2015

Bobik TA, Lehman BP, Yeates TO
Bacterial microcompartments: widespread prokaryotic organelles for isolation and optimization of metabolic pathways.

Mol. Microbiol.. Jul 2015. :. 2015 PMID: 26148529
| 10.1111/mmi.13117

Ort DR, Merchant SS, Alric J, Barkan A, Blankenship RE, Bock R, Croce R, Hanson MR, Hibberd JM, Long SP, Moore TA, Moroney J, Niyogi KK, Parry MA, Peralta-Yahya PP, Prince RC, Redding KE, Spalding MH, van Wijk KJ, Vermaas WF, von Caemmerer S, Weber AP, Yeates TO, Yuan JS, Zhu XG
Redesigning photosynthesis to sustainably meet global food and bioenergy demand.

Proc. Natl. Acad. Sci. U.S.A.. Jun 2015. :. 2015 PMID: 26124102
| 10.1073/pnas.1424031112

McNamara DE, Senese S, Yeates TO, Torres JZ
Structures of potent anticancer compounds bound to tubulin.

Protein Sci.. Jul 2015. 24(7):1164-72. 2015 PMID: 25970265
| 10.1002/pro.2704

Liu Y, Jorda J, Yeates TO, Bobik TA
The PduL Phosphotransacylase Is Used To Recycle Coenzyme A within the Pdu Microcompartment.

J. Bacteriol.. Jul 2015. 197(14):2392-9. 2015 PMID: 25962918
| 10.1128/JB.00056-15

Thompson MC, Cascio D, Leibly DJ, Yeates TO
An allosteric model for control of pore opening by substrate binding in the EutL microcompartment shell protein.

Protein Sci.. Jun 2015. 24(6):956-75. 2015 PMID: 25752492
| PMC4456109 | 10.1002/pro.2672

Chowdhury C, Chun S, Pang A, Sawaya MR, Sinha S, Yeates TO, Bobik TA
Selective molecular transport through the protein shell of a bacterial microcompartment organelle.

Proc. Natl. Acad. Sci. U.S.A.. Mar 2015. 112(10):2990-5. 2015 PMID: 25713376
| PMC4364225 | 10.1073/pnas.1423672112

Jorda J, Liu Y, Bobik TA, Yeates TO
Exploring bacterial organelle interactomes: a model of the protein-protein interaction network in the Pdu microcompartment.

PLoS Comput. Biol.. Feb 2015. 11(2):e1004067. 2015 PMID: 25646976
| PMC4315436 | 10.1371/journal.pcbi.1004067

2014

Thompson MC, Crowley CS, Kopstein J, Bobik TA, Yeates TO
Structure of a bacterial microcompartment shell protein bound to a cobalamin cofactor.

Acta Crystallogr F Struct Biol Commun. Dec 2014. 70(Pt 12):1584-90. 2014 PMID: 25484204
| PMC4315436 | 10.1107/S2053230X1402158X

Lai YT, Reading E, Hura GL, Tsai KL, Laganowsky A, Asturias FJ, Tainer JA, Robinson CV, Yeates TO
Structure of a designed protein cage that self-assembles into a highly porous cube.

Nat Chem. Dec 2014. 6(12):1065-71. 2014 PMID: 25411884
| PMC4239666 | 10.1038/nchem.2107 | NIHMS632817

Bobik TA, Morales EJ, Shin A, Cascio D, Sawaya MR, Arbing M, Yeates TO, Rasche ME
Structure of the methanofuran/methanopterin-biosynthetic enzyme MJ1099 from Methanocaldococcus jannaschii.

Acta Crystallogr F Struct Biol Commun. Nov 2014. 70(Pt 11):1472-9. 2014 PMID: 25372812
| PMC4231847 | 10.1107/S2053230X1402130X

Chowdhury C, Sinha S, Chun S, Yeates TO, Bobik TA
Diverse bacterial microcompartment organelles.

Microbiol. Mol. Biol. Rev.. Sep 2014. 78(3):438-68. 2014 PMID: 25184561
| PMC4187681 | 10.1128/MMBR.00009-14

Thompson MC, Wheatley NM, Jorda J, Sawaya MR, Gidaniyan SD, Ahmed H, Yang Z, McCarty KN, Whitelegge JP, Yeates TO
Identification of a unique Fe-S cluster binding site in a glycyl-radical type microcompartment shell protein.

J. Mol. Biol.. Sep 2014. 426(19):3287-304. 2014 PMID: 25102080
| PMC4175982 | 10.1016/j.jmb.2014.07.018 | NIHMS617253

Jorda J, Sawaya MR, Yeates TO
CrowdPhase: crowdsourcing the phase problem.

Acta Crystallogr. D Biol. Crystallogr.. Jun 2014. 70(Pt 6):1538-48. 2014 PMID: 24914965
| PMC4051500 | 10.1107/S1399004714006427

King NP, Bale JB, Sheffler W, McNamara DE, Gonen S, Gonen T, Yeates TO, Baker D
Accurate design of co-assembling multi-component protein nanomaterials.

Nature. Jun 2014. 510(7503):103-8. 2014 PMID: 24870237
| PMC4137318 | 10.1038/nature13404 | NIHMS613084

Sinha S, Cheng S, Sung YW, McNamara DE, Sawaya MR, Yeates TO, Bobik TA
Alanine scanning mutagenesis identifies an asparagine-arginine-lysine triad essential to assembly of the shell of the Pdu microcompartment.

J. Mol. Biol.. Jun 2014. 426(12):2328-45. 2014 PMID: 24747050
| PMC4089897 | 10.1016/j.jmb.2014.04.012 | NIHMS592738

Jiménez-Osés G, Osuna S, Gao X, Sawaya MR, Gilson L, Collier SJ, Huisman GW, Yeates TO, Tang Y, Houk KN
The role of distant mutations and allosteric regulation on LovD active site dynamics.

Nat. Chem. Biol.. Jun 2014. 10(6):431-6. 2014 PMID: 24727900
| PMC4028369 | 10.1038/nchembio.1503 | NIHMS575619

Okamoto R, Mandal K, Sawaya MR, Kajihara Y, Yeates TO, Kent SB
(Quasi-)racemic X-ray structures of glycosylated and non-glycosylated forms of the chemokine Ser-CCL1 prepared by total chemical synthesis.

