Development and Validation of AMBER-FB15-Compatible Force Field Parameters for Phosphorylated Amino Acids.

ABSTRACT: Phosphorylation of select amino acid residues is one of the most common biological mechanisms for regulating protein structures and functions. While computational modeling can be used to explore the detailed structural changes associated with phosphorylation, most molecular mechanics force fields developed for the simulation of phosphoproteins have been noted to be inconsistent with experimental data. In this work, we parameterize force fields for the phosphorylated forms of the amino acids serine, threonine, and tyrosine using the ForceBalance software package with the goal of improving agreement with experiments for these residues. Our optimized force field, denoted as FB18, is parameterized using high-quality ab initio potential energy scans and is designed to be fully compatible with t

SUBMITTER: Stoppelman JP 

PROVIDER: S-EPMC9649521 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature