Journal Article

Developing a molecular dynamics force field for both folded and disordered protein states

Shaw, David E., Piana, Stefano, Robustelli, Paul

2018

Overview

Molecular dynamics (MD) simulation is a valuable tool for characterizing the structural dynamics of folded proteins and should be similarly applicable to disordered proteins and proteins with both folded and disordered regions. It has been unclear, however, whether any physical model (force field) used in MD simulations accurately describes both folded and disordered proteins. Here, we select a benchmark set of 21 systems, including folded and disordered proteins, simulate these systems with six state-of-theart force fields, and compare the results to over 9,000 available experimental data points. We find that none of the tested force fields simultaneously provided accurate descriptions of folded proteins, of the dimensions of disordered proteins, and of the secondary structure propensities of disordered proteins. Guided by simulation results on a subset of our benchmark, however, we modified parameters of one force field, achieving excellent agreement with experiment for disordered proteins, while maintaining state-of-the-art accuracy for folded proteins. The resulting force field, a99SB-disp, should thus greatly expand the range of biological systems amenable to MD simulation. A similar approach could be taken to improve other force fields.

• Publisher: National Academy of Sciences
• Subject: Benchmarks / Biophysics and Computational Biology / Computer simulation / Data points / Humans / Intrinsically Disordered Proteins - chemistry / Models, Theoretical / Molecular dynamics / Molecular Dynamics Simulation / Molecules / Parameter modification / Physical Sciences / PNAS Plus / Protein Folding / Protein structure / Protein Structure, Secondary / Proteins / Secondary structure / Simulation / State of the art