Computational Protein Engineering: Bridging the Gap between Rational Design and Laboratory Evolution

Gold-Catalyzed One-Step Construction of 2,3-Dihydro-1H-Pyrrolizines with an Electron-Withdrawing group in the 5-position: A Formal Synthesis of 7-Methoxymitosene

(2012) Ze-Yi Yan et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Protein dynamics and enzyme catalysis: the ghost in the machine?

(2012) David R. Glowacki et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Determinants of Reactivity and Selectivity in Soluble Epoxide Hydrolase from Quantum Mechanics/Molecular Mechanics Modeling

(2012) Richard Lonsdale et al.   BIOCHEMISTRY

Catalysis by a De Novo Zinc-Mediated Protein Interface: Implications for Natural Enzyme Evolution and Rational Enzyme Engineering

(2012) Bryan S. Der et al.   BIOCHEMISTRY

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

(2012) Livnat Afriat-Jurnou et al.   BIOCHEMISTRY

Enantioselective, transition metal catalyzed cycloisomerizations

(2012) Angela Marinetti et al.   CHEMICAL SOCIETY REVIEWS

Directed enzyme evolution: beyond the low-hanging fruit

(2012) Moshe Goldsmith et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Catalytic promiscuity inPseudomonas aeruginosaarylsulfatase as an example of chemistry-driven protein evolution

(2012) Jinghui Luo et al.   FEBS LETTERS

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

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

High-valent organometallic copper and palladium in catalysis

(2012) Amanda J. Hickman et al.   NATURE

Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis

(2012) Sagar D Khare et al.   Nature Chemical Biology

Taking Ockham's razor to enzyme dynamics and catalysis

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

Making expensive dirhodium(ii) catalysts cheaper: Rh(ii) recycling methods

(2012) Nuno R. Candeias et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Recent advances and applications of iridium-catalysed asymmetric allylic substitution

(2012) Paolo Tosatti et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

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

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

Probing the Mutational Interplay between Primary and Promiscuous Protein Functions: A Computational-Experimental Approach

(2012) Hector Garcia-Seisdedos et al.   PLoS Computational Biology

Enzymatic Transition States, Transition-State Analogs, Dynamics, Thermodynamics, and Lifetimes

(2011) Vern L. Schramm   Annual Review of Biochemistry

Challenges and Advances in Validating Enzyme Design Proposals: The Case of Kemp Eliminase Catalysis

(2011) Maria P. Frushicheva et al.   BIOCHEMISTRY

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

(2011) Arren Bar-Even et al.   BIOCHEMISTRY

Towards Quantitative Computer-Aided Studies of Enzymatic Enantioselectivity: The Case ofCandida antarcticaLipase A

(2011) Maria P. Frushicheva et al.   CHEMBIOCHEM

Machine Learning Algorithms for Predicting Protein Folding Rates and Stability of Mutant Proteins: Comparison with Statistical Methods

(2011) M. Michael Gromiha et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Divergence and Convergence in Enzyme Evolution: Parallel Evolution of Paraoxonases from Quorum-quenching Lactonases

(2011) Mikael Elias et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

Directed Evolution of Sulfotransferases and Paraoxonases by Ancestral Libraries

(2011) Uria Alcolombri et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural Analyses of Covalent Enzyme–Substrate Analog Complexes Reveal Strengths and Limitations of De Novo Enzyme Design

(2011) Ling Wang et al.   JOURNAL OF MOLECULAR BIOLOGY

Paradynamics: An Effective and Reliable Model for Ab Initio QM/MM Free-Energy Calculations and Related Tasks

(2011) Nikolay V. Plotnikov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Metal-Mediated Affinity and Orientation Specificity in a Computationally Designed Protein Homodimer

(2011) Bryan S. Der et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Chemistry: Enzyme expertise

(2011) Katharine Sanderson   NATURE

"Eppur si muove" (yet it moves)

(2011) V. Moliner   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

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

The linear interaction energy method for the prediction of protein stability changes upon mutation

