Coarse Representations for the Essential Features of the Protein Surface Mark Gerstein (mbg@cb-iris.stanford.edu) The protein surface is usually represented (and viewed) in terms of thousands of intersecting atoms (spheres). The great amount of detail in such a representation obscures the overall shape of the surface and creates computational problems for many popular docking and surface matching schemes. Two approaches are presented for removing unnecessary detail and representing the essential features of the protein surface. (1) Reverse-crystallography: The protein surface is represented in terms of a resolution-dependent Fourier series. This approach allows for hierarchical, resolution-sensitive shape matching and very efficient docking. (2) The hydration surface: The protein surface is defined by the second shell of water molecules surrounding it. The hydration surface is similar to the commonly used molecular surface, but the "probe" water positions are determined in the course of a molecular simulation, rather than just purely geometrically, so it is argued that this surface is more chemically meaningful. MMBJC seminar Beckman 402 3:30 PM Wednesday 8 June 1994 The following references are summarize this work: (1) M Gerstein (1992). "A Resolution-Sensitive Procedure for Comparing Protein Surfaces and its Application to the Comparison of Antigen-Combining Sites," Acta Crystallographica A48: 271-276. (2) M Gerstein & R Lynden-Bell (1993). "Simulation of Water around a Model Protein Helix. 1. Two-dimensional Projections of Solvent Structure," Journal of Physical Chemistry 97: 2982-2990. (3) M Gerstein & R Lynden-Bell (1993). "What is the Natural Boundary for a Protein in Solution?" Journal of Molecular Biology 230: 641-650. (4) M Gerstein & R Lynden-Bell (1993). "Simulation of Water around a Model Protein Helix. 2. The Relative Contributions of Packing, Hydrophobicity, and Hydrogen-Bonding." Journal of Physical Chemistry 97: 2991-2999.