AUG 22, 2013 11:00 AM PDT

Design of protein structures, functions and assemblies

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  • Investigator, Howard Hughes Medical Institute, Professor of Biochemistry, Adjunct Professor of Genome Sciences, Physics, Computer Science, Chemical Engineering, and Bioengineering, University
      The Baker laboratory developed the Rosetta algorithm for ab initio protein structure prediction, which has been extended to a distributed computing project called Rosetta@Home and Foldit. The project aims to produce structural models for protein complexes as well as individual polypeptide chains. The Baker group participates regularly and is recognized for expertise in the CASP structure prediction experiment using ab initio methods, including both manually assisted and automated variants of the Rosetta protocol. Members of the Baker group are also active in the field of protein design; they are recognized as the first group to have designed a protein, known as Top7, with an entirely novel fold. Baker did his graduate work in biochemistry at the University of California, Berkeley in the laboratory of Randy Schekman, where he worked predominantly on protein transport and trafficking in yeast. He did his postdoctoral work with David Agard of University of California, San Francisco. Although well known for development of methods for computational prediction of protein structure and function, Baker is focused on the use of computational methods to drive experimental assessment of biology and therefore the Baker laboratory maintains an active experimental biochemistry group. For his work on protein folding, Baker received the 2008 Sackler International Prize in Biophysics. Baker was elected a Fellow of the American Academy of Arts and Sciences in 2009.

    I will describe recent advances in computational protein design which allow the generation of new protein structures and functions. I will describe the use of these methods to design ultra-stable idealized proteins, flu neutralizing proteins, high affinity ligand binding proteins, and self assembling protein nanomaterials. I will discuss possible applications to therapeutics, vaccines and diagnostics. I will also describe the contributions of the general public to these efforts through the distributed computing project Rosetta@home and the online protein folding and design game FoldIt.

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