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Workflow of this study. All available coenzymes in the PDB were identified according to the CoFactor database (Fischer et al., 2010). The PDB entries of structures bound to coenzymes were downloaded programmatically through the PDBe REST API (pdbe.org/api), including the interatomic cofactor-protein interactions, calculated by Arpeggio (Jubb et al, 2017). The coenzyme binding amino acids were mapped to Uniprot databases via SIFTS (Velankar et al., 2013; Dana et al., 2019). PDB entries were grouped by UniProt code; redundancy was removed by clustering the UniProt sequences by 90% sequence identity. -- biorxiv

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

Coenzyme-Protein Interactions Since Early Life

by Keith CowingNovember 6, 2023November 5, 2023

Recent findings in protein evolution and peptide prebiotic plausibility have been setting the stage for reconsidering the role of peptides in the early stages of life’s origin.

Examples of prebiotic analogue conditions. (A) A boiling, hydrothermal pool on Mount Mutnovsky, an active volcano south of Petropavlovsk, Kamchatka, Russia. The author is pointing at a membranous froth produced by myristic acid added to the pool [4]. Photo credit: Tony Hoffman). (B) Hydrothermal water in Bumpass Hell on Mount Lassen, California (photograph by author). (C) Hydrothermal pools in Hell’s Gate, near Rotorua, New Zealand (Photograph by author). (D) Fly Geyser in the Black Rock playa of northern Nevada (credit: Bruce Damer). -- Life

Extremeophiles and Extreme Environments, Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Origin & Evolution of Life, Status Report

Template-Directed Replication and Chiral Resolution during Wet–Dry Cycling in Hydrothermal Pools

by Keith CowingSeptember 6, 2023September 6, 2023

The commonly supposed template-based format for RNA self-replication requires both duplex assembly and disassembly.

Event data for E. coli ribosome in 2M LiCl. Panel A shows heat map of change in conductance vs. dwell time (time molecule spends disrupting nanopore’s ionic current). Heat map color scale corresponds to a probability of an event being in that region of the heat map. Panel B shows example events interpreted to be an intact ribosome (corresponding to Panel C) and a ribosomal fragment (corresponding to Panel D). Panels C and D show overlaid events within the red boxes C and D on Panel A, plotting all events with a signal-to-noise ratio greater than 10, with time scaled to 1. Event data around a current baseline of 0 pA can be observed in C and D throughout the middle of the scaled events (e.g. events with a current signal close to the baseline along time axis points of 0.4 - 0.6). This is due to instances of the automatic event extraction selecting an event with 2 translocations (due to the translocations happening close to each other temporally). -- biorxiv.org

AI - Data - Apps - Cybernetics, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Status Report, Tricorders & Sensors, Water/Hycean Worlds & Oceanography

Tricorder Tech: Translation As A Biosignature

by Keith CowingAugust 18, 2023August 18, 2023

Life on Earth relies on mechanisms to store heritable information and translate this information into cellular machinery required for biological activity. In all known life, storage, regulation, and translation are […]

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

Discovery Of Novel Primitive Xeno Nucleic Acids As Alternative Genetic Polymers

by Keith CowingJune 23, 2023June 23, 2023

The chemical origin of life on Earth is a puzzle that scientists have been trying to piece together for decades. Many hypotheses have been proposed to explain how life came […]

Chiral molecules can spin polarize magnetic surfaces due to the CISS effect. A. Electron density of a molecule approaching a surface is asymmetrically distributed and a transient charge dipole is created. Charge transport through chiral molecules is spin selective due to the CISS effect and therefore a spin-dipole along the chiral molecular axis accompanies this charge dipole. This transient spin dipole can couple with surface spins due to the spin-exchange interaction (J ≡ [E(↑↑) − E(↑↓)]) and spin polarize the surface along the chiral molecular axis. B. Schematic of the setup used in crystallization experiments for CD detection. Homochiral crystals of RAO are formed on magnetite from their enantiopure solution. These crystals align the magnetic domains under them and interact with the surface spins due to magnetic dipolar coupling—a weaker but longer range coupling compared to the spin-exchange interaction C. A sequence showing the effect of chiral molecules on the magnetic domains. 1 Initially, there is no net magnetization of the magnetic domains. 2 As a layer of RAO is forming, the spins underneath the layer align due to the strong spin-exchange interaction. This is an avalanche magnetization process: molecules align the surface spins and the aligned regions attract more molecules and get larger. 3 The mono-layer grows and covers more surface due to the attraction of chiral molecules to the aligned regions and crystal seeds start forming. 4 Crystals get larger and couple with the magnetic domains due to magnetic dipole-dipole interaction, Edd. D. If an external magnetic field, −→B, is applied, the domains outside the area covered by crystals magnetize. Yet the crystals preserve the magnetization of the domains under them as long as the energy of the dipolar coupling is larger than the magnetic energy. -- physics.chem-ph

