Vohra S, Chintapalli S V, Illingworth C J R, Reeves P J, Mullineaux P M, Clark H S X, Dean M K, Upton G J G, Reynolds C A
Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.
Biochem Soc Trans. 2007 Aug;35(Pt 4):749-54. doi: 10.1042/BST0350749.
A full picture of the similarities between Family A and Family B GPCRs (G-protein coupled receptors) has been frustrated by the lack of clear homology between the respective sequences. Here, we review previous computational studies on GPCR dimerization in which the putative dimerization interfaces have been analysed using entropy, the ET (evolutionary trace) method and related methods. The results derived from multiple sequence alignments of Family A subfamilies have been mapped on to the rhodopsin crystal structure using standard alignments. Similarly, the results for the Family B alignments have been mapped on to the rhodopsin crystal structure using the 'cold-spot' alignment. For both Family A and Family B GPCRs, the sequence analysis indicates that there are functional sites on essentially all transmembrane helices, consistent with the parallel daisy chain model of GPCR oligomerization in which each GPCR makes interactions with a number of neighbouring GPCRs. The results are not too sensitive to the quality of the alignment. Molecular Dynamics simulations of the activation process within a single transmembrane bundle of the rhodopsin and the beta(2)-adrenergic receptor have been reviewed; the key observation, which is consistent with other computational studies, is that there is a translation and bending of helix 6, which contributes to a significant opening out of the intracellular face of the receptor, as shown in the accompanying movies. The simulations required the application of specific experiment-derived harmonic and half-harmonic distance restraints and so the application of such simulations to Family B GPCRs requires considerable care because of the alignment problem. Thus, in order to address the alignment problem, we have exploited the observation that GCR1, a plant GPCR, has homology with Family A, Family B and Family E GPCRs. The resulting alignment for transmembrane helix 3 is presented.
由于A类和B类G蛋白偶联受体（GPCR）各自序列之间缺乏明确的同源性，全面了解它们之间的相似性受到了阻碍。在这里，我们回顾了先前关于GPCR二聚化的计算研究，其中使用熵、进化追踪（ET）方法及相关方法分析了假定的二聚化界面。从A类亚家族的多序列比对得出的结果已使用标准比对映射到视紫红质晶体结构上。同样，B类比对的结果已使用“冷点”比对映射到视紫红质晶体结构上。对于A类和B类GPCR，序列分析表明基本上所有跨膜螺旋上都存在功能位点，这与GPCR寡聚化的平行雏菊链模型一致，即每个GPCR与许多相邻的GPCR相互作用。结果对比对质量不太敏感。对视紫红质和β₂ - 肾上腺素能受体单个跨膜束内激活过程的分子动力学模拟也进行了回顾；与其他计算研究一致的关键观察结果是，螺旋6发生平移和弯曲，这导致受体细胞内面显著张开，如随附的视频所示。这些模拟需要应用特定实验得出的谐波和半谐波距离约束，因此由于比对问题，将此类模拟应用于B类GPCR需要格外小心。因此，为了解决比对问题，我们利用了植物GPCR——GCR1与A类、B类和E类GPCR具有同源性这一观察结果。给出了跨膜螺旋3的最终比对结果。