(2011) Lauren Wickstrom et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

Natural Diversity to Guide Focused Directed Evolution

(2010) Helge Jochens et al.   CHEMBIOCHEM

Biocatalysts by evolution

(2010) Christian Jäckel et al.   CURRENT OPINION IN BIOTECHNOLOGY

Beyond directed evolution—semi-rational protein engineering and design

(2010) Stefan Lutz   CURRENT OPINION IN BIOTECHNOLOGY

Choreographing an enzyme's dance

(2010) Janice Villali et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Conformational diversity and computational enzyme design

(2010) Jonathan K Lassila   CURRENT OPINION IN CHEMICAL BIOLOGY

Examining the case for the effect of barrier compression on tunneling, vibrationally enhanced catalysis, catalytic entropy and related issues

(2010) Shina Caroline Lynn Kamerlin et al.   FEBS LETTERS

Mutational effects and the evolution of new protein functions

(2010) Misha Soskine et al.   NATURE REVIEWS GENETICS

The activation strain model of chemical reactivity

(2010) Willem-Jan van Zeist et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization

(2010) S. C. L. Kamerlin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase

(2010) M. P. Frushicheva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Evaluation and ranking of enzyme designs

(2010) Gert Kiss et al.   PROTEIN SCIENCE

An exciting but challenging road ahead for computational enzyme design

(2010) David Baker   PROTEIN SCIENCE

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

(2010) J. B. Siegel et al.   SCIENCE

Efficient Catalytic Promiscuity for Chemically Distinct Reactions

(2009) Ann C. Babtie et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Toward Accurate Screening in Computer-Aided Enzyme Design†

(2009) Maite Roca et al.   BIOCHEMISTRY

The empirical valence bond as an effective strategy for computer-aided enzyme design

(2009) Alexandra Vardi-Kilshtain et al.   Biotechnology Journal

The EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions

(2009) Shina C. L. Kamerlin et al.   FARADAY DISCUSSIONS

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

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

The Energy Gap as a Universal Reaction Coordinate for the Simulation of Chemical Reactions

(2009) Letif Mones et al.   JOURNAL OF PHYSICAL CHEMISTRY B

An artificial di-iron oxo-protein with phenol oxidase activity

(2009) Marina Faiella et al.   Nature Chemical Biology

Directed evolution drives the next generation of biocatalysts

(2009) Nicholas J Turner   Nature Chemical Biology

Exploring protein fitness landscapes by directed evolution

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

Determining the catalytic role of remote substrate binding interactions in ketosteroid isomerase

(2009) J. P. Schwans et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enzyme millisecond conformational dynamics do not catalyze the chemical step

(2009) A. V. Pisliakov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alteration of enzyme specificity by computational loop remodeling and design

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

Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details

(2009) V. Potapov et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Effective approach for calculations of absolute stability of proteins using focused dielectric constants

(2009) Spyridon Vicatos et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein Design by Directed Evolution

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

Pareto optimization in computational protein design with multiple objectives

(2008) María Suárez et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A New Member of the Alkaline Phosphatase Superfamily with a Formylglycine Nucleophile: Structural and Kinetic Characterisation of a Phosphonate Monoester Hydrolase/Phosphodiesterase from Rhizobium leguminosarum

(2008) Stefanie Jonas et al.   JOURNAL OF MOLECULAR BIOLOGY

Efficient Catalytic Promiscuity in an Enzyme Superfamily: An Arylsulfatase Shows a Rate Acceleration of 1013for Phosphate Monoester Hydrolysis

(2008) Luis F. Olguin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Testing Geometrical Discrimination within an Enzyme Active Site: Constrained Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole

(2008) Paul A. Sigala et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Catalytic Mechanism and Performance of Computationally Designed Enzymes for Kemp Elimination

(2008) Anastassia N. Alexandrova et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Surface Sites for Engineering Allosteric Control in Proteins

(2008) J. Lee et al.   SCIENCE

De Novo Computational Design of Retro-Aldol Enzymes

(2008) L. Jiang et al.   SCIENCE

Enzyme optimization: moving from blind evolution to statistical exploration of sequence–function space

(2008) Richard J. Fox et al.   TRENDS IN BIOTECHNOLOGY

Synthesis of chiral pharmaceutical intermediates by biocatalysis

(2007) Ramesh N. Patel   COORDINATION CHEMISTRY REVIEWS