The dominant perciform suborder Notothenioidei is an excellent study group for assessing the evolution and functional importance of biochemical adaptations to temperature. The availability of notothenioid taxa in a wide range of latitudes (Antarctic and non-Antarctic) provides a tool to enable identification of physiological and biochemical characteristics gained and lost during evolutionary history. Non-Antarctic notothenioids belonging to the most basal families are a crucial source for understanding the evolution of hemoglobin in high-Antarctic cold-adapted fish. This paper focuses on the structure, function and evolution of the oxygen-transport system of Cottoperca gobio, a sub-Antarctic notothenioid fish of the family Bovichtidae, probably derived from ancestral species that evolved in the Antarctic region and later migrated to lower latitudes. Unlike most high-Antarctic notothenioids, but similar to many other acanthomorph teleosts, C. gobio has two major hemoglobins having the beta chain in common. The oxygen-binding equilibria and kinetics of the two hemoglobins have been measured. Hb1 and Hb2 show strong modulation of oxygen-binding equilibria and kinetics by heterotropic effectors, with marked Bohr and Root effects. In Hb1 and Hb2, oxygen affinity and subunit cooperativity are slightly higher than in most high-Antarctic notothenioid hemoglobins. Hb1 and Hb2 show similar rebinding rates, but also show significant dynamic differences that are likely to have functional consequences. Molecular dynamic simulations of C. gobio Hb1 were performed on the dimeric protein in order to obtain a better understanding of the molecular basis of structure/function relationships.
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http://dx.doi.org/10.1111/j.1742-4658.2009.06954.x | DOI Listing |
Science
December 2024
Institute for Geo-Resources and Environment, Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
Methane, a greenhouse gas and energy source, is commonly studied using stable isotope signals as proxies for its formation processes. In subsurface environments, methane often exhibits equilibrium isotopic signals, but the equilibration process has never been demonstrated in the laboratory. We cocultured a hydrogenotrophic methanogen with an H-producing bacterium under conditions (55°C, 10 megapascals) simulating a methane-bearing subsurface.
View Article and Find Full Text PDFBiomolecules
October 2024
Institute of Medical Physics, University of Szeged, 6720 Szeged, Hungary.
The pH dependence of the free energy level of the flash-induced primary charge pair PI was determined by a combination of the results from the indirect charge recombination of PQ and from the delayed fluorescence of the excited dimer (P*) in the reaction center of the photosynthetic bacterium , where the native ubiquinone at the primary quinone binding site Q was replaced by low-potential anthraquinone (AQ) derivatives. The following observations were made: (1) The free energy state of PI was pH independent below pH 10 (-370 ± 10 meV relative to that of the excited dimer P*) and showed a remarkable decrease (about 20 meV/pH unit) above pH 10. A part of the dielectric relaxation of the PI charge pair that is not insignificant (about 120 meV) should come from protonation-related changes.
View Article and Find Full Text PDFNat Commun
October 2024
Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany.
The multi-phase oxidation of S(IV) plays a crucial role in the atmosphere, leading to the formation of haze and severe pollution episodes. We here contribute to its understanding on a molecular level by reporting experimentally determined pK values of the various S(IV) tautomers and reaction barriers for SO formation pathways. Complementary state-of-the-art molecular-dynamics simulations reveal a depletion of bisulfite at low pH at the liquid-vapor interface, resulting in a different tautomer ratio at the interface compared to the bulk.
View Article and Find Full Text PDFAnal Chim Acta
November 2024
GICAPC Research Group, Department of Analytical Chemistry, University of Valencia, Burjassot, Valencia, Spain. Electronic address:
J Chem Phys
October 2024
Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA.
Chemical reactions and vapor-liquid equilibria for molten lithium hydroxide (LiOH) were studied using molecular dynamics simulations and a deep potential (DP) model. The neural network for the model was trained on quantum density functional theory data for a range of conditions. The DP model allows simulations over timescales of hundreds of ns, which provide equilibrium compositions for the systems of interest.
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