Premium
Water in protein cavities: A procedure to identify internal water and exchange pathways and application to fatty acid‐binding protein
Author(s) -
Bakowies Dirk,
van Gunsteren Wilfred F.
Publication year - 2002
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10079
Subject(s) - delaunay triangulation , fatty acid binding protein , chemistry , fatty acid , molecular dynamics , biochemistry , crystallography , computer science , computational chemistry , gene , algorithm
A computational approach based on Delaunay triangulation is presented to identify internal water molecules in proteins and to capture pathways of exchange with the bulk. The implemented procedure is computationally efficient and can easily be applied to long molecular dynamics trajectories of protein simulations. In an application to fatty acid‐binding protein in apo ‐form and with bound palmitate, several protein orifices known from crystal structures have been confirmed to be major portals of solvent exchange. Differences between the two forms of the protein are observed and discussed. Proteins 2002;47:534–545. © 2002 Wiley‐Liss, Inc.