Document Type

Journal Article

Date of this Version

2-15-2009

Publication Source

Proteins: Structure, Function, and Bioinformatics

Volume

74

Issue

3

Start Page

603

Last Page

611

DOI

10.1002/prot.22176

Abstract

Globular proteins often contain structurally well-resolved internal water molecules. Previously, we reported results from a molecular dynamics study that suggested that buried water (Wat3) may play a role in modulating the structure of the FK506 binding protein-12 (FKBP12) (Park and Saven, Proteins 2005; 60:450-463). In particular, simulations suggested that disrupting a hydrogen bond to Wat3 by mutating E60 to either A or Q would cause a structural perturbation involving the distant W59 side chain, which rotates to a new conformation in response to the mutation. This effectively remodels the ligand-binding pocket, as the side chain in the new conformation is likely to clash with bound FK506. To test whether the protein structure is in effect modulated by the binding of a buried water in the distance, we determined high-resolution (0.92-1.29 A) structures of wild-type FKBP12 and its two mutants (E60A, E60Q) by X-ray crystallography. The structures of mutant FKBP12 show that the ligand-binding pocket is indeed remodeled as predicted by the substitution at position 60, even though the water molecule does not directly interact with any of the amino acids of the binding pocket. Thus, these structures support the view that buried water molecules constitute an integral, noncovalent component of the protein structure. Additionally, this study provides an example in which predictions from molecular dynamics simulations are experimentally validated with atomic precision, thus showing that the structural features of protein-water interactions can be reliably modeled at a molecular level.

Copyright/Permission Statement

This is the peer reviewed version of the following article: Proteins. 2009 February 15; 74(3): 603–611. doi:10.1002/prot.22176. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving

Keywords

Binding Sites, Computer Simulation, Crystallography, X-Ray, Hydrogen Bonding, Ligands, Models, Molecular, Protein Conformation, Structure-Activity Relationship, Tacrolimus Binding Protein 1A, Water

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Date Posted: 07 December 2016

This document has been peer reviewed.