BenchIDPs: Evaluation of Conformational Preferences Molecular Mechanics and Solvent Interactions of IDPs across popular Force Fields and Water Models

Abstract

Intrinsically disordered proteins (IDPs), unlike globular proteins, lack stable secondary structure and exist as dynamic ensembles of conformations in physiological conditions. These conformations allow them to adapt to many roles while interacting with other proteins, forming partially folded soluble oligomers or insoluble plaques rich in {beta}-sheet, and are responsible for different pathological diseases. The dynamic nature of IDPs and the lack of well-defined binding sites make drug discovery and development both challenging. Although computational protocols, predominantly involving molecular dynamics (MD) simulations studies, have been complementing in understanding the structure and dynamics of IDPs, the choice of force fields become important in reproducing experimental observations. We herewith provide a systematic study to investigate the structural propensity of four IDPs (A{beta}42, Tau43, amylin and S), using 13 combinations of force field-water models (FF-wm). In addition to validating with NMR observables, we also examine the water dynamics surrounding the chosen IDPs to underscore the generalizability of chosen FF-wms. C36-IDPSFF with amber99sb-dispersion water model (A99SB-disp) is found to perform optimal in simulating IDPs in comparison with other FF-wm combination based on structural propensity and comparison with experimental NMR 3JHN-H-Coupling data as well as dynamical observables.