Leffingwell & Associates
Alchemist WebPick Awarded by the webzine of ChemWeb.com
Leffingwell & Associates provides services and software for the perfume, flavor, food and beverage Industries.
Leffingwell & Associates in a study of the predicted ligand binding sites for certain Human OR's of chromosone 1, have found that the largest cavity (as derived by CastP1-4) in the complimentary regions falls in the transmembrane domains TM 37, especially in the region of TM3-TM5-TM6. This is depicted below for selected Human Olfactory receptors as modeled by Leffingwell. As the CastP technique for determining putative binding cavities and pockets predicts the binding site for retinal in the bovine rhodopsin models 1HXZ (chain A)5 and 1F88 (chain A)6 with an excellent correlation to that previously found11, CastP may provide a simple and fast method for predicting the putative odorant binding sites in olfactory receptors.
Previously, Pilpel & Lancet7 have inferred, that for olfactory receptors, the odorant complementarity determining regions reside in the transmembranal segments 3, 4, and 5. Singer8 in an Analysis of the Molecular Basis for Octanal Interactions in the Expressed Rat I7 Olfactory Receptor makes a strong case that octanal binds with OR-I7 in a pocket ~10 Å from the extracellular surface formed by transmembrane domains 37. In addition, Goddard, et.al.9, have modeled the mouse receptor ORL466 (OR S25) and in docking studies predicted the binding pocket for the compounds hexanol and heptanol. Docking results show that TMs 3, 5, and 6 have residues directly involved in binding and that TM4 may have an important role in binding as it packs against TM3 and TM5 and therefore can alter their relative position if key residues of TM4 are mutated. The presence of a critical Lys on TM7 is similar to the related rhodopsin, where Lys-296 (TM7) binds the retinal chromophore10 and substitutions in this residue may switch receptor specificity toward other functional groups.
Visuals of Receptors and Binding site Cavities
Visual representations (derived from CastP) of the binding site
cavity in rhodopsin and the putative binding sites of a few Human
OR's of chromosone 1 are shown below.
Putative Binding cavity in Human OR1.04.06 derived using CastP
Binding cavity for retinal in Bovine
rhodopsin 1HZX Chain A derived using CastP
Binding cavity for retinal in Bovine
rhodopsin 1F88 Chain A derived using CastP
Putative Binding cavity in Human OR1.04.02 derived using CastP
Putative Binding cavity in Human OR1.06.01 derived using CastP
Sequence data used was from the work of Zozulya, Echeverri & Nguyen of Senomyx who published a paper entitled "The human olfactory receptor repertoire" (June, 2001) in which they reported the identification and physical cloning of 347 putative human full-length odorant receptor genes. Comparative sequence analysis of the predicted gene products allowed them to identify and define a number of consensus sequence motifs and structural features of this vast family of receptors. They believe that these sequences represent the essentially complete repertoire of functional human odorant receptors.12 .They found some differences between their data and those in the HORDE database maintained by Doron Lancet's group at at the Weizmann Institute of Science Crown Human Genome Center13. These included 29 "human OR" (hOR) genes that were apparently identified as pseudogenes in the HORDE database, but encoded as functional hOR candidates in their analysis, as well as 10 hORs not found in HORDE. This online article includes a downloadable file with all 347 hOR's in FASTA format.12a
All the Human OR sequences are now available and cross referenced to sources at the SenseLab Olfactory Receptor DataBase (ORDB).
PDB models of selected Human Olfactory receptors are available from Leffingwell & Associates to interested parties upon request.
Contact: J.C. Leffingwell at Email: firstname.lastname@example.org
Cautionary Statement: The X-ray crystal structures of olfactory receptors have not yet been determined. These theoretical OR models are based on the rhodpsin templates starting first with the OR model with best sequence fit, with other models evolving from the first models. Models were prepared using the Swiss-PdbViewer software as well as Swiss-Model14-16. Certain helical areas were hand corrected to improve conformational issues. Optimized models were checked with the WHAT IF program at Heidelberg. As with most protein models (theoretical or as deterimed by X-ray diffraction), these models are not perfect as analyzed by WHAT IF. As such these models are first approach type models and while they may be useful for determining binding sites and in odorant docking studies, Leffingwell & Associates does not warrant these models suitable for any purpose.
1. Edelsbrunner H, Facello M, Liang J., On the definition and the construction of pockets in macromolecules. Disc. Appl. Math. 88:83-102 (1998).
2. Liang J, Edelsbrunner H, Woodward C., Anatomy of protein pockets and caviteis: measurement of binding site geometry and implications for ligand design. Protein Science. 7:1884-1897 (1998).
3. J. Liang, H. Edelsbrunner, P. Fu, P.V. Sudhakar and S. Subramaniam., Analytical shape computing of macromolecules I: molecular area and volume through alpha shape. Proteins. 33, 1-17 (1998).
4. Liang J, Edelsbrunner H, Fu P, Sudhakar PV, Subramaniam S., Analytical shape computation of macromolecules. II. Identification and computation of inaccessible cavities in proteins. Proteins: Struct. Funct. Genet. 33:18-29 (1998 ).
5. Teller, D. C., Okada, T., Behnke, C. A., Palczewski, K., Stenkamp, R. E.: Advances in Determination of a High-Resolution Three-Dimensional Structure of Rhodopsin, a Model of G-Protein-Coupled Receptors (Gpcrs) Biochemistry 40 pp. 7761 (2001)
6. Palczewski, K., Kumasaka, T., Hori, T., Behnke, C. A., Motoshima, H., Fox, B. A., Le Trong, I., Teller, D. C., Okada, T., Stenkamp, R. E., Yamamoto, M., Miyano, M.: Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor Science 289 pp. 739 (2000)
7. Pilpel, Y. and D. Lancet , The variable and conserved interfaces of modeled olfactory receptor proteins., Protein Sci., May;8(5):969-77 (1999).
8. Singer, Michael S., Analysis of the Molecular Basis for Octanal Interactions in the Expressed Rat I7 Olfactory Receptor,Chem. Senses 25: 155-165, (2000)
9. Floriano WB, Vaidehi N, Goddard WA 3rd, Singer MS, Shepherd GM., Molecular mechanisms underlying differential odor responses of a mouse olfactory receptor. Proc Natl Acad Sci U S A, Sep 26;97(20):10712-6 (2000).
10. Singer, M. S., Weisinger-Lewin, Y., Lancet, D. & Shepherd, G. M., Positive selection moments identify potential functional residues in human olfactory receptors., Recept. Channels 4, 141-147 (1996)
11. Leffingwell, J.C., manuscript in preparation.
12. Sergey Zozulya, Fernando Echeverri & Trieu Nguyen, The human olfactory receptor repertoire, Genome Biology 2001 2(6): research0018.1-0018.12
12a. Zozulya, et. al., http://www.genomebiology.com/2001/2/6/research/0018/gb-2001-2-6-research0018-S1.asp
13. Fuchs T, Glusman G, Horn-Saban S, Lancet D, Pilpel Y, The human olfactory subgenome: from sequence to structure and evolution, Hum Genet 2001 Jan;108(1):1-13; Glusman G, Yanai I, Rubin I, Lancet D., The complete human olfactory subgenome, Genome Res. 2001 May;11(5):685-702
14. Guex, N. and Peitsch, M. C., SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modelling. Electrophoresis 18:2714-2723 (1997).
15. Peitsch, M. C. ProMod and Swiss-Model: Internet-based tools for automated comparative protein modelling. Biochem Soc Trans 24:274-279 (1996).
16. Peitsch, M. C. Protein modeling by E-mail, Bio/Technology 13,658-660 (1995).