从序列和化学位移预测 Xaa-Pro 肽键构象。
Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts.
机构信息
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 126, Bethesda, MD, 20892-0520, USA.
出版信息
J Biomol NMR. 2010 Mar;46(3):199-204. doi: 10.1007/s10858-009-9395-y. Epub 2009 Dec 30.
Abstract
We present a program, named Promega, to predict the Xaa-Pro peptide bond conformation on the basis of backbone chemical shifts and the amino acid sequence. Using a chemical shift database of proteins of known structure together with the PDB-extracted amino acid preference of cis Xaa-Pro peptide bonds, a cis/trans probability score is calculated from the backbone and (13)C(beta) chemical shifts of the proline and its neighboring residues. For an arbitrary number of input chemical shifts, which may include Pro-(13)C(gamma), Promega calculates the statistical probability that a Xaa-Pro peptide bond is cis. Besides its potential as a validation tool, Promega is particularly useful for studies of larger proteins where Pro-(13)C(gamma) assignments can be challenging, and for on-going efforts to determine protein structures exclusively on the basis of backbone and (13)C(beta) chemical shifts.
摘要
我们提出了一个名为 Promega 的程序，用于根据骨架化学位移和氨基酸序列预测 Xaa-Pro 肽键构象。该程序使用已知结构蛋白质的化学位移数据库以及从 PDB 中提取的顺式 Xaa-Pro 肽键的氨基酸偏好，根据脯氨酸及其相邻残基的骨架和 (13)C(beta)化学位移计算顺/反概率得分。对于任意数量的输入化学位移，其中可能包括 Pro-(13)C(gamma)，Promega 计算 Xaa-Pro 肽键为顺式的统计概率。除了作为验证工具的潜力外，Promega 特别适用于较大蛋白质的研究，在这些研究中，Pro-(13)C(gamma)的分配可能具有挑战性，并且适用于正在努力仅根据骨架和 (13)C(beta)化学位移确定蛋白质结构的研究。
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