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Estimating the Directional Flexibility of Proteins from Equilibrium Thermal Fluctuations
preprintsubmitted on 10.10.2020, 07:32 and posted on 12.10.2020, 13:07 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.