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James Bowie » Publications

2008

• Harada BT, Knight MJ, Imai S, Qiao F, Ramachander R, Sawaya MR, Gingery M, Sakane F, Bowie JU. (2008). Regulation of enzyme localization by polymerization: polymer formation by the SAM domain of diacylglycerol kinase delta1. Structure. Mar 2008. 16(3):380-7. [Abstract]
  The diacylglycerol kinase (DGK) enzymes function as regulators of intracellular signaling by altering the levels of the second messengers, diacylglycerol and phosphatidic acid. The DGK delta and eta isozymes possess a common protein-protein interaction module known as a sterile alpha-motif (SAM) domain. In DGK delta, SAM domain self-association inhibits the translocation of DGK delta to the plasma membrane. Here we show that DGK delta SAM forms a polymer and map the polymeric interface by a genetic selection for soluble mutants. A crystal structure reveals that DGKSAM forms helical polymers through a head-to-tail interaction similar to other SAM domain polymers. Disrupting polymerization by polymer interface mutations constitutively localizes DGK delta to the plasma membrane. Thus, polymerization of DGK delta regulates the activity of the enzyme by sequestering DGK delta in an inactive cellular location. Regulation by dynamic polymerization is an emerging theme in signal transduction.
• Gorman PM, Kim S, Guo M, Melnyk RA, McLaurin J, Fraser PE, Bowie JU, Chakrabartty A. (2008). Dimerization of the transmembrane domain of amyloid precursor proteins and familial Alzheimer's disease mutants. BMC neuroscience. 2008. 9:17. [Abstract]
  BACKGROUND: Amyloid precursor protein (APP) is enzymatically cleaved by gamma-secretase to form two peptide products, either Abeta40 or the more neurotoxic Abeta42. The Abeta42/40 ratio is increased in many cases of familial Alzheimer's disease (FAD). The transmembrane domain (TM) of APP contains the known dimerization motif GXXXA. We have investigated the dimerization of both wild type and FAD mutant APP transmembrane domains. RESULTS: Using synthetic peptides derived from the APP-TM domain, we show that this segment is capable of forming stable transmembrane dimers. A model of a dimeric APP-TM domain reveals a putative dimerization interface, and interestingly, majority of FAD mutations in APP are localized to this interface region. We find that FAD-APP mutations destabilize the APP-TM dimer and increase the population of APP peptide monomers. CONCLUSION: The dissociation constants are correlated to both the Abeta42/Abeta40 ratio and the mean age of disease onset in AD patients. We also show that these TM-peptides reduce Abeta production and Abeta42/Abeta40 ratios when added to HEK293 cells overexpressing the Swedish FAD mutation and gamma-secretase components, potentially revealing a new class of gamma-secretase inhibitors.
• Sapra KT, Balasubramanian GP, Labudde D, Bowie JU, Muller DJ. (2008). Point mutations in membrane proteins reshape energy landscape and populate different unfolding pathways. J. Mol. Biol.. Feb 2008. 376(4):1076-90. [Abstract]
  Using single-molecule force spectroscopy, we investigated the effect of single point mutations on the energy landscape and unfolding pathways of the transmembrane protein bacteriorhodopsin. We show that the unfolding energy barriers in the energy landscape of the membrane protein followed a simple two-state behavior and represent a manifestation of many converging unfolding pathways. Although the unfolding pathways of wild-type and mutant bacteriorhodopsin did not change, indicating the presence of same ensemble of structural unfolding intermediates, the free energies of the rate-limiting transition states of the bacteriorhodopsin mutants decreased as the distance of those transition states to the folded intermediate states decreased. Thus, all mutants exhibited Hammond behavior and a change in the free energies of the intermediates along the unfolding reaction coordinate and, consequently, their relative occupancies. This is the first experimental proof showing that point mutations can reshape the free energy landscape of a membrane protein and force single proteins to populate certain unfolding pathways over others.

2007

• Nauli S, Farr S, Lee YJ, Kim HY, Faham S, Bowie JU. (2007). Polymer-driven crystallization. Protein Sci.. Nov 2007. 16(11):2542-51. [Abstract]
  Obtaining well-diffracting crystals of macromolecules remains a significant barrier to structure determination. Here we propose and test a new approach to crystallization, in which the crystallization target is fused to a polymerizing protein module, so that polymer formation drives crystallization of the target. We test the approach using a polymerization module called 2TEL, which consists of two tandem sterile alpha motif (SAM) domains from the protein translocation Ets leukemia (TEL). The 2TEL module is engineered to polymerize as the pH is lowered, which allows the subtle modulation of polymerization needed for crystal formation. We show that the 2TEL module can drive the crystallization of 11 soluble proteins, including three that resisted prior crystallization attempts. In addition, the 2TEL module crystallizes in the presence of various detergents, suggesting that it might facilitate membrane protein crystallization. The crystal structures of two fusion proteins show that the TELSAM polymer is responsible for the majority of contacts in the crystal lattice. The results suggest that biological polymers could be designed as crystallization modules.
• Plotkowski ML, Kim S, Phillips ML, Partridge AW, Deber CM, Bowie JU. (2007). Transmembrane domain of myelin protein zero can form dimers: possible implications for myelin construction. Biochemistry. Oct 2007. 46(43):12164-73. [Abstract]
  Myelin protein zero (MPZ) is the major integral membrane protein of peripheral nerve myelin in higher vertebrates, mediating homoadhesion of the multiple, spiraling wraps of the myelin sheath. Previous studies have shown that full-length MPZ can form dimers and tetramers, and biochemical studies on the extracellular domain (ECD) indicate that it can form a tetramer, albeit very weakly. On the basis of cross-linking studies and equilibrium sedimentation of a transmembrane (TM) domain peptide (MPZ-TM), we find that the MPZ-TM can form homodimers. We further characterized the dimer by measuring the effects of alanine and leucine substitutions on the ability of the TM to dimerize in Escherichia coli membranes. Our results indicate that the primary packing interface for the MPZ TM homodimer is a glycine zipper (GxxxGxxxG) motif. We also find that the G134R mutation, which lies within the glycine zipper packing interface and causes Charcot-Marie-Tooth disease type 1B, severely inhibits dimerization, suggesting that dimerization of the TM domain may be important for the normal functioning of MPZ. By combining our new results with prior work, we suggest a new model for an MPZ lattice that may form during the construction of myelin.
• Pettit FK, Bare E, Tsai A, Bowie JU. (2007). HotPatch: a statistical approach to finding biologically relevant features on protein surfaces. J. Mol. Biol.. Jun 2007. 369(3):863-79. [Abstract]
  We describe a fully automated algorithm for finding functional sites on protein structures. Our method finds surface patches of unusual physicochemical properties on protein structures, and estimates the patches' probability of overlapping functional sites. Other methods for predicting the locations of specific types of functional sites exist, but in previous analyses, it has been difficult to compare methods when they are applied to different types of sites. Thus, we introduce a new statistical framework that enables rigorous comparisons of the usefulness of different physicochemical properties for predicting virtually any kind of functional site. The program's statistical models were trained for 11 individual properties (electrostatics, concavity, hydrophobicity, etc.) and for 15 neural network combination properties, all optimized and tested on 15 diverse protein functions. To simulate what to expect if the program were run on proteins of unknown function, as might arise from structural genomics, we tested it on 618 proteins of diverse mixed functions. In the higher-scoring top half of all predictions, a functional residue could typically be found within the first 1.7 residues chosen at random. The program may or may not use partial information about the protein's function type as an input, depending on which statistical model the user chooses to employ. If function type is used as an additional constraint, prediction accuracy usually increases, and is particularly good for enzymes, DNA-interacting sites, and oligomeric interfaces. The program can be accessed online (at http://hotpatch.mbi.ucla.edu).
• Barwe SP, Kim S, Rajasekaran SA, Bowie JU, Rajasekaran AK. (2007). Janus model of the Na,K-ATPase beta-subunit transmembrane domain: distinct faces mediate alpha/beta assembly and beta-beta homo-oligomerization. J. Mol. Biol.. Jan 2007. 365(3):706-14. [Abstract]
  Na,K-ATPase is a hetero-oligomer of alpha and beta-subunits. The Na,K-ATPase beta-subunit (Na,K-beta) is involved in both the regulation of ion transport activity, and in cell-cell adhesion. By structure prediction and evolutionary analysis, we identified two distinct faces on the Na,K-beta transmembrane domain (TMD) that could mediate protein-protein interactions: a glycine zipper motif and a conserved heptad repeat. Here, we show that the heptad repeat face is involved in the hetero-oligomeric interaction of Na,K-beta with Na,K-alpha, and the glycine zipper face is involved in the homo-oligomerization of Na,K-beta. Point mutations in the heptad repeat motif reduced Na,K-beta binding to Na,K-alpha, and Na,K-ATPase activity. Na,K-beta TMD homo-oligomerized in biological membranes, and mutation of the glycine zipper motif affected oligomerization and cell-cell adhesion. These results provide a structural basis for understanding how Na,K-beta links ion transport and cell-cell adhesion.

2006

• Oberai A, Ihm Y, Kim S, Bowie JU. (2006). A limited universe of membrane protein families and folds. Protein Sci.. Jul 2006. 15(7):1723-34. [Abstract]
  One of the goals of structural genomics is to obtain a structural representative of almost every fold in nature. A recent estimate suggests that 70%-80% of soluble protein domains identified in the first 1000 genome sequences should be covered by about 25,000 structures-a reasonably achievable goal. As no current estimates exist for the number of membrane protein families, however, it is not possible to know whether family coverage is a realistic goal for membrane proteins. Here we find that virtually all polytopic helical membrane protein families are present in the already known sequences so we can make an estimate of the total number of families. We find that only approximately 700 polytopic membrane protein families account for 80% of structured residues and approximately 1700 cover 90% of structured residues. While apparently a finite and reachable goal, we estimate that it will likely take more than three decades to obtain the structures needed for 90% residue coverage, if current trends continue.
• Gundelfinger ED, Boeckers TM, Baron MK, Bowie JU. (2006). A role for zinc in postsynaptic density asSAMbly and plasticity? Trends Biochem. Sci.. Jul 2006. 31(7):366-73. [Abstract]
  Chemical synapses are asymmetric cell junctions that mediate communication between neurons. Multidomain scaffolding proteins of the Shank family act as major organizing elements of the "postsynaptic density"--that is, the cytoskeletal protein matrix associated with the postsynaptic membrane. A recent study has shown that the C-terminal sterile alpha-motif or "SAM domain" of Shank3 (also known as ProSAP2) can form two-dimensional sheets of helical fibers. Assembly and packaging of these fibers are markedly enhanced by the presence of Zn2+ ions. Zn2+ can be released together with glutamate from synaptic vesicles and can enter the postsynaptic cell through specific ionotropic receptors. Based on these observations, we propose a new model of synaptic plasticity in which Zn2+ influx directly and instantly modulates the structure and function of the postsynaptic density.
• Bowie JU. (2006). Flip-flopping membrane proteins. Nat. Struct. Mol. Biol.. Feb 2006. 13(2):94-6. [Abstract]
• Baron MK, Boeckers TM, Vaida B, Faham S, Gingery M, Sawaya MR, Salyer D, Gundelfinger ED, Bowie JU. (2006). An architectural framework that may lie at the core of the postsynaptic density. Science. Jan 2006. 311(5760):531-5. [Abstract]
  The postsynaptic density (PSD) is a complex assembly of proteins associated with the postsynaptic membrane that organizes neurotransmitter receptors, signaling pathways, and regulatory elements within a cytoskeletal matrix. Here we show that the sterile alpha motif domain of rat Shank3/ProSAP2, a master scaffolding protein located deep within the PSD, can form large sheets composed of helical fibers stacked side by side. Zn2+, which is found in high concentrations in the PSD, binds tightly to Shank3 and may regulate assembly. Sheets of the Shank protein could form a platform for the construction of the PSD complex.
• Qiao F, Harada B, Song H, Whitelegge J, Courey AJ, Bowie JU. (2006). Mae inhibits Pointed-P2 transcriptional activity by blocking its MAPK docking site. EMBO J.. Jan 2006. 25(1):70-9. [Abstract]
  During Drosophila melanogaster eye development, signaling through receptor tyrosine kinases (RTKs) leads to activation of a mitogen activated protein tyrosine kinase, called Rolled. Key nuclear targets of Rolled are two antagonistic transcription factors: Yan, a repressor, and Pointed-P2 (Pnt-P2), an activator. A critical regulator of this process, Mae, can interact with both Yan and Pnt-P2 through their SAM domains. Although earlier work showed that Mae derepresses Yan-regulated transcription by depolymerizing the Yan polymer, the mechanism of Pnt-P2 regulation by Mae remained undefined. We find that efficient phosphorylation and consequent activation of Pnt-P2 requires a three-dimensional docking surface on its SAM domain for the MAP kinase, Rolled. Mae binding to Pnt-P2 occludes this docking surface, thereby acting to downregulate Pnt-P2 activity. Docking site blocking provides a new mechanism whereby the cell can precisely modulate kinase signaling at specific targets, providing another layer of regulation beyond the more global changes effected by alterations in the activity of the kinase itself.

