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| http://dx.doi.org/10.1016/j.pbj.2017.07.127 | DOI Listing |
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Fully Atomistic Molecular Dynamics Simulation of Ice Nucleation Near an Antifreeze Protein.
J Am Chem Soc
January 2025
Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, Kowloon 999077, China.
Heterogeneous ice nucleation is a widespread phenomenon in nature. Despite extensive research on ice nucleation near biological antifreeze proteins, a probe for ice nucleation and growth processes at the atomic level is still lacking. Herein, we present simulation evidence of the heterogeneous ice nucleation process on the ice-binding surface (IBS) of the antifreeze protein (TmAFP).
View Article and Find Full Text PDFIron limitation triggers roseoceramide biosynthesis and membrane remodeling in marine roseobacter.
Proc Natl Acad Sci U S A
January 2025
Department of Chemistry, Princeton University, Princeton, NJ 08544.
Chemical communication between marine bacteria and their algal hosts drives population dynamics and ultimately determines the fate of major biogeochemical cycles in the ocean. To gain deeper insights into this small molecule exchange, we screened niche-specific metabolites as potential modulators of the secondary metabolome of the roseobacter, . Metabolomic analysis led to the identification of a group of cryptic lipids that we have termed roseoceramides.
View Article and Find Full Text PDFSymmetry facilitated the evolution of heterospecificity and high-order stoichiometry in vertebrate hemoglobin.
Proc Natl Acad Sci U S A
January 2025
Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637.
Many proteins form paralogous multimers-molecular complexes in which evolutionarily related proteins are arranged into specific quaternary structures. Little is known about the mechanisms by which they acquired their stoichiometry (the number of total subunits in the complex) and heterospecificity (the preference of subunits for their paralogs rather than other copies of the same protein). Here, we use ancestral protein reconstruction and biochemical experiments to study historical increases in stoichiometry and specificity during the evolution of vertebrate hemoglobin (Hb), an αβ heterotetramer that evolved from a homodimeric ancestor after a gene duplication.
View Article and Find Full Text PDFMetabolic activity controls the emergence of coherent flows in microbial suspensions.
Proc Natl Acad Sci U S A
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Experimental Physics V, Department of Physics, University of Bayreuth, D-95447 Bayreuth, Germany.
Photosynthetic microbes have evolved and successfully adapted to the ever-changing environmental conditions in complex microhabitats throughout almost all ecosystems on Earth. In the absence of light, they can sustain their biological functionalities through aerobic respiration, and even in anoxic conditions through anaerobic metabolic activity. For a suspension of photosynthetic microbes in an anaerobic environment, individual cellular motility is directly controlled by its photosynthetic activity, i.
View Article and Find Full Text PDFBayesian Inference of Phylogenetic Distances: Revisiting the Eigenvalue Approach.
Bull Math Biol
January 2025
Section of Epidemiology, University of Copenhagen, Copenhagen, Denmark.
Using genetic data to infer evolutionary distances between molecular sequence pairs based on a Markov substitution model is a common procedure in phylogenetics, in particular for selecting a good starting tree to improve upon. Many evolutionary patterns can be accurately modelled using substitution models that are available in closed form, including the popular general time reversible model (GTR) for DNA data. For more complex biological phenomena, such as variations in lineage-specific evolutionary rates over time (heterotachy), other approaches such as the GTR with rate variation (GTR ) are required, but do not admit analytical solutions and do not automatically allow for likelihood calculations crucial for Bayesian analysis.
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