Role of conformational dynamics in the evolution of novel enzyme function

Isotope Substitution of Promiscuous Alcohol Dehydrogenase Reveals the Origin of Substrate Preference in the Transition State

(2018) Enas M. Behiry et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Mapping the substrate scope of monoamine oxidase (MAO-N) as a synthetic tool for the enantioselective synthesis of chiral amines

(2018) Susanne Herter et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Epoxide Hydrolase Conformational Heterogeneity for the Resolution of Bulky Pharmacologically Relevant Epoxide Substrates

(2018) Eila Serrano-Hervás et al.   CHEMISTRY-A EUROPEAN JOURNAL

Laboratory evolution of protein conformational dynamics

(2018) Eleanor C Campbell et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Exploring the Conversion of a d -Sialic Acid Aldolase into a l -KDO Aldolase

(2018) Adrian Romero-Rivera et al.   EUROPEAN JOURNAL OF ORGANIC CHEMISTRY

The Role of the Active Site Flap in Streptavidin/Biotin Complex Formation

(2018) Nupur Bansal et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Functional Replacement of Histidine in Proteins To Generate Noncanonical Amino Acid Dependent Organisms

(2018) Fei Gan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Rescue of conformational dynamics in enzyme catalysis by directed evolution

(2018) Renee Otten et al.   Nature Communications

Structural and Computational Insight into the Catalytic Mechanism of Limonene Epoxide Hydrolase Mutants in Stereoselective Transformations

(2017) Zhoutong Sun et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Rational design of proteins that exchange on functional timescales

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

Exploring the reversal of enantioselectivity on a zinc-dependent alcohol dehydrogenase

(2017) Miguel A. Maria-Solano et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Exploring the origins of selectivity in soluble epoxide hydrolase from Bacillus megaterium

(2017) Eila Serrano-Hervás et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

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

Networks of Dynamic Allostery Regulate Enzyme Function

(2017) Michael Joseph Holliday et al.   STRUCTURE

Simultaneous engineering of an enzyme's entrance tunnel and active site: the case of monoamine oxidase MAO-N

(2017) Guangyue Li et al.   Chemical Science

De novo active sites for resurrected Precambrian enzymes

(2017) Valeria A. Risso et al.   Nature Communications

Engineering of the Conformational Dynamics of Lipase To Increase Enantioselectivity

(2017) Bin Yang et al.   ACS Catalysis

Role of Conformational Dynamics in the Evolution of Retro-Aldolase Activity

(2017) Adrian Romero-Rivera et al.   ACS Catalysis

NMR reveals a dynamic allosteric pathway in thrombin

(2017) Lindsey D. Handley et al.   Scientific Reports

CADEE: Computer-Aided Directed Evolution of Enzymes

(2017) Beat Anton Amrein et al.   IUCrJ

Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain

(2017) Mohammad M. Sultan et al.   Scientific Reports

New Concepts for Increasing the Efficiency in Directed Evolution of Stereoselective Enzymes

(2016) Zhoutong Sun et al.   CHEMISTRY-A EUROPEAN JOURNAL

Modeling the effect of pathogenic mutations on the conformational landscape of protein kinases

(2016) Giorgio Saladino et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Mechanistic Models of Chemical Exchange Induced Relaxation in Protein NMR

(2016) Simon Olsson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Fast Knoevenagel Condensations Catalyzed by an Artificial Schiff-Base-Forming Enzyme

(2016) Xavier Garrabou et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Continuous changes in structure mapped by manifold embedding of single-particle data in cryo-EM

(2016) Joachim Frank et al.   METHODS

The coming of age of de novo protein design

(2016) Po-Ssu Huang et al.   NATURE

Conformational footprints

(2016) Buyong Ma et al.   Nature Chemical Biology

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

(2016) Eleanor Campbell et al.   Nature Chemical Biology

Discovery of a regioselectivity switch in nitrating P450s guided by molecular dynamics simulations and Markov models

(2016) Sheel C. Dodani et al.   Nature Chemistry

Dynamical network of residue–residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation

(2016) Urmi Doshi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploring the substrate scope of mutants derived from the robust alcohol dehydrogenase TbSADH

