Fast and accurate computation of the 13C chemical shifts for an alanine-rich peptide.
Fast and accurate computation of the 13C chemical shifts for an alanine-rich peptide.
复制标题
快速准确地计算富含丙氨酸的肽的 13C 化学位移。
DOI：
10.1002/prot.20177
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发表时间：
2004
期刊：
影响因子：
--
通讯作者：
Scheraga,HaroldA
中科院分区：
文献类型：
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作者：
Vila,JorgeA;Baldoni,HectorA;Ripoll,DanielR;Scheraga,HaroldA
这项工作的目的是，首先，提出一种快速准确的技术来计算寡肽中每个氨基酸的量子化学13c化学位移的玻尔兹曼平均值，这里通过对肽Ac - XXAAAAAAAOO - NH2的应用来证明（其中X表示二氨基丁酸，a是丙氨酸，O是鸟氨酸）[XAO]，其次，讨论13c α和13c β化学位移区分ppi构象与α -螺旋构象和统计-线圈构象的能力。使用方法的组合，总结如下：(1)通过使用分子力学技术推导构象集合；(2)使用聚类程序形成家族并构建由每个家族的最低能量构象组成的简化构象集，以及(3)使用量子化学方法计算每个家族的最低能量构象的13c化学位移，该方法使用6‐311+G（2d,p）局部密度基集处理选定的残基或残基组，而序列中的剩余残基则使用3‐21G基集处理。整个过程相当精确，并将13c化学位移的玻尔兹曼平均值的计算速度提高了几个数量级。目前的应用揭示了丙氨酸和非丙氨酸残基占据Ramachandran图谱ppii螺旋区域的构象偏好。2004的蛋白质。©2004 Wiley‐Liss, Inc。
The purpose of this work is, first, to present a fast and accurate technique to compute Boltzmann‐averaged values of the quantum‐chemical13C chemical shifts for each amino acid in oligopeptides, demonstrated here by an application to the peptide Ac‐XXAAAAAAAOO‐NH2(where X denotes diaminobutyric acid, A is alanine, and O is ornithine) [XAO] and, second, to discuss the capability of the13Cαand13Cβchemical shifts to distinguish the PPIIconformation from the α‐helix and statistical‐coil conformations. Use is made of a combination of approaches, summarized as follows: (1) derivation of an ensemble of conformations by using a molecular mechanics technique; (2) use of a clustering procedure to form families and build a reduced set of conformations consisting of the lowest‐energy conformations of each family, and (3) computation of the13C chemical shifts for the lowest‐energy conformations of each family, using a quantum‐chemical approach that treats a selected residue, or group of residues, with a 6‐311+G(2d,p)locally‐densebasis set, while the remaining residues in the sequence are treated with a 3‐21G basis set. The whole procedure is quite accurate and speeds up the computation of the Boltzmann‐averaged values of the13C‐chemical shifts by several orders of magnitude. The present application sheds some light on the conformational preference for alanine and non‐alanine residues to occupy the PPIIhelical region of the Ramachandran map. Proteins 2004. © 2004 Wiley‐Liss, Inc.