A comparative study of dynamic structures of proteins by using normal mode analysis database.
利用简正模分析数据库进行蛋白质动态结构的比较研究。
基本信息
- 批准号:15570139
- 负责人:
- 金额:$ 2.24万
- 依托单位:
- 依托单位国家:日本
- 项目类别:Grant-in-Aid for Scientific Research (C)
- 财政年份:2003
- 资助国家:日本
- 起止时间:2003 至 2005
- 项目状态:已结题
- 来源:
- 关键词:
项目摘要
In this study we considered that a comparative study of normal mode analysis for wild-type and mutant lysozymes and for several proteins in the same superfamily could provide some valuable information about dynamic structures of proteins.1.In the study of lysozymes it was found that the changes in the dynamic structures (defined as changes in fluctuations of the amino acid residues here) of the mutant lysozymes from the wild-type one had little correlation with those in the static structures. In order to reveal the basic changes caused by amino acid substitutions we performed a principal component analysis of the fluctuations of amino acid residues with the various mutant lysozymes. As a result, it was found that the domain motions are essential to the fluctuations of the individual amino acid residues. Furthermore, it was found that the correlative movements of the specific atom pairs in the active site should be maintained for the activity of the mutant lysozymes.2.In the comparative … More study of homologous proteins, the proteins were structurally aligned and then the fluctuations of the amino acids were compared at the equivalent sites. Although their amino acid sequences considerably differed in some cases (but their folds were very similar), the fluctuations of the amino acid residues at the equivalent sites in the secondary structure regions agreed well not only qualitatively but also quantitatively with each other. On the other hand, in the loop regions, since the fluctuations were essentially larger and affected by the insertion and deletion of amino acid residues, the changes in the fluctuations differed quantitatively. Furthermore, the dynamic domains were compared. The common regions constructing the dynamic domains among the homologous proteins were detected by visually inspecting their structures best-fitted. Such regions are considered to form a nucleus in the dynamic structure of the superfamily. This kind of observation can be obtained only when several proteins derived from the database we constructed are compared. Less
在本研究中,我们认为对野生型和突变型溶菌酶以及同一超家族中的几种蛋白质进行正态模式分析的比较研究可以为蛋白质的动态结构提供一些有价值的信息。1.在溶菌酶的研究中,发现野生型和突变型溶菌酶的动态结构的变化(这里定义为氨基酸残基的波动)与静态结构的变化几乎没有相关性。为了揭示氨基酸替换引起的基本变化,我们对不同突变的溶菌酶的氨基酸残基的波动进行了主成分分析。结果发现,结构域的运动对单个氨基酸残基的波动是必不可少的。此外,还发现为了保持突变溶菌酶的活性,活性部位的特定原子对应该保持相关的运动。2.在比较…中对同源蛋白质进行更多的研究,对蛋白质进行结构比对,然后比较等效位点处氨基酸的波动。虽然它们的氨基酸序列在某些情况下有很大的差异(但它们的折叠非常相似),但二级结构区等位氨基酸残基的波动不仅在定性上而且在数量上都是一致的。另一方面,在环区,由于波动基本上较大,并且受到氨基酸残基插入和缺失的影响,因此波动的变化在数量上是不同的。此外,还对动态结构域进行了比较。通过肉眼观察同源蛋白之间最匹配的结构来检测构成同源蛋白之间动态结构域的共同区域。这些区域被认为是超家族动态结构中的核心。只有当我们构建的数据库中的几个蛋白质进行比较时,才能获得这种观察结果。较少
项目成果
期刊论文数量(3)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
ProMode:: a database of normal mode analyses on protein molecules with a full-atom model
- DOI:10.1093/bioinformatics/bth197
- 发表时间:2004-09-01
- 期刊:
- 影响因子:5.8
- 作者:Wako, H;Kato, M;Endo, S
- 通讯作者:Endo, S
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WAKO Hiroshi其他文献
WAKO Hiroshi的其他文献
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{{ truncateString('WAKO Hiroshi', 18)}}的其他基金
Normal mode analysis of proteins using an elastic network model in dihedral angle space
使用二面角空间中的弹性网络模型进行蛋白质的正则模式分析
- 批准号:
18500227 - 财政年份:2006
- 资助金额:
$ 2.24万 - 项目类别:
Grant-in-Aid for Scientific Research (C)
Classification and analysis of local structure motifs in protein conformations
蛋白质构象中局部结构基序的分类和分析
- 批准号:
11680666 - 财政年份:1999
- 资助金额:
$ 2.24万 - 项目类别:
Grant-in-Aid for Scientific Research (C)
タンパク質の立体構造の計算機による解析法の開発とそれを用いた立体構造の解析
蛋白质3D结构计算机分析方法的开发及利用该方法的3D结构分析
- 批准号:
01580267 - 财政年份:1989
- 资助金额:
$ 2.24万 - 项目类别:
Grant-in-Aid for General Scientific Research (C)
相似海外基金
Normal mode analysis of proteins using an elastic network model in dihedral angle space
使用二面角空间中的弹性网络模型进行蛋白质的正则模式分析
- 批准号:
18500227 - 财政年份:2006
- 资助金额:
$ 2.24万 - 项目类别:
Grant-in-Aid for Scientific Research (C)
Instantaneous Normal Mode Analysis of Liquids
液体的瞬时简正模分析
- 批准号:
9708055 - 财政年份:1997
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Continuing Grant
Normal Mode Analysis of the Global Ocean Tide
全球海洋潮汐正态模态分析
- 批准号:
7727710 - 财政年份:1978
- 资助金额:
$ 2.24万 - 项目类别:
Continuing Grant
COMPUTATIONAL TOOLS TO SUPPORT BIOPHYSICAL LASER FACILITY: NORMAL MODE ANALYSIS
支持生物物理激光设施的计算工具:正态模式分析
- 批准号:
3873899 - 财政年份:
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