Normal mode analysis of membrane protein dynamics using the vibrational subsystem analysis.

ABSTRACT: The vibrational subsystem analysis is a useful approach that allows for evaluating the spectrum of modes of a given system by integrating out the degrees of freedom accessible to the environment. The approach could be utilized for exploring the collective dynamics of a membrane protein (system) coupled to the lipid bilayer (environment). However, the application to membrane proteins is limited due to high computational costs of modeling a sufficiently large membrane environment unbiased by end effects, which drastically increases the size of the investigated system. We derived a recursive formula for calculating the reduced Hessian of a membrane protein embedded in a lipid bilayer by decomposing the membrane into concentric cylindrical domains with the protein located at the center. The ap

SUBMITTER: Zhang Y 

PROVIDER: S-EPMC8131107 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature