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phosaa14SB and phosaa19SB: Updated Amber Force Field Parameters for Phosphorylated Amino Acids

Journal Article · · Journal of Chemical Theory and Computation
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  1. Stony Brook Univ., NY (United States)
  2. Stony Brook Univ., NY (United States); Yale Univ., New Haven, CT (United States)
  3. Brookhaven National Laboratory (BNL), Upton, NY (United States)
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Phosphorylated amino acids are involved in many cell regulatory networks; proteins containing these post-translational modifications are widely studied both experimentally and computationally. Simulations are used to investigate a wide range of structural and dynamic properties of biomolecules, such as ligand binding, enzyme-reaction mechanisms, and protein folding. However, the development of force field parameters for the simulation of proteins containing phosphorylated amino acids using the Amber program has not kept pace with the development of parameters for standard amino acids, and it is challenging to model these modified amino acids with accuracy comparable to proteins containing only standard amino acids. In particular, the popular ff14SB and ff19SB models do not contain parameters for phosphorylated amino acids. Here, the dihedral parameters for the side chains of the most common phosphorylated amino acids are trained against reference data from QM calculations adopting the ff14SB approach, followed by validation against experimental data. Finally, library files and corresponding parameter files are provided, with versions that are compatible with both ff14SB and ff19SB.
Research Organization:
Brookhaven National Laboratory (BNL), Upton, NY (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF)
Grant/Contract Number:
SC0012704
OSTI ID:
2448262
Report Number(s):
BNL--226136-2024-JAAM
Journal Information:
Journal of Chemical Theory and Computation, Journal Name: Journal of Chemical Theory and Computation Journal Issue: 16 Vol. 20; ISSN 1549-9618
Publisher:
American Chemical SocietyCopyright Statement
Country of Publication:
United States
Language:
English

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Related Subjects

77 NANOSCIENCE AND NANOTECHNOLOGY
chemical structure
conformation
energy
monomers
peptides and proteins