Recent advances in engineering proteins for biocatalysis

Computational Design of Enone-Binding Proteins with Catalytic Activity for the Morita–Baylis–Hillman Reaction

(2013) Sinisa Bjelic et al.   ACS Chemical Biology

Computational Enzyme Design

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

Introduction of selective intersubunit disulfide bonds into self-assembly protein scaffold to enhance an artificial multienzyme complex's activity

(2013) Hidehiko Hirakawa et al.   BIOTECHNOLOGY AND BIOENGINEERING

Protein engineering for metabolic engineering: Current and next-generation tools

(2013) Ryan J. Marcheschi et al.   Biotechnology Journal

Change, exchange, and rearrange: protein engineering for the biotechnological production of fuels, pharmaceuticals, and other chemicals

(2013) Michael A Fisher et al.   CURRENT OPINION IN BIOTECHNOLOGY

Cofactor engineering for advancing chemical biotechnology

(2013) Yipeng Wang et al.   CURRENT OPINION IN BIOTECHNOLOGY

A rational design for trypsin-resistant improvement of Armillariella tabescens β-mannanase MAN47 based on molecular structure evaluation

(2013) Yufeng Li et al.   JOURNAL OF BIOTECHNOLOGY

Improving stability of nitrile hydratase by bridging the salt-bridges in specific thermal-sensitive regions

(2013) Jie Chen et al.   JOURNAL OF BIOTECHNOLOGY

Laboratory Evolution of Enantiocomplementary Candida antarctica Lipase B Mutants with Broad Substrate Scope

(2013) Qi Wu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Screening for Enhanced Triacetic Acid Lactone Production by Recombinant Escherichia coli Expressing a Designed Triacetic Acid Lactone Reporter

(2013) Shuang-Yan Tang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols

(2013) José L Avalos et al.   NATURE BIOTECHNOLOGY

A serine-substituted P450 catalyzes highly efficient carbene transfer to olefins in vivo

(2013) Pedro S Coelho et al.   Nature Chemical Biology

General approach to reversing ketol-acid reductoisomerase cofactor dependence from NADPH to NADH

(2013) S. Brinkmann-Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fusing catalase to an alkane-producing enzyme maintains enzymatic activity by converting the inhibitory byproduct H2O2 to the cosubstrate O2

(2013) C. Andre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nanoreactors by Programmed Enzyme Encapsulation Inside the Capsid of the Bacteriophage P22

(2012) Dustin P. Patterson et al.   ACS Nano

Enantioselective Artificial Metalloenzymes by Creation of a Novel Active Site at the Protein Dimer Interface

(2012) Jeffrey Bos et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Development of an Amine Dehydrogenase for Synthesis of Chiral Amines

(2012) Michael J. Abrahamson et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Improved Production of l-Threonine in Escherichia coli by Use of a DNA Scaffold System

(2012) Jun Hyoung Lee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Engineering nanoscale protein compartments for synthetic organelles

(2012) Edward Y Kim et al.   CURRENT OPINION IN BIOTECHNOLOGY

Triacetic acid lactone as a potential biorenewable platform chemical

(2012) Mei Chia et al.   GREEN CHEMISTRY

Prediction of the solvent affecting site and the computational design of stable Candida antarctica lipase B in a hydrophilic organic solvent

(2012) Hyun June Park et al.   JOURNAL OF BIOTECHNOLOGY

Structure-guided engineering of Lactococcus lactis alcohol dehydrogenase LlAdhA for improved conversion of isobutyraldehyde to isobutanol

(2012) Xiang Liu et al.   JOURNAL OF BIOTECHNOLOGY

Computational Design of Catalytic Dyads and Oxyanion Holes for Ester Hydrolysis

(2012) Florian Richter et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Computational Design of an α-Gliadin Peptidase

(2012) Sydney R. Gordon et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Induced Axial Chirality in Biocatalytic Asymmetric Ketone Reduction

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

Applying Pairwise Combinations of Amino Acid Mutations for Sorting Out Highly Efficient Glucosylation Tools for Chemo-Enzymatic Synthesis of Bacterial Oligosaccharides

(2012) Elise Champion et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Natural strategies for the spatial optimization of metabolism in synthetic biology

