Strong hydrophobic nature of cysteine residues in proteins

The differences between disulfide‐bonding cystine (Cys_SS) and free cysteine (Cys_SH) residues were examined by analyzing the statistical distribution of both types of residue in proteins of known structure. Surprisingly, Cys_SH residues display stronger hydrophobicity than Cys_SS residues. A detailed survey of atoms which come into contact with the sulfhydryl group (sulfur atom) of Cys_SH revealed those atoms are essentially the same in number and variety as those of the methyl group of isoleucine, but are quite different to those of the hydroxyl group of serine. Moreover, the relationships among amino acids were also determined using the 3D‐profile table of known protein structures. Cys_SH was located in the hydrophobic cluster, along with residues such as Met, Trp and Tyr, and was clearly separated from Ser and Thr in the polar cluster. These results imply that free cysteines behave as strongly hydrophobic, and not hydrophilic, residues in proteins.

[1]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[2]  J. Thornton.  Disulphide bridges in globular proteins. , 1981, Journal of molecular biology.

[3]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[4]  L. Poulsen,et al.  Protein disulfide bond synthesis: a possible intracellular mechanism , 1977 .

[5]  W. Taylor,et al.  The classification of amino acid conservation. , 1986, Journal of theoretical biology.

[6]  M. Kanehisa,et al.  Cluster analysis of amino acid indices for prediction of protein structure and function. , 1988, Protein engineering.

[7]  M. Kanehisa,et al.  Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. , 1996, Protein engineering.

[8]  P. Y. Chou,et al.  Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. , 1974, Biochemistry.

[9]  G. Rose,et al.  Hydrophobicity of amino acid residues in globular proteins. , 1985, Science.

[10]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[11]  M. O. Dayhoff,et al.  Atlas of protein sequence and structure , 1965 .

[12]  K. Nishikawa,et al.  Classification of proteins into groups based on amino acid composition and other characters. II. Grouping into four types. , 1983, Journal of biochemistry.

[13]  K Nishikawa,et al.  Assessment of pseudo-energy potentials by the best-five test: a new use of the three-dimensional profiles of proteins. , 1997, Protein engineering.