Molecular mechanism of activation of human musk receptors OR5AN1 and OR1A1 by (R)-muscone and diverse other musk-smelling compounds

We acknowledge support from NSF (CHE-1265679) and NIH (5R01DC014423 subaward) (EB), NIH (5R01 DC014423) (HM), the European Reasearch Council (ERC) and the Engineering Science Research Council (EPSRC) (DO'H), FAPESP and CNPq (RAC), the Chinese Scholarship Council (CSC) for studentship support (MY), National Science Foundation (31070972) (HZ), Science and Technology Commission of Shanghai Municipality (16ZR1418300) (HZ), the Shanghai Eastern Scholar Program (J50201) (HZ). VSB thanks NIH grant 1R01GM106121-01A1 and computational time from NERSC.Understanding olfaction at the molecular level is challenging due to the lack of crystallographic models of odorant receptors (ORs). To better understand the molecular mechanism of OR activation, we focused on chiral (R)-muscone and other musk smelling odorants due to their great importance and widespread use in perfumery and traditional medicine, as well as environmental concerns associated with bioaccumulation of musks with estrogenic/antiestrogenic properties.  We experimentally and computationally examined the activation of human receptors OR5AN1 and OR1A1, recently identified as specifically responding to musk compounds.  OR5AN1 responds at nanomolar concentrations to musk ketone and robustly to macrocyclic sulfoxides and fluorine-substituted macrocyclic ketones; OR1A1 responds only to nitromusks. Structural models of OR5AN1 and OR1A1 based on quantum mechanics/molecular mechanics (QM/MM) hybrid methods were validated through direct comparisons with activation profiles from site-directed mutagenesis experiments and analysis of binding energies for 35 musk-related odorants.  The experimentally found chiral selectivity of OR5AN1 to (R)- over (S)-muscone was also computationally confirmed for muscone and fluorinated (R)-muscone analogs.  Structural models show that OR5AN1, highly responsive to nitromusks over macrocyclic musks, stabilizes odorants by hydrogen bonding to Tyr260 of transmembrane a-helix 6 and hydrophobic interactions with surrounding aromatic residues Phe105, Phe194 and, Phe207.  The binding of OR1A1 to nitromusks is stabilized by hydrogen bonding to Tyr258 along with hydrophobic interactions with surrounding aromatic residues Tyr251 and Phe206.  Hydrophobic/nonpolar and hydrogen bonding interactions contribute, respectively, 77% and 13% to the odorant binding affinities, as shown by an atom-based quantitative structure-activity relationship model.PostprintPeer reviewe

Drawing the Retinal Out of Its Comfort Zone: An ONIOM(QM/MM) Study of Mutant Squid Rhodopsin

Engineering squid rhodopsin with modified retinal analogues is essential for understanding the conserved steric and electrostatic interaction networks that govern the architecture of the Schiff base binding site. Depriving the retinal of its steric and electrostatic contacts affects the positioning of the Schiff-base relative to the key residues Asn87, Tyr111, and Glu180. Displacement of the W1 and W2 positions and the impact on the structural rearrangements near the Schiff base binding region reiterates the need for the presence of internal water molecules and the accessibility of binding sites to them. Also, the dominant role of the Glu180 counterion in inducing the S₁/S₂ state reversal for SBR is shown for the first time in squid rhodopsin

Spectral Tuning in Halorhodopsin: The Chloride Pump Photoreceptor

The spectral tuning of halorhodopsin from Halobacterium salinarum (<i>s</i>hR) during anion transport was analyzed at the molecular level using DFT-QM/MM [SORCI+Q//B3LYP/6-31G­(d):Amber96] hybrid methods. Insights into the influence of Cl^– depletion, Cl^– substitution by N₃^– or NO₃^–, and mutation of key amino acid residues along the ion translocation pathway (H95A, H95R, Q105E, R108H, R108I, R108K, R108Q, T111V, R200A, R200H, R200K, R200Q, and T203V) were analyzed for the first time in a fully atomistic model of the <i>s</i>hR photoreceptor. We found evidence that structural rearrangements mediated by specific hydrogen bonds of internal water molecules and counterions (D238 and Cl^–) in the active site induce changes in the bond-length alternation of the all-<i>trans</i> retinyl chromophore and affect the wavelength of maximal absorption in <i>s</i>hR

