蛋白质虚拟定点突变和饱和突变软件的开发

Development of the protein virtual mutagenesis software for the site-directed and saturation mutagenesis

定点突变和饱和突变是研究蛋白质结构与功能关系、获取新酶的重要手段。如何在计算机上快速、准确地获取突变序列是实施高通量虚拟筛选的首要问题。本文提出一种可满足虚拟突变需求的软件架构,开发出一个蛋白质虚拟突变软件"PMu",拥有序列检查、定点突变和饱和突变3个模块。序列检查模块可代替人工校对,剔除输入序列中潜在的非法字符,为后续分析提供正确的、符合规范的数据。定点突变模块根据用户指定的位点和目标残基,启动对输入序列的自动突变功能,此突变包括替换、删除、插入3种形式。饱和突变模块通过分化参数设置,灵活实现标准饱和突变、自定义饱和突变和亚饱和突变等处理。该软件为相关研究快捷地提供准确的突变序列,可进一步用于同源建模、能量分析、分子动力学模拟以及实际的突变实验等。本文还探讨突变处理中计算机的运算特性,并指出该类型软件今后的2个发展方向。

The site-directed and saturation mutagenesis have been very important methods to probe the structure-function relationship for proteins and to gain novel enzymes.The first problem to implement high throughput screening in silico is how to get mutated sequences quickly and accurately.In this study,the software architecture that satisfies the requirement for virtual mutagenesis has been presented and the protein virtual mutagenesis software named＂PMu＂has been developed.which consists of Sequences Check（SC）,Site-directed Mutagenesis（SdM）,and Site-saturation Mutagenesis（SsM）.The illegal characters potentially existed in the input sequences would be eliminated through SC instead of manual proofreading. Then the checked sequences are applicable to the follow-up processes.With user-defined sites and target residues,automatic mutations that include shift,deletion and insertion can be run by SdM.The standard saturation mutagenesis,customized saturation mutagenesis and sub-saturation mutagenesis are provided in SsM based on ingenious parameter setting.The further applications for the mutated sequences efficiently and exactly supplied by PMu are the homology modeling.the energy analysis,molecular dynamics simulation and the in vitro or in vivo mutation experiment. Operating characteristics of virtual mutagenesis and two development direction of such kind of PMu were discussed.