Simple mechanisms for the evolution of protein complexity

Non-adaptive complexity and biochemical function

(2022) Luca Schulz et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Mapping the energetic and allosteric landscapes of protein binding domains

(2022) Andre J. Faure et al.   NATURE

Constructive Neutral Evolution 20 Years Later

(2021) Sergio A. Muñoz-Gómez et al.   JOURNAL OF MOLECULAR EVOLUTION

Were Ancestral Proteins Less Specific?

(2021) Lucas C Wheeler et al.   MOLECULAR BIOLOGY AND EVOLUTION

A single historical substitution drives an increase in acetylcholine receptor complexity

(2021) Johnathon R. Emlaw et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Contingency and chance erase necessity in the experimental evolution of ancestral proteins

(2021) Victoria Cochran Xie et al.   eLife

How long does it take to fix a favorable mutation, and why should we care?

(2020) Brian Charlesworth   AMERICAN NATURALIST

Origin of complexity in haemoglobin evolution

(2020) Arvind S. Pillai et al.   NATURE

Functional plasticity and evolutionary adaptation of allosteric regulation

(2020) Megan Leander et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A hydrophobic ratchet entrenches molecular complexes

(2020) Georg K. A. Hochberg et al.   NATURE

Engineering Order and Cooperativity in a Disordered Protein

(2019) Sneha Munshi et al.   BIOCHEMISTRY

Evolution of protein interfaces in multimers and fibrils

(2019) W. Jeffrey Zabel et al.   JOURNAL OF CHEMICAL PHYSICS

Engineering orthogonal signalling pathways reveals the sparse occupancy of sequence space

(2019) Conor J. McClune et al.   NATURE

Stepwise shifts underlie evolutionary trends in morphological complexity of the mammalian vertebral column

(2019) Katrina E. Jones et al.   Nature Communications

Accurate Classification of Biological and non-Biological Interfaces in Protein Crystal Structures using Subtle Covariation Signals

(2019) Yoshinori Fukasawa et al.   Scientific Reports

Analysis of allosteric communication in a multienzyme complex by ancestral sequence reconstruction

(2019) Michael Schupfner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery of hidden allosteric sites as novel targets for allosteric drug design

(2018) Shaoyong Lu et al.   DRUG DISCOVERY TODAY

Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein

(2018) Ben E. Clifton et al.   Nature Chemical Biology

Extant fold-switching proteins are widespread

(2018) Lauren L. Porter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

It takes a dimer to tango: Oligomeric small heat shock proteins dissociate to capture substrate

(2018) Indu Santhanagopalan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Engineering allosteric regulation in protein kinases

(2018) David Pincus et al.   Science Signaling

Proteins evolve on the edge of supramolecular self-assembly

(2017) Hector Garcia-Seisdedos et al.   NATURE

Alternative evolutionary histories in the sequence space of an ancient protein

(2017) Tyler N. Starr et al.   NATURE

PDB-wide identification of biological assemblies from conserved quaternary structure geometry

(2017) Sucharita Dey et al.   NATURE METHODS

Structural basis for ligand binding to an enzyme by a conformational selection pathway

(2017) Michael Kovermann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Physicochemical code for quinary protein interactions inEscherichia coli

(2017) Xin Mu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Random protein sequences can form defined secondary structures and are well-tolerated in vivo

(2017) Vyacheslav Tretyachenko et al.   Scientific Reports

Evolution of complex adaptations in molecular systems

(2017) Csaba Pál et al.   Nature Ecology & Evolution

Designing small molecules to target cryptic pockets yields both positive and negative allosteric modulators

(2017) Kathryn M. Hart et al.   PLoS One

Functional determinants of protein assembly into homomeric complexes

(2017) L. Therese Bergendahl et al.   Scientific Reports

Evolution of Protein Quaternary Structure in Response to Selective Pressure for Increased Thermostability

(2016) Nicholas J. Fraser et al.   JOURNAL OF MOLECULAR BIOLOGY

Local fitness landscape of the green fluorescent protein

(2016) Karen S. Sarkisyan et al.   NATURE

Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes

(2016) Benjamin R. Jack et al.   PLOS BIOLOGY

Evolution of an ancient protein function involved in organized multicellularity in animals

(2016) Douglas P Anderson et al.   eLife

Confocal Imaging–Guided Laser Ablation of Basal Cell Carcinomas: An Ex Vivo Study

(2015) Heidy Sierra et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Principles of assembly reveal a periodic table of protein complexes

(2015) S. E. Ahnert et al.   SCIENCE

A protein fold switch joins the circadian oscillator to clock output in cyanobacteria

(2015) Y.-G. Chang et al.   SCIENCE

A structural dissection of large protein-protein crystal packing contacts

(2015) Jiesi Luo et al.   Scientific Reports

Insight into the Allosteric Mechanism of Scapharca Dimeric Hemoglobin

(2014) Jennifer M. Laine et al.   BIOCHEMISTRY

Gradual and contingent evolutionary emergence of leaf mimicry in butterfly wing patterns