Angew. Chem. Int. Ed. Engl.. May 2014. 53(20):5194-8. 2014 PMID: 24692304
| PMC4028369 | 10.1002/anie.201400679

McNamara DE, Cascio D, Jorda J, Bustos C, Wang TC, Rasche ME, Yeates TO, Bobik TA
Structure of dihydromethanopterin reductase, a cubic protein cage for redox transfer.

J. Biol. Chem.. Mar 2014. 289(13):8852-64. 2014 PMID: 24523405
| PMC3979419 | 10.1074/jbc.M113.522342

Wheatley NM, Sundberg CD, Gidaniyan SD, Cascio D, Yeates TO
Structure and identification of a pterin dehydratase-like protein as a ribulose-bisphosphate carboxylase/oxygenase (RuBisCO) assembly factor in the α-carboxysome.

J. Biol. Chem.. Mar 2014. 289(11):7973-81. 2014 PMID: 24459150
| PMC3953307 | 10.1074/jbc.M113.531236

Thompson MC, Yeates TO
A challenging interpretation of a hexagonally layered protein structure.

Acta Crystallogr. D Biol. Crystallogr.. Jan 2014. 70(Pt 1):203-8. 2014 PMID: 24419393
| PMC4030663 | 10.1107/S139900471302422X

2013

Nguyen HB, Hung LW, Yeates TO, Terwilliger TC, Waldo GS
Split green fluorescent protein as a modular binding partner for protein crystallization.

Acta Crystallogr. D Biol. Crystallogr.. Dec 2013. 69(Pt 12):2513-23. 2013 PMID: 24311592
| PMC3852656 | 10.1107/S0907444913024608

Yeates TO, Jorda J, Bobik TA
The shells of BMC-type microcompartment organelles in bacteria.

J. Mol. Microbiol. Biotechnol.. 2013. 23(4-5):290-9. 2013 PMID: 23920492
| PMC3852656 | 10.1159/000351347

Lai YT, Tsai KL, Sawaya MR, Asturias FJ, Yeates TO
Structure and flexibility of nanoscale protein cages designed by symmetric self-assembly.

J. Am. Chem. Soc.. May 2013. 135(20):7738-43. 2013 PMID: 23621606
| PMC3700533 | 10.1021/ja402277f | NIHMS477800

Wheatley NM, Gidaniyan SD, Liu Y, Cascio D, Yeates TO
Bacterial microcompartment shells of diverse functional types possess pentameric vertex proteins.

Protein Sci.. May 2013. 22(5):660-5. 2013 PMID: 23456886
| PMC3649267 | 10.1002/pro.2246

Jorda J, Lopez D, Wheatley NM, Yeates TO
Using comparative genomics to uncover new kinds of protein-based metabolic organelles in bacteria.

Protein Sci.. Feb 2013. 22(2):179-95. 2013 PMID: 23188745
| PMC3588914 | 10.1002/pro.2196

2012

Lai YT, King NP, Yeates TO
Principles for designing ordered protein assemblies.

Trends Cell Biol.. Dec 2012. 22(12):653-61. 2012 PMID: 22975357
| PMC3588914 | 10.1016/j.tcb.2012.08.004

King NP, Sheffler W, Sawaya MR, Vollmar BS, Sumida JP, André I, Gonen T, Yeates TO, Baker D
Computational design of self-assembling protein nanomaterials with atomic level accuracy.

Science. Jun 2012. 336(6085):1171-4. 2012 PMID: 22654060
| PMC4138882 | 10.1126/science.1219364 | HHMIMS613117

Lai YT, Cascio D, Yeates TO
Structure of a 16-nm cage designed by using protein oligomers.

Science. Jun 2012. 336(6085):1129. 2012 PMID: 22654051
| PMC4138882 | 10.1126/science.1219351

Jones EY, Yeates TO
Structure and function in complex macromolecular assemblies: some evolutionary themes.

Curr. Opin. Struct. Biol.. Apr 2012. 22(2):197-9. 2012 PMID: 22444564
| PMC4138882 | 10.1016/j.sbi.2012.03.003

Yeates TO, Kent SB
Racemic protein crystallography.

Annu Rev Biophys. 2012. 41:41-61. 2012 PMID: 22443988
| PMC4138882 | 10.1146/annurev-biophys-050511-102333

Sawaya MR, Pentelute BL, Kent SB, Yeates TO
Single-wavelength phasing strategy for quasi-racemic protein crystal diffraction data.

Acta Crystallogr. D Biol. Crystallogr.. Jan 2012. 68(Pt 1):62-8. 2012 PMID: 22194334
| PMC4138882 | 10.1107/S0907444911049985

Johnson E, Nguyen PT, Yeates TO, Rees DC
Inward facing conformations of the MetNI methionine ABC transporter: Implications for the mechanism of transinhibition.

Protein Sci.. Jan 2012. 21(1):84-96. 2012 PMID: 22095702
| PMC3323783 | 10.1002/pro.765

2011

Tsai SJ, Yeates TO
Bacterial microcompartments insights into the structure, mechanism, and engineering applications.

Prog Mol Biol Transl Sci. 2011. 103:1-20. 2011 PMID: 21999993
| PMC3323783 | 10.1016/B978-0-12-415906-8.00008-X

Pickens LB, Sawaya MR, Rasool H, Pashkov I, Yeates TO, Tang Y
Structural and biochemical characterization of the salicylyl-acyltranferase SsfX3 from a tetracycline biosynthetic pathway.

J. Biol. Chem.. Dec 2011. 286(48):41539-51. 2011 PMID: 21965680
| PMC3308865 | 10.1074/jbc.M111.299859

Jorda J, Yeates TO
Widespread disulfide bonding in proteins from thermophilic archaea.

Archaea. 2011. 2011:409156. 2011 PMID: 21941460
| PMC3177088 | 10.1155/2011/409156

Laganowsky A, Zhao M, Soriaga AB, Sawaya MR, Cascio D, Yeates TO
An approach to crystallizing proteins by metal-mediated synthetic symmetrization.

