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蛋白质结构的三维比对。

The alignment of protein structures in three dimensions.

作者信息

Zuker M, Somorjai R L

出版信息

Bull Math Biol. 1989;51(1):55-78. doi: 10.1007/BF02458836.

DOI:10.1007/BF02458836
PMID:2706402
Abstract

This article extends the use of dynamic programming algorithms in molecular sequence comparison to the alignment of the alpha-carbon (C alpha-) coordinates of two protein structures in three dimensions. The algorithm is described in detail and is applied to the comparison of alpha-lactalbumin with both hen egg white lysozyme and T4 lysozyme. In the first case, the structures are similar, while the second comparison is between two distantly related molecules. References are made to the usual sequence alignments. A variety of complementary methods are introduced to display the results.

摘要

本文将动态规划算法在分子序列比较中的应用扩展到三维空间中两个蛋白质结构的α-碳原子（Cα-）坐标比对。详细描述了该算法，并将其应用于α-乳白蛋白与鸡蛋清溶菌酶和T4溶菌酶的比对。在第一种情况下，结构相似，而第二种比较是在两个远缘相关分子之间进行。文中还提及了常见的序列比对。引入了多种互补方法来展示结果。

相似文献

1
The alignment of protein structures in three dimensions.蛋白质结构的三维比对。
Bull Math Biol. 1989;51(1):55-78. doi: 10.1007/BF02458836.
2
Refined structure of baboon alpha-lactalbumin at 1.7 A resolution. Comparison with C-type lysozyme.分辨率为1.7埃的狒狒α-乳白蛋白的精细结构。与C型溶菌酶的比较。
J Mol Biol. 1989 Jul 5;208(1):99-127. doi: 10.1016/0022-2836(89)90091-0.
3
Crystallographic analysis of the three-dimensional structure of baboon alpha-lactalbumin at low resolution. Homology with lysozyme.低分辨率下狒狒α-乳白蛋白三维结构的晶体学分析。与溶菌酶的同源性。
Biochem J. 1987 Mar 1;242(2):353-60. doi: 10.1042/bj2420353.
4
Comparison of the X-ray structure of baboon alpha-lactalbumin and the tertiary predicted computer models of human alpha-lactalbumin.狒狒α-乳白蛋白的X射线结构与人α-乳白蛋白三级预测计算机模型的比较。
J Comput Aided Mol Des. 1990 Dec;4(4):369-79. doi: 10.1007/BF00117402.
5
A comparative study of peptide models of the alpha-domain of alpha-lactalbumin, lysozyme, and alpha-lactalbumin/lysozyme chimeras allows the elucidation of critical factors that contribute to the ability to form stable partially folded states.对α-乳白蛋白、溶菌酶的α结构域以及α-乳白蛋白/溶菌酶嵌合体的肽模型进行比较研究，有助于阐明促成形成稳定部分折叠状态能力的关键因素。
Biochemistry. 2001 Feb 20;40(7):2138-47. doi: 10.1021/bi001975z.
6
A critical evaluation of the predicted and X-ray structures of alpha-lactalbumin.对α-乳白蛋白预测结构和X射线结构的批判性评估。
J Protein Chem. 1990 Oct;9(5):549-63. doi: 10.1007/BF01025008.
7
Modelling of alpha-lactalbumin from the known structure of hen egg white lysozyme using molecular dynamics.利用分子动力学，基于鸡蛋清溶菌酶的已知结构对α-乳白蛋白进行建模。
J Comput Aided Mol Des. 1987 Apr;1(1):17-22. doi: 10.1007/BF01680554.
8
Molecular divergence of lysozymes and alpha-lactalbumin.溶菌酶和α-乳白蛋白的分子差异
Crit Rev Biochem Mol Biol. 1997;32(4):255-306. doi: 10.3109/10409239709082574.
9
Goose lysozyme structure: an evolutionary link between hen and bacteriophage lysozymes?鹅溶菌酶结构：母鸡与噬菌体溶菌酶之间的进化联系？
Nature. 1983 Jun 30;303(5920):828-31. doi: 10.1038/303828a0.
10
Cooperative folding of the isolated alpha-helical domain of hen egg-white lysozyme.鸡蛋清溶菌酶分离的α-螺旋结构域的协同折叠
J Mol Biol. 2001 Nov 23;314(2):321-9. doi: 10.1006/jmbi.2001.5122.

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Multi-view methods for protein structure comparison using latent dirichlet allocation.

本文引用的文献

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Optimal sequence alignments.最佳序列比对。
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Critical values for testing the significance of amino acid composition indexes.用于检验氨基酸组成指数显著性的临界值。
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Protein sequence and structure alignments within one framework.在一个框架内进行蛋白质序列和结构比对。
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Enhanced graphic matrix analysis of nucleic acid and protein sequences.核酸和蛋白质序列的增强图形矩阵分析
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Comparison of goose-type, chicken-type, and phage-type lysozymes illustrates the changes that occur in both amino acid sequence and three-dimensional structure during evolution.鹅型、鸡型和噬菌体型溶菌酶的比较说明了在进化过程中氨基酸序列和三维结构所发生的变化。
J Mol Evol. 1984;21(2):97-111. doi: 10.1007/BF02100084.
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A general method applicable to the search for similarities in the amino acid sequence of two proteins.一种适用于寻找两种蛋白质氨基酸序列相似性的通用方法。
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