title: Conformation biases of amino acids based on tripeptide microenvironment from PDB database.
abstract: We have constructed a bank (FTTP) of tendentious factors of three states of three-peptide units from PDB database based on conformational dihedral angle library and demonstrated that amino acid biases toward protein secondary structure are present in natural protein sequences. Our research results reveal that 20 standard amino acids fall into three groups: nine residues inclined to alpha-helix with a common character (e.g. direct side chain aliphatic residues or positive/negative charged residues) arrange in three grades, viz EA, QKRLD, and MN, in turn; seven residues are apt to beta-strand with 2'-branched side chain aliphatic residues or benzyl-included residues, namely PV, IYTC, and F, in three ranks; and four residues SHWG show a double tendency to both alpha and beta. Noticeably, proline has the strongest ability to form extended conformation, especially the Re value up to 9.5298 at position 3 (Table 3). Thus, biases of codons show an evident tendency in protein folding, where GC-rich codons are mainly in charge of forming contracted conformation, especially the codon's first letter plays a dominant role in translating the genomic GC signature into protein sequences and structures. So, biases of amino acids will play an important role in protein folding, folding codons, refining domain, structure prediction, and structural genomics/proteomics.
authors.affiliation: Life Science College, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, PR China. yangjie@nju.edu.cn
authors.forename: Jie
authors.initials: J
authors.lastname: Yang
authors.forename: Xian-Chi
authors.initials: XC
authors.lastname: Dong
authors.forename: Yao
authors.initials: Y
authors.lastname: Leng
mesh_terms: D000596:Amino Acids / Q000235:genetics*; D000818:Animals; D003062:Codon; D019295:Computational Biology; D030562:Databases, Protein; D008958:Models, Molecular; D008968:Molecular Conformation; D010455:Peptides / Q000235:genetics*; D017510:Protein Folding; D017433:Protein Structure, Secondary
chemical_list: D000596:Amino Acids; D003062:Codon; D010455:Peptides