2005

• Bowie JU. (2005). Solving the membrane protein folding problem. Nature. Dec 2005. 438(7068):581-9. [Abstract]
  One of the great challenges for molecular biologists is to learn how a protein sequence defines its three-dimensional structure. For many years, the problem was even more difficult for membrane proteins because so little was known about what they looked like. The situation has improved markedly in recent years, and we now know over 90 unique structures. Our enhanced view of the structure universe, combined with an increasingly quantitative understanding of fold determination, engenders optimism that a solution to the folding problem for membrane proteins can be achieved.
• Kim S, Jeon TJ, Oberai A, Yang D, Schmidt JJ, Bowie JU. (2005). Transmembrane glycine zippers: physiological and pathological roles in membrane proteins. Proc. Natl. Acad. Sci. U.S.A.. Oct 2005. 102(40):14278-83. [Abstract]
  We have observed a common sequence motif in membrane proteins, which we call a glycine zipper. Glycine zipper motifs are strongly overrepresented and conserved in membrane protein sequences, and mutations in glycine zipper motifs are deleterious to function in many cases. The glycine zipper has a significant structural impact, engendering a strong driving force for right-handed packing against a neighboring helix. Thus, the presence of a glycine zipper motif leads directly to testable structural hypotheses, particularly for a subclass of glycine zipper proteins that form channels. For example, we suggest that the membrane pores formed by the amyloid-beta peptide in vitro are constructed by glycine zipper packing and find that mutations in the glycine zipper motif block channel formation. Our findings highlight an important structural motif in a wide variety of normal and pathological processes.
• Lorch M, Fahem S, Kaiser C, Weber I, Mason AJ, Bowie JU, Glaubitz C. (2005). How to prepare membrane proteins for solid-state NMR: A case study on the alpha-helical integral membrane protein diacylglycerol kinase from E. coli. Chembiochem. Sep 2005. 6(9):1693-700. [Abstract]
  Several studies have demonstrated that it is viable to use microcrystalline preparations of water-soluble proteins as samples in solid-state NMR experiments [1-5]. Here, we investigate whether this approach holds any potential for studying water-insoluble systems, namely membrane proteins. For this case study, we have prepared proteoliposomes and small crystals of the alpha-helical membrane-protein diacylglycerol kinase (DGK). Preparations were characterised by 13C- and 15N-cross-polarization magic-angle spinning (CPMAS) NMR. It was found that crystalline samples produce better-resolved spectra than proteoliposomes. This makes them more suitable for structural NMR experiments. However, reconstitution is the method of choice for biophysical studies by solid-state NMR. In addition, we discuss the identification of lipids bound to membrane-protein crystals by 31P-MAS NMR.
• Song H, Nie M, Qiao F, Bowie JU, Courey AJ. (2005). Antagonistic regulation of Yan nuclear export by Mae and Crm1 may increase the stringency of the Ras response. Genes Dev.. Aug 2005. 19(15):1767-72. [Abstract]
  Phosphorylation of Yan, a major target of Ras signaling, leads to Crm1-dependent Yan nuclear export, a response that is regulated by Yan polymerization. Yan SAM (sterile alpha motif) domain mutations preventing polymerization result in Ras-independent, but Crm1-dependent Yan nuclear export, suggesting that polymerization prevents Yan export. Mae, which depolymerizes Yan, competes with Crm1 for binding to Yan. Phosphorylation of Yan favors Crm1 in this competition and counteracts inhibition of nuclear export by Mae. These findings suggest that, prior to Ras activation, the Mae/Yan interaction blocks premature nuclear export of Yan monomers. After activation, transcriptional up-regulation of Mae apparently leads to complete depolymerization and export of Yan.
• Qiao F, Bowie JU. (2005). The many faces of SAM. Sci. STKE. May 2005. 2005(286):re7. [Abstract]
  Protein-protein interactions are essential for the assembly, regulation, and localization of functional protein complexes in the cell. SAM domains are among the most abundant protein-protein interaction motifs in organisms from yeast to humans. Although SAM domains adopt similar folds, they are remarkably versatile in their binding properties. Some identical SAM domains can interact with each other to form homodimers or polymers. In other cases, SAM domains can bind to other related SAM domains, to non-SAM domain-containing proteins, and even to RNA. Such versatility earns them functional roles in myriad biological processes, from signal transduction to transcriptional and translational regulation. In this review, we describe the structural basis of SAM domain interactions and highlight their roles in the scaffolding of protein complexes in normal and pathological processes.
• Kim CA, Sawaya MR, Cascio D, Kim W, Bowie JU. (2005). Structural organization of a Sex-comb-on-midleg/polyhomeotic copolymer. J. Biol. Chem.. Jul 2005. 280(30):27769-75. [Abstract]
  The polycomb group proteins are required for the stable maintenance of gene repression patterns established during development. They function as part of large multiprotein complexes created via a multitude of protein-protein interaction domains. Here we examine the interaction between the SAM domains of the polycomb group proteins polyhomeotic (Ph) and Sex-comb-on-midleg (Scm). Previously we showed that Ph-SAM polymerizes as a helical structure. We find that Scm-SAM also polymerizes, and a crystal structure reveals an architecture similar to the Ph-SAM polymer. These results suggest that Ph-SAM and Scm-SAM form a copolymer. Binding affinity measurements between Scm-SAM and Ph-SAM subunits in different orientations indicate a preference for the formation of a single junction copolymer. To provide a model of the copolymer, we determined the structure of the Ph-SAM/Scm-SAM junction. Similar binding modes are observed in both homo- and heterocomplex formation with minimal change in helix axis direction at the polymer joint. The copolymer model suggests that polymeric Scm complexes could extend beyond the local domains of polymeric Ph complexes on chromatin, possibly playing a role in long range repression.
• Faham S, Boulting GL, Massey EA, Yohannan S, Yang D, Bowie JU. (2005). Crystallization of bacteriorhodopsin from bicelle formulations at room temperature. Protein Sci.. Mar 2005. 14(3):836-40. [Abstract]
  We showed previously that high-quality crystals of bacteriorhodopsin (bR) from Halobacterium salinarum can be obtained from bicelle-forming DMPC/CHAPSO mixtures at 37 degrees C. As many membrane proteins are not sufficiently stable for crystallization at this high temperature, we tested whether the bicelle method could be applied at a lower temperature. Here we show that bR can be crystallized at room temperature using two different bicelle-forming compositions: DMPC/CHAPSO and DTPC/CHAPSO. The DTPC/CHAPSO crystals grown at room temperature are essentially identical to the previous, twinned crystals: space group P21 with unit cell dimensions of a = 44.7 A, b = 108.7 A, c = 55.8 A, beta = 113.6 degrees . The room-temperature DMPC/CHAPSO crystals are untwinned, however, and belong to space group C222(1) with the following unit cell dimensions: a = 44.7 A, b = 102.5 A, c = 128.2 A. The bR protein packs into almost identical layers in the two crystal forms, but the layers stack differently. The new untwinned crystal form yielded clear density for a previously unresolved CHAPSO molecule inserted between protein subunits within the layers. The ability to grow crystals at room temperature significantly expands the applicability of bicelle crystallization.
• Bowie JU. (2005). Cell biology: border crossing. Nature. Jan 2005. 433(7024):367-9. [Abstract]
• Edwards MD, Li Y, Kim S, Miller S, Bartlett W, Black S, Dennison S, Iscla I, Blount P, Bowie JU, Booth IR. (2005). Pivotal role of the glycine-rich TM3 helix in gating the MscS mechanosensitive channel. Nat. Struct. Mol. Biol.. Feb 2005. 12(2):113-9. [Abstract]
  The crystal structure of an open form of the Escherichia coli MscS mechanosensitive channel was recently solved. However, the conformation of the closed state and the gating transition remain uncharacterized. The pore-lining transmembrane helix contains a conserved glycine- and alanine-rich motif that forms a helix-helix interface. We show that introducing 'knobs' on the smooth glycine face by replacing glycine with alanine, and substituting conserved alanines with larger residues, increases the pressure required for gating. Creation of a glycine-glycine interface lowers activation pressure. The importance of residues Gly104, Ala106 and Gly108, which flank the hydrophobic seal, is demonstrated. A new structural model is proposed for the closed-to-open transition that involves rotation and tilt of the pore-lining helices. Introduction of glycine at Ala106 validated this model by acting as a powerful suppressor of defects seen with mutations at Gly104 and Gly108.
• Partridge AW, Liu S, Kim S, Bowie JU, Ginsberg MH. (2005). Transmembrane domain helix packing stabilizes integrin alphaIIbbeta3 in the low affinity state. J. Biol. Chem.. Feb 2005. 280(8):7294-300. [Abstract]
  Regulated changes in the affinity of integrin adhesion receptors ("activation") play an important role in numerous biological functions including hemostasis, the immune response, and cell migration. Physiological integrin activation is the result of conformational changes in the extracellular domain initiated by the binding of cytoplasmic proteins to integrin cytoplasmic domains. The conformational changes in the extracellular domain are likely caused by disruption of intersubunit interactions between the alpha and beta transmembrane (TM) and cytoplasmic domains. Here, we reasoned that mutation of residues contributing to alpha/beta interactions that stabilize the low affinity state should lead to integrin activation. Thus, we subjected the entire intracellular domain of the beta3 integrin subunit to unbiased random mutagenesis and selected it for activated mutants. 25 unique activating mutations were identified in the TM and membrane-proximal cytoplasmic domain. In contrast, no activating mutations were identified in the more distal cytoplasmic tail, suggesting that this region is dispensable for the maintenance of the inactive state. Among the 13 novel TM domain mutations that lead to integrin activation were several informative point mutations that, in combination with computational modeling, suggested the existence of a specific TM helix-helix packing interface that maintains the low affinity state. The interactions predicted by the model were used to identify additional activating mutations in both the alpha and beta TM domains. Therefore, we propose that helical packing of the alpha and beta TM domains forms a clasp that regulates integrin activation.

