标题
Conformational dynamics and enzyme evolution
作者
关键词
-
出版物
Journal of the Royal Society Interface
Volume 15, Issue 144, Pages 20180330
出版商
The Royal Society
发表日期
2018-07-18
DOI
10.1098/rsif.2018.0330
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- Challenges and advances in the computational modeling of biological phosphate hydrolysis
- (2018) Dušan Petrović et al. CHEMICAL COMMUNICATIONS
- Cooperativity and flexibility in enzyme evolution
- (2018) Anna Pabis et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Directed Evolution Mimics Allosteric Activation by Stepwise Tuning of the Conformational Ensemble
- (2018) Andrew R. Buller et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- 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
- Conformational Sampling of the Intrinsically Disordered C-Terminal Tail of DERA Is Important for Enzyme Catalysis
- (2018) Marianne Schulte et al. ACS Catalysis
- Iron catalysis at the origin of life
- (2017) Eloi Camprubi et al. IUBMB LIFE
- Similar Active Sites and Mechanisms Do Not Lead to Cross-Promiscuity in Organophosphate Hydrolysis: Implications for Biotherapeutic Engineering
- (2017) Miha Purg et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 1
- (2017) David Blaha-Nelson et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Enzymes at work are enzymes in motion
- (2017) Tamjeed Saleh et al. SCIENCE
- Predicting allosteric mutants that increase activity of a major antibiotic resistance enzyme
- (2017) M. J. Latallo et al. Chemical Science
- De novo active sites for resurrected Precambrian enzymes
- (2017) Valeria A. Risso et al. Nature Communications
- Shuffling Active Site Substate Populations Affects Catalytic Activity: The Case of Glucose Oxidase
- (2017) Dušan Petrović et al. ACS Catalysis
- Role of Conformational Dynamics in the Evolution of Retro-Aldolase Activity
- (2017) Adrian Romero-Rivera et al. ACS Catalysis
- Functional Proteins from Short Peptides: Dayhoff's Hypothesis Turns 50
- (2016) M. Luisa Romero Romero et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Promiscuity in the Enzymatic Catalysis of Phosphate and Sulfate Transfer
- (2016) Anna Pabis et al. BIOCHEMISTRY
- Excess positional mutual information predicts both local and allosteric mutations affecting beta lactamase drug resistance
- (2016) George A. Cortina et al. BIOINFORMATICS
- Multi-input and -output logic circuits based on bioelectrocatalysis with horseradish peroxidase and glucose oxidase immobilized in multi-responsive copolymer films on electrodes
- (2016) Xue Yu et al. BIOSENSORS & BIOELECTRONICS
- Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell
- (2016) Guanghong Wei et al. CHEMICAL REVIEWS
- Promiscuity and electrostatic flexibility in the alkaline phosphatase superfamily
- (2016) Anna Pabis et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Perspective: Defining and quantifying the role of dynamics in enzyme catalysis
- (2016) Arieh Warshel et al. JOURNAL OF CHEMICAL PHYSICS
- β-Lactamases: Why and How
- (2016) R. F. Pratt JOURNAL OF MEDICINAL CHEMISTRY
- 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
- Linking coupled motions and entropic effects to the catalytic activity of 2-deoxyribose-5-phosphate aldolase (DERA)
- (2016) Huan Ma et al. Chemical Science
- Minimization of dynamic effects in the evolution of dihydrofolate reductase
- (2016) J. Javier Ruiz-Pernía et al. Chemical Science
- Modelling proteins’ hidden conformations to predict antibiotic resistance
- (2016) Kathryn M. Hart et al. Nature Communications
- Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes
- (2016) Benjamin R. Jack et al. PLOS BIOLOGY
- Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches
- (2016) Tobias Sikosek et al. PLoS Computational Biology
- The physiology and habitat of the last universal common ancestor
- (2016) Madeline C. Weiss et al. Nature Microbiology
- Molecular Dynamics Explorations of Active Site Structure in Designed and Evolved Enzymes
- (2015) Sílvia Osuna et al. ACCOUNTS OF CHEMICAL RESEARCH
- Are there dynamical effects in enzyme catalysis? Some thoughts concerning the enzymatic chemical step
