Philippe Hervé, Casane Didier, Gribaldo Simonetta, Lopez Philippe, Meunier Julien
Canadian Institute for Advanced Research, Département de Biochimie, Université de Montréal, Succursale Centre-Ville, Montréal, Québec H3C3J7, Canada.
IUBMB Life. 2003 Apr-May;55(4-5):257-65. doi: 10.1080/1521654031000123330.
Study of structure/function relationships constitutes an important field of research, especially for modification of protein function and drug design. However, the fact that rational design (i.e. the modification of amino acid sequences by means of directed mutagenesis, based on knowledge of the three-dimensional structure) appears to be much less efficient than irrational design (i.e. random mutagenesis followed by in vitro selection) clearly indicates that we understand little about the relationships between primary sequence, three-dimensional structure and function. The use of evolutionary approaches and concepts will bring insights to this difficult question. The increasing availability of multigene family sequences that has resulted from genome projects has inspired the creation of novel in silico evolutionary methods to predict details of protein function in duplicated (paralogous) proteins. The underlying principle of all such approaches is to compare the evolutionary properties of homologous sequence positions in paralogs. It has been proposed that the positions that show switches in substitution rate over time--i.e., 'heterotachous sites'--are good indicators of functional divergence. However, it appears that heterotachy is a much more general process, since most variable sites of homologous proteins with no evidence of functional shift are heterotachous. Similarly, it appears that switches in substitution rate are as frequent when paralogous sequences are compared as when orthologous sequences are compared. Heterotachy, instead of being indicative of functional shift, may more generally reflect a less specific process related to the many intra- and inter-molecular interactions compatible with a range of more or less equally viable protein conformations. These interactions will lead to different constraints on the nature of the primary sequences, consistently with theories suggesting the non-independence of substitutions in proteins. However, a specific type of amino acid variation might constitute a good indicator of functional divergence: substitutions occurring at positions that are generally slowly evolving. Such substitutions at constrained sites are indeed much more frequent soon after gene duplication. The identification and analysis of these sites by complementing structural information with evolutionary data may represent a promising direction to future studies dealing with the functional characterization of an ever increasing number of multi-gene families identified by complete genome analysis.
结构/功能关系的研究构成了一个重要的研究领域，特别是对于蛋白质功能的修饰和药物设计而言。然而，合理设计（即基于三维结构知识通过定向诱变修饰氨基酸序列）似乎比非理性设计（即随机诱变后进行体外筛选）效率低得多，这一事实清楚地表明我们对一级序列、三维结构和功能之间的关系了解甚少。进化方法和概念的运用将为这个难题带来新的见解。基因组计划导致多基因家族序列的可得性不断增加，这激发了创建新的计算机进化方法来预测重复（旁系同源）蛋白质中蛋白质功能细节的灵感。所有这些方法的基本原理是比较旁系同源物中同源序列位置的进化特性。有人提出，随着时间推移显示出替代率变化的位置——即“异速位点”——是功能分化的良好指标。然而，异速似乎是一个更为普遍的过程，因为大多数没有功能转移证据的同源蛋白质的可变位点都是异速的。同样，当比较旁系同源序列时，替代率的变化似乎与比较直系同源序列时一样频繁。异速不是功能转移的指标，而可能更普遍地反映了一个不太特定的过程，该过程与一系列或多或少同样可行的蛋白质构象所兼容的许多分子内和分子间相互作用有关。这些相互作用将对一级序列的性质产生不同的限制，这与表明蛋白质中替代并非独立的理论一致。然而，一种特定类型的氨基酸变异可能构成功能分化的良好指标：发生在通常进化缓慢的位置的替代。在基因复制后不久，受约束位点的此类替代确实更为频繁。通过用进化数据补充结构信息来识别和分析这些位点，可能代表了未来研究的一个有前途的方向，这些研究涉及通过全基因组分析鉴定的越来越多的多基因家族的功能表征。
