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METHOD FOR DETERMINING PROTONATION STATES OF PROTEIN ON BASIS OF CONSTANT-PH MOLECULAR DYNAMICS SIMULATION
METHOD FOR DETERMINING PROTONATION STATES OF PROTEIN ON BASIS OF CONSTANT-PH MOLECULAR DYNAMICS SIMULATION
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机译：基于恒定PH分子动力学模拟确定蛋白质质子化状态的方法
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摘要
A method for determining protonation states of a protein on the basis of constant-pH molecular dynamics simulation includes: calculating ΔGelec,ref of a reference compound; setting reasonable initial protonation states according to a simulation target pH value; performing constant-pH molecular dynamics simulation, and restricting positions of protein main chain atoms; setting amino acid residues with a protonation state proportion of higher than 99% or lower than 1% to be not titrated and other amino acid residues to be titrated, performing conventional constant-pH molecular dynamics simulation; setting amino acid residues with a protonation state proportion of higher than 90% or lower than 10% to be not titrated and other amino acid residues to be titrated, performing constant-pH molecular dynamics simulation under conditions of pH−0.5, pH−0.2, pH, pH+0.2, pH+0.5, respectively; performing Hill equation fitting to obtain a final pKa, wherein the protonation state can be determined by pKa.
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