Empirical isotropic chemical shift surfaces
Empirical isotropic chemical shift surfaces
复制标题
DOI：
10.1007/s10858-007-9161-y
复制
发表时间：
2007-08-01
影响因子：
2.7
通讯作者：
Csaszar, Attila G.
中科院分区：
文献类型：
--
作者：
Czinki, Eszter;Csaszar, Attila G.
给出了蛋白质列表，其空间结构（分辨率优于 2.5 埃）可从蛋白质数据库 (PDB) 的条目中获知，各向同性化学位移 (ICS) 值可从与生物磁共振库 (BMRB) 数据库相关的 RefDB 数据库中获知。所选择的结构提供了表征残基主链结构的二面角 phi 和 psi，但不确定性未知。联合使用蛋白质内相同残基的实验 ICS（同样具有大多数未知的不确定性）以及从模型肽 For (L-Ala)(n)-NH2（n = 1、3 和 5）获得的从头算 ICS(phi, psi) 表面，产生了 20 种天然存在的 α-氨基酸的所有主要核的所谓经验 ICS(phi, psi) 表面。在确定的许多经验表面中，C-13(α) ICS(phi, psi) 表面似乎最有希望用于识别主要二级结构类型、α 螺旋、β 链、左手螺旋 (α(D)) 和聚脯氨酸-II。详细的测试表明，丙氨酸是许多天然存在的α-氨基酸的良好模型。二维经验 C-13(α)-H-1(α) ICS(phi, psi) 相关图迄今为止仅通过小肽模型的计算获得，表明其中包含的实验信息的实用性，因此它们应该为蛋白质的结构确定提供有用的约束。
A list of proteins is given for which spatial structures, with a resolution better than 2.5 angstrom, are known from entries in the Protein Data Bank (PDB) and isotropic chemical shift (ICS) values are known from the RefDB database related to the Biological Magnetic Resonance Bank (BMRB) database. The structures chosen provide, with unknown uncertainties, dihedral angles phi and psi characterizing the backbone structure of the residues. The joint use of experimental ICSs of the same residues within the proteins, again with mostly unknown uncertainties, and ab initio ICS(phi, psi) surfaces obtained for the model peptides For (L-Ala)(n)-NH2, with n = 1, 3, and 5, resulted in so-called empirical ICS(phi, psi) surfaces for all major nuclei of the 20 naturally occurring alpha-amino acids. Out of the many empirical surfaces determined, it is the C-13(alpha) ICS(phi, psi) surface which seems to be most promising for identifying major secondary structure types, a-helix, beta-strand, left-handed helix (alpha(D)), and polyproline-II. Detailed tests suggest that Ala is a good model for many naturally occurring a-amino acids. Two-dimensional empirical C-13(alpha)-H-1(alpha) ICS(phi, psi) correlation plots, obtained so far only from computations on small peptide models, suggest the utility of the experimental information contained therein and thus they should provide useful constraints for structure determinations of proteins.