A QM/MM study of the initial excited state dynamics of green-absorbing proteorhodopsin

Molecular Mechanisms Underlying the Spectral Shift in Zebrafish Cone Opsins

Visual pigments are essential for converting light into electrical signals during vision. Composed of an opsin protein and a retinal-based chromophore, pigments in vertebrate rods (Rh1) and cones (Rh2) have different spectral sensitivities, with distinct peak absorption wavelengths determined by the shape and composition of the chromophore binding pocket. Despite advances in understanding Rh1 pigments such as bovine rhodopsin, the molecular basis of spectral shifts in Rh2 cone opsins has been less studied, particularly the E122Q mutation, which accounts for about half of the observed spectral shift in these pigments. In this study, we employed molecular modeling and quantum mechanical techniques to investigate the molecular mechanisms behind the spectral difference in blue-shifted Rh2-1 (absorption peak = 467 nm, 122Q) and green-shifted Rh2-4 (absorption peak = 505 nm, 122E) zebrafish cone opsins. We modeled the pigments 3D structures based on their sequences and conducted all-atom molecular dynamics simulations totaling 2 microseconds. Distance analysis of the trajectories identified three key sites: E113, E181, and E122. The E122Q mutation, previously known, validates our findings, while E181 and E113 are newly identified contributors. Structural analysis revealed key features with differing values that explain the divergent spectral sensitivities of Rh2-1 and Rh2-4: 1) chromophore atom fluctuations and C5-C6 torsion angle, 2) binding pocket volume, 3) hydration patterns, and 4) E113-chromophore interaction stability. Quantum mechanics further confirms the critical role of residue E181 in Rh2-1 and E122 in Rh2-4 for their spectral behavior. Our study provides new insights into the molecular determinants of spectral shifts in cone opsins, and we anticipate that it will serve as a starting point for a broader understanding of the functional diversity of visual pigments.

Understanding the Photoprocesses in Biological Systems: Need for Accurate Multireference Treatment

Light-matter interaction is crucial to life itself and revolves around many of the central processes in biology. The need for understanding these photochemical and photophysical processes cannot be overemphasized. Interaction of light with biological systems starts with the absorption of light and subsequent phenomena that occur in the excited states of the system. However, excited states are typically difficult to understand within the mean field approximation of quantum chemical methods. Therefore, suitable multireference methods and methodologies have been developed to understand these phenomena. In this Perspective, we will describe a few methods and methodologies suitable for these descriptions and discuss some persisting difficulties.

Deciphering the Spectral Tuning Mechanism in Proteorhodopsin: The Dominant Role of Electrostatics Instead of Chromophore Geometry

Proteorhodopsin (PR) is a photoactive proton pump found in marine bacteria. There are two phenotypes of PR exhibiting an environmental adaptation to the ocean's depth which tunes their maximum absorption: blue‐absorbing proteorhodopsin (BPR) and green‐absorbing proteorhodopsin (GPR). This blue/green color‐shift is controlled by a glutamine to leucine substitution at position 105 which accounts for a 20 nm shift. Typically, spectral tuning in rhodopsins is rationalized by the external point charge model but the Q105L mutation is charge neutral. To study this tuning mechanism, we employed the hybrid QM/MM method with sampling from molecular dynamics. Our results reveal that the positive partial charge of glutamine near the C₁₄−C₁₅ bond of retinal shortens the effective conjugation length of the chromophore compared to the leucine residue. The derived mechanism can be applied to explain the color regulation in other retinal proteins and can serve as a guideline for rational design of spectral shifts.

A Unified View on Varied Ultrafast Dynamics of the Primary Process in Microbial Rhodopsins

All-trans to 13-cis photoisomerization of the protonated retinal Schiff base (PRSB) chromophore is the primary step that triggers various biological functions of microbial rhodopsins. While this ultrafast primary process has been extensively studied, it has been recognized that the relevant excited-state relaxation dynamics differ significantly from one rhodopsin to another. To elucidate the origin of the complicated ultrafast dynamics of the primary process in microbial rhodopsins, we studied the excited-state dynamics of proteorhodopsin, its D97N mutant, and bacteriorhodopsin by femtosecond time-resolved absorption (TA) spectroscopy in a wide pH range. The TA data showed that their excited-state relaxation dynamics drastically change when pH approaches the pKa of the counterion residue of the PRSB chromophore in the ground state. This result reveals that the varied excited-state relaxation dynamics in different rhodopsins mainly originate from the difference of the ground-state heterogeneity (i.e., protonation/deprotonation of the PRSB counterion).

Accurate Prediction of Absorption Spectral Shifts of Proteorhodopsin Using a Fragment-Based Quantum Mechanical Method

Many experiments have been carried out to display different colors of Proteorhodopsin (PR) and its mutants, but the mechanism of color tuning of PR was not fully elucidated. In this study, we applied the Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps (EE-GMFCC) method to the prediction of excitation energies of PRs. Excitation energies of 10 variants of Blue Proteorhodopsin (BPR-PR105Q) in residue 105GLN were calculated with the EE-GMFCC method at the TD-B3LYP/6-31G* level. The calculated results show good correlation with the experimental values of absorption wavelengths, although the experimental wavelength range among these systems is less than 50 nm. The ensemble-averaged electric fields along the polyene chain of retinal correlated well with EE-GMFCC calculated excitation energies for these 10 PRs, suggesting that electrostatic interactions from nearby residues are responsible for the color tuning. We also utilized the GMFCC method to decompose the excitation energy contribution per residue surrounding the chromophore. Our results show that residues ASP97 and ASP227 have the largest contribution to the absorption spectral shift of PR among the nearby residues of retinal. This work demonstrates that the EE-GMFCC method can be applied to accurately predict the absorption spectral shifts for biomacromolecules.

Modern quantum chemistry with [Open]Molcas

MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.

A high-throughput computational approach to UV-Vis spectra in protein mutants

In this work we present a high-throughput approach to the computation of absorption UV-Vis spectra tailored to mutagenesis studies. The scheme makes use of a single molecular dynamics trajectory of a reference (non-mutated) species. The shifts in absorption energy caused by a residue mutation are evaluated by building an effective potential of the environment and computing a correction term based on perturbation theory. The sampling is only performed in the phase space of the initial protein. We analyze the robustness of the method by comparing different approximations for the effective potential, the sampling of mutant residue geometries and observing the impact in the prediction of both bathocromic and hypsochromic shifts. As a test subject, we consider a red fluorescent protein variant with potential biotechnological applications.

Low-temperature Raman spectroscopy reveals small chromophore distortion in primary photointermediate of proteorhodopsin

Proteorhodopsin (PR) is a microbial rhodopsin functioning as a light-driven proton pump in aquatic bacteria. We performed low-temperature Raman measurements of PR to obtain the structure of the primary photoproduct, the K intermediate (PR_K ). PR_K showed the hydrogen-out-of-plane modes that are much less intense than those of bacteriorhodopsin as the prototypical light-driven proton pump from haloarchaea. The present results reveal the significantly relaxed chromophore structure in PR_K , which can be coupled to the slow kinetics of the K intermediate. This structure suggests that PR transports protons using the small energy storage within the chromophore at the start of its photocycle.

Different hydrogen bonding environments of the retinal protonated Schiff base control the photoisomerization in channelrhodopsin-2

The first event of the channelrhodopsin-2 (ChR2) photocycle, i.e. trans-to-cis photoisomerization, is studied by means of quantum mechanics/molecular mechanics, taking into account the flexible retinal environment in the ground state.