The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins

• Published in: Journal of chemical information and modeling Vol. 57; no. 5; pp. 1166 - 1178
• Main Authors: Song, Dong, Luo, Ray, Chen, Hai-Feng
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 22.05.2017
• Subjects: Amino acids; Computer Simulation; HIV - chemistry; Intrinsically Disordered Proteins - chemistry; Models, Biological; Molecular Dynamics Simulation; NMR; Nuclear magnetic resonance; Peptides; Protein Folding; Proteins; Residues; Sampling; Simulation; Solvents - chemistry; Stress concentration
• ISSN: 1549-9596; 1549-960X
• DOI: 10.1021/acs.jcim.7b00135

Intrinsically disordered proteins (IDPs) or intrinsically disordered regions do not have a fixed tertiary structure but play key roles in signal regulation, molecule recognition, and drug targeting. However, it is difficult to study the structure and function of IDPs by traditional experimental methods because of their diverse conformations. Limitations of current generic protein force fields and solvent models were reported in the previous simulations of IDPs. We have also explored overcoming these limitations by developing the ff99IDPs and ff14IDPs force fields to correct the dihedral distribution for eight disorder-promoting residues often observed in IDPs and found encouraging improvements. Here we extend our correction of backbone dihedral terms to all 20 naturally occurring amino acids in the IDP-specific force field ff14IDPSFF to further improve the quality of the modeling of IDPs. Extensive tests of seven IDPs and 14 unstructured short peptides show that the simulated Cα chemical shifts obtained with the ff14IDPSFF force field are in quantitative agreement with those from NMR experiments and are more accurate than those obtained with the base generic force field and also our previous ff14IDPs that only corrects the eight disorder-promoting amino acids. The influence of the solvent model was also investigated and found to be less important. Finally, our explicit-solvent MD simulations further show that ff14IDPSFF can still be used to model structural and dynamical properties of two tested folded proteins, with a slightly better agreement in the loop regions for both structural and dynamical properties. These findings confirm that the newly developed IDP-specific force field ff14IDPSFF can improve the conformer sampling of intrinsically disordered proteins.