LAUSR

Intrinsically disordered proteins (IDPs) and folded proteins consist of the family of proteins. Molecular dynamics simulation as an important complement of experiment methods was widely used in the research of protein structure-function relationship. However, the previous tests indicate that the current force fields could not provide accurate descriptions of folded proteins and IDPs. Therefore, a CMAP optimized force field based on ff03 (named ff03CMAP) was developed for balance sampling of folded proteins and IDPs. Extensive tests of typical short peptide, folded proteins, disordered proteins, and fast-folding proteins show that the simulated chemical shifts, J-coupling constants, order parameters, and residual dipolar couplings with the ff03CMAP force field are in quantitatively agreement with those from NMR experiment and are more accurate than other ff03-series force fields. The influences of solvent models were also investigated and TIP4P-Ew combined with ff03CMAP was suitable for folded proteins while ff03CMAP/TIP4PD for disordered proteins. These findings confirm that the newly developed force field ff03CMAP can improve the balance of conformer sampling between folded proteins and intrinsically disordered proteins.