Dynamics and constraints of enzyme evolution

Computational Enzyme Design

(2013) Gert Kiss et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Modulating protein stability - directed evolution strategies for improved protein function

(2013) Raymond D. Socha et al.   FEBS Journal

The Evolutionary Origins of Detoxifying Enzymes

(2013) Hagit Bar-Rogovsky et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

What Makes a Protein Fold Amenable to Functional Innovation? Fold Polarity and Stability Trade-offs

(2013) Eynat Dellus-Gur et al.   JOURNAL OF MOLECULAR BIOLOGY

GroEL/ES Buffering and Compensatory Mutations Promote Protein Evolution by Stabilizing Folding Intermediates

(2013) Kirsten T. Wyganowski et al.   JOURNAL OF MOLECULAR BIOLOGY

Molecular Engineering of Organophosphate Hydrolysis Activity from a Weak Promiscuous Lactonase Template

(2013) Monika M. Meier et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Evolution of a designed retro-aldolase leads to complete active site remodeling

(2013) Lars Giger et al.   Nature Chemical Biology

Evolutionary biochemistry: revealing the historical and physical causes of protein properties

(2013) Michael J. Harms et al.   NATURE REVIEWS GENETICS

The evolutionary paths towards complexity: a metabolic perspective

(2013) Jing-Ke Weng   NEW PHYTOLOGIST

Experimental interrogation of the path dependence and stochasticity of protein evolution using phage-assisted continuous evolution

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

The Environment Affects Epistatic Interactions to Alter the Topology of an Empirical Fitness Landscape

(2013) Kenneth M. Flynn et al.   PLoS Genetics

Stability-mediated epistasis constrains the evolution of an influenza protein

(2013) Lizhi Ian Gong et al.   eLife

Directed evolution of proteins for increased stability and expression using yeast display

(2012) Michael W. Traxlmayr et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Reconstructing a Missing Link in the Evolution of a Recently Diverged Phosphotriesterase by Active-Site Loop Remodeling

(2012) Livnat Afriat-Jurnou et al.   BIOCHEMISTRY

Evolution of Broad Spectrum β-Lactam Resistance in an Engineered Metallo-β-lactamase

(2012) Song Sun et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

Epistasis as the primary factor in molecular evolution

(2012) Michael S. Breen et al.   NATURE

Evolutionary transitions to new DNA methyltransferases through target site expansion and shrinkage

(2012) Liat Rockah-Shmuel et al.   NUCLEIC ACIDS RESEARCH

A transposase strategy for creating libraries of circularly permuted proteins

(2012) Manan M. Mehta et al.   NUCLEIC ACIDS RESEARCH

Intramolecular Epistasis and the Evolution of a New Enzymatic Function

(2012) Sajid Noor et al.   PLoS One

Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates

(2012) R. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epistasis in tomato color mutations involves regulation of phytoene synthase 1 expression by cis-carotenoids

(2012) D. E. Kachanovsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small changes in enzyme function can lead to surprisingly large fitness effects during adaptive evolution of antibiotic resistance

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

TRINS: a method for gene modification by randomized tandem repeat insertions

(2012) Y. Kipnis et al.   PROTEIN ENGINEERING DESIGN & SELECTION

The Rise of Chemodiversity in Plants

(2012) J.-K. Weng et al.   SCIENCE

Network Context and Selection in the Evolution to Enzyme Specificity

(2012) H. Nam et al.   SCIENCE

Real-Time Evolution of New Genes by Innovation, Amplification, and Divergence

(2012) J. Nasvall et al.   SCIENCE

Experimental evolution

(2012) Tadeusz J. Kawecki et al.   TRENDS IN ECOLOGY & EVOLUTION

Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme

(2012) Nobuhiko Tokuriki et al.   Nature Communications

Reconstruction of Ancestral Metabolic Enzymes Reveals Molecular Mechanisms Underlying Evolutionary Innovation through Gene Duplication

