Current-voltage characteristics of metal-protein-metal structures made of proteorhodopsin and bacteriorhodopsin are modeled by using a percolation-like approach. Starting from the tertiary structure pertaining to the single protein, an analogous resistance network is created. Charge transfer inside the network is described as a sequential tunneling mechanism and the current is calculated for each value of the given voltage. The theory is validated with available experiments, in dark and light. The role of the tertiary structure of the single protein and of the mechanisms responsible for the photo-activity is discussed.
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http://dx.doi.org/10.1109/TNB.2016.2617678 | DOI Listing |
J Phys Chem B
October 2024
C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States.
Proteorhodopsin (PR) is a microbial proton pump that plays a significant role in phototrophy of bacteria in marine environments. Fundamental understanding of the structure-function relationship that drives proton pumping in PR has largely been elusive due to a lack of high-resolution structures of the photointermediates in the PR photocycle. Extending upon previous work, we used long-time scale molecular dynamics (MD) simulations to characterize the M state of the blue variant of PR, which represents the first proton transfer that takes place in the photocycle.
View Article and Find Full Text PDFAdv Sci (Weinh)
April 2024
Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, 3012, Switzerland.
Controlling the pH at the microliter scale can be useful for applications in research, medicine, and industry, and therefore represents a valuable application for synthetic biology and microfluidics. The presented vesicular system translates light of different colors into specific pH changes in the surrounding solution. It works with the two light-driven proton pumps bacteriorhodopsin and blue light-absorbing proteorhodopsin Med12, that are oriented in opposite directions in the lipid membrane.
View Article and Find Full Text PDFBiochemistry (Mosc)
October 2023
Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
Retinal-containing light-sensitive proteins - rhodopsins - are found in many microorganisms. Interest in them is largely explained by their role in light energy storage and photoregulation in microorganisms, as well as the prospects for their use in optogenetics to control neuronal activity, including treatment of various diseases. One of the representatives of microbial rhodopsins is ESR, the retinal protein of Exiguobacterium sibiricum.
View Article and Find Full Text PDFJ Phys Chem B
September 2023
Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
Microbial rhodopsins are light-activated retinal-binding membrane proteins that perform a variety of ion transport and photosensory functions. They display several cases of convergent evolution where the same function is present in unrelated or very distant protein groups. Here we report another possible case of such convergent evolution, describing the biophysical properties of a new group of sensory rhodopsins.
View Article and Find Full Text PDFISME Commun
August 2023
State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, 361102, China.
Proton-pump rhodopsin (PPR) in marine microbes can convert solar energy to bioavailable chemical energy. Whereas bacterial PPR has been extensively studied, counterparts in microeukaryotes are less explored, and the relative importance of the two groups is poorly understood. Here, we sequenced whole-assemblage metatranscriptomes and investigated the diversity and expression dynamics of PPR in microbial eukaryotes and prokaryotes at a continental shelf and a slope site in the northern South China Sea.
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