Protein Sci.. Nov 2011. 20(11):1876-90. 2011 PMID: 21898649
| PMC3267952 | 10.1002/pro.727

Yeates TO
Nanobiotechnology: protein arrays made to order.

Nat Nanotechnol. Sep 2011. 6(9):541-2. 2011 PMID: 21804551
| PMC3267952 | 10.1038/nnano.2011.127

Sayre TC, Lee TM, King NP, Yeates TO
Protein stabilization in a highly knotted protein polymer.

Protein Eng. Des. Sel.. Aug 2011. 24(8):627-30. 2011 PMID: 21669955
| PMC3165941 | 10.1093/protein/gzr024

Yeates TO, Thompson MC, Bobik TA
The protein shells of bacterial microcompartment organelles.

Curr. Opin. Struct. Biol.. Apr 2011. 21(2):223-31. 2011 PMID: 21315581
| PMC3070793 | 10.1016/j.sbi.2011.01.006 | NIHMS274656

Forse GJ, Ram N, Banatao DR, Cascio D, Sawaya MR, Klock HE, Lesley SA, Yeates TO
Synthetic symmetrization in the crystallization and structure determination of CelA from Thermotoga maritima.

Protein Sci.. Jan 2011. 20(1):168-78. 2011 PMID: 21082721
| PMC3047073 | 10.1002/pro.550

2010

King NP, Jacobitz AW, Sawaya MR, Goldschmidt L, Yeates TO
Structure and folding of a designed knotted protein.

Proc. Natl. Acad. Sci. U.S.A.. Nov 2010. 107(48):20732-7. 2010 PMID: 21068371
| PMC2996448 | 10.1073/pnas.1007602107

Han GW, Elsliger MA, Yeates TO, Xu Q, Murzin AG, Krishna SS, Jaroszewski L, Abdubek P, Astakhova T, Axelrod HL, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Ernst D, Feuerhelm J, Grant JC, Grzechnik A, Jin KK, Johnson HA, Klock HE, Knuth MW, Kozbial P, Kumar A, Lam WW, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Okach L, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA
Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15.

Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.. Oct 2010. 66(Pt 10):1237-44. 2010 PMID: 20944217
| PMC2954211 | 10.1107/S1744309110025534

Pentelute BL, Mandal K, Gates ZP, Sawaya MR, Yeates TO, Kent SB
Total chemical synthesis and X-ray structure of kaliotoxin by racemic protein crystallography.

Chem. Commun. (Camb.). Nov 2010. 46(43):8174-6. 2010 PMID: 20877851
| PMC2954211 | 10.1039/c0cc03148h

Crowley CS, Cascio D, Sawaya MR, Kopstein JS, Bobik TA, Yeates TO
Structural insight into the mechanisms of transport across the Salmonella enterica Pdu microcompartment shell.

J. Biol. Chem.. Nov 2010. 285(48):37838-46. 2010 PMID: 20870711
| PMC2988387 | 10.1074/jbc.M110.160580

Banigan JR, Mandal K, Sawaya MR, Thammavongsa V, Hendrickx AP, Schneewind O, Yeates TO, Kent SB
Determination of the X-ray structure of the snake venom protein omwaprin by total chemical synthesis and racemic protein crystallography.

Protein Sci.. Oct 2010. 19(10):1840-9. 2010 PMID: 20669184
| PMC2998720 | 10.1002/pro.468

Fan C, Cheng S, Liu Y, Escobar CM, Crowley CS, Jefferson RE, Yeates TO, Bobik TA
Short N-terminal sequences package proteins into bacterial microcompartments.

Proc. Natl. Acad. Sci. U.S.A.. Apr 2010. 107(16):7509-14. 2010 PMID: 20308536
| PMC2867708 | 10.1073/pnas.0913199107

Yeates TO, Crowley CS, Tanaka S
Bacterial microcompartment organelles: protein shell structure and evolution.

Annu Rev Biophys. 2010. 39:185-205. 2010 PMID: 20192762
| PMC3272493 | 10.1146/annurev.biophys.093008.131418 | NIHMS348791

Tanaka S, Sawaya MR, Yeates TO
Structure and mechanisms of a protein-based organelle in Escherichia coli.

Science. Jan 2010. 327(5961):81-4. 2010 PMID: 20044574
| PMC3272493 | 10.1126/science.1179513

2009

Sprinzak E, Cokus SJ, Yeates TO, Eisenberg D, Pellegrini M
Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression.

BMC Syst Biol. 2009. 3:115. 2009 PMID: 20003439
| PMC2804736 | 10.1186/1752-0509-3-115

Gao X, Xie X, Pashkov I, Sawaya MR, Laidman J, Zhang W, Cacho R, Yeates TO, Tang Y
Directed evolution and structural characterization of a simvastatin synthase.

Chem. Biol.. Oct 2009. 16(10):1064-74. 2009 PMID: 19875080
| PMC2798062 | 10.1016/j.chembiol.2009.09.017 | NIHMS152165

Dryden KA, Crowley CS, Tanaka S, Yeates TO, Yeager M
Two-dimensional crystals of carboxysome shell proteins recapitulate the hexagonal packing of three-dimensional crystals.

Protein Sci.. Dec 2009. 18(12):2629-35. 2009 PMID: 19844993
| PMC2821281 | 10.1002/pro.272

Tsai Y, Sawaya MR, Yeates TO
Analysis of lattice-translocation disorder in the layered hexagonal structure of carboxysome shell protein CsoS1C.

Acta Crystallogr. D Biol. Crystallogr.. Sep 2009. 65(Pt 9):980-8. 2009 PMID: 19690376
| PMC2821281 | 10.1107/S0907444909025153

Yu F, Song A, Xu C, Sun L, Li J, Tang L, Yu M, Yeates TO, Hu H, He J
Determining the DUF55-domain structure of human thymocyte nuclear protein 1 from crystals partially twinned by tetartohedry.

Acta Crystallogr. D Biol. Crystallogr.. Mar 2009. 65(Pt 3):212-9. 2009 PMID: 19237743
| PMC2821281 | 10.1107/S0907444908041474

Tanaka S, Sawaya MR, Phillips M, Yeates TO
Insights from multiple structures of the shell proteins from the beta-carboxysome.

