标题：Characterizing hydrophobicity of amino acid side chains in a protein environment via measuring contact angle of a water nanodroplet on planar peptide network
期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2016
卷号：113
期号：46
页码：12946-12951
DOI：10.1073/pnas.1616138113
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：SignificanceQuantitative characterization of hydrophobicity of amino acid side chains in protein environment has important implications to the understanding of the hydrophobic effects and their role in protein folding. Numerous parameters were developed previously to determine hydrophobicity of amino acid residues. However, these hydrophobicity scales are not always correlated consistently. Here, we constructed artificial planar peptide networks composed of unified amino acid side chains, considering both the primary and {beta}-sheet secondary structure of the protein. Using molecular dynamics simulation, we computed the contact angle of a water nanodroplet on the peptide networks for all 20 types of amino acids. Our simulations offer a bridge that can connect thermodynamic hydrophobic data of amino acid residues and contact angle measurement widely used in engineering fields. Hydrophobicity of macroscopic planar surface is conventionally characterized by the contact angle of water droplets. However, this engineering measurement cannot be directly extended to surfaces of proteins, due to the nanometer scale of amino acids and inherent nonplanar structures. To measure the hydrophobicity of side chains of proteins quantitatively, numerous parameters were developed to characterize behavior of hydrophobic solvation. However, consistency among these parameters is not always apparent. Herein, we demonstrate an alternative way of characterizing hydrophobicity of amino acid side chains in a protein environment by constructing a monolayer of amino acids (i.e., artificial planar peptide network) according to the primary and the {beta}-sheet secondary structures of protein so that the conventional engineering measurement of the contact angle of a water droplet can be brought to bear. Using molecular dynamics simulations, contact angles{theta} of a water nanodroplet on the planar peptide network, together with excess chemical potentials of purely repulsive methane-sized Weeks-Chandler-Andersen solute, are computed. All of the 20 types of amino acids and the corresponding planar peptide networks are studied. Expectedly, all of the planar peptide networks with nonpolar amino acids are hydrophobic due to{theta} [IMG] f1.gif" ALT="Formula" BORDER="0"> 90{degrees
