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

Chenfei Shen,Xinsheng Jin,Xiao He,William J Glover

doi:10.3390/molecules26154486

Abstract

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.

Highlights

The rhodopsin proteorhodopsin and related proteins have aroused continuous and extensive interest both experimentally and theoretically among researchers, especially during the past 20 years [1,2,3,4,5]
To handle the full complexities of the PR chromophore-protein interactions, we use Electrostatic Embedded (EE)-GMFCC, which is an extension of GMFCC to include many-body environment effects in each fragment quantum mechanical (QM) calculation using embedding charges that represent the remaining fragments [14,15]
Before applying the EE-GMFCC method to absorption spectrum calculations of PRs, we give a brief description of this quantum fragmentation approach to large biomolecular systems

Summary

Introduction

The rhodopsin proteorhodopsin and related proteins have aroused continuous and extensive interest both experimentally and theoretically among researchers, especially during the past 20 years [1,2,3,4,5]. Rhodopsin is a seven transmembrane α-helices (TM) protein which uses retinal as a chromophore. The aldehyde of vitamin A and a polyene chromophore, is derived from β-carotene and utilized in the all-trans/13-cis configurations in microbial rhodopsins allowing certain microorganisms to convert light into metabolic energy. Proteorhodopsin(PR), as a member of the microbial rhodopsin family, is a light-driven protein found in marine proteobacteria. Borhan and co-workers performed spectral tuning of all-trans-retinal PRs, in which one or multiple residues were mutated by rational mutagenesis, enabling the absorption maximum of the pigment in the range of 425 to 644 nm [11]. Our group developed the Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps (EE-GMFCC) method for quantitatively characterizing properties of proteins with localized excitations (i.e., involving a single chromophore). We hope that this method can be used to help investigate the mechanism of color tuning in PRs, and for the rational design of its mutagenesis

Computational Approaches

The EE-GMFCC Method for Excited State and Its Application for PR105Q

Residue-Based Decomposition of Excitation Energies

Findings

The Local Electric Field along the Retinal