2004

• Ramachander R, Bowie JU. (2004). SAM domains can utilize similar surfaces for the formation of polymers and closed oligomers. J. Mol. Biol.. Oct 2004. 342(5):1353-8. [Abstract]
  The mitogen-activated protein kinase (MAPK) Byr2 and its activator Ste4 are involved in the mating pheromone response pathway of Schizosaccharomyces pombe and interact via their SAM domains. SAM domains can self-associate to form higher-order structures, including dimers, polymers and closed oligomers. Ste4-SAM is adjacent to a trimeric leucine zipper domain and we have shown previously that the two domains together (Ste4-LZ-SAM) bind to a monomeric Byr2-SAM with high affinity (Kd approximately 20 nM), forming a 3:1 complex. Here, we map the surfaces of Byr2-SAM and Ste4-SAM that is involved the interaction. A set of 38 mutants of Byr2-SAM and 33 mutants of Ste4-SAM were prepared, covering most of the protein surfaces. These mutants were purified and screened for binding, yielding a map of residues that are required for binding and a complementary map of residues that are not required. We find that the interface maps to regions of the SAM domains that are known to be important for the formation of SAM polymers. These results indicate that SAM domains can create a variety of oligomeric architectures utilizing common binding surfaces.
• Chamberlain AK, Bowie JU. (2004). Analysis of side-chain rotamers in transmembrane proteins. Biophys. J.. Nov 2004. 87(5):3460-9. [Abstract]
  We measured the frequency of side-chain rotamers in 14 alpha-helical and 16 beta-barrel membrane protein structures and found that the membrane environment considerably perturbs the rotamer frequencies compared to soluble proteins. Although there are limited experimental data, we found statistically significant changes in rotamer preferences depending on the residue environment. Rotamer distributions were influenced by whether the residues were lipid or protein facing, and whether the residues were found near the N- or C-terminus. Hydrogen-bonding interactions with the helical backbone perturbs the rotamer populations of Ser and His. Trp and Tyr favor side-chain conformations that allow their side chains to extend their polar atoms out of the membrane core, thereby aligning the side-chain polarity gradient with the polarity gradient of the membrane. Our results demonstrate how the membrane environment influences protein structures, providing information that will be useful in the structure prediction and design of transmembrane proteins.
• Yohannan S, Yang D, Faham S, Boulting G, Whitelegge J, Bowie JU. (2004). Proline substitutions are not easily accommodated in a membrane protein. J. Mol. Biol.. Jul 2004. 341(1):1-6. [Abstract]
  Proline residues are relatively common in transmembrane helices. This suggests that proline substitutions may be readily tolerated in membrane proteins, even though they invariably produce deviations from canonical helical structure. We have experimentally tested this possibility by making proline substitutions at 15 positions throughout the N-terminal half of bacteriorhodopsin helix B. We find that six of the substitutions yielded no active protein and all the others were destabilizing. Three mutations were only slightly destabilizing, however, reducing stability by about 0.5 kcal/mol, and these all occurred close to the N terminus. This result is consistent with the observation that proline is more common near the ends of TM helices. To learn how proline side-chains could be structurally accommodated at different locations in the helix, we solved the structures of a moderately destabilized mutant positioned near the N terminus of the helix, K41P, and a severely destabilized mutant positioned near the middle of the helix, A51P. The K41P mutation produced only local structural alterations, while the A51P mutation resulted in small, but widely distributed structural changes in helix B. Our results indicate that proline is not easily accommodated in transmembrane helices and that the tolerance to proline substitution is dependent, in a complex way, on the position in the structure.
• Kim S, Chamberlain AK, Bowie JU. (2004). A model of the closed form of the nicotinic acetylcholine receptor m2 channel pore. Biophys. J.. Aug 2004. 87(2):792-9. [Abstract]
  The nicotinic acetylcholine receptor is a neurotransmitter-gated ion channel in the postsynaptic membrane. It is composed of five homologous subunits, each of which contributes one transmembrane helix--the M2 helix--to create the channel pore. The M2 helix from the delta subunit is capable of forming a channel by itself. Although a model of the receptor was recently proposed based on a low-resolution, cryo-electron microscopy density map, we found that the model does not explain much of the other available experimental data. Here we propose a new model of the M2 channel derived solely from helix packing and symmetry constraints. This model agrees well with experimental results from solid-state NMR, chemical reactivity, and mutagenesis experiments. The model depicts the channel pore, the channel gate, and the residues responsible for cation specificity.
• Chamberlain AK, Bowie JU. (2004). Asymmetric amino acid compositions of transmembrane beta-strands. Protein Sci.. Aug 2004. 13(8):2270-4. [Abstract]
  In contrast to water-soluble proteins, membrane proteins reside in a heterogeneous environment, and their surfaces must interact with both polar and apolar membrane regions. As a consequence, the composition of membrane proteins' residues varies substantially between the membrane core and the interfacial regions. The amino acid compositions of helical membrane proteins are also known to be different on the cytoplasmic and extracellular sides of the membrane. Here we report that in the 16 transmembrane beta-barrel structures, the amino acid compositions of lipid-facing residues are different near the N and C termini of the individual strands. Polar amino acids are more prevalent near the C termini than near the N termini, and hydrophobic amino acids show the opposite trend. We suggest that this difference arises because it is easier for polar atoms to escape from the apolar regions of the bilayer at the C terminus of a beta-strand. This new characteristic of beta-barrel membrane proteins enhances our understanding of how a sequence encodes a membrane protein structure and should prove useful in identifying and predicting the structures of trans-membrane beta-barrels.
• Qiao F, Song H, Kim CA, Sawaya MR, Hunter JB, Gingery M, Rebay I, Courey AJ, Bowie JU. (2004). Derepression by depolymerization; structural insights into the regulation of Yan by Mae. Cell. Jul 2004. 118(2):163-73. [Abstract]
  Yan, an ETS family transcriptional repressor, is regulated by receptor tyrosine kinase signaling via the Ras/MAPK pathway. Phosphorylation and downregulation of Yan is facilitated by a protein called Mae. Yan and Mae interact through their SAM domains. We find that repression by Yan requires the formation of a higher order structure mediated by Yan-SAM polymerization. Moreover, a crystal structure of the Yan-SAM/Mae-SAM complex shows that Mae-SAM specifically recognizes a surface on Yan-SAM that is also required for Yan-SAM polymerization. Mae-SAM binds to Yan-SAM with approximately 1000-fold higher affinity than Yan-SAM binds to itself and can effectively depolymerize Yan-SAM. Mutations on Mae that specifically disrupt its SAM domain-dependent interactions with Yan disable the derepression function of Mae in vivo. Depolymerization of Yan by Mae represents a novel mechanism of transcriptional control that sensitizes Yan for regulation by receptor tyrosine kinases.
• Chamberlain AK, Lee Y, Kim S, Bowie JU. (2004). Snorkeling preferences foster an amino acid composition bias in transmembrane helices. J. Mol. Biol.. May 2004. 339(2):471-9. [Abstract]
  By analyzing transmembrane (TM) helices in known structures, we find that some polar amino acids are more frequent at the N terminus than at the C terminus. We propose the asymmetry occurs because most polar amino acids are better able to snorkel their polar atoms away from the membrane core at the N terminus than at the C terminus. Two findings lead us to this proposition: (1) side-chain conformations are influenced strongly by the N or C-terminal position of the amino acid in the bilayer, and (2) the favored snorkeling direction of an amino acid correlates well with its N to C-terminal composition bias. Our results suggest that TM helix predictions should incorporate an N to C-terminal composition bias, that rotamer preferences of TM side-chains are position-dependent, and that the ability to snorkel influences the evolutionary selection of amino acids for the helix N and C termini.
• Kim S, Chamberlain AK, Bowie JU. (2004). Membrane channel structure of Helicobacter pylori vacuolating toxin: role of multiple GXXXG motifs in cylindrical channels. Proc. Natl. Acad. Sci. U.S.A.. Apr 2004. 101(16):5988-91. [Abstract]
  Helicobacter pylori is a human pathogen responsible for severe gastric diseases such as peptic ulcers, gastric adenocarcinoma, and gastric lymphoma. Vacuolating toxin (VacA) is crucial in facilitating the colonization of the gastric lining by inducing cell apoptosis and immune suppression. VacA inserts into membranes and forms a hexameric, anion-selective pore. Here we present a structural model of the VacA pore that strongly resembles the structure of an unrelated anion-selective channel, MscS. In our model, Gly residues in GXXXG motifs pack against small Ala or Val side chains to generate the pore. Our model suggests that the same design of two anion-selective channels was achieved by two different evolutionary paths and provides insight into the mechanism of VacA function.
• Yamaguchi S, Tuzi S, Bowie JU, Saitô H. (2004). Secondary structure and backbone dynamics of Escherichia coli diacylglycerol kinase, as revealed by site-directed solid-state 13C NMR. Biochim. Biophys. Acta. Apr 2004. 1698(1):97-105. [Abstract]
  To gain insight into secondary structure and backbone dynamics, we have recorded (13)C NMR spectra of [3-(13)C]Ala-, [1-(13)C]Val-labeled Escherichia coli diacylglycerol kinase (DGK), using cross-polarization-magic angle spinning (CP-MAS) and single-pulse excitation with dipolar decoupled-magic angle spinning (DD-MAS) methods. DGK was either solubilized in n-decyl-beta-maltoside (DM) micelle or integrated into 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) or 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayers. Surprisingly, the (13)C NMR spectra were broadened to yield rather featureless peaks at physiological temperatures, both in DM solution or lipid bilayers at liquid crystalline phase, due to interference of motional frequencies of DGK with frequencies of magic angle spinning (MAS) or proton decoupling (10(4) or 10(5) Hz, respectively). In gel phase lipids, however, up to six distinct (13)C NMR peaks were well-resolved due to lowered fluctuation frequencies (<10(5) Hz) for the transmembrane region, the amphipathic alpha-helices and loops. While DGK can be tightly packed in gel phase lipids, DGK is less tightly packed at physiological temperatures, where it becomes more mobile. The fact that the enzymatic activity is low under conditions where motion is restricted and high when conformational fluctuations can occur suggests that acquisition of low frequency backbone motions, on the microsecond to millisecond time scale, may facilitate the efficient enzymatic activity of DGK.
• Bowie JU. (2004). Membrane proteins: a new method enters the fold. Proc. Natl. Acad. Sci. U.S.A.. Mar 2004. 101(12):3995-6. [Abstract]
• Yohannan S, Faham S, Yang D, Grosfeld D, Chamberlain AK, Bowie JU. (2004). A C alpha-H...O hydrogen bond in a membrane protein is not stabilizing. J. Am. Chem. Soc.. Mar 2004. 126(8):2284-5. [Abstract]
  Hydrogen bonds involving a carbon donor are very common in protein structures, and energy calculations suggest that Calpha-H...O hydrogen bonds could be about one-half the strength of traditional hydrogen bonds. It has therefore been proposed that these nontraditional hydrogen bonds could be a significant factor in stabilizing proteins, particularly membrane proteins as there is a low dielectric and no competition from water in the bilayer core. Nevertheless, this proposition has never been tested experimentally. Here, we report an experimental test of the significance of Calpha-H...O bonds for protein stability. Thr24 in bacteriorhodopsin, which makes an interhelical Calpha-H...O hydrogen bond to the Calpha of Ala51, was changed to Ala, Val, and Ser, and the thermodynamic stability of the mutants was measured. None of the mutants had significantly reduced stability. In fact, T24A was more stable than the wild-type protein by 0.6 kcal/mol. Crystal structures were determined for each of the mutants, and, while some structural changes were seen for T24S and T24V, T24A showed essentially no apparent structural alteration that could account for the increased stability. Thus, Thr24 appears to destabilize the protein rather than stabilize. Our results suggest that Calpha-H...O bonds are not a major contributor to protein stability.
• Melnyk RA, Kim S, Curran AR, Engelman DM, Bowie JU, Deber CM. (2004). The affinity of GXXXG motifs in transmembrane helix-helix interactions is modulated by long-range communication. J. Biol. Chem.. Apr 2004. 279(16):16591-7. [Abstract]
  Sequence motifs are responsible for ensuring the proper assembly of transmembrane (TM) helices in the lipid bilayer. To understand the mechanism by which the affinity of a common TM-TM interactive motif is controlled at the sequence level, we compared two well characterized GXXXG motif-containing homodimers, those formed by human erythrocyte protein glycophorin A (GpA, high-affinity dimer) and those formed by bacteriophage M13 major coat protein (MCP, low affinity dimer). In both constructs, the GXXXG motif is necessary for TM-TM association. Although the remaining interfacial residues (underlined) in GpA (LIXXGVXXGVXXT) differ from those in MCP (VVXXGAXXGIXXF), molecular modeling performed here indicated that GpA and MCP dimers possess the same overall fold. Thus, we could introduce GpA interfacial residues, alone and in combination, into the MCP sequence to help decrypt the determinants of dimer affinity. Using both in vivo TOXCAT assays and SDS-PAGE gel migration rates of synthetic peptides derived from TM regions of the proteins, we found that the most distal interfacial sites, 12 residues apart (and approximately 18 A in structural space), work in concert to control TM-TM affinity synergistically.
• Yohannan S, Faham S, Yang D, Whitelegge JP, Bowie JU. (2004). The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors. Proc. Natl. Acad. Sci. U.S.A.. Jan 2004. 101(4):959-63. [Abstract]
  One of the hallmarks of membrane protein structure is the high frequency of transmembrane helix kinks, which commonly occur at proline residues. Because the proline side chain usually precludes normal helix geometry, it is reasonable to expect that proline residues generate these kinks. We observe, however, that the three prolines in bacteriorhodopsin transmembrane helices can be changed to alanine with little structural consequences. This finding leads to a conundrum: if proline is not required for helix bending, why are prolines commonly present at bends in transmembrane helices? We propose an evolutionary hypothesis in which a mutation to proline initially induces the kink. The resulting packing defects are later repaired by further mutation, thereby locking the kink in the structure. Thus, most prolines in extant proteins can be removed without major structural consequences. We further propose that nonproline kinks are places where vestigial prolines were later removed during evolution. Consistent with this hypothesis, at 14 of 17 nonproline kinks in membrane proteins of known structure, we find prolines in homologous sequences. Our analysis allows us to predict kink positions with >90% reliability. Kink prediction indicates that different G protein-coupled receptor proteins have different kink patterns and therefore different structures.
• Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D. (2004). The Database of Interacting Proteins: 2004 update. Nucleic Acids Res.. Jan 2004. 32(Database issue):D449-51. [Abstract]
  The Database of Interacting Proteins (http://dip.doe-mbi.ucla.edu) aims to integrate the diverse body of experimental evidence on protein-protein interactions into a single, easily accessible online database. Because the reliability of experimental evidence varies widely, methods of quality assessment have been developed and utilized to identify the most reliable subset of the interactions. This CORE set can be used as a reference when evaluating the reliability of high-throughput protein-protein interaction data sets, for development of prediction methods, as well as in the studies of the properties of protein interaction networks.
• Faham S, Yang D, Bare E, Yohannan S, Whitelegge JP, Bowie JU. (2004). Side-chain contributions to membrane protein structure and stability. J. Mol. Biol.. Jan 2004. 335(1):297-305. [Abstract]
  The molecular forces that stabilize membrane protein structure are poorly understood. To investigate these forces we introduced alanine substitutions at 24 positions in the B helix of bacteriorhodopsin and examined their effects on structure and stability. Although most of the results can be rationalized in terms of the folded structure, there are a number of surprises. (1) We find a remarkably high frequency of stabilizing mutations (17%), indicating that membrane proteins are not highly optimized for stability. (2) Helix B is kinked, with the kink centered around Pro50. The P50A mutation has no effect on stability, however, and a crystal structure reveals that the helix remains bent, indicating that tertiary contacts dominate in the distortion of this helix. (3) We find that the protein is stabilized by about 1kcal/mol for every 38A(2) of surface area buried, which is quite similar to soluble proteins in spite of their dramatically different environments. (4) We find little energetic difference, on average, in the burial of apolar surface or polar surface area, implying that van der Waals packing is the dominant force that drives membrane protein folding.