- (2015) Iñaki Tuñón et al. ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
- The Moderately Efficient Enzyme: Futile Encounters and Enzyme Floppiness
- (2015) Arren Bar-Even et al. BIOCHEMISTRY
- Catalytic Stimulation by Restrained Active-Site Floppiness—The Case of High Density Lipoprotein-Bound Serum Paraoxonase-1
- (2015) Moshe Ben-David et al. JOURNAL OF MOLECULAR BIOLOGY
- Cooperative Electrostatic Interactions Drive Functional Evolution in the Alkaline Phosphatase Superfamily
- (2015) Alexandre Barrozo et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- “Mind the Gap”: Raman Evidence for Rapid Inactivation of CTX-M-9 β-Lactamase Using Mechanism-Based Inhibitors that Bridge the Active Site
- (2015) Hossein Heidari-Torkabadi et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- New Tricks for Old Proteins: Single Mutations in a Nonenzymatic Protein Give Rise to Various Enzymatic Activities
- (2015) Yurii S. Moroz et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Structural analysis of fungus-derived FAD glucose dehydrogenase
- (2015) Hiromi Yoshida et al. Scientific Reports
- Role of Dynamics in Enzyme Catalysis: Substantial versus Semantic Controversies
- (2014) Amnon Kohen ACCOUNTS OF CHEMICAL RESEARCH
- Markov state models of biomolecular conformational dynamics
- (2014) John D Chodera et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Evolutionary Aspects of Enzyme Dynamics
- (2014) Judith P. Klinman et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- Extension and Limits of the Network of Coupled Motions Correlated to Hydride Transfer in Dihydrofolate Reductase
- (2014) Priyanka Singh et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History
- (2014) Valeria A. Risso et al. MOLECULAR BIOLOGY AND EVOLUTION
- Evolution of Conformational Dynamics Determines the Conversion of a Promiscuous Generalist into a Specialist Enzyme
- (2014) T. Zou et al. MOLECULAR BIOLOGY AND EVOLUTION
- The ensemble nature of allostery
- (2014) Hesam N. Motlagh et al. NATURE
- Computational Enzyme Design
- (2013) Gert Kiss et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Hydrogen Tunneling Links Protein Dynamics to Enzyme Catalysis
- (2013) Judith P. Klinman et al. Annual Review of Biochemistry
- Engineering glucose oxidase to minimize the influence of oxygen on sensor response
- (2013) Yohei Horaguchi et al. ELECTROCHIMICA ACTA
- Structural dynamics flexibility informs function and evolution at a proteome scale
- (2013) Zeynep Nevin Gerek et al. Evolutionary Applications
- Hyperstability and Substrate Promiscuity in Laboratory Resurrections of Precambrian β-Lactamases
- (2013) Valeria A. Risso et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Increased Dynamic Effects in a Catalytically Compromised Variant of Escherichia coli Dihydrofolate Reductase
- (2013) J. Javier Ruiz-Pernia 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
- Divergent evolution of protein conformational dynamics in dihydrofolate reductase
- (2013) Gira Bhabha et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Modeling catalytic promiscuity in the alkaline phosphatase superfamily
- (2013) Fernanda Duarte et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- 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
- Unraveling the role of protein dynamics in dihydrofolate reductase catalysis
- (2013) L. Y. P. Luk et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Single Glucose Biofuel Cells Implanted in Rats Power Electronic Devices
- (2013) A. Zebda et al. Scientific Reports
- Efficient, crosswise catalytic promiscuity among enzymes that catalyze phosphoryl transfer
- (2012) Mark F. Mohamed et al. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
- The Origin of Membrane Bioenergetics
- (2012) Nick Lane et al. CELL
- Catalytic promiscuity inPseudomonas aeruginosaarylsulfatase as an example of chemistry-driven protein evolution
- (2012) Jinghui Luo et al. FEBS LETTERS
- Computational Design of Catalytic Dyads and Oxyanion Holes for Ester Hydrolysis