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

Chirality-Induced Magnetization of Magnetite by an RNA Precursor

by Keith CowingJune 18, 2023June 16, 2023

Life is homochiral and homochirality is a fundamental feature of living systems on Earth. While the exact mechanism that led to homochirality is still not fully understood, any realistic scenario […]

The mechanism of spin-selective crystallization due to the CISS effect and the experimental setup. a. As molecules approach a surface, they transiently acquire an induced charge polarization. Due to the CISS effect, transient charge polarization of a chiral molecule is accompanied by spin polarization. The spin state associated with the charge poles is determined by the handedness of the chiral molecule. Because the magnetic surface itself is spin polarized it kinetically favors (akin to a seed crystal) the enantiomer whose transient spin state results in a lower energy spin-exchange interaction. The lower energy overlap with the magnetic surface is singlet-like (red, ↑↓) and the higher energy overlap is triplet-like (blue, ↑↑). The energy difference between these two configurations is higher than the room temperature, kBT, therefore the effect robustly manifests itself. b. Schematic of the setup used in the crystallization experiments and a sample microscope image of the RAO crystals on a magnetite surface from a direct crystallization experiment. The image shows the magnetite surface as the black background and the needle-shaped conglomerate crystals of RAO formed on the surface, as well as the twinned crystals with stochastically arranged needles of D and L-RAO, and racemic RAO in the form of a flaky powder suspended in the water column above the surface. -- physics.chem-ph

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

Origin of Biological Homochirality by Crystallization of an RNA Precursor on a Magnetic Surface

by Keith CowingJune 16, 2023June 16, 2023

Homochirality is a signature of life on Earth yet its origins remain an unsolved puzzle. Achieving homochirality is essential for a high-yielding prebiotic network capable of producing functional polymers like […]

Propagation of homochirality from a common ribonucleotide precursor, RAO, to the entire prebiotic network is illustrated. D-RAO can be transformed into D-ribonucleotides, forming homochiral RNA. L-peptides can be synthesized through the stereoselective binding of L-amino acids to tRNA analogs composed of D-ribonucleotides. This crucial link enables the transfer of homochirality from nucleic acids to peptides. Then L-peptides form L-enzymes, and by enantioselective catalysis a homochiral metabolism can be produced. -- physics.chem-ph

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

The Central Dogma Of Biological Homochirality: How Does Chiral Information Propagate In A Prebiotic Network?

by Keith CowingJune 14, 2023June 14, 2023

Biological systems are homochiral, raising the question of how a racemic mixture of prebiotically synthesized biomolecules could attain a homochiral state at the network level.

Stochastic simulation of a population of water-in-oil droplets containing strands. Heatmaps for A: average fraction of replicase ribozymes per droplet; B: fraction of droplets containing both replicase (R) and replicase encoding DNA template (TdR); C: average reaction propensity of reaction 9 per droplet; with different non-enzymatic ribozyme creation probabilities and error thresholds of enzymatic replications. -- biorxiv.org

Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

The RNA-DNA World And The Emergence Of DNA-encoded Heritable Traits

by Keith CowingMay 28, 2023May 28, 2023

The RNA world hypothesis confers a central role to RNA molecules in information encoding and catalysis.

Secondary structure of the tt_A1P1 construct predicted by mfold (Zuker, 2003). With a ΔG of -64.30 Kcal/mol. Thermus thermophilus numbering system is used. According to this prediction base paring shift occur in H74, H89 and H90. The overall shape of H90 has grown by at least three base pairs at the beginning of the helix compared to the secondary structure of the extant ribosome. -- PNAS

Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

How To Build A Protoribosome

by Keith CowingApril 1, 2023April 1, 2023

NASA-supported scientists have reexamined some previous assumptions about how the ribosome in living cells is constructed. The ribosome is a large molecule found in all living cells that catalyzes the […]

Synthesis of BaTP. Scheme depicting various steps in the chemical synthesis of the prebiotic genetic alphabet Barbitudine and its corresponding triphosphate Barbitudine triphosphate (BaTP) 44 -- biorxiv

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

A Prebiotic Genetic Alphabet As An Early Darwinian Ancestor For Pre-RNA Evolution

by Keith CowingMarch 24, 2023March 24, 2023

RNA-based genetic code is thought to be central to life’s emergence due to its dual ability for information transfer and catalysis. Nonetheless, the genetic code of early life was potentially […]