Prof. Corey S. O'Hern
Yale University
地点：唐仲英楼 B501
时间：2018-05-04 10:30
To make progress in computational protein design, we must have a fundamental understanding of protein structure. We study the extent to which the side chain dihedral angles of residues in protein cores can be predicted using a hard-sphere plus stereochemical constraint model. We show that the hard sphere model can accurately predict the side chain dihedral angle conformations observed in high resolution protein crystal structures. We then demonstrate that protein cores are dense random-packed with packing fractions near 0.56, not 0.74, as described in many biochemistry textbooks. The structure of protein cores is similar to that for random close packing of residue-shaped particles with no constraint on protein backbone connectivity. We show similar results for two other classes of proteins: protein-protein interfaces and transmembrane proteins. In particular, the hard-sphere model is also able to predict the side chain dihedral angle conformations of core residues in these other two classes of proteins. In addition, the core regions of these additional classes of proteins also pack at 0.56.
Professor Corey O’Hern joined the faculty of the School of Engineering and Applied Science at Yale with joint appointments in the Department of Mechanical Engineering & Materials Science (MEMS), Applied Physics, and Physics in July 2002 after postdoctoral fellowships in physics at the University of Chicago and the University of California, Los Angeles. He received tenure at Yale in 2011 and became a full professor in 2018. The O’Hern research group, which currently consists of ten Ph.D. students and two postdocs, tackles a broad range of fundamental questions in soft matter and biological physics using a combination of theoretical and computational techniques. The group seeks a predictive understanding of glass and jamming transitions, in which materials such as granular media, dense colloidal suspensions, and metallic glasses develop solid-like properties over a narrow range of parameters. The group also studies jamming phenomena in biological systems, including tissue and tumor formation, crowding in the cell cytopolasm, and packing in protein cores. Prof. O’Hern’s research has been funded by the National Science Foundation‚ Army Research Office, Defense Threat Reduction Agency, Defense Advanced Research Projects Agency, National Institutes of Health, and the W. M. Keck Foundation. He has authored more than 100 manuscripts in peer-reviewed journals and given more than 150 seminars, colloquia, and presentations at universities and scientific meetings in the US and abroad. He has served in a number of leadership positions in the US soft matter research community, including the Chair of the Topical Group on Statistical and Nonlinear Physics of the American Physical Society. He is a co-founder of the Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), which provides graduate training for Ph.D. students that seek to pursue research at the interface of biology, physics, and engineering, and he is PI of Yale's "Convergent graduate training in engineering, physics, and biology" NIH training grant that funds the IGPPEB. In 2018, he was elected as a Fellow of the American Physical Society.