Protein Sci.. Jan 2009. 18(1):108-20. 2009 PMID: 19177356
| PMC2708042 | 10.1002/pro.14

Beeby M, Bobik TA, Yeates TO
Exploiting genomic patterns to discover new supramolecular protein assemblies.

Protein Sci.. Jan 2009. 18(1):69-79. 2009 PMID: 19177352
| PMC2708037 | 10.1002/pro.1

Xie X, Pashkov I, Gao X, Guerrero JL, Yeates TO, Tang Y
Rational improvement of simvastatin synthase solubility in Escherichia coli leads to higher whole-cell biocatalytic activity.

Biotechnol. Bioeng.. Jan 2009. 102(1):20-8. 2009 PMID: 18988191
| PMC3928684 | 10.1002/bit.22028 | NIHMS552997

2008

Liu J, Mao Y, Lan E, Banatao DR, Forse GJ, Lu J, Blom HO, Yeates TO, Dunn B, Chang JP
Generation of oxide nanopatterns by combining self-assembly of S-layer proteins and area-selective atomic layer deposition.

J. Am. Chem. Soc.. Dec 2008. 130(50):16908-13. 2008 PMID: 19053479
| PMC3928684 | 10.1021/ja803186e

Yeates TO, Yu F
Equations for determining tetartohedral twin fractions.

Acta Crystallogr. D Biol. Crystallogr.. Nov 2008. 64(Pt 11):1158-64. 2008 PMID: 19020354
| PMC3928684 | 10.1107/S0907444908028928

Kudryashov DS, Durer ZA, Ytterberg AJ, Sawaya MR, Pashkov I, Prochazkova K, Yeates TO, Loo RR, Loo JA, Satchell KJ, Reisler E
Connecting actin monomers by iso-peptide bond is a toxicity mechanism of the Vibrio cholerae MARTX toxin.

Proc. Natl. Acad. Sci. U.S.A.. Nov 2008. 105(47):18537-42. 2008 PMID: 19015515
| PMC2587553 | 10.1073/pnas.0808082105

Cheng S, Liu Y, Crowley CS, Yeates TO, Bobik TA
Bacterial microcompartments: their properties and paradoxes.

Bioessays. Nov 2008. 30(11-12):1084-95. 2008 PMID: 18937343
| PMC3272490 | 10.1002/bies.20830 | NIHMS348799

Crowley CS, Sawaya MR, Bobik TA, Yeates TO
Structure of the PduU shell protein from the Pdu microcompartment of Salmonella.

Structure. Sep 2008. 16(9):1324-32. 2008 PMID: 18786396
| PMC3272490 | 10.1016/j.str.2008.05.013

Yeates TO, Kerfeld CA, Heinhorst S, Cannon GC, Shively JM
Protein-based organelles in bacteria: carboxysomes and related microcompartments.

Nat. Rev. Microbiol.. Sep 2008. 6(9):681-91. 2008 PMID: 18679172
| PMC3272490 | 10.1038/nrmicro1913

King NP, Lee TM, Sawaya MR, Cascio D, Yeates TO
Structures and functional implications of an AMP-binding cystathionine beta-synthase domain protein from a hyperthermophilic archaeon.

J. Mol. Biol.. Jun 2008. 380(1):181-92. 2008 PMID: 18513746
| PMC2577872 | 10.1016/j.jmb.2008.04.073 | NIHMS56785

Sawaya MR, Kudryashov DS, Pashkov I, Adisetiyo H, Reisler E, Yeates TO
Multiple crystal structures of actin dimers and their implications for interactions in the actin filament.

Acta Crystallogr. D Biol. Crystallogr.. Apr 2008. 64(Pt 4):454-65. 2008 PMID: 18391412
| PMC2631129 | 10.1107/S0907444908003351

Tanaka S, Kerfeld CA, Sawaya MR, Cai F, Heinhorst S, Cannon GC, Yeates TO
Atomic-level models of the bacterial carboxysome shell.

Science. Feb 2008. 319(5866):1083-6. 2008 PMID: 18292340
| PMC2631129 | 10.1126/science.1151458

2007

Yeates TO, Clubb RT
Biochemistry. How some pili pull.

Science. Dec 2007. 318(5856):1558-9. 2007 PMID: 18063774
| PMC2631129 | 10.1126/science.1151398

Yeates TO, Norcross TS, King NP
Knotted and topologically complex proteins as models for studying folding and stability.

Curr Opin Chem Biol. Dec 2007. 11(6):595-603. 2007 PMID: 17967433
| PMC2179896 | 10.1016/j.cbpa.2007.10.002 | NIHMS35923

Tanaka S, Sawaya MR, Kerfeld CA, Yeates TO
Structure of the RuBisCO chaperone RbcX from Synechocystis sp. PCC6803.

Acta Crystallogr. D Biol. Crystallogr.. Oct 2007. 63(Pt 10):1109-12. 2007 PMID: 17881829
| PMC2179896 | 10.1107/S090744490704228X

King NP, Yeates EO, Yeates TO
Identification of rare slipknots in proteins and their implications for stability and folding.

J. Mol. Biol.. Oct 2007. 373(1):153-66. 2007 PMID: 17764691
| PMC2179896 | 10.1016/j.jmb.2007.07.042

Tsai Y, Sawaya MR, Cannon GC, Cai F, Williams EB, Heinhorst S, Kerfeld CA, Yeates TO
Structural analysis of CsoS1A and the protein shell of the Halothiobacillus neapolitanus carboxysome.

PLoS Biol.. Jun 2007. 5(6):e144. 2007 PMID: 17518518
| PMC1872035 | 10.1371/journal.pbio.0050144

Yeates TO, Tsai Y, Tanaka S, Sawaya MR, Kerfeld CA
Self-assembly in the carboxysome: a viral capsid-like protein shell in bacterial cells.

Biochem. Soc. Trans.. Jun 2007. 35(Pt 3):508-11. 2007 PMID: 17511640
| PMC1872035 | 10.1042/BST0350508

Boutz DR, Cascio D, Whitelegge J, Perry LJ, Yeates TO
Discovery of a thermophilic protein complex stabilized by topologically interlinked chains.

