title: What is the natural boundary of a protein in solution?
abstract: At what distance do proteins in solution interact? Molecular simulation of water around two helices is used to address this question. Calculations are done with two ideal, parallel, polyalanine alpha-helices separated by 9 A, 11 A, 13 A, and 15 A. The second peak in the oxygen density (or loosely the second shell of water molecules) is used to define a hydration surface around the protein, which separates bulk solvent from water molecules strongly influenced by the protein. The hydration surface is contrasted with the Richards-Connolly molecular surface. It indicates that the helices are not completely separate until 15 A, while the molecular surface shows complete separation at 13 A. Suggesting shape-dependent aspects of hydration, the hydration surface only loosely follows the van der Waals outline of the protein surface. In particular, at the 9 A separation, the van der Waals envelopes of the helices make contact; two narrow crevices are formed on either side of the contact; and the water within the crevices is strongly localized in arrangements bridging the helices. A comparison of these 'normal' water simulations with a simulation of a simple, uncharged solvent highlights the importance of hydrogen bonding in structuring liquid water and further contrasts the molecular surface and the hydration surface.
authors: MRC Laboratory of Molecular Biology Hills Road, Cambridge, U.K.
authors: M
authors: M
authors: Gerstein
authors: R M
authors: RM
authors: Lynden-Bell
mesh_terms: D002151:Calorimetry; D008956:Models, Chemical; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012996:Solutions; D014867:Water; D014961:X-Ray Diffraction / Q000379:methods
chemical_list: D010455:Peptides; D011506:Proteins; D012996:Solutions; D014867:Water; C019529:polyalanine