Systems protobiology: origin of life in lipid catalytic networks

Replication of Simulated Prebiotic Amphiphilic Vesicles in a Finite Environment Exhibits Complex Behavior That Includes High Progeny Variability and Competition

(2018) Don L. Armstrong et al.   ASTROBIOLOGY

Quantitative -omic data empowers bottom-up systems biology

(2018) James T Yurkovich et al.   CURRENT OPINION IN BIOTECHNOLOGY

Chemistry of a Unique Polyketide-like Synthase

(2018) Stephanie W. Chun et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Predicting species emergence in simulated complex pre-biotic networks

(2018) Omer Markovitch et al.   PLoS One

Sequence complementarity at the ribosomal Peptidyl Transferase Centre implies self-replicating origin

(2017) Ilana Agmon   FEBS LETTERS

J. B. S. Haldane and the origin of life

(2017) Stéphane Tirard   JOURNAL OF GENETICS

Chemical Evolution and the Evolutionary Definition of Life

(2017) Paul G. Higgs   JOURNAL OF MOLECULAR EVOLUTION

The Origin of Life: Models and Data

(2017) Kathryn A. Lanier et al.   JOURNAL OF MOLECULAR EVOLUTION

Semantic closure demonstrated by the evolution of a universal constructor architecture in an artificial chemistry

(2017) Edward B. Clark et al.   Journal of the Royal Society Interface

Shannon information entropy in the canonical genetic code

(2017) Louis R. Nemzer   JOURNAL OF THEORETICAL BIOLOGY

HMDB 4.0: the human metabolome database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

Re-conceptualizing the origins of life

(2017) Sara I. Walker et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Exploring astrobiology using in silico molecular structure generation

(2017) Markus Meringer et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Prebiotic selection for motifs in a model of template-free elongation of polymers within compartments

(2017) Grant Kinsler et al.   PLoS One

Metabolic flux analysis of heterotrophic growth in Chlamydomonas reinhardtii

(2017) Nanette R. Boyle et al.   PLoS One

Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers

(2017) Elizaveta Guseva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Limits of predictions in thermodynamic systems: a review

(2017) Robert Marsland et al.   REPORTS ON PROGRESS IN PHYSICS

Mineral surface chemistry control for origin of prebiotic peptides

(2017) Valentina Erastova et al.   Nature Communications

Metals promote sequences of the reverse Krebs cycle

(2017) Kamila B. Muchowska et al.   Nature Ecology & Evolution

Opinion: Studies on the origin of life — the end of the beginning

(2017) John D. Sutherland   Nature Reviews Chemistry

Insights into soybean transcriptome reconfiguration under hypoxic stress: Functional, regulatory, structural, and compositional characterization

(2017) Thiago J. Nakayama et al.   PLoS One

Complex Autocatalysis in Simple Chemistries

(2016) Nathaniel Virgo et al.   ARTIFICIAL LIFE

Toward a List of Molecules as Potential Biosignature Gases for the Search for Life on Exoplanets and Applications to Terrestrial Biochemistry

(2016) S. Seager et al.   ASTROBIOLOGY

Coenzyme world model of the origin of life

(2016) Alexei A. Sharov   BIOSYSTEMS

Applications of Discrete Molecular Dynamics in biology and medicine

(2016) Elizabeth A Proctor et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

A prebiotically plausible synthesis of pyrimidine β-ribonucleosides and their phosphate derivatives involving photoanomerization

(2016) Jianfeng Xu et al.   Nature Chemistry

An Experimental Framework for Generating Evolvable Chemical Systems in the Laboratory

(2016) David A. Baum et al.   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

Thermodynamics, Disequilibrium, Evolution: Far-From-Equilibrium Geological and Chemical Considerations for Origin-Of-Life Research

(2016) L. M. Barge et al.   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

Research program for a search of the origin of Darwinian evolution

(2016) Marc Tessera   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

Community detection in networks: A user guide

(2016) Santo Fortunato et al.   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Lipid somersaults: Uncovering the mechanisms of protein-mediated lipid flipping

(2016) Thomas Günther Pomorski et al.   PROGRESS IN LIPID RESEARCH

Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations

(2016) Samuel Hertig et al.   PLoS Computational Biology

Ester-Mediated Amide Bond Formation Driven by Wet-Dry Cycles: A Possible Path to Polypeptides on the Prebiotic Earth

(2015) Jay G. Forsythe et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

An overview of molecular fingerprint similarity search in virtual screening

(2015) Ingo Muegge et al.   Expert Opinion on Drug Discovery

Automated Discovery of Reaction Pathways, Rate Constants, and Transition States Using Reactive Molecular Dynamics Simulations

(2015) Malte Döntgen et al.   Journal of Chemical Theory and Computation

Accelerated molecular dynamics simulations of protein folding

(2015) Yinglong Miao et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Primordial evolvability: Impasses and challenges

