Coenzyme-Protein Interactions since Early Life DOI Open Access
Alma Carolina Sánchez-Rocha, Mikhail Makarov, Lukáš Pravda

et al.

Published: Oct. 16, 2024

Recent findings in protein evolution and peptide prebiotic plausibility have been setting the stage for reconsidering role of peptides early stages life’s origin. Ancient families found to share common themes proteins reduced composition prebiotically plausible amino acids reported capable structure formation key functions, such as binding RNA. While this may suggest relevance life, their functional repertoire when composed a limited number residues (missing some most sophisticated groups today’s alphabet) has debated.Cofactors enrich scope about half extant enzymes but whether they could also bind lacking evolutionary late remains speculative. The aim study was resolve propensity organic cofactors by analysis protein-coenzyme interactions across Protein Data Bank (PDB). We find that are more abundant sites ancient coenzymes rely frequently on involvement backbone atoms metal ion cofactors. Moreover, we identified few select examples where coenzyme is supported solely available acids. These results imply coenzyme-peptide collaboration preceding establishment Central Dogma full alphabet evolution.

Language: Английский

Coenzyme-Protein Interactions since Early Life DOI Open Access
Alma Carolina Sánchez-Rocha, Mikhail Makarov, Lukáš Pravda

et al.

Published: Feb. 26, 2024

Recent findings in protein evolution and peptide prebiotic plausibility have been setting the stage for reconsidering role of peptides early stages life’s origin. Ancient families found to share common themes proteins reduced composition prebiotically plausible amino acids reported capable structure formation key functions, such as binding RNA. While this may suggest relevance life, their functional repertoire when composed a limited number residues (missing some most sophisticated groups today’s alphabet) has debated.Cofactors enrich scope about half extant enzymes but whether they could also bind lacking evolutionary late remains speculative. The aim study was resolve propensity organic cofactors by analysis protein-coenzyme interactions across Protein Data Bank (PDB). We find that are more abundant sites ancient coenzymes rely frequently on involvement backbone atoms metal ion cofactors. Moreover, we identified few select examples where coenzyme is supported solely available acids. These results imply coenzyme-peptide collaboration preceding establishment Central Dogma full alphabet evolution.

Language: Английский

Citations

4
A Systematic Investigation of TMB Substrate Composition for Signal Enhancement in ELISA DOI
Pavel Khramtsov, Anastasia Novokshonova,

Zarina Galaeva

et al.

Analytical Biochemistry, Journal Year: 2025, Volume and Issue: 704, P. 115908 - 115908

Published: May 23, 2025

Language: Английский

Citations

0
Peptides En Route from Prebiotic to Biotic Catalysis DOI Creative Commons
Klára Hlouchová

Accounts of Chemical Research, Journal Year: 2024, Volume and Issue: 57(15), P. 2027 - 2037

Published: July 17, 2024

ConspectusIn the quest to understand prebiotic catalysis, different molecular entities, mainly minerals, metal ions, organic cofactors, and ribozymes, have been implied as key players. Of these, inorganic cofactors gained attention for their ability catalyze a wide array of reactions central modern metabolism frequently participate in these within enzymes. Nevertheless, bridging gap between remains fundamental question origins life.In this Account, peptides are investigated potential bridge linking catalysis by minerals/cofactors enzymes that dominate life's chemical reactions. Before ribosomal synthesis emerged, random sequences were plausible on early Earth. This was made possible sources amino acid delivery synthesis, well condensation under variety conditions. Early proteins probably exhibited distinct compositions, enriched small aliphatic acidic residues. An increase abundance acids with larger side chains canonical basic groups most likely dependent emergence more challenging (bio)synthesis. Pressing questions thus arise: how did composition influence peptide properties, what extent could they contribute metabolism?Recent research from our group colleagues shows highly peptides/proteins comprising only presumably "early" fact competent at secondary structure formation even possess adaptive folding characteristics such spontaneous refoldability chaperone independence achieve soluble structures. Moreover, we showed can still bind RNA utilizing ions carboxylate phosphoester functional groups. And finally, ancient shown be capable binding considered prebiotically plausible, supporting properties providing groups, which would nominate them catalytic hubs great relevance.These findings underscore biochemical plausibility an peptide/protein world devoid complex yet collaborating other species. Drawing mechanistic protein-cofactor it is speculated here peptide/protein-cofactor ensemble facilitate similar range reactions, albeit lower rates. hypothesis invites systematic experimental test.Nonetheless, Account does not exclude scenarios prebiotic-to-biotic or prioritize any specific pathways syntheses. The objective examine availability, composition, among various factors involved life.

