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-小分子或功能基团-放置在蛋白质表面，以确定最有利的结合位置。X射线结晶学和核磁共振谱表明，不同大小和极性的有机溶剂聚集在蛋白质上的有限数量的位置。最近开发的一种映射算法可以可靠地识别不同探针分子结合的共识位点。这些位置与已有的实验数据符合得很好。一个非常重要的结果是，酶中的共同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与酶的特定配体(底物、抑制剂和过渡态类似物)结合。因此，计算映射可用于识别和表征功能位点。与对接方法相比，该方法对蛋白质结构的变化不那么敏感，并且对算法和能量参数的变化具有显著的鲁棒性。这项建议的目标包括开发高通量自动测绘软件，通过绘制一些已被熟知的酶的图谱来验证该方法，并将该方法应用于尽可能多的特性不佳的酶。这些结果有望提供大量关于酶结合位点的新信息，至少应该表明哪些残基应该通过定点突变实验进行研究。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产生越来越多特征不佳的蛋白质的结构，而根据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它们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.