Energetics of the H-Bond Network in Rhodopsin

Overview

Journal Biochemistry

Specialty Biochemistry

Date 2024 May 15

PMID 38745402

Authors

Tomoyasu Noji

Yoshihiro Chiba

Keisuke Saito

Hiroshi Ishikita

Affiliations

Soon will be listed here.

Abstract

rhodopsin (ESR) functions as a light-driven proton pump utilizing Lys96 for proton uptake and maintaining its activity over a wide pH range. Using a combination of methodologies including the linear Poisson-Boltzmann equation and a quantum mechanical/molecular mechanical approach with a polarizable continuum model, we explore the microscopic mechanisms underlying its pumping activity. Lys96, the primary proton uptake site, remains deprotonated owing to the loss of solvation in the ESR protein environment. Asp85, serving as a proton acceptor group for Lys96, does not form a low-barrier H-bond with His57. Instead, deprotonated Asp85 forms a salt-bridge with protonated His57, and the proton is predominantly located at the His57 moiety. Glu214, the only acidic residue at the end of the H-bond network exhibits a p value of ∼6, slightly elevated due to solvation loss. It seems likely that the H-bond network [Asp85···His57···HO···Glu214] serves as a proton-conducting pathway toward the protein bulk surface.

Citing Articles

Direct evidence for a deprotonated lysine serving as a H-bond "acceptor" in a photoreceptor protein.

Nagae T, Takeda M, Noji T, Saito K, Aoyama H, Miyanoiri Y Proc Natl Acad Sci U S A. 2024; 121(36):e2404472121.

PMID: 39190358 PMC: 11388336. DOI: 10.1073/pnas.2404472121.

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