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

Olga O Lebedenko, Vladislav A Salikov, Sergei A Izmailov, Ivan S Podkorytov, Nikolai R Skrynnikov

https://www.sciencedirect.com/science/article/abs/pii/S0006349523007208

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, our analysis of the diffusion data indicates that MD simulations of N-H4 in the TIP4P-Ew water give rise to an overly compact conformational ensemble for this peptide. In contrast, TIP4P-D and OPC simulations produce the ensembles that are consistent with the experimental D_tr result. These observations are supported by the analyses of the ¹⁵N spin relaxation rates. We also tested a number of empirical methods to predict D_tr based on IDP’s coordinates extracted from the MD snapshots. In particular, we show that the popular approach involving the program HYDROPRO can produce misleading results. This happens because HYDROPRO is not intended to predict the diffusion properties of highly flexible biopolymers such as IDPs. Likewise, recent empirical schemes that exploit the relationship between the small-angle x-ray scattering-informed conformational ensembles of IDPs and the respective experimental D_tr values also prove to be problematic. In this sense, the first-principle calculations of D_tr from the MD simulations, such as demonstrated in this work, should provide a useful benchmark for future efforts in this area.

Тэги: Измайлов, Лебеденко, Подкорытов, Саликов, Скрынников