J. Mol. Biol.. May 2007. 368(5):1332-44. 2007 PMID: 17395198
| PMC1955483 | 10.1016/j.jmb.2007.02.078 | NIHMS22846

Yeates TO
Protein structure: evolutionary bridges to new folds.

Curr. Biol.. Jan 2007. 17(2):R48-50. 2007 PMID: 17240325
| PMC1955483 | 10.1016/j.cub.2006.12.003

2006

Yeates TO, Beeby M
Biochemistry. Proteins in a small world.

Science. Dec 2006. 314(5807):1882-3. 2006 PMID: 17185587
| PMC1955483 | 10.1126/science.1137400

Banatao DR, Cascio D, Crowley CS, Fleissner MR, Tienson HL, Yeates TO
An approach to crystallizing proteins by synthetic symmetrization.

Proc. Natl. Acad. Sci. U.S.A.. Oct 2006. 103(44):16230-5. 2006 PMID: 17050682
| PMC1637565 | 10.1073/pnas.0607674103

Laidman J, Forse GJ, Yeates TO
Conformational change and assembly through edge beta strands in transthyretin and other amyloid proteins.

Acc. Chem. Res.. Sep 2006. 39(9):576-83. 2006 PMID: 16981673
| PMC1637565 | 10.1021/ar050017s

Norcross TS, Yeates TO
A framework for describing topological frustration in models of protein folding.

J. Mol. Biol.. Sep 2006. 362(3):605-21. 2006 PMID: 16930616
| PMC1637565 | 10.1016/j.jmb.2006.07.054

Sawaya MR, Cannon GC, Heinhorst S, Tanaka S, Williams EB, Yeates TO, Kerfeld CA
The structure of beta-carbonic anhydrase from the carboxysomal shell reveals a distinct subclass with one active site for the price of two.

J. Biol. Chem.. Mar 2006. 281(11):7546-55. 2006 PMID: 16407248
| PMC1637565 | 10.1074/jbc.M510464200

2005

Bowers PM, O’Connor BD, Cokus SJ, Sprinzak E, Yeates TO, Eisenberg D
Utilizing logical relationships in genomic data to decipher cellular processes.

FEBS J.. Oct 2005. 272(20):5110-8. 2005 PMID: 16218945
| PMC1637565 | 10.1111/j.1742-4658.2005.04946.x

Chaudhuri BN, Yeates TO
A computational method to predict genetically encoded rare amino acids in proteins.

Genome Biol.. 2005. 6(9):R79. 2005 PMID: 16168086
| PMC1242214 | 10.1186/gb-2005-6-9-r79

Kudryashov DS, Sawaya MR, Adisetiyo H, Norcross T, Hegyi G, Reisler E, Yeates TO
The crystal structure of a cross-linked actin dimer suggests a detailed molecular interface in F-actin.

Proc. Natl. Acad. Sci. U.S.A.. Sep 2005. 102(37):13105-10. 2005 PMID: 16141336
| PMC1196358 | 10.1073/pnas.0506429102

Beeby M, O’Connor BD, Ryttersgaard C, Boutz DR, Perry LJ, Yeates TO
The genomics of disulfide bonding and protein stabilization in thermophiles.

PLoS Biol.. Sep 2005. 3(9):e309. 2005 PMID: 16111437
| PMC1188242 | 10.1371/journal.pbio.0030309

Kerfeld CA, Sawaya MR, Tanaka S, Nguyen CV, Phillips M, Beeby M, Yeates TO
Protein structures forming the shell of primitive bacterial organelles.

Science. Aug 2005. 309(5736):936-8. 2005 PMID: 16081736
| PMC1188242 | 10.1126/science.1113397

2004

Bowers PM, Cokus SJ, Eisenberg D, Yeates TO
Use of logic relationships to decipher protein network organization.

Science. Dec 2004. 306(5705):2246-9. 2004 PMID: 15618515
| PMC1188242 | 10.1126/science.1103330

O’Connor BD, Yeates TO
GDAP: a web tool for genome-wide protein disulfide bond prediction.

Nucleic Acids Res.. Jul 2004. 32(Web Server issue):W360-4. 2004 PMID: 15215411
| PMC441514 | 10.1093/nar/gkh376

Bowers PM, Pellegrini M, Thompson MJ, Fierro J, Yeates TO, Eisenberg D
Prolinks: a database of protein functional linkages derived from coevolution.

Genome Biol.. 2004. 5(5):R35. 2004 PMID: 15128449
| PMC416471 | 10.1186/gb-2004-5-5-r35

Chaudhuri BN, Chan S, Perry LJ, Yeates TO
Crystal structure of the apo forms of psi 55 tRNA pseudouridine synthase from Mycobacterium tuberculosis: a hinge at the base of the catalytic cleft.

J. Biol. Chem.. Jun 2004. 279(23):24585-91. 2004 PMID: 15028724
| PMC416471 | 10.1074/jbc.M401045200

2003

Strong M, Graeber TG, Beeby M, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D
Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps.

Nucleic Acids Res.. Dec 2003. 31(24):7099-109. 2003 PMID: 14654685
| PMC291866

Kerfeld CA, Sawaya MR, Bottin H, Tran KT, Sugiura M, Cascio D, Desbois A, Yeates TO, Kirilovsky D, Boussac A
Structural and EPR characterization of the soluble form of cytochrome c-550 and of the psbV2 gene product from the cyanobacterium Thermosynechococcus elongatus.

Plant Cell Physiol.. Jul 2003. 44(7):697-706. 2003 PMID: 12881497
| PMC291866

Chaudhuri BN, Sawaya MR, Kim CY, Waldo GS, Park MS, Terwilliger TC, Yeates TO
The crystal structure of the first enzyme in the pantothenate biosynthetic pathway, ketopantoate hydroxymethyltransferase, from M tuberculosis.

Structure. Jul 2003. 11(7):753-64. 2003 PMID: 12842039
| PMC291866

Padilla JE, Yeates TO
A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning.