(2016) Zhoutong Sun et al.   TETRAHEDRON LETTERS

Catalytic Asymmetric Reduction of Difficult-to-Reduce Ketones: Triple-Code Saturation Mutagenesis of an Alcohol Dehydrogenase

(2016) Zhoutong Sun et al.   ACS Catalysis

Molecular Dynamics Explorations of Active Site Structure in Designed and Evolved Enzymes

(2015) Sílvia Osuna et al.   ACCOUNTS OF CHEMICAL RESEARCH

A Promiscuous De Novo Retro-Aldolase Catalyzes Asymmetric Michael Additions via Schiff Base Intermediates

(2015) Xavier Garrabou et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Enantioselective Enzymes by Computational Design and In Silico Screening

(2015) Hein J. Wijma et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

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

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

(2015) Andrew Currin et al.   CHEMICAL SOCIETY REVIEWS

Contact- and distance-based principal component analysis of protein dynamics

(2015) Matthias Ernst et al.   JOURNAL OF CHEMICAL PHYSICS

Accelerated molecular dynamics simulations of protein folding

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

Thermoanaerobacter ethanolicus secondary alcohol dehydrogenase mutants with improved racemization activity

(2015) Musa M. Musa et al.   JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC

An excess of catalytically required motions inhibits the scavenger decapping enzyme

(2015) Ancilla Neu et al.   Nature Chemical Biology

Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models

(2015) Nuria Plattner et al.   Nature Communications

Amine Oxidation Mediated by N-Methyltryptophan Oxidase: Computational Insights into the Mechanism, Role of Active-Site Residues, and Covalent Flavin Binding

(2015) Bora Karasulu et al.   ACS Catalysis

Distinguishing induced fit from conformational selection

(2014) Stefano Gianni et al.   BIOPHYSICAL CHEMISTRY

Active Site Plasticity of a Computationally Designed Retro-Aldolase Enzyme

(2014) Richard Obexer et al.   ChemCatChem

A theoretical view of protein dynamics

(2014) Modesto Orozco   CHEMICAL SOCIETY REVIEWS

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

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

Computationally Efficient and Accurate Enantioselectivity Modeling by Clusters of Molecular Dynamics Simulations

(2014) Hein J. Wijma et al.   Journal of Chemical Information and Modeling

Variational Approach to Molecular Kinetics

(2014) Feliks Nüske et al.   Journal of Chemical Theory and Computation

POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics

(2014) Jacob D. Durrant et al.   Journal of Chemical Theory and Computation

Amino Acid Networks in a (β/α)8 Barrel Enzyme Change during Catalytic Turnover

(2014) Jennifer M. Axe et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

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

Trajectories of the ribosome as a Brownian nanomachine

(2014) Ali Dashti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering of an epoxide hydrolase for efficient bioresolution of bulky pharmaco substrates

(2014) X.-D. Kong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering of Flexible Loops in Enzymes

(2014) Bettina M. Nestl et al.   ACS Catalysis

Computational Enzyme Design

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

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

De novo enzymes by computational design

(2013) Hajo Kries et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Molecular determinants of drug–receptor binding kinetics

(2013) Albert C. Pan et al.   DRUG DISCOVERY TODAY

Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure based independent component analysis

(2013) Yusuke Naritomi et al.   JOURNAL OF CHEMICAL PHYSICS

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Engineering an Enantioselective Amine Oxidase for the Synthesis of Pharmaceutical Building Blocks and Alkaloid Natural Products

(2013) Diego Ghislieri et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs

(2013) Ron O. Dror et al.   NATURE

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

Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics

(2013) D. Granata et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational Selection or Induced Fit? A Critical Appraisal of the Kinetic Mechanism

(2012) Austin D. Vogt et al.   BIOCHEMISTRY

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

Induced Axial Chirality in Biocatalytic Asymmetric Ketone Reduction

(2012) Rubén Agudo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Taking Ockham's razor to enzyme dynamics and catalysis

(2012) David R. Glowacki et al.   Nature Chemistry

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

Engineering a model protein cavity to catalyze the Kemp elimination

(2012) M. Merski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Multistate approaches in computational protein design

