Malkov Sasa N, Zivković Miodrag V, Beljanski Milos V, Hall Michael B, Zarić Snezana D
Department of Mathematics, University of Belgrade, Studentski trg 16, 11000, Belgrade, Serbia.
J Mol Model. 2008 Aug;14(8):769-75. doi: 10.1007/s00894-008-0313-0. Epub 2008 May 27.
The correlation between the primary and secondary structures of proteins was analysed using a large data set from the Protein Data Bank. Clear preferences of amino acids towards certain secondary structures classify amino acids into four groups: alpha-helix preferrers, strand preferrers, turn and bend preferrers, and His and Cys (the latter two amino acids show no clear preference for any secondary structure). Amino acids in the same group have similar structural characteristics at their Cbeta and Cgamma atoms that predicts their preference for a particular secondary structure. All alpha-helix preferrers have neither polar heteroatoms on Cbeta and Cgamma atoms, nor branching or aromatic group on the Cbeta atom. All strand preferrers have aromatic groups or branching groups on the Cbeta atom. All turn and bend preferrers have a polar heteroatom on the Cbeta or Cgamma atoms or do not have a Cbeta atom at all. These new rules could be helpful in making predictions about non-natural amino acids.
利用来自蛋白质数据库的大量数据集，分析了蛋白质一级结构与二级结构之间的相关性。氨基酸对某些二级结构有明显偏好，据此可将氨基酸分为四类：偏好α螺旋的氨基酸、偏好β折叠的氨基酸、偏好转角和弯曲的氨基酸，以及组氨酸和半胱氨酸（后两种氨基酸对任何二级结构都没有明显偏好）。同一组中的氨基酸在其Cβ和Cγ原子处具有相似的结构特征，这预示了它们对特定二级结构的偏好。所有偏好α螺旋的氨基酸在Cβ和Cγ原子上既没有极性杂原子，在Cβ原子上也没有支链或芳香基团。所有偏好β折叠的氨基酸在Cβ原子上有芳香基团或支链基团。所有偏好转角和弯曲的氨基酸在Cβ或Cγ原子上有极性杂原子，或者根本没有Cβ原子。这些新规则可能有助于对非天然氨基酸进行预测。
