A mechanistic view of enzyme evolution

Resolving dynamics and function of transient states in single enzyme molecules

(2020) Hugo Sanabria et al.   Nature Communications

Comprehensive exploration of the translocation, stability and substrate recognition requirements in VIM-2 lactamase

(2020) John Z Chen et al.   eLife

The Causes and Consequences of Genetic Interactions (Epistasis)

(2019) Júlia Domingo et al.   Annual Review of Genomics and Human Genetics

Protein engineering: the potential of remote mutations

(2019) Matthew Wilding et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Futile encounter engineering of the DSR-M dextransucrase modifies the resulting polymer length

(2019) Marion Claverie et al.   BIOCHEMISTRY

Cryptic genetic variation shapes the adaptive evolutionary potential of enzymes

(2019) Florian Baier et al.   eLife

Deciphering the Allosterically-driven Conformational Ensemble in Tryptophan Synthase Evolution

(2019) Miguel A. Maria-Solano et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme

(2019) Michael C. Thompson et al.   Nature Chemistry

Higher-order epistasis shapes the fitness landscape of a xenobiotic-degrading enzyme

(2019) Gloria Yang et al.   Nature Chemical Biology

Enzyme Evolution: An Epistatic Ratchet versus a Smooth Reversible Transition

(2019) Moshe Ben-David et al.   MOLECULAR BIOLOGY AND EVOLUTION

Directed Evolution of Protein Catalysts

(2018) Cathleen Zeymer et al.   Annual Review of Biochemistry

Role of conformational dynamics in the evolution of novel enzyme function

(2018) Miguel A. Maria-Solano et al.   CHEMICAL COMMUNICATIONS

Enzyme evolution: innovation is easy, optimization is complicated

(2018) Matilda S .Newton et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Compensatory mutations and epistasis for protein function

(2018) Jay F Storz   CURRENT OPINION IN STRUCTURAL BIOLOGY

Conformational dynamics and enzyme evolution

(2018) Dušan Petrović et al.   Journal of the Royal Society Interface

Evolution of chalcone isomerase from a noncatalytic ancestor

(2018) Miriam Kaltenbach et al.   Nature Chemical Biology

Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein

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

Evolutionary repurposing of a sulfatase: A new Michaelis complex leads to efficient transition state charge offset

(2018) Charlotte M. Miton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rescue of conformational dynamics in enzyme catalysis by directed evolution

(2018) Renee Otten et al.   Nature Communications

The evolution of multiple active site configurations in a designed enzyme

(2018) Nan-Sook Hong et al.   Nature Communications

Scalable, Continuous Evolution of Genes at Mutation Rates above Genomic Error Thresholds

(2018) Arjun Ravikumar et al.   CELL

Relaxation of nonproductive binding and increased rate of coenzyme release in an alcohol dehydrogenase increases turnover with a nonpreferred alcohol enantiomer

(2017) Emil Hamnevik et al.   FEBS Journal

Differential catalytic promiscuity of the alkaline phosphatase superfamily bimetallo core reveals mechanistic features underlying enzyme evolution

(2017) Fanny Sunden et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Optimization of Enzyme Mechanism along the Evolutionary Trajectory of a Computationally Designed (Retro-)Aldolase

(2017) Cathleen Zeymer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Alternative evolutionary histories in the sequence space of an ancient protein

(2017) Tyler N. Starr et al.   NATURE

Rational design of proteins that exchange on functional timescales

(2017) James A Davey et al.   Nature Chemical Biology

Nonribosomal biosynthesis of backbone-modified peptides

(2017) David L. Niquille et al.   Nature Chemistry

Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily

(2017) Eyal Akiva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural and functional innovations in the real-time evolution of new (βα)8barrel enzymes

(2017) Matilda S. Newton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Overcoming an optimization plateau in the directed evolution of highly efficient nerve agent bioscavengers

(2017) Moshe Goldsmith et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Single-mutation fitness landscapes for an enzyme on multiple substrates reveal specificity is globally encoded

(2017) Emily E. Wrenbeck et al.   Nature Communications

A Panel of TrpB Biocatalysts Derived from Tryptophan Synthase through the Transfer of Mutations that Mimic Allosteric Activation

(2016) Javier Murciano-Calles et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The Evolution of New Catalytic Mechanisms for Xenobiotic Hydrolysis in Bacterial Metalloenzymes

(2016) Elena Sugrue et al.   AUSTRALIAN JOURNAL OF CHEMISTRY

Conformational Tinkering Drives Evolution of a Promiscuous Activity through Indirect Mutational Effects

(2016) Gloria Yang et al.   BIOCHEMISTRY

Evolution of Enzyme Superfamilies: Comprehensive Exploration of Sequence–Function Relationships

(2016) F. Baier et al.   BIOCHEMISTRY

Optimization of Conformational Dynamics in an Epistatic Evolutionary Trajectory

(2016) Mariano M. González et al.   MOLECULAR BIOLOGY AND EVOLUTION

The role of protein dynamics in the evolution of new enzyme function

(2016) Eleanor Campbell et al.   Nature Chemical Biology

Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase

(2016) Richard Obexer et al.   Nature Chemistry

Epistasis in protein evolution

(2016) Tyler N. Starr et al.   PROTEIN SCIENCE

How mutational epistasis impairs predictability in protein evolution and design

(2016) Charlotte M. Miton et al.   PROTEIN SCIENCE

Using mutability landscapes of a promiscuous tautomerase to guide the engineering of enantioselective Michaelases

