Thompson Elaine E, Kornev Alexandr P, Kannan Natarajan, Kim Choel, Ten Eyck Lynn F, Taylor Susan S
Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, 92093, USA.
Protein Sci. 2009 Oct;18(10):2016-26. doi: 10.1002/pro.209.
Identifying conserved pockets on the surfaces of a family of proteins can provide insight into conserved geometric features and sites of protein-protein interaction. Here we describe mapping and comparison of the surfaces of aligned crystallographic structures, using the protein kinase family as a model. Pockets are rapidly computed using two computer programs, FADE and Crevasse. FADE uses gradients of atomic density to locate grooves and pockets on the molecular surface. Crevasse, a new piece of software, splits the FADE output into distinct pockets. The computation was run on 10 kinase catalytic cores aligned on the alphaF-helix, and the resulting pockets spatially clustered. The active site cleft appears as a large, contiguous site that can be subdivided into nucleotide and substrate docking sites. Substrate specificity determinants in the active site cleft between serine/threonine and tyrosine kinases are visible and distinct. The active site clefts cluster tightly, showing a conserved spatial relationship between the active site and alphaF-helix in the C-lobe. When the alphaC-helix is examined, there are multiple mechanisms for anchoring the helix using spatially conserved docking sites. A novel site at the top of the N-lobe is present in all the kinases, and there is a large conserved pocket over the hinge and the alphaC-beta4 loop. Other pockets on the kinase core are strongly conserved but have not yet been mapped to a protein-protein interaction. Sites identified by this algorithm have revealed structural and spatially conserved features of the kinase family and potential conserved intermolecular and intramolecular binding sites.
识别一族蛋白质表面上的保守口袋可以深入了解保守的几何特征以及蛋白质 - 蛋白质相互作用位点。在此，我们以蛋白激酶家族为模型，描述比对的晶体结构表面的图谱绘制及比较。使用两个计算机程序FADE和Crevasse快速计算口袋。FADE利用原子密度梯度在分子表面定位凹槽和口袋。新软件Crevasse将FADE的输出结果分割成不同的口袋。计算在10个在αF - 螺旋上比对的激酶催化核心上运行，得到的口袋在空间上聚类。活性位点裂隙呈现为一个大的连续位点，可细分为核苷酸和底物对接位点。丝氨酸/苏氨酸激酶和酪氨酸激酶之间活性位点裂隙中的底物特异性决定因素清晰且不同。活性位点裂隙紧密聚类，显示出活性位点与C叶中的αF - 螺旋之间存在保守的空间关系。当检查αC - 螺旋时，存在多种利用空间保守对接位点固定该螺旋的机制。所有激酶中都存在N叶顶部的一个新位点，并且在铰链和αC - β4环上方有一个大的保守口袋。激酶核心上的其他口袋高度保守，但尚未映射到蛋白质 - 蛋白质相互作用。通过该算法识别的位点揭示了激酶家族的结构和空间保守特征以及潜在的保守分子间和分子内结合位点。