Acta Crystallogr. D Biol. Crystallogr.. Jul 2003. 59(Pt 7):1124-30. 2003 PMID: 12832754
| PMC291866

Kerfeld CA, Yoshida S, Tran KT, Yeates TO, Cascio D, Bottin H, Berthomieu C, Sugiura M, Boussac A
The 1.6 A resolution structure of Fe-superoxide dismutase from the thermophilic cyanobacterium Thermosynechococcus elongatus.

J. Biol. Inorg. Chem.. Sep 2003. 8(7):707-14. 2003 PMID: 12827458
| PMC291866 | 10.1007/s00775-003-0469-0

Elam JS, Taylor AB, Strange R, Antonyuk S, Doucette PA, Rodriguez JA, Hasnain SS, Hayward LJ, Valentine JS, Yeates TO, Hart PJ
Amyloid-like filaments and water-filled nanotubes formed by SOD1 mutant proteins linked to familial ALS.

Nat. Struct. Biol.. Jun 2003. 10(6):461-7. 2003 PMID: 12754496
| PMC291866 | 10.1038/nsb935

Rudolph MG, Kelker MS, Schneider TR, Yeates TO, Oseroff V, Heidary DK, Jennings PA, Wilson IA
Use of multiple anomalous dispersion to phase highly merohedrally twinned crystals of interleukin-1beta.

Acta Crystallogr. D Biol. Crystallogr.. Feb 2003. 59(Pt 2):290-8. 2003 PMID: 12554939
| PMC291866

Kerfeld CA, Sawaya MR, Brahmandam V, Cascio D, Ho KK, Trevithick-Sutton CC, Krogmann DW, Yeates TO
The crystal structure of a cyanobacterial water-soluble carotenoid binding protein.

Structure. Jan 2003. 11(1):55-65. 2003 PMID: 12517340
| PMC291866

2002

Larsen NA, Heine A, de Prada P, Redwan el-R, Yeates TO, Landry DW, Wilson IA
Structure determination of a cocaine hydrolytic antibody from a pseudomerohedrally twinned crystal.

Acta Crystallogr. D Biol. Crystallogr.. Dec 2002. 58(Pt 12):2055-9. 2002 PMID: 12454464
| PMC291866

Nitao LK, Yeates TO, Reisler E
Conformational dynamics of the SH1-SH2 helix in the transition states of myosin subfragment-1.

Biophys. J.. Nov 2002. 83(5):2733-41. 2002 PMID: 12414706
| PMC1302358 | 10.1016/S0006-3495(02)75283-1

Yeates TO
Structures of SET domain proteins: protein lysine methyltransferases make their mark.

Cell. Oct 2002. 111(1):5-7. 2002 PMID: 12372294
| PMC1302358

Serag AA, Altenbach C, Gingery M, Hubbell WL, Yeates TO
Arrangement of subunits and ordering of beta-strands in an amyloid sheet.

Nat. Struct. Biol.. Oct 2002. 9(10):734-9. 2002 PMID: 12219081
| PMC1302358 | 10.1038/nsb838

Yeates TO, Padilla JE
Designing supramolecular protein assemblies.

Curr. Opin. Struct. Biol.. Aug 2002. 12(4):464-70. 2002 PMID: 12163069
| PMC1302358

Mallick P, Boutz DR, Eisenberg D, Yeates TO
Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds.

Proc. Natl. Acad. Sci. U.S.A.. Jul 2002. 99(15):9679-84. 2002 PMID: 12107280
| PMC124975 | 10.1073/pnas.142310499

Kerfeld CA, Sawaya MR, Krogmann DW, Yeates TO
Structure of cytochrome c6 from Arthrospira maxima: an assembly of 24 subunits in a nearly symmetric shell.

Acta Crystallogr. D Biol. Crystallogr.. Jul 2002. 58(Pt 7):1104-10. 2002 PMID: 12077429
| PMC124975

Ryttersgaard C, Griffith SC, Sawaya MR, MacLaren DC, Clarke S, Yeates TO
Crystal structure of human L-isoaspartyl methyltransferase.

J. Biol. Chem.. Mar 2002. 277(12):10642-6. 2002 PMID: 11792715
| PMC124975 | 10.1074/jbc.M200229200

Thapar N, Griffith SC, Yeates TO, Clarke S
Protein repair methyltransferase from the hyperthermophilic archaeon Pyrococcus furiosus. Unusual methyl-accepting affinity for D-aspartyl and N-succinyl-containing peptides.

J. Biol. Chem.. Jan 2002. 277(2):1058-65. 2002 PMID: 11694513
| PMC124975 | 10.1074/jbc.M108261200

2001

Griffith SC, Sawaya MR, Boutz DR, Thapar N, Katz JE, Clarke S, Yeates TO
Crystal structure of a protein repair methyltransferase from Pyrococcus furiosus with its L-isoaspartyl peptide substrate.

J. Mol. Biol.. Nov 2001. 313(5):1103-16. 2001 PMID: 11700066
| PMC124975 | 10.1006/jmbi.2001.5095

Sawaya MR, Krogmann DW, Serag A, Ho KK, Yeates TO, Kerfeld CA
Structures of cytochrome c-549 and cytochrome c6 from the cyanobacterium Arthrospira maxima.

Biochemistry. Aug 2001. 40(31):9215-25. 2001 PMID: 11478889
| PMC124975

Serag AA, Altenbach C, Gingery M, Hubbell WL, Yeates TO
Identification of a subunit interface in transthyretin amyloid fibrils: evidence for self-assembly from oligomeric building blocks.

Biochemistry. Aug 2001. 40(31):9089-96. 2001 PMID: 11478875
| PMC124975

Padilla JE, Colovos C, Yeates TO
Nanohedra: using symmetry to design self assembling protein cages, layers, crystals, and filaments.

Proc. Natl. Acad. Sci. U.S.A.. Feb 2001. 98(5):2217-21. 2001 PMID: 11226219
| PMC30118 | 10.1073/pnas.041614998

2000

Colovos C, Toth EA, Yeates TO
Evaluation of phase accuracy via topological and geometrical analysis of electron-density maps.

Acta Crystallogr. D Biol. Crystallogr.. Nov 2000. 56(Pt 11):1421-9. 2000 PMID: 11053840
| PMC30118

Toth EA, Worby C, Dixon JE, Goedken ER, Marqusee S, Yeates TO
The crystal structure of adenylosuccinate lyase from Pyrobaculum aerophilum reveals an intracellular protein with three disulfide bonds.

