Integrating solvation shell structure in experimentally driven molecular dynamics using x-ray solution scattering data.

ABSTRACT: In the past few decades, prediction of macromolecular structures beyond the native conformation has been aided by the development of molecular dynamics (MD) protocols aimed at exploration of the energetic landscape of proteins. Yet, the computed structures do not always agree with experimental observables, calling for further development of the MD strategies to bring the computations and experiments closer together. Here, we report a scalable, efficient MD simulation approach that incorporates an x-ray solution scattering signal as a driving force for the conformational search of stable structural configurations outside of the native basin. We further demonstrate the importance of inclusion of the hydration layer effect for a precise description of the processes involving large changes in

SUBMITTER: Hsu DJ 

PROVIDER: S-EPMC7255814 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature