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首页> 外文期刊>Journal of Molecular Biology >The relationship between protein structure and function: a comprehensive survey with application to the yeast genome.
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The relationship between protein structure and function: a comprehensive survey with application to the yeast genome.

机译：蛋白质结构与功能之间的关系：全面调查及其在酵母基因组中的应用。

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For most proteins in the genome databases, function is predicted via sequence comparison. In spite of the popularity of this approach, the extent to which it can be reliably applied is unknown. We address this issue by systematically investigating the relationship between protein function and structure. We focus initially on enzymes functionally classified by the Enzyme Commission (EC) and relate these to by structurally classified domains the SCOP database. We find that the major SCOP fold classes have different propensities to carry out certain broad categories of functions. For instance, alpha/beta folds are disproportionately associated with enzymes, especially transferases and hydrolases, and all-alpha and small folds with non-enzymes, while alpha+beta folds have an equal tendency either way. These observations for the database overall are largely true for specific genomes. We focus, in particular, on yeast, analyzing it with many classifications in addition to SCOP and EC (i.e. COGs, CATH, MIPS), and find clear tendencies for fold-function association, across a broad spectrum of functions. Analysis with the COGs scheme also suggests that the functions of the most ancient proteins are more evenly distributed among different structural classes than those of more modern ones. For the database overall, we identify the most versatile functions, i.e. those that are associated with the most folds, and the most versatile folds, associated with the most functions. The two most versatile enzymatic functions (hydro-lyases and O-glycosyl glucosidases) are associated with seven folds each. The five most versatile folds (TIM-barrel, Rossmann, ferredoxin, alpha-beta hydrolase, and P-loop NTP hydrolase) are all mixed alpha-beta structures. They stand out as generic scaffolds, accommodating from six to as many as 16 functions (for the exceptional TIM-barrel). At the conclusion of our analysis we are able to construct a graph giving the chance that a functional annotation can be reliably transferred at different degrees of sequence and structural similarity. Supplemental information is available from http://bioinfo.mbb.yale.edu/genome/foldfunc++ +. Copyright 1999 Academic Press.
机译：对于基因组数据库中的大多数蛋白质，功能是通过序列比较来预测的。尽管这种方法很流行，但其可靠应用的程度尚不清楚。我们通过系统地研究蛋白质功能和结构之间的关系来解决这个问题。我们最初专注于酶委员会（EC）功能分类的酶，并将其与SCOP数据库的结构分类域相关联。我们发现，主要的SCOP折叠类具有执行某些广泛功能类别的不同倾向。例如，α/β折叠与酶（尤其是转移酶和水解酶）不成比例地相关，而全α和小折叠与非酶结合，而α+β折叠在任一方向上都具有相同的趋势。总体而言，这些对数据库的观察对于特定的基因组基本上是正确的。我们特别关注酵母，除了SCOP和EC（即COG，CATH，MIPS）外，还通过许多分类对它进行分析，并在广泛的功能范围内发现了折叠功能关联的明确趋势。通过COGs方案进行的分析还表明，与较现代的蛋白质相比，大多数古代蛋白质的功能在不同的结构类别中分布更均匀。对于整个数据库，我们确定最通用的功能，即与最多折叠相关的功能，以及最通用的与最多功能相关的折叠。两种最通用的酶功能（水解酶和O-糖基葡萄糖苷酶）分别具有七折。五个最通用的折叠（TIM桶，Rossmann，铁氧还蛋白，α-β水解酶和P环NTP水解酶）都是混合的α-β结构。它们作为通用脚手架脱颖而出，可容纳6到多达16个功能（用于特殊的TIM枪管）。在我们的分析结束时，我们能够构建一个图，使功能注释可以在不同程度的序列和结构相似性下可靠地转移。可从http://bioinfo.mbb.yale.edu/genome/foldfunc++ +获得补充信息。版权所有1999，学术出版社。

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