Language: Английский

Citations

1
Protocellular Heme and Iron–Sulfur Clusters DOI Creative Commons
Daniele Rossetto, Nemanja Cvjetan, Peter Walde

et al.

Accounts of Chemical Research, Journal Year: 2024, Volume and Issue: 57(16), P. 2293 - 2302

Published: Aug. 5, 2024

ConspectusCentral to the quest of understanding emergence life is uncover role metals, particularly iron, in shaping prebiotic chemistry. Iron, as most abundant accessible transition metals on Earth, played a pivotal early biochemical processes and continues be indispensable modern biology. Here, we discuss our recent contributions probing plausibility complexes with including heme iron-sulfur clusters, mediating chemistry beneficial protocell. Laboratory experiments spectroscopic findings suggest plausible pathways, often facilitated by UV light, for synthesis clusters. Once formed, displays catalytic, peroxidase-like activity when complexed amphiphiles. This could have been two ways. First, catalytically removed molecule (H

Language: Английский

Citations

1
Coenzyme-Protein Interactions since Early Life DOI Creative Commons
Alma Carolina Sánchez-Rocha, Mikhail Makarov, Lukáš Pravda

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 1, 2023

Abstract Recent findings in protein evolution and peptide prebiotic plausibility have been setting the stage for reconsidering role of peptides early stages life’s origin. Ancient families found to share common themes proteins reduced composition prebiotically plausible amino acids reported capable structure formation key functions, such as binding RNA. While this may suggest relevance life, their functional repertoire when composed a limited number residues (missing some most sophisticated groups today’s alphabet) has debated. Cofactors enrich scope about half extant enzymes but whether they could also bind lacking evolutionary late remains speculative. The aim study was resolve propensity organic cofactors by analysis protein-coenzyme interactions across Protein Data Bank (PDB). We find that are more abundant sites ancient coenzymes rely frequently on involvement backbone atoms metal ion cofactors. Moreover, we identified few select examples where coenzyme is supported solely available acids. These results imply coenzyme-peptide collaboration preceding establishment Central Dogma full alphabet evolution.

Language: Английский

Citations

2
Coenzyme-Protein Interactions since Early Life DOI Open Access
Alma Carolina Sánchez-Rocha, Mikhail Makarov, Lukáš Pravda

et al.

Published: Feb. 26, 2024

Recent findings in protein evolution and peptide prebiotic plausibility have been setting the stage for reconsidering role of peptides early stages life’s origin. Ancient families found to share common themes proteins reduced composition prebiotically plausible amino acids reported capable structure formation key functions, such as binding RNA. While this may suggest relevance life, their functional repertoire when composed a limited number residues (missing some most sophisticated groups today’s alphabet) has debated.Cofactors enrich scope about half extant enzymes but whether they could also bind lacking evolutionary late remains speculative. The aim study was resolve propensity organic cofactors by analysis protein-coenzyme interactions across Protein Data Bank (PDB). We find that are more abundant sites ancient coenzymes rely frequently on involvement backbone atoms metal ion cofactors. Moreover, we identified few select examples where coenzyme is supported solely available acids. These results imply coenzyme-peptide collaboration preceding establishment Central Dogma full alphabet evolution.

Language: Английский

Citations

0
Coenzyme-Protein Interactions since Early Life DOI Open Access
Alma Carolina Sánchez-Rocha, Mikhail Makarov, Lukáš Pravda

et al.

Published: Oct. 16, 2024

Recent findings in protein evolution and peptide prebiotic plausibility have been setting the stage for reconsidering role of peptides early stages life’s origin. Ancient families found to share common themes proteins reduced composition prebiotically plausible amino acids reported capable structure formation key functions, such as binding RNA. While this may suggest relevance life, their functional repertoire when composed a limited number residues (missing some most sophisticated groups today’s alphabet) has debated.Cofactors enrich scope about half extant enzymes but whether they could also bind lacking evolutionary late remains speculative. The aim study was resolve propensity organic cofactors by analysis protein-coenzyme interactions across Protein Data Bank (PDB). We find that are more abundant sites ancient coenzymes rely frequently on involvement backbone atoms metal ion cofactors. Moreover, we identified few select examples where coenzyme is supported solely available acids. These results imply coenzyme-peptide collaboration preceding establishment Central Dogma full alphabet evolution.

Language: Английский

Citations

0