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Improved Sampling Strategies for Protein Model Refinement based on Molecular Dynamics Simulation

preprint
submitted on 29.11.2020, 17:54 and posted on 01.12.2020, 08:40 by Lim Heo, Collin Arbour, Michael Feig
Protein structures provide valuable information for understanding biological processes. Protein structures can be determined by experimental methods such as X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, or cryogenic electron microscopy. As an alternative, in silico methods can be used to predict protein structures. Those methods utilize protein structure databases for structure prediction via template-based modeling or for training machine-learning models to generate predictions. Structure prediction for proteins distant from proteins with known structures often results in lower accuracy with respect to the true physiological structures. Physics-based protein model refinement methods can be applied to improve model accuracy in the predicted models. Refinement methods rely on conformational sampling around the predicted structures, and if structures closer to the native states are sampled, improvements in the model quality become possible. Molecular dynamics simulations have been especially successful for improving model qualities but although consistent refinement can be achieved, the improvements in model qualities are still moderate. To extend the refinement performance of a simulation-based protocol, we explored new schemes that focus on an optimized use of biasing functions and the application of increased simulation temperatures. In addition, we tested the use of alternative initial models so that the simulations can explore conformational space more broadly. Based on the insight of this analysis we are proposing a new refinement protocol that significantly outperformed previous state-of-the-art molecular dynamics simulation-based protocols in the benchmark tests described here.

Funding

Modeling and dynamics of biomolecules on cellular scales

National Institute of General Medical Sciences

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History

Email Address of Submitting Author

mfeiglab@gmail.com

Institution

Michigan State University

Country

USA

ORCID For Submitting Author

0000-0001-9380-6422

Declaration of Conflict of Interest

The authors have no conflict of interest to declare.

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