(2016) Jan-Ytzen van der Meer et al.   Nature Communications

Distinct Metal Isoforms Underlie Promiscuous Activity Profiles of Metalloenzymes

(2015) Florian Baier et al.   ACS Chemical Biology

Expanding the Enzyme Universe: Accessing Non-Natural Reactions by Mechanism-Guided Directed Evolution

(2015) Hans Renata et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The Moderately Efficient Enzyme: Futile Encounters and Enzyme Floppiness

(2015) Arren Bar-Even et al.   BIOCHEMISTRY

Evolvability as a Function of Purifying Selection in TEM-1 β-Lactamase

(2015) Michael A. Stiffler et al.   CELL

In vivo continuous directed evolution

(2015) Ahmed H Badran et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

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

Integrative, dynamic structural biology at atomic resolution—it's about time

(2015) Henry van den Bedem et al.   NATURE METHODS

Contingency and entrenchment in protein evolution under purifying selection

(2015) Premal Shah et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Directed evolution of the tryptophan synthase β-subunit for stand-alone function recapitulates allosteric activation

(2015) Andrew R. Buller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An evolutionary biochemist's perspective on promiscuity

(2015) Shelley D. Copley   TRENDS IN BIOCHEMICAL SCIENCES

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

(2015) Miriam Kaltenbach et al.   eLife

Keep on Moving: Discovering and Perturbing the Conformational Dynamics of Enzymes

(2014) Gira Bhabha et al.   ACCOUNTS OF CHEMICAL RESEARCH

Maintenance of Native-like Protein Dynamics May Not Be Required for Engineering Functional Proteins

(2014) Sophie M.C. Gobeil et al.   CHEMISTRY & BIOLOGY

A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain

(2014) C. Anders Olson et al.   CURRENT BIOLOGY

The robustness and innovability of protein folds

(2014) Ágnes Tóth-Petróczy et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Enzyme Promiscuity: Engine of Evolutionary Innovation

(2014) Chetanya Pandya et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

Comprehensive mutational scanning of a kinasein vivoreveals substrate-dependent fitness landscapes

(2014) Alexandre Melnikov et al.   NUCLEIC ACIDS RESEARCH

Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase

(2014) N. Preiswerk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An atomic-resolution view of neofunctionalization in the evolution of apicomplexan lactate dehydrogenases

(2014) Jeffrey I Boucher et al.   eLife

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

(2014) Ryota Moriuchi et al.   AMB Express

Flexibility and Reactivity in Promiscuous Enzymes

(2013) Pietro Gatti-Lafranconi et al.   CHEMBIOCHEM

Modulating protein stability - directed evolution strategies for improved protein function

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

Precision is essential for efficient catalysis in an evolved Kemp eliminase

(2013) Rebecca Blomberg et al.   NATURE

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

(2013) Lars Giger et al.   Nature Chemical Biology

Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein

(2013) D. Melamed et al.   RNA

Efficient, crosswise catalytic promiscuity among enzymes that catalyze phosphoryl transfer

(2012) Mark F. Mohamed et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Catalytic Versatility and Backups in Enzyme Active Sites: The Case of Serum Paraoxonase 1

(2012) Moshe Ben-David et al.   JOURNAL OF MOLECULAR BIOLOGY

Intramolecular Epistasis and the Evolution of a New Enzymatic Function

(2012) Sajid Noor et al.   PLoS One

Iterative approach to computational enzyme design

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

Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59

(2012) O. Khersonsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Robust design and optimization of retroaldol enzymes

(2012) Eric A. Althoff et al.   PROTEIN SCIENCE

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

(2012) J. Nasvall et al.   SCIENCE

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

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

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

Directed Evolution of a Gatekeeper Domain in Nonribosomal Peptide Synthesis

(2011) Benoit Villiers et al.   CHEMISTRY & BIOLOGY

Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution

(2011) Olga Khersonsky et al.   JOURNAL OF MOLECULAR BIOLOGY

Deep mutational scanning: assessing protein function on a massive scale

(2011) Carlos L. Araya et al.   TRENDS IN BIOTECHNOLOGY

Enzyme Promiscuity: A Mechanistic and Evolutionary Perspective

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

Mining electron density for functionally relevant protein polysterism in crystal structures

(2010) James S. Fraser et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

What makes an enzyme promiscuous?

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

Enzyme dynamics point to stepwise conformational selection in catalysis

(2010) Buyong Ma et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

A single-molecule enzymatic assay in a directly accessible femtoliter droplet array

(2010) Shouichi Sakakihara et al.   LAB ON A CHIP

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 Optimization of Computationally Designed Enzymes: Kemp Eliminases of the KE07 Series

(2009) Olga Khersonsky et al.   JOURNAL OF MOLECULAR BIOLOGY

Hidden alternative structures of proline isomerase essential for catalysis

(2009) James S. Fraser et al.   NATURE

Protein promiscuity and its implications for biotechnology

(2009) Irene Nobeli et al.   NATURE BIOTECHNOLOGY

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

Protein Dynamism and Evolvability

(2009) N. Tokuriki et al.   SCIENCE

Evolutionary History of a Specialized P450 Propane Monooxygenase

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

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