Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States

• Published in: The journal of physical chemistry. B Vol. 119; no. 16; pp. 5113 - 5123
• Main Authors: Piana, Stefano, Donchev, Alexander G, Robustelli, Paul, Shaw, David E
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 23.04.2015
• Subjects: Computer simulation; Dispersions; Fluid dynamics; Molecular dynamics; Molecular Dynamics Simulation; Molecular Structure; Physical simulation; Proteins; Proteins - chemistry; Quantum Theory; Simulation; Water - chemistry
• ISSN: 1520-6106; 1520-5207; 1520-5207
• DOI: 10.1021/jp508971m

Many proteins can be partially or completely disordered under physiological conditions. Structural characterization of these disordered states using experimental methods can be challenging, since they are composed of a structurally heterogeneous ensemble of conformations rather than a single dominant conformation. Molecular dynamics (MD) simulations should in principle provide an ideal tool for elucidating the composition and behavior of disordered states at an atomic level of detail. Unfortunately, MD simulations using current physics-based models tend to produce disordered-state ensembles that are structurally too compact relative to experiments. We find that the water models typically used in MD simulations significantly underestimate London dispersion interactions, and speculate that this may be a possible reason for these erroneous results. To test this hypothesis, we create a new water model, TIP4P-D, that approximately corrects for these deficiencies in modeling water dispersion interactions while maintaining compatibility with existing physics-based models. We show that simulations of solvated proteins using this new water model typically result in disordered states that are substantially more expanded and in better agreement with experiment. These results represent a significant step toward extending the range of applicability of MD simulations to include the study of (partially or fully) disordered protein states.