(2012) Karin Voordeckers et al.   PLOS BIOLOGY

Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies

(2012) Nicholas Furnham et al.   PLoS Computational Biology

Systematic Detection of Epistatic Interactions Based on Allele Pair Frequencies

(2012) Marit Ackermann et al.   PLoS Genetics

Exploring the Complexity of the HIV-1 Fitness Landscape

(2012) Roger D. Kouyos et al.   PLoS Genetics

Quantifying the Adaptive Potential of an Antibiotic Resistance Enzyme

(2012) Martijn F. Schenk et al.   PLoS Genetics

Replaying the Tape of Life: Quantification of the Predictability of Evolution

(2012) Alexander E. Lobkovsky et al.   Frontiers in Genetics

The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters

(2011) Arren Bar-Even et al.   BIOCHEMISTRY

The Enzyme Function Initiative

(2011) John A. Gerlt et al.   BIOCHEMISTRY

Enhancing the Thermal Robustness of an Enzyme by Directed Evolution: Least Favorable Starting Points and Inferior Mutants Can Map Superior Evolutionary Pathways

(2011) Yosephine Gumulya et al.   CHEMBIOCHEM

Strategy and success for the directed evolution of enzymes

(2011) Paul A Dalby   CURRENT OPINION IN STRUCTURAL BIOLOGY

Divergent Evolution in Enolase Superfamily: Strategies for Assigning Functions

(2011) John A. Gerlt et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A system for the continuous directed evolution of biomolecules

(2011) Kevin M. Esvelt et al.   NATURE

Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme

(2011) Eric J. Hayden et al.   NATURE

Evolutionary paths to antibiotic resistance under dynamically sustained drug selection

(2011) Erdal Toprak et al.   NATURE GENETICS

Systems-biology approaches for predicting genomic evolution

(2011) Balázs Papp et al.   NATURE REVIEWS GENETICS

Fitness Trade-Offs in the Evolution of Dihydrofolate Reductase and Drug Resistance in Plasmodium falciparum

(2011) Marna S. Costanzo et al.   PLoS One

The causes of epistasis

(2011) J. A. G. M. de Visser et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population

(2011) A. I. Khan et al.   SCIENCE

Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation

(2011) H.-H. Chou et al.   SCIENCE

Nonlinear Fitness Landscape of a Molecular Pathway

(2011) Lilia Perfeito et al.   PLoS Genetics

Reciprocal Sign Epistasis between Frequently Experimentally Evolved Adaptive Mutations Causes a Rugged Fitness Landscape

(2011) Daniel J. Kvitek et al.   PLoS Genetics

Prevalence of Epistasis in the Evolution of Influenza A Surface Proteins

(2011) Sergey Kryazhimskiy et al.   PLoS Genetics

Initial Mutations Direct Alternative Pathways of Protein Evolution

(2011) Merijn L. M. Salverda et al.   PLoS Genetics

Enzyme Promiscuity: A Mechanistic and Evolutionary Perspective

(2010) Olga Khersonsky and Dan S. Tawfik   Annual Review of Biochemistry

Protein kinetic stability

(2010) Jose M. Sanchez-Ruiz   BIOPHYSICAL CHEMISTRY

Multiple peaks and reciprocal sign epistasis in an empirically determined genotype-phenotype landscape

(2010) Alexandre Dawid et al.   CHAOS

What makes an enzyme promiscuous?

(2010) Ann Babtie et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Diminishing Returns From Beneficial Mutations and Pervasive Epistasis Shape the Fitness Landscape for Rifampicin Resistance in Pseudomonas aeruginosa

(2010) R. C. MacLean et al.   GENETICS

Multiple Global Suppressors of Protein Stability Defects Facilitate the Evolution of Extended-Spectrum TEM β-Lactamases

(2010) Nicholas G. Brown et al.   JOURNAL OF MOLECULAR BIOLOGY

Compensatory Mutations Restore Fitness during the Evolution of Dihydrofolate Reductase

(2010) K. M. Brown et al.   MOLECULAR BIOLOGY AND EVOLUTION

Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5′-phosphate synthesis

(2010) Juhan Kim et al.   Molecular Systems Biology

Constraints and plasticity in genome and molecular-phenome evolution

(2010) Eugene V. Koonin et al.   NATURE REVIEWS GENETICS

Mutational effects and the evolution of new protein functions

(2010) Misha Soskine et al.   NATURE REVIEWS GENETICS

The evolution of gene duplications: classifying and distinguishing between models

