Table 4 Comparison of the sequences defining the transmembrane helices of pairs of models for bovine rhodopsin and hGalR1. The models of bovine rhodopsin and hGalR1 built using the group A sequences onto the Baldwin template give the lipid-corrected compatibility scores of 107.76 and 110.0, respectively. According to the REPIMPS method these are the best models for bovine rhodopsin and hGalR1 among 78,125 models built for each of these GPCRs. Group B sequences are those derived from alignment of sequences of 493 GPCRs proposed by Baldwin et al. [3]. The lipid-corrected compatibility score for bovine rhodopsin and hGalR1 modelled using group B sequences were 85.6 and 89.8, respectively.
From: Modelling the structures of G protein-coupled receptors aided by three-dimensional validation
Helix | Alignment | Sequences for bovine rhodopsin | Sequences for hGalR1 |
|---|---|---|---|
I | A | 37 FSML AAYMFLLIMLGFPINFLT LYVTV 63 | Â Â Â Â 35VTLV VFGLIFALGVLGNSLVIT VLARS61 |
| Â | B | 38 SMLA AYMFLLIMLGFPINFLTL YVTVQ 64 | 34 FVTL VVFGLIFALGVLGNSLVI TVLAR 60 |
II | A | Â Â Â Â 70TPLNY ILLNLAVADLFMVFGGFT TTLY96 | 67 RSTTN LFILNLSIADLAYLLFCI PFQA 93 |
| Â | B | 69 RTPLN YILLNLAVADLFMVFGGF TTTL 95 | 67 RSTTN LFILNLSIADLAYLLFCI PFQA 93 |
III | A | 106 GPTGCNL EGFFATLGGEIALWSLVV LAIERYVVVC 140 | 106 FICKFIH YFFTVSMLVSIFTLAAMS VDRYVAIVHS 140 |
| Â | B | Â Â Â Â Â Â Â Â Â 108TGCNLEG FFATLGGEIALWSLVVLA IERYVVVCKP142 | 106 FICKFIH YFFTVSMLVSIFTLAAMS VDRYVAIVHS 140 |
IV | A | Â Â Â Â 152HAIMG VAFTWVMALACAAPPL VGWS176 | 148 VSRNA LLGVGCIWALSIAMAS PVAY 172 |
| Â | B | 151 NHAIM GVAFTWVMALACAAPP LVGW 175 | Â Â Â Â Â Â Â Â Â 150RNALL GVGCIWALSIAMASPV AYHQ174 |
V | A | 202 SFV IYMFVVHFIIPLIVIFFC YGQLVFTVK 231 | 199 AYV VCTFVFGYLLPLLLICFC YAKVLNHLH 228 |
| Â | B | Â Â Â Â Â Â 204VIY MFVVHFIIPLIVIFFCYG QLVFTVKEA233 | Â Â Â Â Â Â Â 201VVC TFVFGYLLPLLLICFCYA KVLNHLHKK230 |
VI | A | Â Â Â Â Â Â 247EKEVTRMVIIM VIAFLICWLPYAGVAF YIF276 | 240 ASKKKTAQTV LVVVVVFGISWLPHHII HLW 269 |
| Â | B | 245 KAEKEVTRMVI IMVIAFLICWLPYAGV AFY 274 | 240 ASKKKTAQTV LVVVVVFGISWLPHHII HLW 269 |
VII | A | 286 IFMT IPAFFAKTSAVYNPVI YIMM 309 | 284 FRIT AHCLAYSNSSVNPIIY AFLS 307 |
| Â | B | Â Â Â Â Â Â 288MTIP AFFAKTSAVYNPVIYI MMNK311 | Â Â Â Â 285RITA HCLAYSNSSVNPIIYA FLSE308 |