(2015) Vera Vasas et al.   JOURNAL OF THEORETICAL BIOLOGY

Prebiotic network evolution: six key parameters

(2015) Philippe Nghe et al.   Molecular BioSystems

Lipid vesicles trigger α-synuclein aggregation by stimulating primary nucleation

(2015) Céline Galvagnion et al.   Nature Chemical Biology

Evolution of Autocatalytic Sets in Computational Models of Chemical Reaction Networks

(2015) Wim Hordijk   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

Pathways for abiotic organic synthesis at submarine hydrothermal fields

(2015) Jill M. McDermott et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Self-reproducing catalyst drives repeated phospholipid synthesis and membrane growth

(2015) Michael D. Hardy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Membranes serve as allosteric activators of phospholipase A2, enabling it to extract, bind, and hydrolyze phospholipid substrates

(2015) Varnavas D. Mouchlis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Hydrophobic Temperature Dependence of Amino Acids Directly Calculated from Protein Structures

(2015) Erik van Dijk et al.   PLoS Computational Biology

Towards Co-Evolution of Membrane Proteins and Metabolism

(2015) Michael A. Wilson et al.   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

Uncertainty of Prebiotic Scenarios: The Case of the Non-Enzymatic Reverse Tricarboxylic Acid Cycle

(2015) Dmitry Yu Zubarev et al.   Scientific Reports

Chain-Length Heterogeneity Allows for the Assembly of Fatty Acid Vesicles in Dilute Solutions

(2014) Itay Budin et al.   BIOPHYSICAL JOURNAL

Quasispecies in population of compositional assemblies

(2014) Renan Gross et al.   BMC EVOLUTIONARY BIOLOGY

Competition and Cooperation in Dynamic Replication Networks

(2014) Zehavit Dadon et al.   CHEMISTRY-A EUROPEAN JOURNAL

Opportunities for merging chemical and biological synthesis

(2014) Stephen Wallace et al.   CURRENT OPINION IN BIOTECHNOLOGY

Abiotic synthesis of RNA in water: a common goal of prebiotic chemistry and bottom-up synthetic biology

(2014) Brian J Cafferty et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Multispecies population dynamics of prebiotic compositional assemblies

(2014) Omer Markovitch et al.   JOURNAL OF THEORETICAL BIOLOGY

Oleic Acid Phase Behavior from Molecular Dynamics Simulations

(2014) J. Joel Janke et al.   LANGMUIR

Non-enzymatic glycolysis and pentose phosphate pathway-like reactions in a plausible Archean ocean

(2014) M. A. Keller et al.   Molecular Systems Biology

Conditions for Evolvability of Autocatalytic Sets: A Formal Example and Analysis

(2014) Wim Hordijk et al.   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

Evolution of oil droplets in a chemorobotic platform

(2014) Juan Manuel Parrilla Gutierrez et al.   Nature Communications

Prebiotic Systems Chemistry: New Perspectives for the Origins of Life

(2013) Kepa Ruiz-Mirazo et al.   CHEMICAL REVIEWS

Visible Light Photoredox Catalysis with Transition Metal Complexes: Applications in Organic Synthesis

(2013) Christopher K. Prier et al.   CHEMICAL REVIEWS

The Origin of RNA and “My Grandfather’s Axe”

(2013) Nicholas V. Hud et al.   CHEMISTRY & BIOLOGY

The Evolutionary Origin of Biological Function and Complexity

(2013) Addy Pross   JOURNAL OF MOLECULAR EVOLUTION

Competition between model protocells driven by an encapsulated catalyst

(2013) Katarzyna Adamala et al.   Nature Chemistry

Quantifying Disorder through Conditional Entropy: An Application to Fluid Mixing

(2013) Giovanni B. Brandani et al.   PLoS One

Systems of Creation: The Emergence of Life from Nonliving Matter

(2012) Stephen Mann   ACCOUNTS OF CHEMICAL RESEARCH

Lipid-like Self-Assembling Peptides

(2012) Shuguang Zhang   ACCOUNTS OF CHEMICAL RESEARCH

From Prelife to Life: How Chemical Kinetics Become Evolutionary Dynamics

(2012) Irene A. Chen et al.   ACCOUNTS OF CHEMICAL RESEARCH

Excess Mutual Catalysis Is Required for Effective Evolvability

(2012) Omer Markovitch et al.   ARTIFICIAL LIFE

Membranes, Murchison, and Mars: An Encapsulated Life in Science

(2012) David Deamer   ASTROBIOLOGY

Spontaneous chiral symmetry breaking in early molecular networks

(2012) Ran Kafri et al.   Biology Direct

The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)a

(2012) Harold S Bernhardt   Biology Direct

Evolution before genes

(2012) Vera Vasas et al.   Biology Direct

The algorithmic origins of life

(2012) S. I. Walker et al.   Journal of the Royal Society Interface

ECMDB: The E. coli Metabolome Database

(2012) An Chi Guo et al.   NUCLEIC ACIDS RESEARCH

How Does Biology Emerge From Chemistry?