2003

• Kim CA, Bowie JU. (2003). SAM domains: uniform structure, diversity of function. Trends Biochem. Sci.. Dec 2003. 28(12):625-8. [Abstract]
  Sterile alpha motif (SAM) domains are known to exhibit diverse protein-protein interaction modes. They can form multiple self-association architectures and also bind to various non-SAM domain-containing proteins. Surprising new work adds a completely unanticipated function for some SAM domains - the ability to bind RNA. Such functional diversity within a homologous protein family presents a significant challenge for bioinformatic function assignment.
• Rajasekaran SA, Anilkumar G, Oshima E, Bowie JU, Liu H, Heston W, Bander NH, Rajasekaran AK. (2003). A novel cytoplasmic tail MXXXL motif mediates the internalization of prostate-specific membrane antigen. Mol. Biol. Cell. Dec 2003. 14(12):4835-45. [Abstract]
  Prostate-specific membrane antigen (PSMA) is a transmembrane protein expressed at high levels in prostate cancer and in tumor-associated neovasculature. In this study, we report that PSMA is internalized via a clathrin-dependent endocytic mechanism and that internalization of PSMA is mediated by the five N-terminal amino acids (MWNLL) present in its cytoplasmic tail. Deletion of the cytoplasmic tail abolished PSMA internalization. Mutagenesis of N-terminal amino acid residues at position 2, 3, or 4 to alanine did not affect internalization of PSMA, whereas mutation of amino acid residues 1 or 5 to alanine strongly inhibited internalization. Using a chimeric protein composed of Tac antigen, the alpha-chain of interleukin 2-receptor, fused to the first five amino acids of PSMA (Tac-MWNLL), we found that this sequence is sufficient for PSMA internalization. In addition, inclusion of additional alanines into the MWNLL sequence either in the Tac chimera or the full-length PSMA strongly inhibited internalization. From these results, we suggest that a novel MXXXL motif in the cytoplasmic tail mediates PSMA internalization. We also show that dominant negative micro2 of the adaptor protein (AP)-2 complex strongly inhibits the internalization of PSMA, indicating that AP-2 is involved in the internalization of PSMA mediated by the MXXXL motif.
• Kim S, Chamberlain AK, Bowie JU. (2003). A simple method for modeling transmembrane helix oligomers. J. Mol. Biol.. Jun 2003. 329(4):831-40. [Abstract]
  We describe an effective procedure for modeling the structures of simple transmembrane helix homo-oligomers. The method differs from many previous approaches in that the only structural constraint we use to help select the correct model is the oligomerization state of the protein. The method involves the following steps: (1) perform 100-250 independent Monte Carlo energy minimizations of helix pairs to produce a large collection of well-packed structures; (2) filter the minimized structures to find those that are consistent with the expected symmetry of the oligomer; (3) cluster the structures that pass the symmetry filter; and (4) select a representative of the most populous cluster as the final prediction. We applied the method to the transmembrane helices of five proteins and compare our results to the available experimental data. Our predictions of glycophorin A, neu, the M2 channel and phospholamban resulted in a single model for each protein that agreed with the experimental results. In the case of erbB-2, however, we obtained three structurally distinct clusters of approximately equal sizes, so it was not possible to identify a clearly favored structure. This may reflect a real heterogeneity of packing modes for erbB-2, which is known to interact with different receptor subunits. Our method should be useful for obtaining structural models of transmembrane domains, improving our understanding of structure/function relationships for particular membrane proteins.
• Partridge AW, Melnyk RA, Yang D, Bowie JU, Deber CM. (2003). A transmembrane segment mimic derived from Escherichia coli diacylglycerol kinase inhibits protein activity. J. Biol. Chem.. Jun 2003. 278(24):22056-60. [Abstract]
  The function of membrane proteins is inextricably linked to the proper packing and assembly of their independently helical transmembrane (TM) segments. Here we examined whether an externally added TM peptide analogue could specifically inhibit the function of the membrane protein from which it is derived by competing for native TM helix packing sites, thereby producing a non-functional peptide-protein complex. This hypothesis was tested using Lys-tagged peptides synthesized with sequences corresponding to the three TM segments of the homotrimeric Escherichia coli diacylglycerol kinase (DGK). The peptide corresponding to wild-type DGK TM-2 inhibited the protein's enzymatic activity in a dose-dependent manner through formation of an inactive pseudo-complex, whereas peptides derived from TM-1 and TM-3 were benign toward DGK structure/function. Also, substitution of a conserved residue (Glu-69) within the TM-2 peptide abolished these effects, demonstrating the strict sequence requirements for TM-2-mediated association. This strategy, coupled with the practical advantages of the water solubility of Lys-tagged TM peptides, may constitute an attractive approach for the design of therapeutic membrane protein modulators even in the absence of a high resolution structure.
• Chamberlain AK, Faham S, Yohannan S, Bowie JU. (2003). Construction of helix-bundle membrane proteins. Adv. Protein Chem.. 2003. 63:19-46. [Abstract]

