Origin and Consequences of Steric Strain in the Rhodopsin Binding Pocket

Abstract

To study the origin and the effects of steric strain on the chromophore conformation in rhodopsin, we have performed quantum-mechanical calculations on the wild-type retinal chromophore and four retinal derivatives, 13-demethyl-, 10-methyl-13-demethyl-, 10-methyl-, and 9-demethylretinal. For the dynamics of the whole protein, a combined quantum mechanics/molecular mechanics method (DFTB/CHARMM) was used and for the calculation of excited-state properties the nonempirical CASSCF/CASPT2 method. After relaxation inside the protein, all chromophores show significant nonplanar distortions from C10 to C13, most strongly for 10-methylretinal and least pronounced for 9-demethylretinal. In all five cases, the dihedral angle of the C10-C11=C12-C13 bond is negative which attests to the strong chiral discrimination exerted by the protein pocket. The calculations show that the nonplanar distortion of the chromophore, including the sense of rotation, is caused by a combination of two effects: the fitting of both ends to the protein matrix which imposes a distance constraint and the bonding arrangement at the Schiff base terminus. With both the counterion Glu113 and Lys296 displaced off the plane of the chromophore, their binding to N16 exerts a torque on the chromophore. As a result, the polyene chain, from N16 to C13, is twisted in a clockwise manner against the remaining part of the chromophore, leading to a C11=C12 bond with the observed negative dihedral angle. Shifts of the absorption maxima are reproduced correctly, in particular, the red shift of the 10-methyl and the strong blue shift of the 9-demethyl analogue relative to the wild type. Calculated positive rotatory strengths of the alpha-CD bands are in agreement with the calculated absolute conformation of the mutant chromophores.

Dynamic Structure of Retinylidene Ligand of Rhodopsin Probed by Molecular Simulations

“…For retinal bound to rhodopsin, the two torsions adjacent to the cis-double bond are significantly perturbed from their planar state; the C10-C11 torsion angle is 164±12° and the C12-C13 torsion angle is 161±9°, in accord with 2 H NMR data for rhodopsin in the dark state 33 . The torsional deformation alleviates the steric clashes between the C13-methyl group and the H10 hydrogen 38 . Results of the MD simulations are generally consistent with three planes of unsaturation for retinal within the binding cavity of rhodopsin 16,33,41 , a model previously used to interpret 2 H NMR results 33 .…”

“…However, interactions of the β-ionone ring within its binding pocket are nonspecific, and the cavity is large enough to allow conformational heterogeneity. It follows that activation of rhodopsin can be considered in terms of three (sub)sites for binding of the ligand to the receptor 16,25,33,38 . These correspond to (i) the protonated Schiff base and its associated counterion 14,[58][59][60] , (ii) the mid-portion of the polyene chain 25,28 , and lastly (iii) the β-ionone ring within its hydrophobic binding pocket 31,33 .…”

“…Multiple retinal conformations 31 could be important for understanding conflicting reports in the literature that address isomerization of the β -ionone ring [32][33][34]38,40,55,63 . Up until now, most investigators have assumed that the β-ionone ring of retinal adopts a single conformer.…”

“…Although several calculations have focused on the structure of the retinal 38 , none considered the possibility of multiple retinal conformers. In part, this is because such transitions occur very rarely on the time scale of typical molecular dynamics calculations.…”

Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum chemistry

“…Later, Birge and Hubbard (6) reported a different semiempirical study of an explicit chromophore-counterion pair evolving along a single coordinate. While the first simulation of the retinal photoisomerization using a full atomic-level protein model (7) was reported for the related receptor bacterio-Rh (bR), attempts to simulate the PSB11 excited-state motion in a complete Rh model are more recent (8)(9)(10). On the other hand, a quantitative evaluation of the isomerization coordinate and time scale requires, as a prerequisite, an accurate excited-state force field for PSB11 in Rh.…”