A study of the hydrophobicity of amino acids on the structure of proteins by molecular dynamics simulation
Aims:This paper aims to study the effect of hydrophobicity of different amino acids,including the size of side chain,charged residue and disulfide bond,on the protein structures.Methods:The protein models with different hydrophilic or hydrophobic amino acids were constructed by VMD software;and the system was simulated by the molecular dynamics method.Results:Bond-stretching energy and bond-bending energy of the protein chain were not related to the hydrophobicity of the amino acids directly.Meanwhile,the VDW energy of the protein chains constructed by hydrophobic amino acids was lower than those constructed by hydrophilic amino acids.The hydrophobicity of amino acids could affect the secondary structure of protein chains.It was obtained by analyzing the root mean square fluctuation and root mean square deviation of the protein chain.The protein chains constructed by hydrophobic amino acids could maintain the α-helix structure during the simulations.Conclusions:The study of the relationship between the hydrophobicity of amino acids,the potential energy and the structure of proteins can provide theoretical support for the subsequent understanding of the conformation of protein and its application in biology.
molecular dynamics simulationproteinhydrophobicity of amino acidsα-helix
万方数据
维普
