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Exploring Biomolecular Interaction Between the Molecular Chaperone Hsp90 and Its Client Protein Kinase Cdc37 using Field-Effect Biosensing Technology

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Structural coupling between FKBP12 and buried water.

Szilvia Szep¹, Sheldon Park, Eric T Boder

¹Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

|August 16, 2008

Summary

Buried water molecules are integral to protein structure. Mutating FKBP12 (FK506 binding protein-12) confirmed that disrupting internal water interactions alters protein structure and ligand-binding pockets, validating molecular dynamics simulations.

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Bimolecular Fluorescence Complementation

Bimolecular Fluorescence Complementation

Published on: April 15, 2011

Area of Science:

Structural biology
Computational biophysics
Protein dynamics

Background:

Globular proteins often contain internal water molecules.
Previous molecular dynamics simulations suggested buried water (Wat3) modulates FKBP12 structure.
Mutations disrupting Wat3 hydrogen bonds were predicted to alter the W59 side chain and ligand-binding pocket.

Purpose of the Study:

To experimentally validate the role of buried water in protein structure modulation.
To determine high-resolution structures of wild-type FKBP12 and E60A/E60Q mutants.
To assess the accuracy of molecular dynamics simulations in predicting structural changes due to internal water interactions.

Main Methods:

X-ray crystallography at high resolution (0.92-1.29 Å).
Determination of structures for wild-type FKBP12, FKBP12 E60A mutant, and FKBP12 E60Q mutant.
Comparison of experimental structures with predictions from molecular dynamics simulations.

Main Results:

Experimental structures confirmed remodeling of the FKBP12 ligand-binding pocket in mutants E60A and E60Q.
The observed structural changes in the binding pocket were consistent with molecular dynamics predictions.
The internal water molecule (Wat3) did not directly interact with binding pocket amino acids, yet its disruption caused significant structural changes.

Conclusions:

Buried water molecules are integral, noncovalent components of protein structure.
Molecular dynamics simulations can accurately predict structural consequences of altered protein-water interactions.
This study provides atomic-level validation for modeling protein-water interactions.