(2014) Takao K Suzuki et al.   BMC EVOLUTIONARY BIOLOGY

Evolutionary relationship of two ancient protein superfolds

(2014) José Arcadio Farías-Rico et al.   Nature Chemical Biology

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

Prediction and Analysis of Surface Hydrophobic Residues in Tertiary Structure of Proteins

(2014) Shambhu Malleshappa Gowder et al.   TheScientificWorldJOURNAL

Vestigialization of an Allosteric Switch: Genetic and Structural Mechanisms for the Evolution of Constitutive Activity in a Steroid Hormone Receptor

(2014) Jamie T. Bridgham et al.   PLoS Genetics

A Distal Mutation Perturbs Dynamic Amino Acid Networks in Dihydrofolate Reductase

(2013) David D. Boehr et al.   BIOCHEMISTRY

Exploitation of Latent Allostery Enables the Evolution of New Modes of MAP Kinase Regulation

(2013) Scott M. Coyle et al.   CELL

Protein Complexes Are under Evolutionary Selection to Assemble via Ordered Pathways

(2013) Joseph A. Marsh et al.   CELL

The Designability of Protein Switches by Chemical Rescue of Structure: Mechanisms of Inactivation and Reactivation

(2013) Yan Xia et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Evolutionary diversification of the multimeric states of proteins

(2013) M. Lynch   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational selection and adaptation to ligand binding in T4 lysozyme cavity mutants

(2013) C. J. Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Eye evolution and its functional basis

(2013) DAN-E. NILSSON   VISUAL NEUROSCIENCE

Constructive neutral evolution: exploring evolutionary theory’s curious disconnect

(2012) Arlin Stoltzfus   Biology Direct

An α Helix to β Barrel Domain Switch Transforms the Transcription Factor RfaH into a Translation Factor

(2012) Björn M. Burmann et al.   CELL

Designing Allosteric Control into Enzymes by Chemical Rescue of Structure

(2012) Katelyn Deckert et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Evolution of increased complexity in a molecular machine

(2012) Gregory C. Finnigan et al.   NATURE

Structure of an Engineered β-Lactamase Maltose Binding Protein Fusion Protein: Insights into Heterotropic Allosteric Regulation

(2012) Wei Ke et al.   PLoS One

Allosteric pathways in imidazole glycerol phosphate synthase

(2012) I. Rivalta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hot Spots for Allosteric Regulation on Protein Surfaces

(2011) Kimberly A. Reynolds et al.   CELL

The Evolution of Multimeric Protein Assemblages

(2011) M. Lynch   MOLECULAR BIOLOGY AND EVOLUTION

Stepwise evolution of stable sociality in primates

(2011) Susanne Shultz et al.   NATURE

Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB

(2011) Vincent J. Lynch et al.   NATURE

How to Change the Oligomeric State of a Circular Protein Assembly: Switch from 11-Subunit to 12-Subunit TRAP Suggests a General Mechanism

(2011) Chao-Sheng Chen et al.   PLoS One

Experimental illumination of a fitness landscape

(2011) R. T. Hietpas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analyzing protein structure and function using ancestral gene reconstruction

(2010) Michael J Harms et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A Simple Definition of Structural Regions in Proteins and Its Use in Analyzing Interface Evolution

(2010) Emmanuel D. Levy   JOURNAL OF MOLECULAR BIOLOGY

Crystal Structure of the First Plant Urease from Jack Bean: 83 Years of Journey from Its First Crystal to Molecular Structure

(2010) Anuradha Balasubramanian et al.   JOURNAL OF MOLECULAR BIOLOGY

Engineering a protein-protein interface using a computationally designed library

(2010) G. Guntas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering allosteric regulation into the hinge region of a circularly permuted TEM-1 β-lactamase

(2010) Valéry Mathieu et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Irremediable Complexity?

(2010) M. W. Gray et al.   SCIENCE

Engineering Allosteric Regulation into Biological Catalysts

(2009) Jacques Fastrez   CHEMBIOCHEM

Allostery in the LacI/GalR family: variations on a theme

(2009) Liskin Swint-Kruse et al.   CURRENT OPINION IN MICROBIOLOGY

NMR spectroscopy brings invisible protein states into focus

(2009) Andrew J Baldwin et al.   Nature Chemical Biology

A minimal sequence code for switching protein structure and function

(2009) Patrick A. Alexander et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein Dynamism and Evolvability

(2009) N. Tokuriki et al.   SCIENCE

The rate at which asexual populations cross fitness valleys

(2009) Daniel B. Weissman et al.   THEORETICAL POPULATION BIOLOGY

Designed Protein-Protein Association

(2008) D. Grueninger et al.   SCIENCE