Back to Search
Start Over
Energetics of the H-Bond Network in Exiguobacterium sibiricum Rhodopsin.
- Source :
-
Biochemistry [Biochemistry] 2024 Jun 04; Vol. 63 (11), pp. 1505-1512. Date of Electronic Publication: 2024 May 14. - Publication Year :
- 2024
-
Abstract
- Exiguobacterium sibiricum 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 K <subscript>a</subscript> value of ∼6, slightly elevated due to solvation loss. It seems likely that the H-bond network [Asp85···His57···H <subscript>2</subscript> O···Glu214] serves as a proton-conducting pathway toward the protein bulk surface.
- Subjects :
- Protons
Bacterial Proteins chemistry
Bacterial Proteins metabolism
Proton Pumps metabolism
Proton Pumps chemistry
Hydrogen-Ion Concentration
Models, Molecular
Rhodopsins, Microbial metabolism
Rhodopsins, Microbial chemistry
Rhodopsins, Microbial genetics
Hydrogen Bonding
Exiguobacterium metabolism
Exiguobacterium chemistry
Subjects
Details
- Language :
- English
- ISSN :
- 1520-4995
- Volume :
- 63
- Issue :
- 11
- Database :
- MEDLINE
- Journal :
- Biochemistry
- Publication Type :
- Academic Journal
- Accession number :
- 38745402
- Full Text :
- https://doi.org/10.1021/acs.biochem.4c00182