J. Mol. Biol.. Aug 2000. 301(2):433-50. 2000 PMID: 10926519
| PMC30118 | 10.1006/jmbi.2000.3970

Eisenberg D, Marcotte EM, Xenarios I, Yeates TO
Protein function in the post-genomic era.

Nature. Jun 2000. 405(6788):823-6. 2000 PMID: 10866208
| PMC30118 | 10.1038/35015694

1999

Pellegrini M, Yeates TO
Searching for frameshift evolutionary relationships between protein sequence families.

Proteins. Nov 1999. 37(2):278-83. 1999 PMID: 10584072
| PMC30118

Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D
A combined algorithm for genome-wide prediction of protein function.

Nature. Nov 1999. 402(6757):83-6. 1999 PMID: 10573421
| PMC30118 | 10.1038/47048

Marcotte EM, Pellegrini M, Yeates TO, Eisenberg D
A census of protein repeats.

J. Mol. Biol.. Oct 1999. 293(1):151-60. 1999 PMID: 10512723
| PMC30118 | 10.1006/jmbi.1999.3136

Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D
Detecting protein function and protein-protein interactions from genome sequences.

Science. Jul 1999. 285(5428):751-3. 1999 PMID: 10427000
| PMC30118

Pellegrini M, Marcotte EM, Yeates TO
A fast algorithm for genome-wide analysis of proteins with repeated sequences.

Proteins. Jun 1999. 35(4):440-6. 1999 PMID: 10382671
| PMC30118

Yeates TO, Fam BC
Protein crystals and their evil twins.

Structure. Feb 1999. 7(2):R25-9. 1999 PMID: 10368291
| PMC30118

Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO
Assigning protein functions by comparative genome analysis: protein phylogenetic profiles.

Proc. Natl. Acad. Sci. U.S.A.. Apr 1999. 96(8):4285-8. 1999 PMID: 10200254
| PMC16324

1998

Colovos C, Cascio D, Yeates TO
The 1.8 A crystal structure of the ycaC gene product from Escherichia coli reveals an octameric hydrolase of unknown specificity.

Structure. Oct 1998. 6(10):1329-37. 1998 PMID: 9782055
| PMC16324

Kerfeld CA, Salmeen AE, Yeates TO
Crystal structure and possible dimerization of the high-potential iron-sulfur protein from Chromatium purpuratum.

Biochemistry. Oct 1998. 37(40):13911-7. 1998 PMID: 9760225
| PMC16324 | 10.1021/bi9810252

1997

Kerfeld CA, Wu YP, Chan C, Krogmann DW, Yeates TO
Crystals of the carotenoid protein from Arthrospira maxima containing uniformly oriented pigment molecules.

Acta Crystallogr. D Biol. Crystallogr.. Nov 1997. 53(Pt 6):720-3. 1997 PMID: 15299860
| PMC16324 | 10.1107/S0907444997006999

Pellegrini M, Grønbech-Jensen N, Kelly JA, Pfluegl GM, Yeates TO
Highly constrained multiple-copy refinement of protein crystal structures.

Proteins. Dec 1997. 29(4):426-32. 1997 PMID: 9408940
| PMC16324

Bell CE, Yeates TO, Eisenberg D
Unusual conformation of nicotinamide adenine dinucleotide (NAD) bound to diphtheria toxin: a comparison with NAD bound to the oxidoreductase enzymes.

Protein Sci.. Oct 1997. 6(10):2084-96. 1997 PMID: 9336832
| PMC2143571 | 10.1002/pro.5560061004

Pellegrini M, Wukovitz SW, Yeates TO
Simulation of protein crystal nucleation.

Proteins. Aug 1997. 28(4):515-21. 1997 PMID: 9261867
| PMC2143571

Yeates TO
Detecting and overcoming crystal twinning.

Meth. Enzymol.. 1997. 276:344-58. 1997 PMID: 9048378
| PMC2143571

1996

Kerfeld CA, Chan C, Hirasawa M, Kleis-SanFrancisco S, Yeates TO, Knaff DB
Isolation and characterization of soluble electron transfer proteins from Chromatium purpuratum.

Biochemistry. Jun 1996. 35(24):7812-8. 1996 PMID: 8672482
| PMC2143571 | 10.1021/bi952731v

Redinbo MR, Eide SM, Stone RL, Dixon JE, Yeates TO
Crystallization and preliminary structural analysis of Bacillus subtilis adenylosuccinate lyase, an enzyme implicated in infantile autism.

Protein Sci.. Apr 1996. 5(4):786-8. 1996 PMID: 8845770
| PMC2143394 | 10.1002/pro.5560050425

Kelly JA, Feigon J, Yeates TO
Reconciliation of the X-ray and NMR structures of the thrombin-binding aptamer d(GGTTGGTGTGGTTGG).

J. Mol. Biol.. Mar 1996. 256(3):417-22. 1996 PMID: 8604127
| PMC2143394 | 10.1006/jmbi.1996.0097

1995

Wukovitz SW, Yeates TO
Why protein crystals favour some space-groups over others.

Nat. Struct. Biol.. Dec 1995. 2(12):1062-7. 1995 PMID: 8846217
| PMC2143394

Kerfeld CA, Anwar HP, Interrante R, Merchant S, Yeates TO
The structure of chloroplast cytochrome c6 at 1.9 A resolution: evidence for functional oligomerization.

J. Mol. Biol.. Jul 1995. 250(5):627-47. 1995 PMID: 7623381
| PMC2143394 | 10.1006/jmbi.1995.0404

Yeates TO
Algorithms for evaluating the long-range accessibility of protein surfaces.

J. Mol. Biol.. Jun 1995. 249(4):804-15. 1995 PMID: 7602592
| PMC2143394 | 10.1006/jmbi.1995.0339

1994

Kelly JA, Singer E, Osslund TD, Yeates TO
Crystallization and preliminary structural studies of neurotrophin-3.

Protein Sci.. Jun 1994. 3(6):982-3. 1994 PMID: 8069227
| PMC2142878 | 10.1002/pro.5560030614

Kerfeld CA, Yeates TO, Thornber JP
Biochemical and spectroscopic characterization of the reaction center-LH1 complex and the carotenoid-containing B820 subunit of Chromatium purpuratum.