- (2012) Florian Richter et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Good vibrations in enzyme-catalysed reactions
- (2012) Sam Hay et al. Nature Chemistry
- Rational Redesign of Glucose Oxidase for Improved Catalytic Function and Stability
- (2012) J. Todd Holland et al. PLoS One
- Robust design and optimization of retroaldol enzymes
- (2012) Eric A. Althoff et al. PROTEIN SCIENCE
- Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme
- (2012) Nobuhiko Tokuriki et al. Nature Communications
- Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts
- (2012) Tobias Sikosek et al. PLoS Computational Biology
- Flexibility, Diversity, and Cooperativity: Pillars of Enzyme Catalysis
- (2011) Gordon G. Hammes et al. BIOCHEMISTRY
- Engineering of Glucose Oxidase for Direct Electron Transfer via Site-Specific Gold Nanoparticle Conjugation
- (2011) J. Todd Holland et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Design of a switchable eliminase
- (2011) I. V. Korendovych et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions
- (2011) A. J. Adamczyk et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Examining the promiscuous phosphatase activity of Pseudomonas aeruginosa arylsulfatase: A comparison to analogous phosphatases
- (2011) Jinghui Luo et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- A Dynamic Knockout Reveals That Conformational Fluctuations Influence the Chemical Step of Enzyme Catalysis
- (2011) G. Bhabha et al. SCIENCE
- Enzyme Promiscuity: A Mechanistic and Evolutionary Perspective
- (2010) Olga Khersonsky and Dan S. Tawfik Annual Review of Biochemistry
- Role of conservative mutations in protein multi-property adaptation
- (2010) David Rodriguez-Larrea et al. BIOCHEMICAL JOURNAL
- Update 1 of: Tunneling and Dynamics in Enzymatic Hydride Transfer
- (2010) Zachary D. Nagel et al. CHEMICAL REVIEWS
- Everything you wanted to know about Markov State Models but were afraid to ask
- (2010) Vijay S. Pande et al. METHODS
- The evolution of gene duplications: classifying and distinguishing between models
- (2010) Hideki Innan et al. NATURE REVIEWS GENETICS
- A Glucose BioFuel Cell Implanted in Rats
- (2010) Philippe Cinquin et al. PLoS One
- 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
- Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction
- (2010) J. B. Siegel et al. SCIENCE
- Overlap between folding and functional energy landscapes for adenylate kinase conformational change
- (2010) Ulrika Olsson et al. Nature Communications
- Integrated Enzyme-Based Biofuel Cells-A Review
- (2009) I. Willner et al. Fuel Cells
- A 21st century revisionist's view at a turning point in enzymology
- (2009) Zachary D Nagel et al. Nature Chemical Biology
- The evolutionary consequences of erroneous protein synthesis
- (2009) D. Allan Drummond et al. NATURE REVIEWS GENETICS
- Diversity of chemical mechanisms in thioredoxin catalysis revealed by single-molecule force spectroscopy
- (2009) Raul Perez-Jimenez et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Potential role of phenotypic mutations in the evolution of protein expression and stability
- (2009) M. Goldsmith et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- 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
- Conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase
- (2009) C. J. Jackson et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Mapping catalytic promiscuity in the alkaline phosphatase superfamily
- (2009) Stefanie Jonas et al. PURE AND APPLIED CHEMISTRY
- Protein Dynamism and Evolvability
- (2009) N. Tokuriki et al. SCIENCE
- The look-ahead effect of phenotypic mutations
- (2008) Dion J Whitehead et al. Biology Direct
- Kemp elimination catalysts by computational enzyme design
- (2008) Daniela Röthlisberger et al. NATURE
- How do bacterial cells ensure that metalloproteins get the correct metal?
- (2008) Kevin J. Waldron et al. NATURE REVIEWS MICROBIOLOGY
- De Novo Computational Design of Retro-Aldol Enzymes
- (2008) L. Jiang et al. SCIENCE
- Electrochemical Glucose Biosensors
- (2007) Joseph Wang CHEMICAL REVIEWS
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started