Computational Mapping of Proteins for Binding of Ligands

描述（由申请人提供）：计算溶剂作图方法将分子探针-小分子或官能团-放置在蛋白质表面，以确定最有利的结合位置。x射线晶体学和核磁共振表明，不同大小和极性的有机溶剂聚集在蛋白质上有限的位置。最近开发的一种映射算法可靠地确定了不同探针分子结合的一致位点。这些位置与现有的实验数据符合得很好。一个非常重要的结果是，酶中的共识位点是底物结合位点的主要亚位点，与探针相互作用的氨基酸残基也结合酶的特定配体（底物、抑制剂和过渡态类似物）。因此，计算映射可用于功能位点的识别和表征。与对接方法相比，该方法对蛋白质结构的变化不太敏感，并且对算法和能量参数的变化具有显著的鲁棒性。该提案的目标包括开发用于高通量自动制图的软件，通过绘制许多已被充分理解的酶来验证该方法，并将该方法应用于尽可能多的未被充分表征的酶。这些结果有望提供大量关于酶结合位点的新信息，并且至少应该建议哪些残基应该通过位点定向突变实验进行研究。溶剂图谱还将测试其识别其他类型蛋白质功能位点的能力。一种可靠的作图方法将特别有用，因为结构基因组学方法可能会为越来越多的特征不明显的蛋白质产生结构，而基于蛋白质结构识别功能位点的计算方法很少。作为第二个应用，氨基酸将被用作探针。并将研究单个氨基酸残基的有利结合位置与其在结合肽中的实际位置之间的关系。

DESCRIPTION (provided by applicant): Computational solvent mapping methods place molecular probes - small molecules or functional groups - on a protein surface in order to identify the most favorable binding positions. X-ray crystallography and NMR show that organic solvents with different sizes and polarities cluster at a limited number of sites on a protein. A recently developed mapping algorithm reliably identifies the consensus sites at which different probe molecules bind. These sites are in good agreement with the available experimental data. A very important result is that the consensus sites in enzymes are major subsites of the substrate binding site, and the amino acid residues that interact with the probes also bind the specific ligands (substrates, inhibitors, and transition state analogs) of the enzyme. Thus, computational mapping can be used for the identification and characterization of functional sites. The approach is less sensitive to variations in the structure of the protein than docking methods, and is remarkably robust against changes in the algorithm and energy parameters. The goals of this proposal include the development of software for high-throughput automatic mapping, validation of the approach by the mapping of a number of well understood enzymes, and application of the method to as many poorly characterized enzymes as possible. The results are expected to provide a substantial body of new information on enzyme binding sites, and at the very least should suggest which residues should be studied by site-directed mutation experiments. Solvent mapping will also be tested for its ability to identify functional sites in other types of proteins. A reliable mapping method will be particularly useful, as structural genomics approaches are likely to produce structures for an increasing number of poorly characterized proteins, and there are very few computational methods for identifying functional sites on the basis of protein structure, As a second application, amino acids will be used as probes, and the relationship between favorable binding positions of individual amino acid residues and their actual positions in bound peptides will be studied.