proteomics Archives

Phylogenetic relationship among known OmcA/MtrC decaheme c-type cytochromes from diverse bacteria and the newly identified D. acetexigens MtrC detected in this study. Maximum-likelihood phylogenetic tree constructed from a concatenated alignment of the known diversity of OmcA/MtrC decaheme c-type cytochromes and the D. acetexigens MtrC detected in this study. Color codes were assigned by taxonomic order. Bootstrap support values ≥90% from 1000 resamples are indicated with filled black circles. The scale bar represents average changes per amino acid position. MtrC, OmcA, MtrH, MtrG, UndA, and MtrF indicate members of the MtrC family of proteins. MtrC of D. acetexigens is indicated with a red dot. A full resolution image of the tree is available in Supplementary Fig. 11. -- The ISME Journal

Extremeophiles and Extreme Environments, Genomics, Proteomics, Bioinformatics, Magnetic Fields, Electromagnetism, bioelectricity,, Microbiology & Virology, Press Release

Bacteria Reveal Hidden Powers Of Electricity Transfer

by Keith CowingJanuary 14, 2026January 14, 2026

Editor’s note: as we delve further into the myriad of ways that life on Earth operates, modes of operation once thought to be rare or limited to small niches are […]

popEVE combines variation from across evolutionary sequences, modeled with EVE and ESM-1v, with variation within the human population (UKBB17 or GnomAD18), using a Gaussian process to learn the relationship between evolutionary scores and missense constraint.

AI - Data - Apps - Cybernetics, Biochemistry & Organic Chemistry, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Nanotechnology & SynBio, Press Release

AI Learns From The Tree Of Life To Support Rare Disease Diagnosis

by Keith CowingJanuary 13, 2026January 13, 2026

Editor’s note: If we aspire to mount expeditions to new worlds and then embrace the task of characterizing and quantifying whatever life forms we find, the ability to map and […]

Conceptual model for the evolution of exoenzymes and the recycling of organic matter across the Great Oxidation Event (GOE). (A) In the Archean Ocean, prior to the GOE, the recycling of organic matter depended entirely on the activity of fermenters. This resulted in low recycling efficiency, elevated carbon burial, and limited regeneration of essential nutrients back into seawater. This scarcity of particulate organic matter (POM) also reduced the availability of niches for microbial colonization, thus limiting the selective pressure for the evolution of exoenzyme systems. (b) Following the GOE, rising oxygen levels increased the availability of high-energy electron acceptors (e.g. O2, nitrate and ferric iron), supporting the expansion of metabolic groups with high exoenzyme capacity, such as aerobic heterotrophs, dissimilatory nitrate reducers and dissimilatory ferric iron reducers. Concurrently, increases in POM abundance and microbial cell densities would have amplified the selective pressure to produce exoenzymes. Collectively, these changes in the Paleoproterozoic promoted more efficient recycling of organic matter and regeneration of nutrients back into the water column, ultimately fueling greater primary productivity and oxygen release. This feedback between exoenzyme evolution, nutrient cycling, and oxygen production would have amplified Earth’s progressive oxygenation. -- biorxiv.org

Atmospheres, Climate, Weather, Biochemistry & Organic Chemistry, Biogeochemical Cycles & Geobiology, Biophysics, Biosignatures & Paleobiology, Gaia - Planetary Perspectives, Origin & Evolution of Life, Status Report, Water/Hycean Worlds & Oceanography

Microbial Exoenzymes Catalyzed The Transition To An Oxygenated Earth

by Keith CowingOctober 11, 2025October 11, 2025

Microbial exoenzymes—extracellular enzymes secreted to degrade complex organic polymers— are essential for recycling carbon and nutrients, thus sustaining primary productivity in today’s oceans.

Pohang University of Science & Technology (POSTECH)

Biochemistry & Organic Chemistry, Biophysics, Genomics, Proteomics, Bioinformatics, Nanotechnology & SynBio, Origin & Evolution of Life, Press Release

SynBio: A Ring Has Been Added Onto Existing Ribosome Proteins

by Keith CowingOctober 8, 2025October 8, 2025

Inside our cells, ribosomes-the tireless “protein factories” of life-have just shown off a new skill they haven’t used in billions of years.

