How mutational epistasis impairs predictability in protein evolution and design

Simultaneous Use of in Silico Design and a Correlated Mutation Network as a Tool To Efficiently Guide Enzyme Engineering

(2015) Alberto Nobili et al.   CHEMBIOCHEM

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

(2015) Andrew Currin et al.   CHEMICAL SOCIETY REVIEWS

Negative Epistasis and Evolvability in TEM-1 β-Lactamase—The Thin Line between an Enzyme's Conformational Freedom and Disorder

(2015) Eynat Dellus-Gur et al.   JOURNAL OF MOLECULAR BIOLOGY

Quantitative Description of a Protein Fitness Landscape Based on Molecular Features

(2015) María-Rocío Meini et al.   MOLECULAR BIOLOGY AND EVOLUTION

Methods for the directed evolution of proteins

(2015) Michael S. Packer et al.   NATURE REVIEWS GENETICS

Pervasive degeneracy and epistasis in a protein-protein interface

(2015) A. I. Podgornaia et al.   SCIENCE

Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes

(2015) Adam C. Palmer et al.   Nature Communications

Reverse evolution leads to genotypic incompatibility despite functional and active site convergence

(2015) Miriam Kaltenbach et al.   eLife

Evolution of DNA Specificity in a Transcription Factor Family Produced a New Gene Regulatory Module

(2014) Alesia N. McKeown et al.   CELL

Computational tools for designing and engineering enzymes

(2014) Jiri Damborsky et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Role of pleiotropy during adaptation of TEM-1β-lactamase to two novel antibiotics

(2014) Martijn F. Schenk et al.   Evolutionary Applications

Dynamics and constraints of enzyme evolution

(2014) Miriam Kaltenbach et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Extreme Synergistic Mutational Effects in the Directed Evolution of a Baeyer–Villiger Monooxygenase as Catalyst for Asymmetric Sulfoxidation

(2014) Zhi-Gang Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Differential Effects of a Mutation on the Normal and Promiscuous Activities of Orthologs: Implications for Natural and Directed Evolution

(2014) Akhil Khanal et al.   MOLECULAR BIOLOGY AND EVOLUTION

Epistasis Constrains Mutational Pathways of Hemoglobin Adaptation in High-Altitude Pikas

(2014) Danielle M. Tufts et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dynamics and hydration explain failed functional transformation in dehalogenase design

(2014) Jan Sykora et al.   Nature Chemical Biology

The role of distant mutations and allosteric regulation on LovD active site dynamics

(2014) Gonzalo Jiménez-Osés et al.   Nature Chemical Biology

Design of activated serine–containing catalytic triads with atomic-level accuracy

(2014) Sridharan Rajagopalan et al.   Nature Chemical Biology

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

Empirical fitness landscapes and the predictability of evolution

(2014) J. Arjan G.M. de Visser et al.   NATURE REVIEWS GENETICS

Evolution of oligomeric state through allosteric pathways that mimic ligand binding

(2014) Tina Perica et al.   SCIENCE

Epistatic Adaptive Evolution of Human Color Vision

(2014) Shozo Yokoyama et al.   PLoS Genetics

Stepwise enhancement of catalytic performance of haloalkane dehalogenase LinB towards β-hexachlorocyclohexane

(2014) Ryota Moriuchi et al.   AMB Express

Design of Protein Catalysts

(2013) Donald Hilvert   Annual Review of Biochemistry

Accounting for epistatic interactions improves the functional analysis of protein structures

(2013) Angela D. Wilkins et al.   BIOINFORMATICS

Should evolutionary geneticists worry about higher-order epistasis?

(2013) Daniel M Weinreich et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

SELECTION BIASES THE PREVALENCE AND TYPE OF EPISTASIS ALONG ADAPTIVE TRAJECTORIES

(2013) Jeremy A. Draghi et al.   EVOLUTION

Accessible Mutational Trajectories for the Evolution of Pyrimethamine Resistance in the Malaria Parasite Plasmodium vivax

(2013) Pan-Pan Jiang et al.   JOURNAL OF MOLECULAR EVOLUTION

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

Mutational effects on stability are largely conserved during protein evolution

(2013) O. Ashenberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin

(2013) C. Natarajan et al.   SCIENCE

Stability-mediated epistasis constrains the evolution of an influenza protein

(2013) Lizhi Ian Gong et al.   eLife

The spatial architecture of protein function and adaptation

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

Intramolecular Epistasis and the Evolution of a New Enzymatic Function

(2012) Sajid Noor et al.   PLoS One

Repeatability and Contingency in the Evolution of a Key Innovation in Phage Lambda

(2012) J. R. Meyer et al.   SCIENCE

Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme

(2012) Nobuhiko Tokuriki et al.   Nature Communications

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

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

The causes of epistasis

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

Network Models of TEM β-Lactamase Mutations Coevolving under Antibiotic Selection Show Modular Structure and Anticipate Evolutionary Trajectories

(2011) Violeta Beleva Guthrie et al.   PLoS Computational Biology

Initial Mutations Direct Alternative Pathways of Protein Evolution

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

Fitness Epistasis and Constraints on Adaptation in a Human Immunodeficiency Virus Type 1 Protein Region

(2010) J. da Silva et al.   GENETICS

Pervasive Cryptic Epistasis in Molecular Evolution

(2010) Mark Lunzer et al.   PLoS Genetics

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

Revealing evolutionary pathways by fitness landscape reconstruction

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

Laboratory Evolution of Robust and Enantioselective Baeyer−Villiger Monooxygenases for Asymmetric Catalysis

(2009) Manfred T. Reetz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Directed Evolution of an Enantioselective Epoxide Hydrolase: Uncovering the Source of Enantioselectivity at Each Evolutionary Stage

(2009) Manfred T. Reetz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Macromolecular Modeling with Rosetta

(2008) Rhiju Das et al.   Annual Review of Biochemistry

Constructing and Analyzing the Fitness Landscape of an Experimental Evolutionary Process

(2008) Manfred T. Reetz et al.   CHEMBIOCHEM

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

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli

(2008) Z. D. Blount et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA