Residue-Specific Force Field Improving the Sample of Intrinsically Disordered Proteins and Folded Proteins

Intrinsically disordered proteins and regions (IDPs and IDRs) have attracted increasing interest with their abundance in the human proteome and critical roles in various human diseases. However, the characterization of structural dynamics of IDPs presents a challenge to general experimental methods due to their highly heterogeneous ensembles. Molecular dynamics (MD) simulation has been an alternative method with recent advances in computation power. Nevertheless, it is imperative that eligible predictions are determined by a highly precise force field, but traditional force fields sometimes give a collapsed disorder structure and overestimate the stability of IDPs. Here, we present a novel residue-specific force field, OPLSIDPSFF, to correct backbone dihedral terms for all 20 natural amino acids based on OPLS-AA/L. Extensive tests of 11 IDPs and two short peptides show that the simulated chemical shifts and J-coupling with the OPLSIDPSFF force field are in quantitative agreement with those from NMR experimental observables and are more accurate than the base generic force field. The influences of solvent models were also investigated, and it was found that TIP4P-D water had positive effects on limited observables. Furthermore, OPLSIDPSFF can still be used to model structural and dynamic properties of two tested folded proteins and fast-folding proteins. These findings confirm that the newly developed residue-specific force field OPLSIDPSFF can improve the conformer sampling of intrinsically disordered and folded proteins.