Using NMR diffusion data to validate MD models of disordered proteins: Test case of N-terminal tail of histone H4.

ABSTRACT: MD simulations can provide uniquely detailed models of intrinsically disordered proteins (IDPs). However, these models need careful experimental validation. The coefficient of translational diffusion D_tr, measurable by pulsed field gradient NMR, offers a potentially useful piece of experimental information related to the compactness of the IDP's conformational ensemble. Here, we investigate, both experimentally and via the MD modeling, the translational diffusion of a 25-residue N-terminal fragment from histone H4 (N-H4). We found that the predicted values of D_tr, as obtained from mean-square displacement of the peptide in the MD simulations, are largely determined by the viscosity of the MD water (which has been reinvestigated as a part of our study). Beyond that, ou

SUBMITTER: Lebedenko OO 

PROVIDER: S-EPMC10808029 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature