Pal D, Chakrabarti P
Department of Biochemistry, Bose Institute, Calcutta, India.
J Biomol Struct Dyn. 2000 Oct;18(2):273-80. doi: 10.1080/07391102.2000.10506665.
Various amino acid similarity matrices have been derived using data on physicochemical properties and molecular evolution. Conformational similarity indices, CS(XX'), between different residues are computed here using the distribution of the main-chain and side-chain torsion angles and the values have been used to cluster amino acids in proteins. A subset of these parameters, CS(AX') indicates the extent of similarity in the main-chain and side-chain conformations (phi,psi and chi1) of different residues (X) with Ala (A) and is found to have strong correlation with alpha-helix propensities. However, no subset of CS(XX') provides any linear relationship with beta-sheet propensities, suggesting that the conformational feature favouring the location of a residue in an alpha-helix is different from the one favouring the beta-sheet. Conformationally similar residues (close CS(AX) values) have similar steric framework of the side-chain (linear/branched, aliphatic/aromatic), irrespective of the polarity or hydrophobicity. Cooperative nucleation of helix may be facile for a contiguous stretch of residues with high overall CS(AX) values.
人们利用物理化学性质和分子进化的数据推导出了各种氨基酸相似性矩阵。本文利用主链和侧链扭转角的分布计算了不同残基之间的构象相似性指数CS(XX')，这些值已被用于对蛋白质中的氨基酸进行聚类。这些参数的一个子集CS(AX')表示不同残基(X)与丙氨酸(A)在主链和侧链构象(φ、ψ和χ1)上的相似程度，发现其与α-螺旋倾向有很强的相关性。然而，CS(XX')的任何子集都与β-折叠倾向没有线性关系，这表明有利于残基位于α-螺旋中的构象特征与有利于β-折叠的构象特征不同。构象相似的残基(CS(AX)值相近)具有相似的侧链空间框架(线性/分支、脂肪族/芳香族)，而与极性或疏水性无关。对于具有高总体CS(AX)值的连续残基片段，螺旋的协同成核可能很容易。
