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| Ruhong Zhou, IBM Thomas J. Watson Research Center |
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| Ruhong Zhou is currently a Research Staff Scientist at the Computational Biology Center, IBM Watson Research Lab, and an Adjunct Professor at the Chemistry Department, Columbia University. He received his Ph.D. with Prof. Bruce Berne in chemical physics from Columbia University in 1997. He joined IBM's Thomas J. Watson Research Center in 2000, after spending two and a half years working with Prof. Richard Friesner (Columbia) and Prof. William Jorgensen (Yale) on polarizable force fields and protein-ligand binding mechanisms when he was at Schrodinger. He has authored and co-authored more than 50 journal publications and 6 patents, and has delivered numerous invited talks at major conferences and universities. He has won the Hammette Award for best PhD graduates from Columbia University in 1997, the American Chemical Society Award (DEC Award) on Computational Chemistry in 1995, and IBM Invention Achievement Awards in 2002-2003. His current research interests include development of novel methods and algorithms for computational biology and bioinformatics, computer-aided drug design, and large scale simulations for protein structure prediction and protein folding.
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Dewetting in nanoscale hydrophobic plates collapse and multi-domain protein folding
Ruhong Zhou, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA and
Department of Chemistry, Columbia University, New York, NY 10027, USA
The dewetting (water drying) between protein domains of a two-domain protein, BphC enzyme, is studied and compared with the drying between two nanoscale paraffin-like hydrophobic plates. The BphC enzyme, which is selected from all two-domain proteins in PDB by hydrophobicity profiling analysis, shows an excellent hydrophobic interface for the purposes of comparison. It is found that there exists strong dewetting transition (SDT) with vapor regions up to 2-3 water layers between the two hydrophobic plates when they collapse, whereas in the multi-domain protein folding, no drying transition has been observed even at very small inter-domain separations. Only weak water depletion (WWD), with a water density about 10-15% lower than the bulk, is found in the inter-domain gap region. Water depletion and hydrophobic collapse occur on a nanosecond time scale, two orders of magnitude slower than that found in the collapse of idealized paraffin-like plates. When the electrostatic protein-water forces are turned off, a dewetting or water drying transition occurs in the inter-domain region and the collapse speeds up by more than an order of magnitude. When attractive van derWaals forces are further turned off, the dewetting in the inter-domain region becomes more profound with the collapse even faster, and the protein domains behave just like the hydrophobic plates.
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