Comparative genomics of protein structure and function

描述（由申请人提供）：这项工作旨在鉴定蛋白质功能决定因素，并在蛋白质组中比较它们以预测蛋白质功能。该方法基于一种系统基因组算法，即进化痕迹（ET），该算法识别蛋白质中的关键功能残基；以及ET Annotation （ETA）算法，该算法从ET分析3D模板中提取，描述参与结合或催化的关键残基的组成和构象，然后在其他结构中搜索与这些3D模板的几何匹配，从而表明它们具有共同的功能。初步数据已经通过计算和实验广泛验证了ETA，并且ETA已经成为结构基因组蛋白功能注释的有用工具。然而，这两种方法仍然可以获得灵敏度，特异性和可扩展性。为此，我们在目标1中提出，首先，通过优化输入序列的选择和残基功能重要性的新度量来改进关键功能残基的ET识别，其次，改进3D模板的选择。在Aim 2中，我们提出了一种新的基于网络的注释扩散方法来一次性比较所有3D模板匹配，并添加来自其他来源的功能信息，例如来自未知结构的蛋白质。目标3是实验性的，它将通过对具有直接医学意义的蛋白质的突变和分析来检验我们的预测，其中包括一种控制细菌耐药性的蛋白质和另一种疟疾耐药性标志的蛋白质。从长远来看，这些结果应该有助于将蛋白质工程和药物设计的重点放在蛋白质最功能和治疗相关的部分上，并且，更广泛地说，将大量指数级增长的原始序列和结构数据与生物功能及其分子基础联系起来。

DESCRIPTION (provided by applicant): This work aims to identify protein functional determinants and to compare them across the proteome to predict protein function. The approach is predicated on a phylogenomic algorithm, the Evolutionary Trace (ET), that identifies key functional residues in proteins; and on ET Annotation (ETA) algorithms, which extract from ET analysis 3D templates, describing the composition and conformation of key residues involved in binding or in catalysis, and then search in other structures for geometric matches to these 3D templates that suggest a common function. Preliminary data have extensively validated ET, both computationally and through experiments, and ETA has become a useful tool to annotate function on structural genomics proteins. Both methods, however, can still gain in sensitivity, specificity and scalability. To do so we propose in Aim 1, first, to improve the ET identification of key functional residues, by optimizing the selection of the input sequences and by a new measure of residue functional importance, and, second, to refine the selection of 3D templates. In Aim 2, we propose a new network-based annotation diffusion method to compare all 3D template matches at once and to add in functional information from other sources, such as from proteins without known structure. Aim 3 is experimental and it will test our predictions through mutations and assays on proteins of direct medical interest including one that controls drug resistance in bacteria and another that is a marker of drug resistance in malaria. In the long term, these results should help to focus protein engineering and drug design to the most functionally and therapeutically relevant parts of a protein, and, most broadly, link the massive and exponentially growing amounts of raw sequence and structure data to biological function and its molecular basis.