2002

• Chamberlain AK, Bowie JU. (2002). Evaluation of C-H cdots, three dots, centered O hydrogen bonds in native and misfolded proteins. J. Mol. Biol.. Sep 2002. 322(3):497-503. [Abstract]
  Non-traditional C-H cdots, three dots, centered Y hydrogen bonds, in which a carbon atom acts as the hydrogen donor and an electronegative atom Y (Y=N, O or S) acts as the acceptor, have been reported in proteins, but their importance in protein structures is not well established. Here, we present the results of three computational tests that examine the significance of C-H cdots, three dots, centered Y bonds involving the C(alpha) in proteins. First, we compared the number of C(alpha)-H cdots, three dots, centered Y bonds in native structures with two sets of compact, energy-minimized decoy structures. The decoy structures contain about as many C(alpha)-H cdots, three dots, centered Y bonds as the native structures, indicating that the constraints of chain connectivity and compactness can lead to incidental formation of C(alpha)-H cdots, three dots, centered Y bonds. Secondly, we examined whether short C(alpha)-H cdots, three dots, centered Y bonds have a tendency to be linear, as is expected for a cohesive hydrogen-bonding interaction. The native structures do show this trend, but so does one of the decoy sets, suggesting that this criterion is also not sufficient to indicate a stabilizing interaction. Finally, we examined the preference for C(alpha)-H cdots, three dots, centered Y bond donors to be near to strong hydrogen bond acceptors. In the native proteins, the alpha protons attract strong acceptors like oxygen atoms more than weak acceptors. In contrast, hydrogen bond donors in the decoy structures do not distinguish between strong and weak acceptors. Thus, any individual C(alpha)-H cdots, three dots, centered Y bond may be fortuitous and occur due to the polypeptide connectivity and compactness. Taken collectively, however, C(alpha)-H cdots, three dots, centered Y bonds provide a weakly cohesive force that stabilizes proteins.
• Tran HH, Kim CA, Faham S, Siddall MC, Bowie JU. (2002). Native interface of the SAM domain polymer of TEL. BMC Struct. Biol.. Aug 2002. 2:5. [Abstract]
  BACKGROUND: TEL is a transcriptional repressor containing a SAM domain that forms a helical polymer. In a number of hematologic malignancies, chromosomal translocations lead to aberrant fusions of TEL-SAM to a variety of other proteins, including many tyrosine kinases. TEL-SAM polymerization results in constitutive activation of the tyrosine kinase domains to which it becomes fused, leading to cell transformation. Thus, inhibitors of TEL-SAM self-association could abrogate transformation in these cells. In previous work, we determined the structure of a mutant TEL-SAM polymer bearing a Val to Glu substitution in center of the subunit interface. It remained unclear how much the mutation affected the architecture of the polymer, however. RESULTS: Here we determine the structure of the native polymer interface. To accomplish this goal, we introduced mutations that block polymer extension, producing a heterodimer with a wild-type interface. We find that the structure of the wild-type polymer interface is quite similar to the mutant structure determined previously. With the structure of the native interface, it is possible to evaluate the potential for developing therapeutic inhibitors of the interaction. We find that the interacting surfaces of the protein are relatively flat, containing no obvious pockets for the design of small molecule inhibitors. CONCLUSION: Our results confirm the architecture of the TEL-SAM polymer proposed previously based on a mutant structure. The fact that the interface contains no obvious potential binding pockets suggests that it may be difficult to find small molecule inhibitors to treat malignancies in this way.
• Ramachander R, Kim CA, Phillips ML, Mackereth CD, Thanos CD, McIntosh LP, Bowie JU. (2002). Oligomerization-dependent association of the SAM domains from Schizosaccharomyces pombe Byr2 and Ste4. J. Biol. Chem.. Oct 2002. 277(42):39585-93. [Abstract]
  SAM (sterile alpha motif) domains are protein-protein interaction modules found in a large number of regulatory proteins. Byr2 and Ste4 are two SAM domain-containing proteins in the mating pheromone response pathway of the fission yeast, Schizosaccharomyces pombe. Byr2 is a mitogen-activated protein kinase kinase kinase that is regulated by Ste4. Tu et al. (Tu, H., Barr, M., Dong, D. L., and Wigler, M. (1997) Mol. Cell. Biol. 17, 5876-5887) showed that the isolated SAM domain of Byr2 binds a fragment of Ste4 that contains both a leucine zipper (Ste4-LZ) domain as well as a SAM domain, suggesting that Byr2-SAM and Ste4-SAM may form a hetero-oligomer. Here, we show that the individual SAM domains of Ste4 and Byr2 are monomeric at low concentrations and bind to each other in a 1:1 stoichiometry with a relatively weak dissociation constant of 56 +/- 3 microm. Inclusion of the Ste4-LZ domain, which determines the oligomeric state of Ste4, has a dramatic effect on binding affinity, however. We find that the Ste4-LZ domain is trimeric and, when included with the Ste4-SAM domain, yields a 3:1 Ste4-LZ-SAM:Byr2-SAM complex with a tight dissociation constant of 19 +/- 4 nm. These results suggest that the Ste4-LZ-SAM protein may recognize multiple binding sites on Byr2-SAM, indicating a new mode of oligomeric organization for SAM domains. The fact that high affinity binding occurs only with the addition of an oligomerization domain suggests that it may be necessary to include ancillary oligomerization modules when searching for binding partners of SAM domains.
• Kim CA, Gingery M, Pilpa RM, Bowie JU. (2002). The SAM domain of polyhomeotic forms a helical polymer. Nat. Struct. Biol.. Jun 2002. 9(6):453-7. [Abstract]
  The polycomb group (PcG) proteins are important in the maintenance of stable repression patterns during development. Several PcG members contain a protein protein interaction module called a SAM domain (also known as SPM, PNT and HLH). Here we report the high-resolution structure of the SAM domain of polyhomeotic (Ph). Ph-SAM forms a helical polymer structure, providing a likely mechanism for the extension of PcG complexes. The structure of the polymer resembles that formed by the SAM domain of another transcriptional repressor, TEL. The formation of these polymer structures by SAM domains in two divergent repressors suggests a conserved mode of repression involving a higher order chromatin structure.
• Faham S, Bowie JU. (2002). Bicelle crystallization: a new method for crystallizing membrane proteins yields a monomeric bacteriorhodopsin structure. J. Mol. Biol.. Feb 2002. 316(1):1-6. [Abstract]
  Obtaining crystals of membrane proteins that diffract to high resolution remains a major stumbling block in structure determination. Here we present a new method for crystallizing membrane proteins from a bicelle forming lipid/detergent mixture. The method is flexible and simple to use. As a test case, bacteriorhodopsin (bR) from Halobacterium salinarum was crystallized from a bicellar solution, yielding a new bR crystal form. The crystals belong to space group P2(1) with unit cell dimensions of a=45.0 A, b=108.9 A, c=55.9 A, beta=113.58 degrees and a dimeric asymmetric unit. The structure was solved by molecular replacement and refined at 2.0 A resolution. In all previous bR structures the protein is organized as a parallel trimer, but in the crystals grown from bicelles, the individual bR subunits are arranged in an antiparallel fashion.

2001

• Bowie JU. (2001). Stabilizing membrane proteins. Curr. Opin. Struct. Biol.. Aug 2001. 11(4):397-402. [Abstract]
  Membrane proteins can be extremely stable in a bilayer environment, but are often unstable and rapidly lose activity after detergent solubilization. Poor stability can preclude the detailed characterization of many membrane proteins. One way to alleviate this problem is to find more stable mutants of a membrane protein of interest. This approach is made tractable by the finding that stability-enhancing mutations appear to be relatively common in membrane proteins.
• Kim CA, Phillips ML, Kim W, Gingery M, Tran HH, Robinson MA, Faham S, Bowie JU. (2001). Polymerization of the SAM domain of TEL in leukemogenesis and transcriptional repression. EMBO J.. Aug 2001. 20(15):4173-82. [Abstract]
  TEL is a transcriptional repressor that is a frequent target of chromosomal translocations in a large number of hematalogical malignancies. These rearrangements fuse a potent oligomerization module, the SAM domain of TEL, to a variety of tyrosine kinases or transcriptional regulatory proteins. The self-associating property of TEL-SAM is essential for cell transformation in many, if not all of these diseases. Here we show that the TEL-SAM domain forms a helical, head-to-tail polymeric structure held together by strong intermolecular contacts, providing the first clear demonstration that SAM domains can polymerize. Our results also suggest a mechanism by which SAM domains could mediate the spreading of transcriptional repression complexes along the chromosome.
• Zhou Y, Lau FW, Nauli S, Yang D, Bowie JU. (2001). Inactivation mechanism of the membrane protein diacylglycerol kinase in detergent solution. Protein Sci.. Feb 2001. 10(2):378-83. [Abstract]
  We have examined the irreversible inactivation mechanism of the membrane protein diacylglycerol kinase in the detergents n-octyl-beta-D-glucopyranoside (OG) at 55 degrees C and n-decyl-maltopyranoside (DM) at 80 degrees C. Under no inactivation conditions did we find any direct evidence for the chemical modifications that are commonly found in soluble proteins. Moreover, protein inactivated at 55 degrees C in OG could be reactivated by an unfolding and refolding protocol, suggesting that the protein is inactivated by a stable conformational change, not a covalent modification. We also found that the inactivation rate decreased with both increasing protein concentration and increasing thermodynamic stability, consistent with an inactivation pathway involving transient dissociation and/or unfolding of the protein. Our results suggest that the primary cause of diacylglycerol kinase inactivation is not low solubility, but poor intrinsic stability in the detergent environment.

2000

• Bowie JU. (2000). Are we destined to repeat history? Curr. Opin. Struct. Biol.. Aug 2000. 10(4):435-7. [Abstract]
• Nagy JK, Lau FW, Bowie JU, Sanders CR. (2000). Mapping the oligomeric interface of diacylglycerol kinase by engineered thiol cross-linking: homologous sites in the transmembrane domain. Biochemistry. Apr 2000. 39(14):4154-64. [Abstract]
  This work represents the first stage of thiol-based cross-linking studies to map the oligomeric interface of the homotrimeric membrane protein diacylglycerol kinase (DAGK). A total of 53 single-cysteine mutants spanning DAGK's three transmembrane segments and the first part of a cytoplasmic domain were purified and subjected to catalytic oxidation in mixed micelles. Four mutants (A52C, I53C, A74C, and I75C) were observed to undergo intratrimer disulfide bond formation between homologous sites on adjacent subunits. To establish whether the homologous sites are proximal in the ground-state conformation of DAGK or whether the disulfide bonds formed as a result of motions that brought normally distal sites into transient proximity, additional cross-linking experiments were carried out in three different milieus of varying fluidity [mixed micelles, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) vesicles, and Escherichia coli membranes]. Cross-linking experiments included disulfide bond formation under three different catalytic conditions [Cu(II)-phenanthroline oxidation, I(2) oxidation, and thionitrobenzoate-based thiol exchange] and reactions with a set of bifunctional thiol-reactive chemical cross-linkers presenting two different reactive chemistries and several spacer lengths. On the basis of these studies, residues 53 and 75 are judged to be in stable proximity within the DAGK homotrimer, while position 52 appears to be more distal and forms disulfide bonds only as a result of protein motions. Results for position 74 were ambiguous. In lipid vesicles and mixed micelles DAGK appears to execute motions that are not present in native membranes, with mobility also being higher for DAGK in mixed micelles than in POPC vesicles.
• Zhou Y, Bowie JU. (2000). Building a thermostable membrane protein. J. Biol. Chem.. Mar 2000. 275(10):6975-9. [Abstract]
  The poor stability of membrane proteins in detergent solution is one of the main technical barriers to their structural and functional characterization. Here we describe a solution to this problem for diacylglycerol kinase (DGK), an integral membrane protein from Escherichia coli. Twelve enhanced stability mutants of DGK were obtained using a simple screen. Four of the mutations were combined to create a quadruple mutant that had improved stability in a wide range of detergents. In n-octylglucoside, the wild-type DGK had a thermal inactivation half-life of 6 min at 55 degrees C, while the quadruple mutant displayed a half-life of 35 min at 80 degrees C. In addition, the quadruple mutant had improved thermodynamic stability. Our approach should be applicable to other membrane proteins that can be conveniently assayed.
• Bowie JU. (2000). Understanding membrane protein structure by design. Nat. Struct. Biol.. Feb 2000. 7(2):91-4. [Abstract]
  In contrast to soluble proteins, the primary interactions that specify and stabilize membrane protein structures are still largely a matter of speculation. Although van der Waals interactions have been gaining increasing favor as the dominant player, new results demonstrate the strength of hydrogen bonding in a membrane environment.