Assembly formed by primordial peptides as observed by bright field Microscopy Credit Frenkel-Pinter Lab

Biochemistry & Organic Chemistry, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Press Release

New Study Reveals Why Nature Picked Today’s Proteins

by Keith CowingOctober 1, 2025October 1, 2025

Why did life on Earth choose alpha amino acids as the building blocks of proteins? A new study suggests the answer lies in the stability of their inter-molecular interactions.

The four helices conserved across the Lipocone superfamily constitute a cone-like structure, with the helices tending to coalesce on one end and open out into a pocket on the other, lined by the conserved sequence positions. Image credit: Burroughs, Nicastro and L. Aravind (CC BY 4.0)

Biochemistry & Organic Chemistry, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

Origins Of Wnt Signalling Reveals A Protein Superfamily Across The Tree of Life

by Keith CowingSeptember 11, 2025September 18, 2025

Researchers have described a large set of previously unrecognised enzymatic domains – named the Lipocone superfamily – and outlined their evolutionary pathway from bacterial defence molecules to key players in […]

Archaeal proteomes were systematically scanned to identify EPs with potential antimicrobial activity. Circular bars denote the log10-transformed average active (red) and inactive (blue) EPs discovered by APEX. A peptide was classified as active if its predicted mean MIC against tested bacterial strains was ≤100 μmol l−1. The values were normalized by the number of proteins per organism scanned. Archaea with peptides that were synthesized are indicated by a light red square, and those experimentally validated as active are highlighted with a dark red square. -- Nature Microbiology

AI - Data - Apps - Cybernetics, Astropharmacy / Biotechnology, Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Commercial & Private Sector, Extremeophiles and Extreme Environments, Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Press Release, Sample Return

AI Uncovers New Antibiotics In Archaea Microbes

by Keith CowingAugust 17, 2025August 17, 2025

They’ve survived for billions of years in boiling acid, deep-sea vents and salt flats. Now, some of Earth’s oldest life forms — microbes called Archaea — are offering a new […]

The Protein Domain Insertion Optimizer, abbreviated as ProDomino, can forecast which protein domains – like domino tiles – have to be fitted together to engineer a merged protein with new properties. | © Jan Mathony, Benedict Wolf

Astropharmacy / Biotechnology, Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Nanotechnology & SynBio, Origin & Evolution of Life, Status Report

How An Artificial Protein Emerges From Fitting Together Individual Components

by Keith CowingAugust 6, 2025

The targeted engineering of artificial proteins with unique properties – that is possible with the assistance of a novel method developed by a research team led by Prof. Dr Dominik […]

Distribution of sample locations across sabkha units of different ages along the northern coast of the United Arab Emirates. (a) Sampling locations at various outcrops, including Sample A from modern deposits and Samples B and C from a young sabkha terrace. (b) Detailed view of the sampling site for Sample A in the modern sabkha. (c) Image of the lower sabkha terrace where Samples B and C were collected, along with the location of Sample E, which was obtained from a precipitated brine in modern sabkha waters. (d) Upper sabkha terrace showing the sampling site for Sample D. (e) Overview of the five analyzed samples used for protein studies. International Journal of Molecular Sciences via PubMed

Analog Studies, Astrogeology, Biosignatures & Paleobiology, Impact events, Mapping, Geodesy, Cartography, Bathymetry, Mars, Meteorites & Asteroids, Status Report

Comparing Protein Stability in Modern and Ancient Sabkha Environments: Implications for Molecular Remnants on Ancient Mars

by Keith CowingAugust 6, 2025August 6, 2025

Understanding the mechanisms of protein preservation in extreme environments is essential for identifying potential molecular biosignatures on Mars.

The core (gold and black) and surface (silver) residues that were randomised Credit Albert Escobedo/Centro de Regulación Genómica

Astropharmacy / Biotechnology, Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Commercial & Private Sector, Genomics, Proteomics, Bioinformatics, Nanotechnology & SynBio, Press Release

One Billion-year-old Rules Of Protein Stability Revealed

by Keith CowingJuly 25, 2025

Proteins are life’s molecular workhorses, doing everything from turning sunlight into food to fighting viruses. They are built from 20 different types of amino acid molecules, so even a small […]