(2012) Christina M Agapakis et al.   Nature Chemical Biology

Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis

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

Synthetic cascades are enabled by combining biocatalysts with artificial metalloenzymes

(2012) V. Köhler et al.   Nature Chemistry

Engineered Protein Nano-Compartments for Targeted Enzyme Localization

(2012) Swati Choudhary 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

Comparison of random mutagenesis and semi-rational designed libraries for improved cytochrome P450 BM3-catalyzed hydroxylation of small alkanes

(2012) M. M. Y. Chen et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Robust design and optimization of retroaldol enzymes

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

Olefin Cyclopropanation via Carbene Transfer Catalyzed by Engineered Cytochrome P450 Enzymes

(2012) P. S. Coelho et al.   SCIENCE

Biotinylated Rh(III) Complexes in Engineered Streptavidin for Accelerated Asymmetric C-H Activation

(2012) T. K. Hyster et al.   SCIENCE

Virus-like particle nanoreactors: programmed encapsulation of the thermostable CelB glycosidase inside the P22 capsid

(2012) Dustin P. Patterson et al.   Soft Matter

Improvement of the Redox Balance Increases l-Valine Production by Corynebacterium glutamicum under Oxygen Deprivation Conditions

(2011) Satoshi Hasegawa et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Protein and RNA engineering to customize microbial molecular reporting

(2011) Joseph A. Gredell et al.   Biotechnology Journal

Manipulating the Expression Rate and Enantioselectivity of an Epoxide Hydrolase by Using Directed Evolution

(2011) Manfred T. Reetz et al.   CHEMBIOCHEM

An artificial metalloenzyme for olefin metathesis

(2011) Clemens Mayer et al.   CHEMICAL COMMUNICATIONS

Revisiting the Lipase from Pseudomonas aeruginosa: Directed Evolution of Substrate Acceptance and Enantioselectivity Using Iterative Saturation Mutagenesis

(2011) Shreenath Prasad et al.   CHEMPHYSCHEM

Cytochrome P450: taming a wild type enzyme

(2011) Sang Taek Jung et al.   CURRENT OPINION IN BIOTECHNOLOGY

The N-Terminal Region of the Medium Subunit (PduD) Packages Adenosylcobalamin-Dependent Diol Dehydratase (PduCDE) into the Pdu Microcompartment

(2011) C. Fan et al.   JOURNAL OF BACTERIOLOGY

Synthetic scaffolds increased resveratrol biosynthesis in engineered yeast cells

(2011) Yechun Wang et al.   JOURNAL OF BIOTECHNOLOGY

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

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

Engineered ketol-acid reductoisomerase and alcohol dehydrogenase enable anaerobic 2-methylpropan-1-ol production at theoretical yield in Escherichia coli

(2011) Sabine Bastian et al.   METABOLIC ENGINEERING

Regio- and stereoselectivity of P450-catalysed hydroxylation of steroids controlled by laboratory evolution

(2011) Sabrina Kille et al.   Nature Chemistry

Hydrolytic catalysis and structural stabilization in a designed metalloprotein

(2011) Melissa L. Zastrow et al.   Nature Chemistry

DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency

(2011) Robert J. Conrado et al.   NUCLEIC ACIDS RESEARCH

Computational design of a thermostable mutant of cocaine esterase via molecular dynamics simulations

(2011) Xiaoqin Huang et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

De Novo Enzyme Design Using Rosetta3

(2011) Florian Richter et al.   PLoS One

Design of a switchable eliminase

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

Directed Evolution of a Protein Container

(2011) B. Worsdorfer et al.   SCIENCE

Organization of Intracellular Reactions with Rationally Designed RNA Assemblies

(2011) C. J. Delebecque et al.   SCIENCE

An Artificial Metalloenzyme: Creation of a Designed Copper Binding Site in a Thermostable Protein

(2010) John Podtetenieff et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

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

Diversion of Flux toward Sesquiterpene Production inSaccharomyces cerevisiaeby Fusion of Host and Heterologous Enzymes

(2010) Line Albertsen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Contribution of a Xylan-Binding Module to the Degradation of a Complex Cellulosic Substrate by Designer Cellulosomes

(2010) S. Morais et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Practically Useful: What the RosettaProtein Modeling Suite Can Do for You