1999

• Bowie JU. (1999). Helix-bundle membrane protein fold templates. Protein Sci.. Dec 1999. 8(12):2711-9. [Abstract]
  In the fold recognition approach to structure prediction, a sequence is tested for compatibility with an already known fold. For membrane proteins, however, few folds have been determined experimentally. Here the feasibility of computing the vast majority of likely membrane protein folds is tested. The results indicate that conformation space can be effectively sampled for small numbers of helices. The vast majority of potential monomeric membrane protein structures can be represented by about 30-folds for three helices, but increases exponentially to about 1,500,000 folds for seven helices. The generated folds could serve as templates for fold recognition or as starting points for conformational searches that are well distributed throughout conformation space.
• Thanos CD, Faham S, Goodwill KE, Cascio D, Phillips M, Bowie JU. (1999). Monomeric structure of the human EphB2 sterile alpha motif domain. J. Biol. Chem.. Dec 1999. 274(52):37301-6. [Abstract]
  The sterile alpha motif (SAM) domain is a protein module found in many diverse signaling proteins. SAM domains in some systems have been shown to self-associate. Previous crystal structures of an EphA4-SAM domain dimer (Stapleton, D., Balan, I., Pawson, T., and Sicheri, F. (1999) Nat. Struct. Biol. 6, 44-49) and a possible EphB2-SAM oligomer (Thanos, C. D., Goodwill, K. E., and Bowie, J. U. (1999) Science 283, 833-836) both revealed large interfaces comprising an exchange of N-terminal peptide arms. Within the arm, a conserved hydrophobic residue (Tyr-8 in the EphB2-SAM structure or Phe-910 in the EphA4-SAM structure) is anchored into a hydrophobic cleft on a neighboring molecule. Here we have solved a new crystal form of the human EphB2-SAM domain that has the same overall SAM domain fold yet has no substantial intermolecular contacts. In the new structure, the N-terminal peptide arm of the EphB2-SAM domain protrudes out from the core of the molecule, leaving both the arm (including Tyr-8) and the hydrophobic cleft solvent-exposed. To verify that Tyr-8 is solvent-exposed in solution, we made a Tyr-8 to Ala-8 mutation and found that the EphB2-SAM domain structure and stability were only slightly altered. These results suggest that Tyr-8 is not part of the hydrophobic core of the EphB2-SAM domain and is conserved for functional reasons. Cystallographic evidence suggests a possible role for the N-terminal arm in oligomerization. In the absence of a direct demonstration of biological relevance, however, the functional role of the N-terminal arm remains an open question.
• Thanos CD, Bowie JU. (1999). p53 Family members p63 and p73 are SAM domain-containing proteins. Protein Sci.. Aug 1999. 8(8):1708-10. [Abstract]
  Homologs of the tumor suppressor p53, called p63 and p73, have been identified. The p63 and p73 family members possess a domain structure similar to p53, but contain variable C-terminal extensions. We find that some of the C-terminal extensions contain Sterile Alpha Motif (SAM) domains. SAM domains are protein modules that are involved in protein-protein interactions. Consistent with this role, the C-terminal SAM domains of the p63 and p73 may regulate function by recruiting other protein effectors.
• Lau FW, Nauli S, Zhou Y, Bowie JU. (1999). Changing single side-chains can greatly enhance the resistance of a membrane protein to irreversible inactivation. J. Mol. Biol.. Jul 1999. 290(2):559-64. [Abstract]
  The thermal inactivation rates of a set of 20 cysteine-substituted variants of the integral membrane protein diacylglycerol kinase were measured. Two of the mutations, I53C and I70C, were found to significantly prolong the half-life of the enzyme in detergent solution. By combining the single mutants to create a double mutant, I53C/I70C, the half-life of the enzyme was improved from less than a minute at 70 degrees C to 51 minutes. These results demonstrate that individual side-chain substitutions can significantly improve the properties of membrane proteins in detergent solution.
• Lau FW, Chen X, Bowie JU. (1999). Active sites of diacylglycerol kinase from Escherichia coli are shared between subunits. Biochemistry. Apr 1999. 38(17):5521-7. [Abstract]
  We show that residues from different subunits participate in forming the active site of the trimeric membrane protein diacylglycerol kinase (DGK) from Escherichia coli. Five likely active-site mutants were identified: A14Q, N72S, E76L, K94L, and D95N. All five of these mutants possessed significantly impaired catalytic function, without evidence of gross structural alterations as judged by their similar near-UV and far-UV circular dichroism spectra. We found that mixtures of either A14Q or E76L with N72S or K94L possessed much greater activity than the mutant proteins by themselves, suggesting that Ala14 and Glu76 may be on one half-site while Asn72 and Lys94 are on another half-site. Consistent with the shared site model, we also found that (1) peak activity of A14Q and N72S subunit mixtures occur at equimolar concentrations; (2) the maximum activity of the A14Q and N72S mixture was 20% of the wild-type enzyme, in good agreement with the theoretical maximum of 25%; (3) the activity of mutant subunits could not be recovered by mixing with the wild-type subunits; (4) a double mutant, A14Q/N72S, bearing mutations in both putative half-sites was found to inactivate wild-type subunits; (5) the concentration dependence of inactivation by the A14Q/N72S mutant could be well described by a shared site model for a trimeric protein. Unexpectedly, we found that the single mutant D95N behaved in a manner similar to the double mutant, A14Q/N72S, inactivating wild-type subunits. We propose that Asp95 plays a role in more than one active site.
• Thanos CD, Goodwill KE, Bowie JU. (1999). Oligomeric structure of the human EphB2 receptor SAM domain. Science. Feb 1999. 283(5403):833-6. [Abstract]
  The sterile alpha motif (SAM) domain is a protein interaction module that is present in diverse signal-transducing proteins. SAM domains are known to form homo- and hetero-oligomers. The crystal structure of the SAM domain from an Eph receptor tyrosine kinase, EphB2, reveals two large interfaces. In one interface, adjacent monomers exchange amino-terminal peptides that insert into a hydrophobic groove on each neighbor. A second interface is composed of the carboxyl-terminal helix and a nearby loop. A possible oligomer, constructed from a combination of these binding modes, may provide a platform for the formation of larger protein complexes.
• Pettit FK, Bowie JU. (1999). Protein surface roughness and small molecular binding sites. J. Mol. Biol.. Jan 1999. 285(4):1377-82. [Abstract]
  Pharmaceutical design is usually directed at developing small molecules that can specifically bind and alter the activity of a target protein. Here, we show that high-affinity binding of small molecules requires a rough patch on a protein surface. Drug design strategies should therefore be targeted to rough areas on a protein. Our results indicate that the roughness of small functional sites may reflect the complex local shapes needed to fit specific interactions into small areas.

1997

• Zhou Y, Wen J, Bowie JU. (1997). A passive transmembrane helix. Nat. Struct. Biol.. Dec 1997. 4(12):986-90. [Abstract]
• Bowie JU. (1997). Helix packing in membrane proteins. J. Mol. Biol.. Oct 1997. 272(5):780-9. [Abstract]
  A survey of 45 transmembrane (TM) helices and 88 helix packing interactions in three independent transmembrane protein structures reveals the following features. (1) Helix lengths range from 14 to 36 residues with an average length of 26.4 residues. There is a preference for lengths greater than 20 residues. (2) The helices are tilted with respect to the bilayer normal by an average of 21 degrees, but there is a decided preference for smaller tilt angles. (3) The distribution of helix packing angles is very different than for soluble proteins. The most common packing angles for TM helices are centered around +20 degrees while for soluble proteins packing angles of around -35 degrees are the most prevalent. (4) The average distance of closest approach is 9.6 A, which is the same as soluble proteins. (5) There is no preference for the positioning of the point of closest approach along the length of the helices. (6) It is almost a rule that TM helices pack against neighbors in the sequence. Of the 37 helices that have a sequence neighbor, 36 of them are in significant contact with a neighbor. (7) An antiparallel orientation is more prevalent than a parallel orientation and antiparallel interactions are more intimate on average. The general features of helix bundle membrane protein architecture described in this survey should prove useful in the modeling of helix bundle transmembrane proteins.
• Bowie JU. (1997). Helix packing angle preferences. Nat. Struct. Biol.. Nov 1997. 4(11):915-7. [Abstract]
  The distribution of interaxial angles between packed alpha-helices has been explained by a number of elegant models describing how side chains on helices can interdigitate without steric conflicts. Here I show that much of the apparent preference for particular angles is due to statistical bias and that true packing angle preferences are not well described by regular packing models.
• Lau FW, Bowie JU. (1997). A method for assessing the stability of a membrane protein. Biochemistry. May 1997. 36(19):5884-92. [Abstract]
  The integral membrane protein diacylglycerol kinase (DGK) from Escherichia coli has been reversibly unfolded in a protein/detergent/mixed micelle system by varying the molar ratio of n-decyl beta-D-maltoside (DM) and sodium dodecyl sulfate (SDS). Unfolding was monitored by circular dichroism (CD) and ultraviolet (UV) absorbance spectroscopy. When unfolding is monitored by measuring changes in absorbance at 294 nm, two distinct denaturation phases are observed, indicative of a stable intermediate. When CD is used as a conformational probe, the resulting denaturation curve contains only one major transition, which corresponds to the first unfolding phase observed by absorbance changes. The unfolding behavior of several mutant proteins in which the tryptophan residues were selectively replaced made it possible to assign the first unfolding phase to a denaturation event in a cytoplasmic domain and the second phase to denaturation of the membrane-embedded portion of the protein. The denaturation curves fit well to a model which assumes two cooperative transitions and a linear relationship between unfolding free energy and SDS concentration. Extrapolation back to zero denaturant indicates an unfolding free energy of 6 kcal/mol for the cytoplasmic domain and 16 kcal/mol for the transmembrane domain. The high apparent stability of the transmembrane domain could explain the high degree of tolerance to amino acid substitutions seen for DGK and other membrane proteins. The approach described in this paper may be applicable to other membrane protein systems.
• Eisenberg D, Lüthy R, Bowie JU. (1997). VERIFY3D: assessment of protein models with three-dimensional profiles. Meth. Enzymol.. 1997. 277:396-404. [Abstract]

1996

• Thanos CD, Bowie JU. (1996). Developmentally expressed myosin heavy-chain kinase possesses a diacylglycerol kinase domain. Protein Sci.. Apr 1996. 5(4):782-5. [Abstract]
  In Dictyostelium, an ordered actin and myosin assembly-disassembly process is necessary for proper development, differentiation, and motility (Yumura S, Fukui F, 1985, Nature 314(6007): 194-196; Ravid S, Spudich JA, 1989, J Biol Chem 264(25): 15144-15150), and phosphorylation of myosin heavy chains has been implicated in the myosin assembly-disassembly process (Egelhoff TT, Lee RJ, Spudich JA, 1993, Cell 75(2):363-371). The developmentally expressed 84-kDa myosin heavy-chain kinase (MHCK) from Dictyostelium (Ravid S, Spudich JA, 1992, Proc Natl Acad Sci USA 89(13):5877-5881) is known to be a member of the protein kinase C (PKC) family. We have observed a rather striking homology between the large central domain of MHCK and the catalytic domain of diacylglycerol kinase (DGK), indicating that MHCK is in fact a gene fusion between a DGK and a PKC, possessing two separate kinase domains. The combined diacylglycerol kinase/myosin heavy-chain kinase (DGK/MHCK) may therefore have dual functionality, possessing the ability to phosphorylate both protein and lipid. We present a hypothesis that DGK/MHCK can antagonize both actin and myosin assembly, as well as other cellular processes, by coordinated down regulation of signaling via myosin heavy-chain kinase activity and diacylglycerol kinase activity.
• Wen J, Chen X, Bowie JU. (1996). Exploring the allowed sequence space of a membrane protein. Nat. Struct. Biol.. Feb 1996. 3(2):141-8. [Abstract]
  We present a comprehensive view of the tolerance of a membrane protein to sequence substitution. We find that the protein, diacylglycerol kinase from Escherichia coli, is extremely tolerant to sequence changes with three-quarters of the residues tolerating non-conservative changes. The conserved residues are distributed with approximately the same frequency in the soluble and transmembrane portions of the protein, but the most critical active-site residues appear to residue in the second cytoplasmic domain. It is remarkable that a unique structure of the membrane embedded portion of the protein can be encoded by a sequence that is so tolerant to substitution.
• Bowie JU, Zhang K, Wilmanns M, Eisenberg D. (1996). Three-dimensional profiles for measuring compatibility of amino acid sequence with three-dimensional structure. Meth. Enzymol.. 1996. 266:598-616. [Abstract]
• Fischer D, Rice D, Bowie JU, Eisenberg D. (1996). Assigning amino acid sequences to 3-dimensional protein folds. FASEB J.. Jan 1996. 10(1):126-36. [Abstract]
  With the advent of genome sequencing projects, the amino acid sequences of thousands of proteins are determined every year. Each of these protein sequences must be identified with its function and its 3-dimensional structure for us to gain a full understanding of the molecular biology of organisms. To meet this challenge, new methods are being developed for fold recognition, the computational assignment of newly determined amino acid sequences to 3-dimensional protein structures. These methods start with a library of known 3-dimensional target protein structures. The new probe sequence is then aligned to each target protein structure in the library and the compatibility of the sequence for that structure is scored. If a target structure is found to have a significantly high compatibility score, it is assumed that the probe sequence folds in much the same way as the target structure. The fundamental assumptions of this approach are that many different sequences fold in similar ways and there is a relatively high probability that a new sequence possesses a previously observed fold. We review various approaches to fold recognition and break down the process into its main steps: creation of a library of target folds; representation of the folds; alignment of the probe sequence to a target fold using a sequence-to-structure compatibility scoring function; and assessment of significance of compatibility. We emphasize that even though this new field of fold recognition has made rapid progress, technical problems remain to be solved in most of the steps. Standard benchmarks may help identify the problem steps and find solutions to the problems.

1995

• Bowie JU, Pakula AA, Simon MI. (1995). The three-dimensional structure of the aspartate receptor from Escherichia coli. Acta Crystallogr. D Biol. Crystallogr.. Mar 1995. 51(Pt 2):145-54. [Abstract]
  The crystal structure of the periplasmic domain of the aspartate receptor from Escherichia coli has been solved and refined to an R-factor of 0.203 at 2.3 A, resolution. The dimeric protein is largely helical, with four helices from each monomer forming a four-helix bundle. The dimer interface is constructed from four helices, two from each subunit, also packed together in a four-helix bundle arrangement. A sulfate ion occupies the aspartate-binding site. All hydrogen bonds made to aspartate are substituted by direct or water-mediated hydrogen bonds to the sulfate. Comparison of the Escherichia coli aspartate-receptor structure with that of Salmonella typhimurium [Milburn, Prive, Milligan, Scott, Yeh, Jancarik, Koshland & Kim (1991). Science, 254, 1342-1347; Scott, Milligan, Milburn, Prive, Yeh, Koshland & Kim (1993). J. Mol. Biol. 232, 555-573] reveals strong conservation in the structure of the monomer, but more divergence in the orientation of the subunits with respect to one another. Mutations that render the Escherichia coli receptor incapable of responding to maltose are either located in spatially conserved sites or in regions of the structures that have high temperature factors and are therefore likely to be quite flexible. The inability of the receptor from Salmonella typhimurium to respond to maltose may, therefore, be because of differences in amino acids located on the binding surface rather than structural differences.

1994

• Bowie JU, Eisenberg D. (1994). An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function. Proc. Natl. Acad. Sci. U.S.A.. May 1994. 91(10):4436-40. [Abstract]
  Three short protein sequences have been guided by computer to folds resembling their crystal structures. Initially, peptide fragment conformations ranging in size from 9 to 25 residues were selected from a database of known protein structures. A fragment was selected if it was compatible with a segment of the sequence to be folded, as judged by three-dimensional profile scores. By linking the selected fragment conformations together, hundreds of trial structures were generated of the same length and sequence as the protein to be folded. These starting trial structures were then improved by an evolutionary algorithm. Selection pressure for improving the structures was provided by an energy function that was designed to guide the conformational search procedure toward the correct structure. We find that by evolution of only 400 structures for fewer than 1400 generations, the overall fold of some small helical proteins can be computed from the sequence, with deviations from observed structures of 2.5-4.0 A for C alpha atoms.

1992

• Lüthy R, Bowie JU, Eisenberg D. (1992). Assessment of protein models with three-dimensional profiles. Nature. Mar 1992. 356(6364):83-5. [Abstract]
  As methods for determining protein three-dimensional (3D) structure develop, a continuing problem is how to verify that the final protein model is correct. The revision of several protein models to correct errors has prompted the development of new criteria for judging the validity of X-ray and NMR structures, as well as the formation of energetic and empirical methods to evaluate the correctness of protein models. The challenge is to distinguish between a mistraced or wrongly folded model, and one that is basically correct, but not adequately refined. We show that an effective test of the accuracy of a 3D protein model is a comparison of the model to its own amino-acid sequence, using a 3D profile, computed from the atomic coordinates of the structure 3D profiles of correct protein structures match their own sequences with high scores. In contrast, 3D profiles for protein models known to be wrong score poorly. An incorrectly modelled segment in an otherwise correct structure can be identified by examining the profile score in a moving-window scan. The accuracy of a protein model can be assessed by its 3D profile, regardless of whether the model has been derived by X-ray, NMR or computational procedures.
• Eisenberg D, Bowie JU, Lüthy R, Choe S. (1992). Three-dimensional profiles for analysing protein sequence-structure relationships. Faraday Discuss.. 1992. (93):25-34. [Abstract]
  In the method of 3D (three-dimensional) profiles, each residue position in a protein is characterized by its environment and is represented by a row of 20 numbers in a table, the profile. These numbers are the statistical preferences (called 3D-1D scores) of each of the 20 amino acids for this environment. A profile is computed from the coordinates of a protein model, and it gives a score S for any amino acid sequence folded as the model. To date 3D profiles have found three applications. The first is to identify other protein sequences which are folded in the same general pattern as the structure from which the profile was prepared. These are sequences which have high scores for the profile computed from the model. The second is to assess the validity of protein models, however determined. Correct models are found to give profiles that have high scores for their own amino acid sequences, and incorrect models are found to have lower scores. The example of the X-ray structure determination of diphtheria toxin is discussed. The third application is to assess which is the stable oligomeric state of a folded protein. Several examples suggest that the highest profile score for a sequence is achieved when the protein is aggregated into its most stable oligomeric state.

1991

• Bowie JU, Lüthy R, Eisenberg D. (1991). A method to identify protein sequences that fold into a known three-dimensional structure. Science. Jul 1991. 253(5016):164-70. [Abstract]
  The inverse protein folding problem, the problem of finding which amino acid sequences fold into a known three-dimensional (3D) structure, can be effectively attacked by finding sequences that are most compatible with the environments of the residues in the 3D structure. The environments are described by: (i) the area of the residue buried in the protein and inaccessible to solvent; (ii) the fraction of side-chain area that is covered by polar atoms (O and N); and (iii) the local secondary structure. Examples of this 3D profile method are presented for four families of proteins: the globins, cyclic AMP (adenosine 3',5'-monophosphate) receptor-like proteins, the periplasmic binding proteins, and the actins. This method is able to detect the structural similarity of the actins and 70- kilodalton heat shock proteins, even though these protein families share no detectable sequence similarity.
• Mossing MC, Bowie JU, Sauer RT. (1991). A streptomycin selection for DNA-binding activity. Meth. Enzymol.. 1991. 208:604-19. [Abstract]
• Reidhaar-Olson JF, Bowie JU, Breyer RM, Hu JC, Knight KL, Lim WA, Mossing MC, Parsell DA, Shoemaker KR, Sauer RT. (1991). Random mutagenesis of protein sequences using oligonucleotide cassettes. Meth. Enzymol.. 1991. 208:564-86. [Abstract]

1990

• Brown BM, Bowie JU, Sauer RT. (1990). Arc repressor is tetrameric when bound to operator DNA. Biochemistry. Dec 1990. 29(51):11189-95. [Abstract]
  The Arc repressor of bacteriophage P22 is a member of a family of DNA-binding proteins that use N-terminal residues in a beta-sheet conformation for operator recognition. Here, Arc is shown to bind to its operator site as a tetramer. When mixtures of Arc (53 residues) and an active variant of Arc (78 residues) are used in gel retardation experiments, five discrete protein-DNA complexes are observed. This result is as expected for operators bearing heterotetramers containing 4:0, 3:1, 2:2, 1:3, and 0:4 ratios of the two proteins. Direct measurements of binding stoichiometry support the conclusion that Arc binds to a single 21-base-pair operator site as a tetramer. The Arc-operator binding reaction is highly cooperative (Hill constant = 3.5) and involves at least two coupled equilibria. In the first reaction, two unfolded monomers interact to form a folded dimer (Bowie & Sauer, 1989a). Rapid dilution experiments indicate that the Arc dimer is the kinetically significant DNA-binding species and allow an estimate of the equilibrium dissociation constant for dimerization [K1 = 5 (+/- 3) x 10(-9) M]. The rate of association of Arc-operator complexes shows the expected second-order dependence on the concentration of free Arc dimers, with k2 = 2.8 (+/- 0.7) x 10(18) M-2 s-1. The dissociation of Arc-operator complexes is a first-order process with k-2 = 1.6 (+/- 0.6) x 10(-4) s-1. The ratio of these kinetic constants [K2 = 5.7 (+/- 2.3) x 10(-23) M2] provides an estimate for the equilibrium constant for dissociation of the DNA-bound tetramer to two free Arc dimers and the operator. An independent determination of this complex equilibrium constant [K2 = 7.8 (+/- 4.8) x 10(-23) M2] was obtained from equilibrium binding experiments.
• Bowie JU, Reidhaar-Olson JF, Lim WA, Sauer RT. (1990). Deciphering the message in protein sequences: tolerance to amino acid substitutions. Science. Mar 1990. 247(4948):1306-10. [Abstract]
  An amino acid sequence encodes a message that determines the shape and function of a protein. This message is highly degenerate in that many different sequences can code for proteins with essentially the same structure and activity. Comparison of different sequences with similar messages can reveal key features of the code and improve understanding of how a protein folds and how it performs its function.
• Bowie JU, Sauer RT. (1990). TraY proteins of F and related episomes are members of the Arc and Mnt repressor family. J. Mol. Biol.. Jan 1990. 211(1):5-6. [Abstract]
  Amino acid changes known to be structurally allowed in Arc repressor were used to aid in the identification of proteins with sequence similarity to Arc and the related Mnt repressor. The sequences of the TraY proteins from the F episome and related episomes were found to be similar to those of Arc and Mnt.
• Bowie JU, Clarke ND, Pabo CO, Sauer RT. (1990). Identification of protein folds: matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures. Proteins. 1990. 7(3):257-64. [Abstract]
  Hydrophobic side chains often are buried in the interior of a protein, and evolutionarily related proteins usually maintain the hydrophobic character of buried positions. In this paper we show that a pattern of hydrophobicity values derived from a set of related protein sequences is well correlated with the linear pattern of side-chain solvent accessibility values, calculated from a known protein structure representative of the sequences. In several cases, information from aligned sequences can be used to select the correct tertiary fold from a large data base of protein structures.

