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How the protonation state of a phosphorylated amino acid governs molecular recognition: insights from classical molecular dynamics simulations
Author(s) -
Kawade Raiji,
Kuroda Daisuke,
Tsumoto Kouhei
Publication year - 2020
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1002/1873-3468.13674
Subject(s) - protonation , molecular dynamics , phosphorylation , chemistry , amino acid , molecular recognition , biophysics , computational chemistry , biochemistry , molecule , biology , ion , organic chemistry
Physicochemical properties of proteins are controlled mainly by post‐translational modifications such as amino acid phosphorylation. Although molecular dynamics simulations have been shown to be a valuable tool for studying the effects of phosphorylation on protein structure and dynamics, most of the previous studies assumed that the phosphate group was in the unprotonated ( PO 3 2 - ) state, even though the protonation state could in fact vary at physiological pH. In this study, we performed molecular dynamics simulations of four different protein‐phosphorylated peptide complexes both in the PO 3 2 -and PO 3 H − states. Our simulations delineate different dynamics and energetics between the two states, suggesting importance of the protonation state of a phosphorylated amino acid in molecular recognition.