In Silico Prediction of Ligand Binding Energies in Multiple Therapeutic Targets and Diverse Ligand SetsA Case Study on BACE1, TYK2, HSP90, and PERK Proteins

We present here the use of QM/MM LIE (linear interaction energy) based binding free energy calculations that greatly improve the precision and accuracy of predicting experimental binding affinities, in comparison to most current binding free energy methodologies, while maintaining reasonable computational times. Calculations are done for four sets of ligand–protein complexes, chosen on the basis of diversity of protein types and availability of experimental data, totaling 140 ligands binding to therapeutic protein targets BACE1, TYK2, HSP90, and PERK. This method allows calculations for a diverse set of ligands and multiple protein targets without the need for parametrization or extra calculations. The accuracy achieved with this method can be used to guide small molecule computational drug design programs

Color Vision: “OH-Site” Rule for Seeing Red and Green

Eyes gather information, and color forms an extremely important component of the information, more so in the case of animals to forage and navigate within their immediate environment. By using the ONIOM (QM/MM) (ONIOM = our own <i>N-</i>layer integrated molecular orbital plus molecular mechanics) method, we report a comprehensive theoretical analysis of the structure and molecular mechanism of spectral tuning of monkey red- and green-sensitive visual pigments. We show that interaction of retinal with three hydroxyl-bearing amino acids near the β-ionone ring part of the retinal in opsin, A164S, F261Y, and A269T, increases the electron delocalization, decreases the bond length alternation, and leads to variation in the wavelength of maximal absorbance of the retinal in the red- and green-sensitive visual pigments. On the basis of the analysis, we propose the “OH-site” rule for seeing red and green. This rule is also shown to account for the spectral shifts obtained from hydroxyl-bearing amino acids near the Schiff base in different visual pigments: at site 292 (A292S, A292Y, and A292T) in bovine and at site 111 (Y111) in squid opsins. Therefore, the OH-site rule is shown to be site-specific and not pigment-specific and thus can be used for tracking spectral shifts in any visual pigment

Spectral tuning of ultraviolet cone pigments: An interhelical lock mechanism

Ultraviolet (UV) cone pigments can provide insights into the molecular evolution of vertebrate vision since they are nearer to ancestral pigments than the dim-light rod photoreceptor rhodopsin. While visible-absorbing pigments contain an 11-cis retinyl chromophore with a protonated Schiff-base (PSB11), UV pigments uniquely contain an unprotonated Schiff-base (USB11). Upon F86Y mutation in model UV pigments, both the USB11 and PSB11 forms of the chromophore are found to coexist at physiological pH. The origin of this intriguing equilibrium remains to be understood at the molecular level. Here, we address this phenomenon and the role of the USB11 environment in spectral tuning by combining mutagenesis studies with spectroscopic (UV-vis) and theoretical [DFT-QM/MM (SORCI+Q//B3LYP/6-31G(d): Amber96)] analysis. We compare structural models of the wild-type (WT), F86Y, S90A and S90C mutants of Siberian hamster ultraviolet (SHUV) cone pigment to explore structural rearrangements that stabilize USB11 over PSB11. We find that the PSB11 forms upon F86Y mutation and is stabilized by an "inter-helical lock" (IHL) established by hydrogen-bonding networks between transmembrane (TM) helices TM6, TM2, and TM3 (including water w2c and amino acid residues Y265, F86Y, G117, S118, A114, and E113). The findings implicate the involvement of the IHL in constraining the displacement of TM6, an essential component of the activation of rhodopsin, in the spectral tuning of UV pigments. \ua9 2013 American Chemical Society

Ultrafast OH-stretching frequency shifts of hydrogen- bonded 2-naphthol photoacid-base complexes in solution

We characterize the transient solvent-dependent OH-stretching frequency shifts of photoacid 2-naphthol hydrogen-bonded with CH3CN in the S0- and S1-states using a combined experimental and theoretical approach, and disentangle specific hydrogen-bonding contributions from nonspecific dielectric response