(2012) Addy Pross   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

Autopoiesis 40 years Later. A Review and a Reformulation

(2012) Pablo Razeto-Barry   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

Search for the Most Primitive Membranes: Some Remaining Problems

(2012) Yoichi Nakatani et al.   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

Is There an Optimal Level of Open-Endedness in Prebiotic Evolution?

(2012) Omer Markovitch et al.   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

Kinetic characterization of the critical step in HIV-1 protease maturation

(2012) S. K. Sadiq et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Exit Cavity Was Crucial to the Polymerase Activity of the Early Ribosome

(2011) George E. Fox et al.   ASTROBIOLOGY

Origin of Evolution versus Origin of Life: A Shift of Paradigm

(2011) Marc Tessera   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Required Levels of Catalysis for Emergence of Autocatalytic Sets in Models of Chemical Reaction Systems

(2011) Wim Hordijk et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

LIPID MAPS-Nature Lipidomics Gateway: An Online Resource for Students and Educators Interested in Lipids

(2011) Manish Sud et al.   JOURNAL OF CHEMICAL EDUCATION

The future of molecular dynamics simulations in drug discovery

(2011) David W. Borhani et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Membrane Assembly Driven by a Biomimetic Coupling Reaction

(2011) Itay Budin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Predicting template-based catalysis rates in a simple catalytic reaction model

(2011) Wim Hordijk et al.   JOURNAL OF THEORETICAL BIOLOGY

Self-reproduction of supramolecular giant vesicles combined with the amplification of encapsulated DNA

(2011) Kensuke Kurihara et al.   Nature Chemistry

Membrane catalysis of peptide–receptor bindingThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.

(2010) David N. Langelaan et al.   Biochemistry and Cell Biology

Vesicles with charged domains

(2010) Cíntia C. Vequi-Suplicy et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Non-enzymatic transfer of sequence information under plausible prebiotic conditions

(2010) Felix Olasagasti et al.   BIOCHIMIE

Autocatalytic Sets and the Origin of Life

(2010) Wim Hordijk et al.   Entropy

Influence of Montmorillonite on Nucleotide Oligomerization Reactions: A Molecular Dynamics Study

(2010) Damien C. Mathew et al.   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

What is Life? Defining Life in the Context of Emergent Complexity

(2010) Bruce H. Weber   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

Which Way to Life?

(2010) Antonio Lazcano   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

Lack of evolvability in self-sustaining autocatalytic networks constraints metabolism-first scenarios for the origin of life

(2010) V. Vasas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stochastic Simulation of the Chemoton

(2009) Sven Van Segbroeck et al.   ARTIFICIAL LIFE

Chemical Evolution of Amphiphiles: Glycerol Monoacyl Derivatives Stabilize Plausible Prebiotic Membranes

(2009) S.E. Maurer et al.   ASTROBIOLOGY

Self-organization in dissipative structures: A thermodynamic theory for the emergence of prebiotic cells and their epigenetic evolution

(2009) R.M. Pulselli et al.   BIOSYSTEMS

Coenzyme Autocatalytic Network on the Surface of Oil Microspheres as a Model for the Origin of Life

(2009) Alexei Sharov   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Mutations and Lethality in Simulated Prebiotic Networks

(2009) Aron Inger et al.   JOURNAL OF MOLECULAR EVOLUTION

The Origin of Life: Chemical Evolution of a Metabolic System in a Mineral Honeycomb?

(2009) Sergio Branciamore et al.   JOURNAL OF MOLECULAR EVOLUTION

Darwin’s warm little pond revisited: from molecules to the origin of life

(2009) Hartmut Follmann et al.   NATURWISSENSCHAFTEN

Life Began When Evolution Began: A Lipidic Vesicle-Based Scenario

(2009) Marc Tessera   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

Self-assembly and function of primitive cell membranes

(2009) Andrew Pohorille et al.   RESEARCH IN MICROBIOLOGY

Chemistry and the Missing Era of Evolution

(2008) A. Graham Cairns-Smith   CHEMISTRY-A EUROPEAN JOURNAL

Evolution and self-assembly of protocells

(2008) Ricard V. Solé   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Nucleobase Mediated, Photocatalytic Vesicle Formation from an Ester Precursor

(2008) Michael S. DeClue et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Hydrothermal vents and the origin of life

(2008) William Martin et al.   NATURE REVIEWS MICROBIOLOGY

Membrane lipids: where they are and how they behave

(2008) Gerrit van Meer et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Abiotic Formation of Hydrocarbons from Dissolved CO2 Under Hydrothermal Conditions with Cobalt-Bearing Magnetite

(2008) Fuwu Ji et al.   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

Prevolutionary dynamics and the origin of evolution

(2008) M. A. Nowak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coarse-Grained MD Simulations of Membrane Protein-Bilayer Self-Assembly

(2008) Kathryn A. Scott et al.   STRUCTURE

The Implausibility of Metabolic Cycles on the Prebiotic Earth

(2008) Leslie E Orgel   PLOS BIOLOGY

The origin of autonomous agents by natural selection

(2007) Chrisantha Fernando et al.   BIOSYSTEMS