Conformational Dynamics of Supramolecular Protein Assemblies in the EMDB

TL;DR

This paper introduces an unsupervised computational framework using normal mode analysis to analyze and visualize the conformational dynamics of supramolecular protein assemblies in the EMDB, enhancing understanding of their biological functions.

Contribution

It presents a novel method for analyzing conformational dynamics of EMDB entries using finite element normal mode analysis, with results validated against all-atom models.

Findings

Analyzed 452 EMDB entries for conformational dynamics.

Validated results with all-atom models.

Provided detailed dynamics for hepatitis B capsid, RF2, and GroEL.

Abstract

The Electron Microscopy Data Bank (EMDB) is a rapidly growing repository for the dissemination of structural data from single-particle reconstructions of supramolecular protein assemblies including motors, chaperones, cytoskeletal assemblies, and viral capsids. While the static structure of these assemblies provides essential insight into their biological function, their conformational dynamics and mechanics provide additional important information regarding the mechanism of their biological function. Here, we present an unsupervised computational framework to analyze and store for public access the conformational dynamics of supramolecular protein assemblies deposited in the EMDB. Conformational dynamics are analyzed using normal mode analysis in the finite element framework, which is used to compute equilibrium thermal fluctuations, cross-correlations in molecular motions, and strain energy distributions for 452 of the 681 entries stored in the EMDB at present. Results for the viral capsid of hepatitis B, ribosome-bound termination factor RF2, and GroEL are presented in detail and validated with all-atom based models. The conformational dynamics of protein assemblies in the EMDB may be useful in the interpretation of their biological function, as well as in the classification and refinement of EM-based structures.