Biochim. Biophys. Acta. Apr 1994. 1185(2):193-202. 1994 PMID: 8167136
| PMC2142878

Redinbo MR, Yeates TO, Merchant S
Plastocyanin: structural and functional analysis.

J. Bioenerg. Biomembr.. Feb 1994. 26(1):49-66. 1994 PMID: 8027022
| PMC2142878

1993

Redinbo MR, Cascio D, Choukair MK, Rice D, Merchant S, Yeates TO
The 1.5-A crystal structure of plastocyanin from the green alga Chlamydomonas reinhardtii.

Biochemistry. Oct 1993. 32(40):10560-7. 1993 PMID: 8399201
| PMC2142878

Colovos C, Yeates TO
Verification of protein structures: patterns of nonbonded atomic interactions.

Protein Sci.. Sep 1993. 2(9):1511-9. 1993 PMID: 8401235
| PMC2142462 | 10.1002/pro.5560020916

Kerfeld CA, Thornber JP, Yeates TO
Crystallization of two integral membrane pigment-protein complexes from the purple-sulfur bacterium Chromatium purpuratum.

Protein Sci.. Aug 1993. 2(8):1352-5. 1993 PMID: 8401219
| PMC2142436 | 10.1002/pro.5560020818

Redinbo MR, Yeates TO
Structure determination of plastocyanin from a specimen with a hemihedral twinning fraction of one-half.

Acta Crystallogr. D Biol. Crystallogr.. Jul 1993. 49(Pt 4):375-80. 1993 PMID: 15299512
| PMC2142436 | 10.1107/S090744499300294X

Yeates TO, Zhang KY
Ambiguities in ab initio phasing.

Science. Mar 1993. 259(5102):1771-2. 1993 PMID: 17816893
| PMC2142436 | 10.1126/science.259.5102.1771

Yeates TO
The asymmetric regions of rotation functions between Patterson functions of arbitrarily high symmetry.

Acta Crystallogr., A, Found. Crystallogr.. Jan 1993. 49 ( Pt 1):138-41. 1993 PMID: 8442929
| PMC2142436

1991

Yeates TO, Jacobson DH, Martin A, Wychowski C, Girard M, Filman DJ, Hogle JM
Three-dimensional structure of a mouse-adapted type 2/type 1 poliovirus chimera.

EMBO J.. Sep 1991. 10(9):2331-41. 1991 PMID: 1651227
| PMC452928

1990

Yeates TO
Determination of the correct reference frame from an atomic coordinate list.

Acta Crystallogr., A, Found. Crystallogr.. Jul 1990. 46 ( Pt 7):625-6. 1990 PMID: 2206485
| PMC452928

Yeates TO, Rini JM
Intensity-based domain refinement of oriented but unpositioned molecular replacement models.

Acta Crystallogr., A, Found. Crystallogr.. May 1990. 46 ( Pt 5):352-9. 1990 PMID: 2198887
| PMC452928

1989

Rees DC, Komiya H, Yeates TO, Allen JP, Feher G
The bacterial photosynthetic reaction center as a model for membrane proteins.

Annu. Rev. Biochem.. 1989. 58:607-33. 1989 PMID: 2673018
| PMC452928 | 10.1146/annurev.bi.58.070189.003135

1988

Komiya H, Yeates TO, Rees DC, Allen JP, Feher G
Structure of the reaction center from Rhodobacter sphaeroides R-26 and 2.4.1: symmetry relations and sequence comparisons between different species.

Proc. Natl. Acad. Sci. U.S.A.. Dec 1988. 85(23):9012-6. 1988 PMID: 3057498
| PMC282652

Yeates TO, Komiya H, Chirino A, Rees DC, Allen JP, Feher G
Structure of the reaction center from Rhodobacter sphaeroides R-26 and 2.4.1: protein-cofactor (bacteriochlorophyll, bacteriopheophytin, and carotenoid) interactions.

Proc. Natl. Acad. Sci. U.S.A.. Nov 1988. 85(21):7993-7. 1988 PMID: 3186702
| PMC282340

Allen JP, Feher G, Yeates TO, Komiya H, Rees DC
Structure of the reaction center from Rhodobacter sphaeroides R-26: protein-cofactor (quinones and Fe2+) interactions.

Proc. Natl. Acad. Sci. U.S.A.. Nov 1988. 85(22):8487-91. 1988 PMID: 3054889
| PMC282483

Yeates TO
Simple statistics for intensity data from twinned specimens.

Acta Crystallogr., A, Found. Crystallogr.. Mar 1988. 44 ( Pt 2):142-4. 1988 PMID: 3272147
| PMC282483

1987

Yeates TO, Komiya H, Rees DC, Allen JP, Feher G
Structure of the reaction center from Rhodobacter sphaeroides R-26: membrane-protein interactions.

Proc. Natl. Acad. Sci. U.S.A.. Sep 1987. 84(18):6438-42. 1987 PMID: 3306679
| PMC299092

Allen JP, Feher G, Yeates TO, Komiya H, Rees DC
Structure of the reaction center from Rhodobacter sphaeroides R-26: the protein subunits.

Proc. Natl. Acad. Sci. U.S.A.. Sep 1987. 84(17):6162-6. 1987 PMID: 2819866
| PMC299029

Allen JP, Feher G, Yeates TO, Komiya H, Rees DC
Structure of the reaction center from Rhodobacter sphaeroides R-26: the cofactors.

Proc. Natl. Acad. Sci. U.S.A.. Aug 1987. 84(16):5730-4. 1987 PMID: 3303032
| PMC298936

1986

Allen JP, Feher G, Yeates TO, Rees DC, Deisenhofer J, Michel H, Huber R
Structural homology of reaction centers from Rhodopseudomonas sphaeroides and Rhodopseudomonas viridis as determined by x-ray diffraction.

Proc. Natl. Acad. Sci. U.S.A.. Nov 1986. 83(22):8589-93. 1986 PMID: 3022298
| PMC386976

0


. . :. 0 PMID: 0
| PMC386976