(2010) Hideki Innan et al.   NATURE REVIEWS GENETICS

Artificial gene amplification reveals an abundance of promiscuous resistance determinants in Escherichia coli

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

An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily

(2010) B. van Loo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Permissive Secondary Mutations Enable the Evolution of Influenza Oseltamivir Resistance

(2010) J. D. Bloom et al.   SCIENCE

Biocatalytic Asymmetric Synthesis of Chiral Amines from Ketones Applied to Sitagliptin Manufacture

(2010) C. K. Savile et al.   SCIENCE

Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction

(2010) J. B. Siegel et al.   SCIENCE

Pervasive Cryptic Epistasis in Molecular Evolution

(2010) Mark Lunzer et al.   PLoS Genetics

Evolutionary Trajectories of Beta-Lactamase CTX-M-1 Cluster Enzymes: Predicting Antibiotic Resistance

(2010) Ângela Novais et al.   PLoS Pathogens

One plasmid selection system for the rapid evolution of aminoacyl-tRNA synthetases

(2009) Charles E. Melançon et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Revealing evolutionary pathways by fitness landscape reconstruction

(2009) Manjunatha Kogenaru et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Directed enzyme evolution: climbing fitness peaks one amino acid at a time

(2009) Cara A Tracewell et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Questioning our perceptions about evolution of biodegradative enzymes

(2009) Lawrence P Wackett   CURRENT OPINION IN MICROBIOLOGY

Stability effects of mutations and protein evolvability

(2009) Nobuhiko Tokuriki et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

An epistatic ratchet constrains the direction of glucocorticoid receptor evolution

(2009) Jamie T. Bridgham et al.   NATURE

Evolution of efficient pathways for degradation of anthropogenic chemicals

(2009) Shelley D Copley   Nature Chemical Biology

Exploring protein fitness landscapes by directed evolution

(2009) Philip A. Romero et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Stepwise acquisition of pyrimethamine resistance in the malaria parasite

(2009) E. R. Lozovsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive landscapes and protein evolution

(2009) M. Carneiro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In the light of directed evolution: Pathways of adaptive protein evolution

(2009) J. D. Bloom 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

Inferring Stabilizing Mutations from Protein Phylogenies: Application to Influenza Hemagglutinin

(2009) Jesse D. Bloom et al.   PLoS Computational Biology

Evolutionary History of a Specialized P450 Propane Monooxygenase

(2008) Rudi Fasan et al.   JOURNAL OF MOLECULAR BIOLOGY

A Study in Molecular Contingency: Glutamine Phosphoribosylpyrophosphate Amidotransferase is a Promiscuous and Evolvable Phosphoribosylanthranilate Isomerase

(2008) Wayne M. Patrick et al.   JOURNAL OF MOLECULAR BIOLOGY

Intense Neutral Drifts Yield Robust and Evolvable Consensus Proteins

(2008) Shimon Bershtein et al.   JOURNAL OF MOLECULAR BIOLOGY

Ohno's Model Revisited: Measuring the Frequency of Potentially Adaptive Mutations under Various Mutational Drifts

(2008) Shimon Bershtein et al.   MOLECULAR BIOLOGY AND EVOLUTION

Kemp elimination catalysts by computational enzyme design

(2008) Daniela Röthlisberger et al.   NATURE

Neutralism and selectionism: a network-based reconciliation

(2008) Andreas Wagner   NATURE REVIEWS GENETICS

Turning a hobby into a job: How duplicated genes find new functions

(2008) Gavin C. Conant et al.   NATURE REVIEWS GENETICS

Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems

(2008) Patrick C. Phillips   NATURE REVIEWS GENETICS

Adaptive protein evolution grants organismal fitness by improving catalysis and flexibility

(2008) P. E. Tomatis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A compromise required by gene sharing enables survival: Implications for evolution of new enzyme activities

(2008) S. Y. McLoughlin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Protein Stability and New Functions Trade Off

(2008) Nobuhiko Tokuriki et al.   PLoS Computational Biology

From Classical Genetics to Quantitative Genetics to Systems Biology: Modeling Epistasis

(2008) David L. Aylor et al.   PLoS Genetics