Molecular Mechanism of Wide Photoabsorption Spectral Shifts of Color Variants of Human Cellular Retinol Binding Protein II

Abstract

Color variants of human cellular retinol binding protein II (hCRBPII) created by protein engineering were recently shown to exhibit anomalously wide photoabsorption spectral shifts over ∼200 nm across the visible region. The remarkable phenomenon provides a unique opportunity to gain insight into the molecular basis of the color tuning of retinal binding proteins for understanding of color vision as well as for engineering of novel color variants of retinal binding photoreceptor proteins employed in optogenetics. Here, we report a theoretical investigation of the molecular mechanism underlying the anomalously wide spectral shifts of the color variants of hCRBPII. Computational modeling of the color variants with hybrid molecular simulations of free energy geometry optimization succeeded in reproducing the experimentally observed wide spectral shifts, and revealed that protein flexibility, through which the active site structure of the protein and bound water molecules is altered by remote mutations, plays a significant role in inducing the large spectral shifts.

Tuning the Protein‐Induced Absorption Shifts of Retinal in Engineered Rhodopsin Mimics

“…During the completion of this work, a new QM/MM study on the hCRBPII models was published by Cheng et al . Their QM systems comprised the retinal moiety, similar to our “small QM” system (see Figure ), but treated at the XMCQDPT2(12,12)/6‐31G** level of theory, whereas the MM environment was modeled as a mean electrostatic field of the protein residues.…”

Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores

“…The mechanism through which proteins influence the absorption wavelength λmax of the chromophore is known as color tuning or spectral tuning, a topic that has been widely studied computationally [50][51][52][53] and experimentally. 54,55 Other Δ E(S1-S0) and Δ E(S2-S1) modulating effects are achieved by changing the effective length of the conjugated chain via single bond twisting (e.g. the C6-C7 double bond in rPSB11).…”

Counterion-controlled spectral tuning of the protonated Schiff-base retinal

“…The chromophore is found within a multitude of different opsin proteins which absorb light at different parts of the visible and ultra-violet spectrum, as well as in bacteriorhodopsin proteins found in Archaea. The color tunability of the chromophore, often referred to as the opsin shift, has been widely studied [5][6][7][8][9][10], mainly through comparison of protein absorption measurements to quantum chemical calculations. Spectral analysis of the tuning induced by the protein environment has led to a debate about the nature of the most important contribution to the observed large shifts.…”

“…Spectral analysis of the tuning induced by the protein environment has led to a debate about the nature of the most important contribution to the observed large shifts. While some work has identified the geometric effect (torsion of the retinal or change in the bond length alternation) as the major source for tuning [11], other work attributed it to the electrostatic effect of the counterion [5,6] or the sum of interactions from the binding pocket [10,12,13].…”