Cofactors as Molecular Fossils To Trace the Origin and Evolution of Proteins

Short and simple sequences favored the emergence of N-helix phospho-ligand binding sites in the first enzymes

(2020) Liam M. Longo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small protein folds at the root of an ancient metabolic network

(2020) Hagai Raanan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Autocatalytic chemical networks at the origin of metabolism

(2020) Joana C. Xavier et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Carbon–Metal Bonds: Rare and Primordial in Metabolism

(2019) William F. Martin   TRENDS IN BIOCHEMICAL SCIENCES

Protein three-dimensional structures at the origin of life

(2019) E. James Milner-White   Interface Focus

UniProt: the universal protein knowledgebase

(2018) The UniProt Consortium   NUCLEIC ACIDS RESEARCH

DNA Local-Flexibility-Dependent Assembly of Phase-Separated Liquid Droplets

(2018) Anisha Shakya et al.   BIOPHYSICAL JOURNAL

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

(2018) Stephen K Burley et al.   NUCLEIC ACIDS RESEARCH

Multiple prebiotic metals mediate translation

(2018) Marcus S. Bray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simple yet functional phosphate-loop proteins

(2018) Maria Luisa Romero Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes

(2018) Joana C. Xavier et al.   PLoS Computational Biology

Ribosomal proteins as documents of the transition from unstructured (poly)peptides to folded proteins

(2017) Andrei N. Lupas et al.   JOURNAL OF STRUCTURAL BIOLOGY

Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes

(2017) Joana C. Xavier et al.   METABOLIC ENGINEERING

Frozen in Time: The History of Proteins

(2017) Nicholas A. Kovacs et al.   MOLECULAR BIOLOGY AND EVOLUTION

Iron mediates catalysis of nucleic acid processing enzymes: support for Fe(II) as a cofactor before the great oxidation event

(2017) C. Denise Okafor et al.   NUCLEIC ACIDS RESEARCH

ATP controls the crowd

(2017) Allyson M. Rice et al.   SCIENCE

ATP as a biological hydrotrope

(2017) Avinash Patel et al.   SCIENCE

The TIM Barrel Architecture Facilitated the Early Evolution of Protein-Mediated Metabolism

(2016) Aaron David Goldman et al.   JOURNAL OF MOLECULAR EVOLUTION

Evolution of the global phosphorus cycle

(2016) Christopher T. Reinhard et al.   NATURE

ATP selection in a random peptide library consisting of prebiotic amino acids

(2015) Shou-Kai Kang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Proteopedia: Rossmann fold: A beta-alpha-beta fold at dinucleotide binding sites

(2015) Israel Hanukoglu   BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION

Nucleotide binding database NBDB – a collection of sequence motifs with specific protein-ligand interactions

(2015) Zejun Zheng et al.   NUCLEIC ACIDS RESEARCH

A vocabulary of ancient peptides at the origin of folded proteins

(2015) Vikram Alva et al.   eLife

Origin and Evolution of Protein Fold Designs Inferred from Phylogenomic Analysis of CATH Domain Structures in Proteomes

(2013) Syed Abbas Bukhari et al.   PLoS Computational Biology

Bioinformatic Identification of the Most Ancient Copper Protein Architecture

(2012) Hong-Fang Ji et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Towards functional repertoire of the earliest proteins

(2012) Y. Sobolevsky et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Selective Stabilization of a Partially Unfolded Protein by a Metabolite

(2012) Pei-Fen Liu et al.   JOURNAL OF MOLECULAR BIOLOGY

The Enzymatic and Metabolic Capabilities of Early Life

(2012) Aaron David Goldman et al.   PLoS One

A synthetic hexapeptide designed to resemble a proteinaceous p-loop nest is shown to bind inorganic phosphate

(2012) Antonio Bianchi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein Domain Structure Uncovers the Origin of Aerobic Metabolism and the Rise of Planetary Oxygen

(2012) Kyung Mo Kim et al.   STRUCTURE

Proteins from an Unevolved Library of de novo Designed Sequences Bind a Range of Small Molecules

(2012) Izhack Cherny et al.   ACS Synthetic Biology

Computational reconstruction of primordial prototypes of elementary functional loops in modern proteins

(2011) Alexander Goncearenco et al.   BIOINFORMATICS

The Phylogenomic Roots of Modern Biochemistry: Origins of Proteins, Cofactors and Protein Biosynthesis

(2011) Gustavo Caetano-Anollés et al.   JOURNAL OF MOLECULAR EVOLUTION

MACiE: exploring the diversity of biochemical reactions

(2011) Gemma L. Holliday et al.   NUCLEIC ACIDS RESEARCH

Prototypes of elementary functional loops unravel evolutionary connections between protein functions

(2010) Alexander Goncearenco et al.   BIOINFORMATICS

The evolution and functional repertoire of translation proteins following the origin of life

(2010) Aaron D Goldman et al.   Biology Direct

On the abundance of zinc in the evolutionarily old protein domains

(2010) A. Y. Mulkidjanian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

History of biological metal utilization inferred through phylogenomic analysis of protein structures

(2010) C. L. Dupont et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Characteristics of Novel Protein Folds

(2010) Narcis Fernandez-Fuentes et al.   PLoS Computational Biology

A Synthetic Protein Selected for Ligand Binding Affinity Mediates ATP Hydrolysis

(2009) Chad R. Simmons et al.   ACS Chemical Biology

The origin, evolution and structure of the protein world

(2009) Gustavo Caetano-Anollés et al.   BIOCHEMICAL JOURNAL

Evolutionary formation of new protein folds is linked to metallic cofactor recruitment

(2009) Hong-Fang Ji et al.   BIOESSAYS

Metal-MACiE: a database of metals involved in biological catalysis

(2009) Claudia Andreini et al.   BIOINFORMATICS

A four-column theory for the origin of the genetic code: tracing the evolutionary pathways that gave rise to an optimized code

(2009) Paul G Higgs   Biology Direct

On the origin of life in the Zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth

(2009) Armen Y Mulkidjanian et al.   Biology Direct

The Continuing Puzzle of the Great Oxidation Event

(2009) Alex L. Sessions et al.   CURRENT BIOLOGY

Early Earth: Oxygen for heavy-metal fans

(2009) Timothy W. Lyons et al.   NATURE

A recurrent magnesium-binding motif provides a framework for the ribosomal peptidyl transferase center

(2009) Chiaolong Hsiao et al.   NUCLEIC ACIDS RESEARCH

Protein Dynamism and Evolvability

(2009) N. Tokuriki et al.   SCIENCE

Organic cofactors participated more frequently than transition metals in redox reactions of primitive proteins

(2008) Hong‐Fang Ji et al.   BIOESSAYS

The Last Universal Common Ancestor: emergence, constitution and genetic legacy of an elusive forerunner

(2008) Nicolas Glansdorff et al.   Biology Direct

Parallel adaptations to high temperatures in the Archaean eon

(2008) Bastien Boussau et al.   NATURE

Relevance of the flavin binding to the stability and folding of engineered cholesterol oxidase containing noncovalently bound FAD

(2008) Laura Caldinelli et al.   PROTEIN SCIENCE

OCEANS: Elements and Evolution

(2008) A. D. Anbar   SCIENCE

Characters of very ancient proteins

(2007) Bin-Guang Ma et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS