Luki Goldschmidt
I'm a Staff Research Associate in Dr. Eisenberg's laboratory at the Molecular Biology Institute at University of California, Los Angeles. We are primarily a structural biology laboratory specializing in the determination of protein structures by x-ray crystallography, however, our group explores a variety of research areas in structural genomics and proteomics, and bioinformatics.
My responsibilities include the development of algorithms and services provided by the laboratory, including the ZipperDB and SERp web services, and the maintenance and operation of the in-house high performance distributed computing infrastructure.
If you are new to MBI and need help getting your computational project started or have questions about our computations resources, come find me in Boyer Hall 105.
The SER Server
I developed the Surface Entropy Reduction (SER) prediction server in collaboration with Zygmunt Derewenda's laboratory at University of Virginia. Crystallizability is the key limiting step of macromolecular structure determination by x-ray crystallography. This server suggests mutations designed to enhance crystallizability of proteins to obtain higher quality crystals, which then can be used to solve atomic structures such as those found in the protein data bank (PDB). The server has been online and available to the public since January 2006 and is used by many researchers daily.
Energetics of Amyloid Formation
Amyloid diseases, including Alzheimer's and prion diseases, are associated with elongated protein fibrils. Under destabilizing conditions, natural proteins that typically have an important cellular function undergo a conformational change and form fibrils. In collaboration with Kiril Tsemekhman and David Baker at the University of Washington in Seattle, we use both classical electrostatics and the quantum density functional theory to investigate the energetics of formation of such amyloid fibers. The accurately known atomic structure of the heptameric peptide with amino acid sequence GNNQQNY from the yeast prion Sup35 (shown on the left), whose structure was recently solved in our laboratory, serves as the first "amyloid backbone" in this endeavor.
Another part of this project aims to detect segments within proteins responsible for the conversion of innocuous proteins to fibrils. At the core of this computational method is the program RosettaDesign, developed in David Baker's laboratory. I'm continuing the development of the method for identifying fibril-forming segments of proteins, and developing a web server interface for viewing of the prediction results for all proteins processed on our new computing cluster.
ZipperDB
A web server to access our predictions of fibrillogenic segments within proteins is in development. Our database of predictions computed so far is available at: http://services.mbi.ucla.edu/zipperdb.
GPU-sc
The gpu-sc program is a port of CCP4's sc program that calculates the Lawrence and Coleman shape complementarity statistic of two interacting molecular surfaces. It takes advantage of CUDA-capable GPUs (such as NVIDIA GeForce, Quadro or Tesla video cards) to achieve an up to 200x speed up of run time without scarifying accuracy. The C++ source code and pre-comiled binaries are freely available here.
Publications
- Neil P. King, Alex w. Jackobitz, Michael R. Sawaya, Lukasz Goldschmidt, Todd O. Yeates (2010). Structure and folding of a designed knotted protein. PNAS, 107(48): 20732-20737.
- Lukasz Goldschmidt, Poh K. Teng, Roland Riek, David Eisenberg (2010). The amylome, all proteins capable of forming amyloid-like fibrils. PNAS, 107(8): 3784-3492.
- Jed J.W. Wiltzius, Meytal Landau, Rebecca Nelson, Michael R. Sawaya, Marcin I. Apostol, Lukasz Goldschmidt, Angela B. Soriaga, Duilio Cascio, Kanagalaghatta Rajashankar, David Eisenberg (2009). Molecular mechanisms for protein-encoded inheritance. Nature Structural & Molecular Biology. 16: 973-798.
- Rodolfo Guardado-Mendoza, Alberto M. Davalli, Alberto O. Chavez, Gene B. Hubbard, Edward J. Dick, Abraham Majluf-Cruz, Carlos E. Tene-Perez, Lukasz Goldschmidt, John Hart, Carla Perego, Anthony G. Comuzzie, Maria Elizabeth Tejero, Giovanna Finzi, Claudia Placidi, Stefano La Rosa, Carlo Capella, Glenn Halff, Amalia Gastaldellia, Ralph A. DeFronzoa, Franco Follia. (2009). Pancreatic islet amyloidosis, beta-cell apoptosis, and α-cell proliferation are determinants of islet remodeling in type-2 diabetic baboons. PNAS, ePub July 30, 2009.
- Lukasz Goldschmidt, David Cooper, Zygmunt Derewenda, David Eisenberg. (2007). Toward rational protein crystallization: A Web server for the design of crystallizable protein variants. Protein Science. 16:1569-1576 (2007 Aug).
- Kiril Tsemekhman, Lukasz Goldschmidt, David Eisenberg, David Baker. (2007). Cooperative Hydrogen-Bonding in Amyloid Formation. Protein Science. 16:761-764 (2007 Feb).
Back Track
I currently live in Santa Monica, CA, just a few blocks away from the Pacific ocean. It's a fun place to live! I found my way to Los Angeles in fall of 2004 for graduate school. Previously I received my B.Sc. in Cell & Molecular Biology from the University of Washington, in Seattle, WA. About a decade ago I moved from Hamburg, Germany to the little town of Rainier, WA that I called home for a few years. Prior to that I spent a good chunk of my life growing up in Poland. And the rest is history...
Lab Contact Info
105 Boyer Hall
611 Charles E. Young Dr. E.
Los Angeles, CA 90095
Lab Phone: 310.206.3907