(2012) James A. Davey et al.   PROTEIN SCIENCE

Comparison of designed and randomly generated catalysts for simple chemical reactions

(2012) Yakov Kipnis et al.   PROTEIN SCIENCE

Robust design and optimization of retroaldol enzymes

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

An Unusual (R)-Selective Epoxide Hydrolase with High Activity for Facile Preparation of Enantiopure Glycidyl Ethers

(2011) Jing Zhao et al.   ADVANCED SYNTHESIS & CATALYSIS

Equilibrium Sampling in Biomolecular Simulations

(2011) Daniel M. Zuckerman   Annual Review of Biophysics

Flexibility, Diversity, and Cooperativity: Pillars of Enzyme Catalysis

(2011) Gordon G. Hammes et al.   BIOCHEMISTRY

Modulation of Substrate Specificities of d-Sialic Acid Aldolase through Single Mutations of Val-251

(2011) Chien-Yu Chou et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

Comparison of Methods to Obtain Force-Field Parameters for Metal Sites

(2011) LiHong Hu et al.   Journal of Chemical Theory and Computation

NCIPLOT: A Program for Plotting Noncovalent Interaction Regions

(2011) Julia Contreras-García et al.   Journal of Chemical Theory and Computation

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

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

Studying functional dynamics in bio-molecules using accelerated molecular dynamics

(2011) Phineus R. L. Markwick et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

De Novo Enzyme Design Using Rosetta3

(2011) Florian Richter et al.   PLoS One

Simplifying the representation of complex free-energy landscapes using sketch-map

(2011) Michele Ceriotti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design of a switchable eliminase

(2011) I. V. Korendovych et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Femtosecond dynamics coupled to chemical barrier crossing in a Born-Oppenheimer enzyme

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

A Dynamic Knockout Reveals That Conformational Fluctuations Influence the Chemical Step of Enzyme Catalysis

(2011) G. Bhabha et al.   SCIENCE

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Laboratory Evolution of Stereoselective Enzymes: A Prolific Source of Catalysts for Asymmetric Reactions

(2010) Manfred T. Reetz   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Enzyme Promiscuity: A Mechanistic and Evolutionary Perspective

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

Designing ensembles in conformational and sequence space to characterize and engineer proteins

(2010) Gregory D Friedland et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Revealing Noncovalent Interactions

(2010) Erin R. Johnson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Origins of catalysis by computationally designed retroaldolase enzymes

(2010) J. K. Lassila et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluation and ranking of enzyme designs

(2010) Gert Kiss et al.   PROTEIN SCIENCE

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

A Single Point Mutation Reverses the Enantiopreference ofThermoanaerobacter ethanolicusSecondary Alcohol Dehydrogenase

(2009) Musa M. Musa et al.   ChemCatChem

Backbone flexibility in computational protein design

(2009) Daniel J Mandell et al.   CURRENT OPINION IN BIOTECHNOLOGY

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

(2009) M. J. Harvey et al.   Journal of Chemical Theory and Computation

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

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

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

NMR spectroscopy brings invisible protein states into focus

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

A 21st century revisionist's view at a turning point in enzymology

(2009) Zachary D Nagel et al.   Nature Chemical Biology

Exploring protein fitness landscapes by directed evolution

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

Protein Dynamism and Evolvability

(2009) N. Tokuriki et al.   SCIENCE

Protein Design by Directed Evolution

(2008) Christian Jäckel et al.   Annual Review of Biophysics

Kemp elimination catalysts by computational enzyme design

(2008) Daniela Röthlisberger et al.   NATURE

What is principal component analysis?

(2008) Markus Ringnér   NATURE BIOTECHNOLOGY

Activity and selectivity of W110A secondary alcohol dehydrogenase from Thermoanaerobacter ethanolicus in organic solvents and ionic liquids: mono- and biphasic media

(2008) Musa M. Musa et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

De Novo Computational Design of Retro-Aldol Enzymes

(2008) L. Jiang et al.   SCIENCE

Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations

(2002) Buyong Ma et al.   PROTEIN SCIENCE