1989

• Zagorski MG, Bowie JU, Vershon AK, Sauer RT, Patel DJ. (1989). NMR studies of Arc repressor mutants: proton assignments, secondary structure, and long-range contacts for the thermostable proline-8----leucine variant of Arc. Biochemistry. Dec 1989. 28(25):9813-25. [Abstract]
  Arc repressor is a 53-residue sequence-specific DNA binding protein. We report the assignment of the proton NMR spectrum and the secondary structure for the thermostable PL8 variant of Arc. This mutant, which differs from wild type by a Pro-8----Leu substitution, was chosen for study because its enhanced stability allows spectra to be acquired at elevated temperatures where spectral resolution is higher. The first five residues of the protein play important roles in DNA binding but appear to be disordered in solution. Residues 6-14 form the remaining part of the N-terminal DNA binding region of the protein and assume an antiparallel beta-conformation. This indicates that Arc is a member of a new class of DNA binding proteins. The observed interresidue nuclear Overhauser effects are consistent with a beta-strand, gamma-turn, beta-strand structure for the residue 6-14 region, although other structures are also consistent with the data. The remaining portion of the protein is predominantly alpha-helical. Residues 16-26 and 35-50 form amphipathic alpha-helices which may pack together in a four-helix bundle in the protein dimer.
• Bowie JU, Sauer RT. (1989). Equilibrium dissociation and unfolding of the Arc repressor dimer. Biochemistry. Sep 1989. 28(18):7139-43. [Abstract]
  The equilibrium unfolding reaction of Arc repressor, a dimeric DNA binding protein encoded by bacteriophage P22, can be monitored by fluorescence or circular dichroism changes. The stability of Arc is concentration dependent, and the unfolding reaction is well described as a two-state transition from folded dimer to unfolded monomer. The stability of the protein is decreased at low pH and increased by high salt concentration. The salt dependence suggests that two ions bind preferentially to the folded protein. In 10 mM potassium phosphate (pH 7.3) and 100 mM KCl, the unfolding free energy reaches a maximum near room temperature. The results suggest that at the low protein concentrations where operator DNA binding is normally measured, Arc is predominantly monomeric and unfolded.
• Bowie JU, Sauer RT. (1989). Identification of C-terminal extensions that protect proteins from intracellular proteolysis. J. Biol. Chem.. May 1989. 264(13):7596-602. [Abstract]
  Revertants of defective mutants in the Arc repressor of bacteriophage P22 were isolated. Five of the six reverting mutations were frameshifts near the end of the coding sequence which resulted in proteins with C-terminal extensions. Each of the reverting mutations prolong the half-lives in vivo of the proteins in which they reside, yet they do not alter the thermodynamic stability, structure, oligomeric form, or DNA-binding properties of these proteins. Fusion of one of these tails to the C-terminal end of a mutant form of the N-terminal domain of lambda repressor also prevented proteolysis of this protein. These C-terminal sequences may prevent degradation by blocking the recognition of unstable proteins by the proteolytic machinery in the cell.
• Bowie JU, Sauer RT. (1989). Identifying determinants of folding and activity for a protein of unknown structure. Proc. Natl. Acad. Sci. U.S.A.. Apr 1989. 86(7):2152-6. [Abstract]
  We have generated an extensive genetic map of functionally allowed and/or structurally allowed amino acid substitutions in Arc repressor, a DNA binding protein of unknown structure. Analysis of the allowed substitution patterns identifies residues that are likely to be involved in protein function and identifies side chains that play important structural roles, including residues likely to form the hydrophobic core. The identities of approximately one-third of the residues in Arc repressor are functionally important, about one-half are structurally important, and the remainder are unimportant for either structure or function. The patterns of obligatory hydrophobic positions permit strong predictions of secondary structure.
• Knight KL, Bowie JU, Vershon AK, Kelley RD, Sauer RT. (1989). The Arc and Mnt repressors. A new class of sequence-specific DNA-binding protein. J. Biol. Chem.. Mar 1989. 264(7):3639-42. [Abstract]
  Genetic, biochemical, and biophysical studies have begun to reveal details of the structures of Arc and Mnt and show that these repressors use residues at their N-terminal ends for operator recognition and binding. Some of the DNA contacts made by these residues have been identified, and this information together with NMR studies has permitted the construction of models of the DNA binding region. Although the accuracy of these models remains to be determined, it seems clear that Arc and Mnt are members of a new class of DNA-binding proteins.

1986

• Vershon AK, Bowie JU, Karplus TM, Sauer RT. (1986). Isolation and analysis of arc repressor mutants: evidence for an unusual mechanism of DNA binding. Proteins. Dec 1986. 1(4):302-11. [Abstract]
  We have isolated 64 different missense mutations at 36 out of 53 residue positions in the Arc repressor of bacteriophage P22. Many of the mutant proteins with substitutions in the C-terminal 40 residues of Arc have reduced intracellular levels and probably have altered structures or stabilities. Mutations in the N-terminal ten residues of Arc cause large decreases in operator DNA binding affinity without affecting the ability of Arc to fold into a stable three-dimensional structure. We argue that these N-terminal residues are important for operator recognition but that they are not part of a conventional helix-turn-helix DNA binding structure. These results suggest that Arc may use a new mechanism for sequence specific DNA binding.

1984

• Bowie JU, Gray GR. (1984). Synthesis and mass spectra of the partially methylated and partially ethylated anhydro-D-mannitol acetates derived by reductive cleavage of permethylated and perethylated Saccharomyces cerevisiae D-mannans. Carbohydr. Res.. Jul 1984. 129:87-97. [Abstract]
  Reductive cleavage of per-O-ethylated or per-O-methylated Saccharomyces cerevisiae D-mannans and subsequent acetylation had previously been shown to produce the expected derivatives of 1,5-anhydro-D-mannitol. Described herein is the independent synthesis of each of these derivatives, namely, 1,5-anhydro-2,3,4,6-tetra-O-methyl-, -2,3,4,6-tetra-O-ethyl-, -2-O-acetyl-3,4,6-tri-O-methyl-, -2-O-acetyl-3,4,6-tri-O-ethyl-, -3-O-acetyl-2,4,6-tri-O-methyl-, -3-O-acetyl-2,4,6-tri-O-ethyl-, -6-O-acetyl-2,3,4-tri-O-methyl-, -6-O-acetyl-2,3,4-tri-O-ethyl-, -2,6-di-O-acetyl-3,4-di-O-methyl-, -2,6-di-O-acetyl-3,4-di-O-ethyl-, -3,6-di-O-acetyl-2,4-di-O-methyl-, and -3,6-di-O-acetyl-2,4-di-O-ethyl-D-mannitol. The 1H-n.m.r. spectra, chemical-ionization (NH3) mass spectra, and electron-impact mass spectra for all of these derivatives are tabulated.
• Bowie JU, Trescony PV, Gray GR. (1984). Analysis of linkage positions in Saccharomyces cerevisiae D-mannans by the reductive-cleavage method. Carbohydr. Res.. Feb 1984. 125(2):301-7. [Abstract]
  The positions of linkage in the D-mannans derived from Saccharomyces cerevisiae X2180 and its mutants, mnn1, mnn2, and mnn4, were established by perethylation and subsequent reductive cleavage with triethylsilane in the presence of boron trifluoride etherate (BF3 . Et2O) or trimethylsilyl trifluoromethanesulfonate. With the latter as the catalyst, all glycosidic carbon-oxygen bonds were cleaved, to produce a mixture of ethylated 1,5-anhydro-D-mannitol derivatives. With BF3 . Et2O as the catalyst, 2-, 3-, and 6-linked residues were incompletely cleaved, and residues linked at both O-2 and O-6 were not cleaved at all. It was concluded that reductive cleavage is an attractive method for determination of the structure of polysaccharides.
• Wright CD, Bowie JU, Nelson RD. (1984). Influence of yeast mannan on release of myeloperoxidase by human neutrophils: determination of structural features of mannan required for formation of myeloperoxidase-mannan-neutrophil complexes. Infect. Immun.. Feb 1984. 43(2):467-71. [Abstract]
  Structural features of mannan which participate in the formation of myeloperoxidase-mannan-neutrophil complexes have been studied by using a battery of structurally modified mannans. Mannan was isolated from Saccharomyces cerevisiae X2180 wild type and modified by strong alkaline degradation, selective (mild) alkaline degradation, and selective acetolysis. Mannose oligosaccharides bound to the peptide portion of mannan appeared to be required for binding of mannan to the neutrophil. The interaction of mannan with myeloperoxidase appeared to occur through phosphate groups of the mannan outer chain. The myeloperoxidase-mannan interaction was determined to be ionic in nature. The mannan-neutrophil interaction may involve cell membrane receptors for mannose.

1983

• Wright CD, Bowie JU, Gray GR, Nelson RD. (1983). Candidacidal activity of myeloperoxidase: mechanisms of inhibitory influence of soluble cell wall mannan. Infect. Immun.. Oct 1983. 42(1):76-80. [Abstract]
  We have previously demonstrated the ability of human neutrophil myeloperoxidase to bind to mannan isolated from Candida albicans. Mannan may therefore be a primary component of the yeast cell wall which provides for binding of myeloperoxidase, a requirement potentially important for the candidacidal activity of the enzyme. In this report, we describe experiments to consider the relationship of the mannan-binding activity of myeloperoxidase to its candidacidal activity and the possibility that free mannan may inhibit myeloperoxidase-mediated candidacidal activity. We observed that binding of myeloperoxidase to the target yeasts was required for killing of C. albicans. We also observed that addition of soluble mannan significantly reduced myeloperoxidase-mediated killing of the yeasts in a dose-dependent manner by antagonizing binding of myeloperoxidase. Soluble mannan was demonstrated to have a similar dose-dependent inhibitory effect on neutrophil-mediated candidacidal activity without influencing phagocytosis of the organism. On the basis of these observations, we speculate that mannan solubilized in plasma and tissue fluid may interfere with neutrophil-mediated host defense against Candida infection.