(2010) Kristian W. Kaufmann et al.   BIOCHEMISTRY

Combinatorial Alanine Substitution Enables Rapid Optimization of Cytochrome P450BM3 for Selective Hydroxylation of Large Substrates

(2010) Jared C. Lewis et al.   CHEMBIOCHEM

Engineering Enzyme Specificity Using Computational Design of a Defined-Sequence Library

(2010) Shaun M. Lippow et al.   CHEMISTRY & BIOLOGY

Beyond directed evolution—semi-rational protein engineering and design

(2010) Stefan Lutz   CURRENT OPINION IN BIOTECHNOLOGY

Status of protein engineering for biocatalysts: how to design an industrially useful biocatalyst

(2010) Andreas S Bommarius et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Enhanced thermostability of methyl parathion hydrolase from Ochrobactrum sp. M231 by rational engineering of a glycine to proline mutation

(2010) Jian Tian et al.   FEBS Journal

Structural Insight into the Mechanisms of Transport across theSalmonella entericaPdu Microcompartment Shell

(2010) Christopher S. Crowley et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Thermostabilization of Bacillus circulans xylanase via computational design of a flexible surface cavity

(2010) Jeong Chan Joo et al.   JOURNAL OF BIOTECHNOLOGY

Enhanced cellulose degradation by nano-complexed enzymes: Synergism between a scaffold-linked exoglucanase and a free endoglucanase

(2010) Sarah Moraïs et al.   JOURNAL OF BIOTECHNOLOGY

Thermostabilization of Bacillus circulans xylanase: Computational optimization of unstable residues based on thermal fluctuation analysis

(2010) Jeong Chan Joo et al.   JOURNAL OF BIOTECHNOLOGY

Manipulating the Stereoselectivity of Limonene Epoxide Hydrolase by Directed Evolution Based on Iterative Saturation Mutagenesis

(2010) Huabao Zheng et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Iterative Saturation Mutagenesis Accelerates Laboratory Evolution of Enzyme Stereoselectivity: Rigorous Comparison with Traditional Methods

(2010) Manfred T. Reetz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli

(2010) Tae Seok Moon et al.   METABOLIC ENGINEERING

Short N-terminal sequences package proteins into bacterial microcompartments

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

Expanding metabolism for total biosynthesis of the nonnatural amino acid L-homoalanine

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

Induced allostery in the directed evolution of an enantioselective Baeyer-Villiger monooxygenase

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

Structure and Mechanisms of a Protein-Based Organelle in Escherichia coli

(2010) S. Tanaka et al.   SCIENCE

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

(2010) J. B. Siegel et al.   SCIENCE

Cellulase-Xylanase Synergy in Designer Cellulosomes for Enhanced Degradation of a Complex Cellulosic Substrate

(2010) S. Morais et al.   mBio

Reversal of coenzyme specificity of 2,3-butanediol dehydrogenase fromSaccharomyces cerevisaeand in vivo functional analysis

(2009) Maryam Ehsani et al.   BIOTECHNOLOGY AND BIOENGINEERING

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

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

Synthetic protein scaffolds provide modular control over metabolic flux

(2009) John E Dueber et al.   NATURE BIOTECHNOLOGY

Rational stabilization of enzymes by computational redesign of surface charge–charge interactions

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

Computational design-based molecular engineering of the glycosyl hydrolase family 11 B. subtilis XynA endoxylanase improves its acid stability

(2009) T. Belien et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Computational design ofCandida boidiniixylose reductase for altered cofactor specificity

(2009) George A. Khoury et al.   PROTEIN SCIENCE

The Ehrlich Pathway for Fusel Alcohol Production: a Century of Research on Saccharomyces cerevisiae Metabolism

(2008) L. A. Hazelwood et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Addressing the Numbers Problem in Directed Evolution

(2008) Manfred T. Reetz et al.   CHEMBIOCHEM

Kemp elimination catalysts by computational enzyme design

(2008) Daniela Röthlisberger et al.   NATURE

Protein-based organelles in bacteria: carboxysomes and related microcompartments

(2008) Todd O. Yeates et al.   NATURE REVIEWS MICROBIOLOGY

De Novo Computational Design of Retro-Aldol Enzymes

(2008) L. Jiang et al.   SCIENCE