Petrossian Tanya C, Clarke Steven G
Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA.
Mol Cell Proteomics. 2009 Jul;8(7):1516-26. doi: 10.1074/mcp.M900025-MCP200. Epub 2009 Apr 7.
A new program (Multiple Motif Scanning) was developed to scan the Saccharomyces cerevisiae proteome for Class I S-adenosylmethionine-dependent methyltransferases. Conserved Motifs I, Post I, II, and III were identified and expanded in known methyltransferases by primary sequence and secondary structural analysis through hidden Markov model profiling of both a yeast reference database and a reference database of methyltransferases with solved three-dimensional structures. The roles of the conserved amino acids in the four motifs of the methyltransferase structure and function were then analyzed to expand the previously defined motifs. Fisher-based negative log statistical matrix sets were developed from the prevalence of amino acids in the motifs. Multiple Motif Scanning is able to scan the proteome and score different combinations of the top fitting sequences for each motif. In addition, the program takes into account the conserved number of amino acids between the motifs. The output of the program is a ranked list of proteins that can be used to identify new methyltransferases and to reevaluate the assignment of previously identified putative methyltransferases. The Multiple Motif Scanning program can be used to develop a putative list of enzymes for any type of protein that has one or more motifs conserved at variable spacings and is freely available (www.chem.ucla.edu/files/MotifSetup.Zip). Finally hidden Markov model profile clustering analysis was used to subgroup Class I methyltransferases into groups that reflect their methyl-accepting substrate specificity.
开发了一个新程序（多重基序扫描），用于在酿酒酵母蛋白质组中搜索I类依赖S-腺苷甲硫氨酸的甲基转移酶。通过对酵母参考数据库和具有已解析三维结构的甲基转移酶参考数据库进行隐马尔可夫模型分析，通过一级序列和二级结构分析，在已知甲基转移酶中鉴定并扩展了保守基序I、I后、II和III。然后分析甲基转移酶结构和功能的四个基序中保守氨基酸的作用，以扩展先前定义的基序。基于Fisher的负对数统计矩阵集是根据基序中氨基酸的出现频率开发的。多重基序扫描能够扫描蛋白质组，并对每个基序的最佳匹配序列的不同组合进行评分。此外，该程序还考虑了基序之间保守的氨基酸数量。该程序的输出是一个蛋白质排名列表,可用于识别新的甲基转移酶，并重新评估先前鉴定的推定甲基转移酶的归属。多重基序扫描程序可用于为任何类型的蛋白质开发一个推定的酶列表，这些蛋白质具有一个或多个在可变间距处保守的基序，并且可免费获取（www.chem.ucla.edu/files/MotifSetup.Zip）。最后，使用隐马尔可夫模型轮廓聚类分析将I类甲基转移酶亚组为反映其甲基接受底物特异性的组。
