protein Archives

Computational Modeling Of An RNA-peptide World

by Keith CowingSeptember 25, 2026September 25, 2026

[biorxiv.org] Emergence and evolution of functional RNA and protein structures are the central problems for understanding the origin of life.

Structure of the PoXeR monomer (left) and trimer (right) predicted using AlphaFold 3. The trimeric structure was observed from the cytoplasmic side, and the C-terminal tails with low pLDDT scores were omitted. W45 and W130 are labeled according to their residue numbers. -- Nature

Biophysics

How A Deep-sea Protein Adapts To An Extreme Environment

by Keith CowingSeptember 11, 2026September 11, 2026

[Kyushu University] Life in the deep sea is under immense pressure—literally. Such extreme conditions can disrupt the delicate structures of proteins essential to life. Yet somehow, the proteins in deep-sea […]

Origin & Evolution of Life

The History Of Enzyme Evolution Embedded In Metabolism

by Keith CowingSeptember 11, 2026September 11, 2026

[PNAS]. Whereas phylogenetic reconstructions are a primary record of protein evolution, it is unknown whether the deep history of enzymes is encoded at higher levels of biological organization.

Molecular dynamics simulations of Orn_6, Dab_6, and Dap_6. (A) Representative structures with the DZBB form used for the MD simulations. (B) Normalized RMSD vs. Rg plots. (C) Free energy landscapes constructed from the dominant principal components. The first two principal components capture the essential collective motions, and the corresponding trace values reflect differences in conformational sampling. Panels (A) to (C) show representative figures for Orn_6, Dab_6, and Dap_6, respectively. (D) Root mean square fluctuation (RMSF) profiles. (E) Intramolecular hydrogen bonds across 20,000 frames. (F) Secondary structure elements (%). Structure = α-helix + β-sheet + β-bridge + Turn. -- biorxiv.org

Origin & Evolution of Life

Prebiotic Cationic Amino Acids Support Formation Of An Ancient Protein Fold

by Keith CowingSeptember 4, 2026September 4, 2026

[biorxiv.org] The evolutionary basis for the selection of the standard proteinogenic amino acids remains elusive, particularly for the long cationic amino acids, lysine and arginine, which were likely scarce in […]

A symbiotic scenario for co-evolution of the ribosome and the replicase. Two variations of the scenario are depicted, whereby the peptidyltransferase center (PTC) and the replicase (REP) ribozymes are encoded by distinct (A) or the same (B) RNA molecule. The figure depicts three major stages of cellular evolution from the primordial RNA world (left) to the intermediate RNA-protein world (center) and the last universal cellular ancestor (LUCA, right). The major events occurring during each stage are briefly described in the corresponding information boxes at the bottom of the figure. -- [q-bio.PE]

Genomics, Proteomics, Bioinformatics

The Selfish Ribosome

by Keith CowingAugust 28, 2026August 28, 2026

[q-bio.PE]. The ribosome is responsible for protein synthesis in all cells, and is the largest energy consumer in the cell.

The diverging paths of iron (Fe) and nickel (Ni) from minerals to proteins. Fe-based metabolisms flourish both before and after Earth’s oxygenation. Ni-based metabolisms are almost exclusively anaerobic, reflecting their origin in the reducing Archean. Fe is used by biology as a generalist, due to its flexibility, which can be seen both in its diverse mineral chemistry and in metal-binding centers of proteins. Ni is less flexible mineralogically, chemically in proteins, and more evolutionarily constrained, as reflected by its metabolic exclusion from oxidized environments. -- LIFE

Astrogeology

Diverging Mineral Chemistry of Iron and Nickel Throughout Earth’s Changing Redox Conditions Reveals Foundation for Their Evolution as Protein Cofactors

by Keith CowingJuly 14, 2026July 14, 2026

[LIFE] Iron (Fe) and nickel (Ni) were both foundational to early metabolism, yet their biological trajectories diverged as Earth’s surface redox state changed. Here, we integrate mineral chemistry network analysis, […]

A newly developed framework for understanding the photoproperties of both natural organic matter and eumelanin, a natural pigment responsible for dark colors in organisms, may inspire advanced sustainable technologies, scientists say. -- ACS Central Science

Biochemistry & Organic Chemistry

Unraveling The Building Blocks Of Earth’s Pigments

by Keith CowingJuly 1, 2026July 1, 2026

[Ohio State] Although they are some of the most widespread substances on Earth, not much is known about eumelanin, or natural organic matter (NOM) — a dark-colored substance formed by […]

To test the method, the team analyzed more than 100 organic and inorganic samples, including material from three-billion-year-old Earth rocks, dinosaur eggshells and fossilized dinosaur feathers caught in amber, as well as samples collected in space from the Ryugu and Bennu asteroids. Asteroid Bennu. Credit: NASA/Goddard/University of Arizona

Astrochemistry, Astronomy & Telescopes, Biochemistry & Organic Chemistry, Biogeochemical Cycles & Geobiology, Biophysics, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Habitable Zones, Imaging & Spectroscopy, Origin & Evolution of Life, Press Release, Water/Hycean Worlds & Oceanography

Before The Aliens, The Amino Acids

by Keith CowingJune 11, 2026June 11, 2026

Before any wrinkled, wide-eyed creature from a distant civilization asks to be taken home, the first success in the search for life beyond Earth might be more prosaic. A clue […]

The primary structural framework is fabricated from Al 6061 alloy, while the biological and electrochemical chambers are constructed from polycarbonate. Printed circuit boards (PCBs) are manufactured using FR4 fiberglass-reinforced epoxy laminate due to its mechanical strength, electrical insulation, and flame-retardant properties. MAEx follows a fully modular, non-welded structural design in which all components are assembled using fasteners, spacers, and interlocking structural elements. The three experimental modules are vertically stacked using spacers for mechanical separation and subsystem protection, while electronic boards are mounted within a dedicated cage structure secured to the payload walls. These strategies provide structural rigidity, thermal isolation, and vibration tolerance during launch conditions. induced vibrations while also maintaining appropriate thermal and electrical isolation between subsystems. -- astro-ph.IM

Biosignatures & Paleobiology, Commercial & Private Sector, Cubesats and smallsats, Microbiology & Virology, Microgravity, Missions & Hardware, Nanotechnology & SynBio, Radiation, Space Life Science, Status Report

Development and Demonstration of a Modular Astrobiological Experiments (MAEx) Payload for Autonomous Biological Monitoring in Low Earth Orbit (LEO)

by Keith CowingMay 29, 2026May 29, 2026

The spaceflight environment presents unique physicochemical conditions, including microgravity, ionizing radiation, altered fluid transport, and confined engineered habitats, which influence biological systems and biomolecular assembly processes.