Deupi Xavier
Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland.
Methods Mol Biol. 2012;914:219-35. doi: 10.1007/978-1-62703-023-6_13.
A substantial part of the structural and much of the functional information about G protein-coupled receptors (GPCRs) comes from studies on rhodopsin. Thus, analysis tools for detailed structure comparison are key to see to what extent this information can be extended to other GPCRs. Among the methods to evaluate protein structures and, in particular, helix distortions, HELANAL has the advantage that it provides data (local bend and twist angles) that can be easily translated to structural effects, as a local opening/tightening of the helix.In this work I show how HELANAL can be used to extract detailed structural information of the transmembrane bundle of GPCRs, and I provide some examples on how these data can be interpreted to study basic principles of protein structure, to compare homologous proteins and to study mechanisms of receptor activation. Also, I show how in combination with the sequence analysis tools provided by the program GMoS, distortions in individual receptors can be put in the context of the whole Class A GPCR family. Specifically, quantification of the strong proline-induced distortions in the transmembrane bundle of rhodopsin shows that they are not standard proline kinks. Moreover, the helix distortions in transmembrane helix (TMH) 5 and TMH 6 of rhodopsin are also present in the rest of GPCR crystal structures obtained so far, and thus, rhodopsin-based homology models have modeled correctly these strongly distorted helices. While in some cases the inherent "rhodopsin bias" of many of the GPCR models to date has not been a disadvantage, the availability of more templates will clearly result in better homology models. This type of analysis can be, of course, applied to any protein, and it may be particularly useful for the structural analysis of other membrane proteins. A detailed knowledge of the local structural changes related to ligand binding and how they are translated into larger-scale movements of transmembrane domains is key to understand receptor activation.
关于G蛋白偶联受体（GPCRs）的大量结构信息和许多功能信息都来自对视紫红质的研究。因此，用于详细结构比较的分析工具是了解这些信息能在多大程度上扩展到其他GPCRs的关键。在评估蛋白质结构，尤其是螺旋扭曲的方法中，HELANAL的优势在于它提供的数据（局部弯曲和扭转角度）可以很容易地转化为结构效应，比如螺旋的局部打开/收紧。在这项工作中，我展示了如何使用HELANAL来提取GPCRs跨膜束的详细结构信息，并提供了一些例子来说明如何解释这些数据以研究蛋白质结构的基本原理、比较同源蛋白质以及研究受体激活机制。此外，我还展示了如何结合程序GMoS提供的序列分析工具，将单个受体中的扭曲置于整个A类GPCR家族的背景下。具体而言，对视紫红质跨膜束中强烈的脯氨酸诱导扭曲的量化表明，它们不是标准的脯氨酸扭结。此外，视紫红质的跨膜螺旋（TMH）5和TMH 6中的螺旋扭曲也存在于迄今为止获得的其他GPCR晶体结构中，因此，基于视紫红质的同源模型正确地模拟了这些严重扭曲的螺旋。虽然在某些情况下，迄今为止许多GPCR模型固有的“视紫红质偏差”并不是一个劣势，但更多模板的可用性显然会产生更好的同源模型。当然，这种类型的分析可以应用于任何蛋白质，并且它可能对其他膜蛋白的结构分析特别有用。了解与配体结合相关的局部结构变化以及它们如何转化为跨膜结构域的更大规模运动是理解受体激活的关键。
