ff19SB: Amino-acid specific protein backbone parameters trained against quantum mechanics energy surfaces in solution

Tian, Chuan; Kasavajhala, Koushik; Belfon, Kellon A. A.; Raguette, Lauren; Huang, He; Migues, Angela N.; Bickel, John; Wang, Yuzhang; Pincay, Jorge; Wu, Qin; Simmerling, Carlos

doi:10.1021/acs.jctc.9b00591

Title: ff19SB: Amino-acid specific protein backbone parameters trained against quantum mechanics energy surfaces in solution

Journal Article · Tue Nov 12 00:00:00 EST 2019 · Journal of Chemical Theory and Computation

DOI:https://doi.org/10.1021/acs.jctc.9b00591· OSTI ID:1574918

Tian, Chuan ^[1]; Kasavajhala, Koushik ^[1]; Belfon, Kellon A. A. ^[1]; Raguette, Lauren ^[1]; Huang, He ^[1]; Migues, Angela N. ^[2]; Bickel, John ^[3]; Wang, Yuzhang ^[1]; Pincay, Jorge ^[3];

^[4]; Simmerling, Carlos ^[1]

Stony Brook Univ., Stony Brook, NY (United States). Dept. of Chemistry and Laufer Center for Physical and Quantitative Biology
Stony Brook Univ., Stony Brook, NY (United States). Laufer Center for Physical and Quantitative Biology
Stony Brook Univ., Stony Brook, NY (United States). Dept. of Chemistry
Brookhaven National Lab. (BNL), Upton, NY (United States). Center for Functional Nanomaterials

Molecular dynamics (MD) simulations have become increasingly popular in studying the motions and functions of biomolecules. The accuracy of the simulation, however, is highly determined by the molecular mechanics (MM) force field (FF), a set of functions with adjustable parameters to compute the potential energies from atomic positions. However, the overall quality of the FF, such as our previously published ff99SB and ff14SB, can be limited by assumptions that were made years ago. In the updated model presented here (ff19SB), we have significantly improved the backbone profiles for all 20 amino acids. We fit coupled Φ/ψ parameters using 2D Φ/ψ conformational scans for multiple amino acids, using as reference data the entire 2D quantum mechanics (QM) energy surface. We address the polarization inconsistency during dihedral parameter fitting by using both QM and MM in solution. Finally, we examine possible dependency of the backbone fitting on side chain rotamer. To extensively validate ff19SB parameters, we have performed a total of ~5 milliseconds MD simulations in explicit solvent. Here, our results show that after amino-acid specific training against QM data with solvent polarization, ff19SB not only reproduces the differences in amino acid specific Protein Data Bank (PDB) Ramachandran maps better, but also shows significantly improved capability to differentiate amino acid dependent properties such as helical propensities. We also conclude that an inherent underestimation of helicity is present in ff14SB, which is (inexactly) compensated by an increase in helical content driven by the TIP3P bias toward overly compact structures. In summary, ff19SB, when combined with a more accurate water model such as OPC, should have better predictive power for modeling sequence-specific behavior, protein mutations, and also rational protein design.

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Research Organization:: Brookhaven National Lab. (BNL), Upton, NY (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: SC0012704

OSTI ID:: 1574918

Report Number(s):: BNL-212345-2019-JAAM; TRN: US2001253

Journal Information:: Journal of Chemical Theory and Computation, Vol. 16, Issue 1; ISSN 1549-9618

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 336 works

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