Department of Pharmaceutical Chemistry, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem 91120
The receptor C5aR is a protein of 350 amino acids, found in the membranes of polymorphonuclear leukocytes. When activated by its ligand, C5a, a very potent chemoatractant, a few events occur. One of the most important ones is the amplification of the inflammatory process.
C5aR belongs to the superfamily of G Protein-Coupled Receptors (GPCR), which includes over a 100 members, who are involved in many important biological activities. The structure of these proteins has not been determined yet.
One of the very few membranal proteins whose structure was solved is bacteriorhodopsin, a membranal proton pump from Halobacterium halobium[1]. It consists of seven transmembranal helices, connected by extra- and intra- cellular hydrophylic loops, an extra-cellular N-terminal and an intra- cellular C-terminal. Bacteriorhodopsin is not a GPCR and has little homology with the proteins of this family, yet there is experimental evidence that demonstrates a similar topology with the GPCRs.
Our three-dimensional model for C5aR is based on the structure of bacteriorhodopsin, since it is the only known protein with a similar structure. Seven regions along the sequence, which are assumed to contain the seven transmembranal helices, were found by means of hydrophobicity prophiles and multiple sequence alignment with other GPCRs, with the program Homology[2]. These seven regions are the input to a program, which suggests the limits of each helix. The program threads the seven sequences simultaniously on the coordinates of bacteriorhodopsin, combining all the options for each helix. It looks for the best structure by calculating the overall contact energy[3] or by summing up the hydrophobicity values[4,5,6,7] in the membrane and outside.
Two best structures were found by combining the results of two versions of the program. The results enable us to align the two proteins in order to transfer the coordinates of bacteriorhodopsin to C5aR. The next step is to refine the orientation of the side chains, many of which are different in C5aR compared to bacteriorhodopsin, in order to avoid collisions between them.
References:
1. Henderson, R. et al. (1990). J. Immun. 153, 4200-4205.
2. Biosym Technologies (1993). Homology user guide, version 2.3 San Diego:
ch. 2, 1-41.
3. Miyazawa, S. and Jernigan, R. (1985). Macromolocules 18, 534-552.
4. Argos, P. et al. (1982). Eur. J. Biochem. 128, 534-552.
5. Engleman, D. M. et al. (1986). Ann. Rev. Biophys. Biophys. Chem. 15, 321-353.
6. Kyte, J. and Doolittle, R. F. (1982). J. Mol. Biol. 157, 105-132.
7. Von Heijne, G. (1981). Eur. J. Biochem 116, 419-422.