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Estimating the Directional Flexibility of Proteins from Equilibrium Thermal Fluctuations

preprint
submitted on 10.10.2020 and posted on 12.10.2020 by SANJOY PAUL, Ravindra Venkatramani
In this manuscript, we demonstrate the abilities of atomistic MD trajectories to estimate the directional spring constants of proteins. The MD-derived spring constants are cross-correlated with single-molecule force spectropcopy (SMFS) experimental data for 5 different globular proteins. We employ the framework to predict the mechanical anisotropy of ubiquitin and associated changes in the anisotropy with functionally relevant protein-protein interactions. Finally, we use the MD-based framework to benchmark and improve computationally inexpensive and scalable elastic network model (ENM) based methods to estimate protein directional flexibility.

Funding

Department of Atomic Energy, Government of India, under Project No. 12-R&D-TFR-5.10-0100.

History

Email Address of Submitting Author

ravi.venkatramani@gmail.com

Institution

Tata Institute of Fundamental Research

Country

India

ORCID For Submitting Author

0000-0001-8893-2352

Declaration of Conflict of Interest

No conflict of interest

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