How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding
How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding
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DOI：
10.1016/j.jmb.2006.09.062
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发表时间：
2007-01-05
影响因子：
5.6
通讯作者：
Nussinov, Ruth
中科院分区：
文献类型：
--
作者：
Gunasekaran, Kannan;Nussinov, Ruth
蛋白质是动态分子，在配体结合时经常发生构象变化。人们普遍认为柔性环区在酶中具有关键的功能作用。缺乏对结合位点灵活性的考虑导致了预测蛋白质功能和配体与蛋白质受体成功对接的失败。在这里，我们解决这个问题：哪些序列和结构特征区分结构柔性和刚性结合位点？我们分析了 41 种蛋白质的配体结合 (holo) 和游离 (apo) 形式的高分辨率晶体结构，其中配体结合后未发生构象变化，其中 35 种蛋白质具有中等构象变化，22 种蛋白质观察到较大构象变化。我们发现每个残基观察到的残基-残基接触数量（接触密度）不能区分柔性和刚性结合位点，这表明特定相互作用和氨基酸在调节构象变化中的作用。对氢键和疏水相互作用的检查表明，不发生构象变化的情况具有构成结合袋的高极性相互作用。有趣的是，大的芳香族氨基酸色氨酸很容易出现在已注意到大的构象变化的例子的结合位点处。此外，在大构象变化的例子中，疏水性-疏水性、芳香族-芳香族和疏水性-极性残基对相互作用占主导地位。对 Ramachandran 二面角 (phi,psi) 的进一步分析表明，在刚性和柔性情况下都发现采用不允许构象的残基。更重要的是，采用不允许构象的结合位点残基狭窄地聚集在 L-Ala Ramachandran 图谱的两个特定区域中。对配体结合时二面角变化的检查表明，phi、psi 变化的幅度通常很小，尽管可以看到一些较大的变化，特别是在右手 α 螺旋和延伸构象之间。我们的工作进一步提供了二面角空间构象变化的解释。这里报告的发现预计将有助于提供预测蛋白质-配体复合物和基于模板的蛋白质功能预测的框架。
Proteins are dynamic molecules and often undergo conformational change upon ligand binding. It is widely accepted that flexible loop regions have a critical functional role in enzymes. Lack of consideration of binding site flexibility has led to failures in predicting protein functions and in successfully docking ligands with protein receptors. Here we address the question: which sequence and structural features distinguish the structurally flexible and rigid binding sites? We analyze high-resolution crystal structures of ligand bound (holo) and free (apo) forms of 41 proteins where no conformational change takes place upon ligand binding, 35 examples with moderate conformational change, and 22 cases where a large conformational change has been observed. We find that the number of residue-residue contacts observed per-residue (contact density) does not distinguish flexible and rigid binding sites, suggesting a role for specific interactions and amino acids in modulating the conformational changes. Examination of hydrogen bonding and hydrophobic interactions reveals that cases that do not undergo conformational change have high polar interactions constituting the binding pockets. Intriguingly, the large, aromatic amino acid tryptophan has a high propensity to occur at the binding sites of examples where a large conformational change has been noted. Further, in large conformational change examples, hydrophobic-hydrophobic, aromatic-aromatic, and hydrophobic-polar residue pair interactions are dominant. Further analysis of the Ramachandran dihedral angles (phi,psi) reveals that the residues adopting disallowed conformations are found in both rigid and flexible cases. More importantly, the binding site residues adopting disallowed conformations clustered narrowly into two specific regions of the L-Ala Ramachandran map. Examination of the dihedral angles changes upon ligand binding shows that the magnitude of phi, psi changes are in general minimal, although some large changes particularly between right-handed alpha-helical and extended conformations are seen. Our work further provides an account of conformational changes in the dihedral angles space. The findings reported here are expected to assist in providing a framework for predicting protein-ligand complexes and for template-based prediction of protein function.