Luki Goldschmidt
I'm a Ph.D. graduate student 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 current research projects include the implementation of the Surface Entropy Reduction Prediction Server and modeling of the energetics in amyloid formation.
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 GRID computing cluster.
Publications
- Kiril Tsemekhman, Lukasz Goldschmidt, David Eisenberg, David Baker. (2007). Cooperative Hydrogen-Bonding in Amyloid Formation. Protein Science. 16:761-764 (2007 Feb).
- Lukasz Goldschmidt, David Cooper, Zygmunt Derewenda, David Eisenberg. (2007). The Surface Entropy Reduction Server. Protein Science. 16:1569-1576 (2007 Aug).
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
The Insitute of Dungeonomics
105 Boyer Hall
611 Charles E. Young Dr. E.
Los Angeles, CA 90095
Lab Phone: 310.206.3907
Lab Fax: 310.206.3914
