基于一级结构和三维结构预测蛋白质脱酰胺化速率。
Prediction of protein deamidation rates from primary and three-dimensional structure.
作者信息
Robinson N E, Robinson A B
机构信息
Division of Chemistry, California Institute of Technology, Pasadena, CA 91125, USA.
出版信息
Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4367-72. doi: 10.1073/pnas.071066498.
Abstract
A method for the quantitative estimation of instability with respect to deamidation of the asparaginyl (Asn) residues in proteins is described. The procedure involves the observation of several simple aspects of the three-dimensional environment of each Asn residue in the protein and a calculation that includes these observations, the primary amino acid residue sequence, and the previously reported complete set of sequence-dependent rates of deamidation for Asn pentapeptides. This method is demonstrated and evaluated for 23 proteins in which 31 unstable and 167 stable Asn residues have been reported and for 7 unstable and 63 stable Asn residues that have been reported in 61 human hemoglobin variants. The relative importance of primary structure and three-dimensional structure in Asn deamidation is estimated.
摘要
描述了一种用于定量评估蛋白质中天冬酰胺（Asn）残基脱酰胺作用不稳定性的方法。该程序涉及观察蛋白质中每个Asn残基三维环境的几个简单方面，以及一个计算，该计算包括这些观察结果、一级氨基酸残基序列，以及先前报道的Asn五肽完整的序列依赖性脱酰胺速率集。对23种蛋白质进行了该方法的论证和评估，其中已报道31个不稳定Asn残基和167个稳定Asn残基，以及对61种人类血红蛋白变体中报道的7个不稳定Asn残基和63个稳定Asn残基进行了评估。估计了一级结构和三维结构在Asn脱酰胺中的相对重要性。
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2
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3
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4
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5
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7
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10
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