Test of the Binding Threshold Hypothesis for olfactory receptors: Explanation of the differential binding of ketones to the mouse and human orthologs of olfactory receptor 912‐93

We tested the Binding Threshold Hypothesis (BTH) for activation of olfactory receptors (ORs): To activate an OR, the odorant must bind to the OR with binding energy above some threshold value. The olfactory receptor (OR) 912‐93 is known experimentally to be activated by ketones in mouse, but is inactive to ketones in human, despite an amino acid sequence identity of ∼66%. To investigate the origins of this difference, we used the MembStruk first‐principles method to predict the tertiary structure of the mouse OR 912‐93 (mOR912‐93), and the HierDock first‐principles method to predict the binding site for ketones to this receptor. We found that the strong binding of ketones to mOR912‐93 is dominated by a hydrogen bond of the ketone carbonyl group to Ser105. All ketones predicted to have a binding energy stronger than EBindThresh = 26 kcal/mol were observed experimentally to activate this OR, while the two ketones predicted to bind more weakly do not. In addition, we predict that 2‐undecanone and 2‐dodecanone both bind sufficiently strongly to activate mOR912‐93. A similar binding site for ketones was predicted in hOR912‐93, but the binding is much weaker because the human ortholog has a Gly at the position of Ser105. We predict that mutating this Gly to Ser in human should lead to activation of hOR912‐93 by these ketones. Experimental substantiations of the above predictions would provide further tests of the validity of the BTH, our predicted 3D structures, and our predicted binding sites for these ORs.

[1]  L. Turin,et al.  A spectroscopic mechanism for primary olfactory reception. , 1996, Chemical senses.

[2]  Doron Lancet,et al.  Prediction of the odorant binding site of olfactory receptor proteins by human–mouse comparisons , 2004, Protein science : a publication of the Protein Society.

[3]  G. Schertler,et al.  Structure of rhodopsin , 1998, Eye.

[4]  R. H. S. Carpenter,et al.  Reply to 'Putting noise into neurophysiological models of simple decision making' , 2001, Nature Neuroscience.

[5]  Pieter F. W. Stouten,et al.  Fast prediction and visualization of protein binding pockets with PASS , 2000, J. Comput. Aided Mol. Des..

[6]  W. Goddard,et al.  Atomic level simulations on a million particles: The cell multipole method for Coulomb and London nonbond interactions , 1992 .

[7]  M. S. Singer,et al.  Analysis of the molecular basis for octanal interactions in the expressed rat 17 olfactory receptor. , 2000, Chemical senses.

[8]  Wely B. Floriano,et al.  Interaction of e. coli outer‐membrane protein A with sugars on the receptors of the brain microvascular endothelial cells , 2002, Proteins.

[9]  L. Buck,et al.  The mouse olfactory receptor gene family , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Peter L. Freddolino,et al.  Prediction of structure and function of G protein-coupled receptors , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[11]  Peter L. Freddolino,et al.  Predicted 3D structure for the human beta 2 adrenergic receptor and its binding site for agonists and antagonists. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[12]  L. Buck,et al.  The human olfactory receptor gene family. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[13]  D. Eisenberg,et al.  The hydrophobic moment detects periodicity in protein hydrophobicity. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[14]  L. Vosshall,et al.  A psychophysical test of the vibration theory of olfaction , 2004, Nature Neuroscience.

[15]  Hiroshi Kataoka,et al.  Molecular Bases of Odor Discrimination: Reconstitution of Olfactory Receptors that Recognize Overlapping Sets of Odorants , 2001, The Journal of Neuroscience.

[16]  J M Blaney,et al.  A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.

[17]  Todd J. A. Ewing,et al.  Critical evaluation of search algorithms for automated molecular docking and database screening , 1997, J. Comput. Chem..

[18]  Nagarajan Vaidehi,et al.  Virtual screening for binding of phenylalanine analogues to phenylalanyl-tRNA synthetase. , 2002, Journal of the American Chemical Society.

[19]  S. Firestein,et al.  The olfactory receptor gene superfamily of the mouse , 2002, Nature Neuroscience.

[20]  Roland L. Dunbrack,et al.  Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. , 1997, Journal of molecular biology.

[21]  Patrice Mollard,et al.  A single olfactory receptor specifically binds a set of odorant molecules , 2002, The European journal of neuroscience.

[22]  Abhinandan Jain,et al.  Protein simulations using techniques suitable for very large systems: The cell multipole method for nonbond interactions and the Newton‐Euler inverse mass operator method for internal coordinate dynamics , 1994, Proteins.

[23]  G. Zamanakos A fast and accurate analytical method for the computation of solvent effects in molecular simulations , 2002 .

[24]  B. Trask,et al.  A gene recently inactivated in human defines a new olfactory receptor family in mammals. , 1998, Human molecular genetics.

[25]  Abhinandan Jain,et al.  A fast recursive algorithm for molecular dynamics simulation , 1993 .

[26]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[27]  William A. Goddard,et al.  Fidelity of Phenylalanyl-tRNA Synthetase in Binding the Natural Amino Acids , 2003 .

[28]  J. Gasteiger,et al.  ITERATIVE PARTIAL EQUALIZATION OF ORBITAL ELECTRONEGATIVITY – A RAPID ACCESS TO ATOMIC CHARGES , 1980 .

[29]  Nagarajan Vaidehi,et al.  First principles predictions of the structure and function of g-protein-coupled receptors: validation for bovine rhodopsin. , 2004, Biophysical journal.

[30]  K. Mikoshiba,et al.  Functional expression of a mammalian odorant receptor. , 1998, Science.

[31]  S. L. Mayo,et al.  DREIDING: A generic force field for molecular simulations , 1990 .

[32]  Stephen Taylor,et al.  Molecular dynamics for very large systems on massively parallel computers: The MPSim program , 1997, J. Comput. Chem..

[33]  A. Sali,et al.  Comparative protein structure modeling by iterative alignment, model building and model assessment. , 2003, Nucleic acids research.

[34]  L. Buck,et al.  Combinatorial Receptor Codes for Odors , 1999, Cell.

[35]  Peter L. Freddolino,et al.  The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antagonists. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[36]  Abhinandan Jain,et al.  Constant temperature constrained molecular dynamics: The Newton-Euler inverse mass operator method , 1996 .

[37]  G M Shepherd,et al.  Molecular mechanisms underlying differential odor responses of a mouse olfactory receptor. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[38]  W. Goddard,et al.  Mechanism for antibody catalysis of the oxidation of water by singlet dioxygen , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[39]  R. Axel,et al.  A novel multigene family may encode odorant receptors: A molecular basis for odor recognition , 1991, Cell.

[40]  R. Araneda,et al.  The molecular receptive range of an odorant receptor , 2000, Nature Neuroscience.

[41]  L. Stubbs,et al.  Sequence and chromosomal localization of the mouse ortholog of the human olfactory receptor gene 912-93 , 1999, Mammalian Genome.

[42]  Nagarajan Vaidehi,et al.  Making sense of olfaction through predictions of the 3-D structure and function of olfactory receptors. , 2004, Chemical senses.

[43]  Nagarajan Vaidehi,et al.  HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases. , 2004, Journal of medicinal chemistry.

[44]  Nagarajan Vaidehi,et al.  Predicted 3-D structures for mouse I7 and rat I7 olfactory receptors and comparison of predicted odor recognition profiles with experiment. , 2004, Chemical senses.

[45]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[46]  Peter Mombaerts,et al.  Odorant Receptor Expression Defines Functional Units in the Mouse Olfactory System , 2002, The Journal of Neuroscience.

[47]  P. Mombaerts Seven-transmembrane proteins as odorant and chemosensory receptors. , 1999, Science.

[48]  Dietmar Krautwurst,et al.  Identification of Ligands for Olfactory Receptors by Functional Expression of a Receptor Library , 1998, Cell.