Peng Jeffrey W, Wilson Brian D, Namanja Andrew T
Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
J Biomol NMR. 2009 Sep;45(1-2):171-83. doi: 10.1007/s10858-009-9349-4. Epub 2009 Jul 29.
Flexible ligands pose challenges to standard structure-activity studies since they frequently reorganize their conformations upon protein binding and catalysis. Here, we demonstrate the utility of side chain (13)C relaxation dispersion measurements to identify and quantify the conformational dynamics that drive this reorganization. The dispersion measurements probe methylene (13)CH(2) and methyl (13)CH(3) groups; the latter are highly prevalent side chain moieties in known drugs. Combining these side chain studies with existing backbone dispersion studies enables a comprehensive investigation of mus-ms conformational dynamics related to binding and catalysis. We perform these measurements at natural (13)C abundance, in congruence with common pharmaceutical research settings. We illustrate these methods through a study of the interaction of a phosphopeptide ligand with the peptidyl-prolyl isomerase, Pin1. The results illuminate the side-chain moieties that undergo conformational readjustments upon complex formation. In particular, we find evidence that multiple exchange processes influence the side chain dispersion profiles. Collectively, our studies illustrate how side-chain relaxation dispersion can shed light on ligand conformational transitions required for activity, and thereby suggest strategies for its optimization.
柔性配体对标准的构效关系研究提出了挑战，因为它们在与蛋白质结合及催化过程中常常会重新组织其构象。在此，我们展示了侧链¹³C弛豫色散测量在识别和量化驱动这种重新组织的构象动力学方面的效用。色散测量探测亚甲基¹³CH₂和甲基¹³CH₃基团；后者是已知药物中高度普遍的侧链部分。将这些侧链研究与现有的主链色散研究相结合，能够全面研究与结合和催化相关的毫秒级构象动力学。我们在天然¹³C丰度下进行这些测量，这与常见的药物研究环境一致。我们通过研究磷酸肽配体与肽基脯氨酰异构酶Pin1的相互作用来说明这些方法。结果揭示了在复合物形成时经历构象重新调整的侧链部分。特别地，我们发现有证据表明多个交换过程影响侧链色散谱。总体而言，我们的研究说明了侧链弛豫色散如何能够阐明活性所需的配体构象转变，从而为其优化提出策略。
