Why are large conformational changes well described by harmonic normal modes?

ABSTRACT: Low-frequency normal modes generated by elastic network models tend to correlate strongly with large conformational changes of proteins, despite their reliance on the harmonic approximation, which is only valid in close proximity of the native structure. We consider 12 variants of the torsional network model (TNM), an elastic network model in torsion angle space, that adopt different sets of torsion angles as degrees of freedom and reproduce with similar quality the thermal fluctuations of proteins but present drastic differences in their agreement with conformational changes. We show that these differences are related to the extent of the deviations from the harmonic approximation, assessed through an anharmonic energy function whose harmonic approximation coincides with the TNM. Our resu

SUBMITTER: Dehouck Y 

PROVIDER: S-EPMC8715200 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature