X-ray crystallography Archives

Conceptual model illustrating a possible evolutionary trajectory of ATP-generating enzymes. Under prebiotic conditions with a limited amino acid repertoire, kinase-like proteins resembling Arc1-12KR or Arc1-11K may have generated ATP through ADP disproportionation (2ADP → ATP + AMP). As the amino acid alphabet expanded toward the LUCA era, this chemistry was likely superseded by the emergence of modern NDKs, which catalyze phosphoryl transfer between NTPs and NDPs, and by adenylate kinases, which catalyze the reversible reaction 2ADP ⇌ ATP + AMP. Ultimately, the evolution of rotary ATP synthases enabled efficient ATP production from ADP and inorganic phosphate. -- biorxiv.org

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

Emergence Of A Potentially Ancestral ATP-synthesizing Activity Under Prebiotic Amino Acid Constraints

by Keith CowingFebruary 25, 2026February 25, 2026

The earliest enzymes are thought to have been composed of the limited amino acid repertoire available on prebiotic Earth. However, how such compositional simplicity shaped catalytic capability remains unclear.

Open and closed conformations of rcPEPCK along the reaction coordinate. Superposition of the open and closed structures (N-terminal domain residues 3-250) of rcPEPCK, indicating conformational changes of A) the global structure and B) the active site. Holo rcPEPCK (open) is shown in steel blue (PDB 2QEW), and its Ω-loop in light grey, R-loop in coral, and P loop in lilac. Oxalate- (enol-pyruvate intermediate mimic) GTP bound rcPEPCK (closed) is shown in gold (PDB 3DT2) and its Ω-loop in grey, R-loop in firebrick red, and P-loop in purple. Oxalate9 and GTP are shown bound to the active site and atoms are colored by type (red – oxygen, blue – nitrogen, green – carbon, purple – phosphorous, pink – manganese). -- biorxiv.org

Biochemistry & Organic Chemistry, Biosignatures & Paleobiology, Extremeophiles and Extreme Environments, Microgravity, Status Report

A Structural Perspective on the Temperature-dependent Activity of Enzymes

by Keith CowingSeptember 3, 2024September 2, 2024

Enzymes are biomolecular catalysts whose activity varies with temperature. Unlike for small-molecule catalysts, the structural ensembles of enzymes can vary substantially with temperature, and it is in general unclear how […]

X-ray crystallography

Emergence Of A Potentially Ancestral ATP-synthesizing Activity Under Prebiotic Amino Acid Constraints

A Structural Perspective on the Temperature-dependent Activity of Enzymes

How High-pressure Ices On Large Ocean Worlds Can Support Habitability: The Compatibility Of Amino Acids Into Ice VI And VII

Ice Drives The Emergence Of Functional Protocells

Chemical Abundance Patterns at z=1-7: Carbon, Nitrogen, Neon, Sulphur, and Argon Abundances From JWST Spectroscopy

Optimization of Petal-Shaped Occulters for Exo-Earth Observation

Topographically Forced Stationary Waves Can Explain The Near-Surface Zonal Winds Observed By Huygens On Titan