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。Mapping Protein Structural Evolution upon Unfolding
Veena Shankar Avadhani et al.
BIOCHEMISTRY (2022)
Ancestral sequence reconstruction of ancient lipase from family I.3 bacterial lipolytic enzymes
Mohamad Farihan Afnan Mohd Rozi et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2022)
Ancestral Sequence Reconstruction of a Cytochrome P450 Family Involved in Chemical Defense Reveals the Functional Evolution of a Promiscuous, Xenobiotic-Metabolizing Enzyme in Vertebrates
Kurt L. Harris et al.
MOLECULAR BIOLOGY AND EVOLUTION (2022)
Engineering of Ancestors as a Tool to Elucidate Structure, Mechanism, and Specificity of Extant Terpene Cyclase
Karen Schriever et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)
Hexamerization and thermostability emerged very early during geranylgeranylglyceryl phosphate synthase evolution
Cosimo Kropp et al.
PROTEIN SCIENCE (2021)
A Reconstructed Common Ancestor of the Fatty Acid Photo-decarboxylase Clade Shows Photo-decarboxylation Activity and Increased Thermostability
Yue Sun et al.
CHEMBIOCHEM (2021)
A rooted phylogeny resolves early bacterial evolution
Gareth A. Coleman et al.
SCIENCE (2021)
Ancestral sequence reconstruction for protein engineers
Matthew A. Spence et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2021)
Resurrection and characterization of ancestral CYP11A1 enzymes
Philip Hartz et al.
FEBS JOURNAL (2021)
Highly accurate protein structure prediction with AlphaFold
John Jumper et al.
NATURE (2021)
Machine Learning in Enzyme Engineering
Stanislav Mazurenko et al.
ACS CATALYSIS (2020)
Exploring the therapeutic potential of modern and ancestral phenylalanine/tyrosine ammonia-lyases as supplementary treatment of hereditary tyrosinemia
Natalie M. Hendrikse et al.
SCIENTIFIC REPORTS (2020)
Structure of an ancestral mammalian family 1B1 cytochrome P450 with increased thermostability
Aaron G. Bart et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2020)
Approaching boiling point stability of an alcohol dehydrogenase through computationally-guided enzyme engineering
Friso S. Aalbers et al.
ELIFE (2020)
Evaluating Protein Engineering Thermostability Prediction Tools Using an Independently Generated Dataset
Peishan Huang et al.
ACS OMEGA (2020)
Practically useful protein-design methods combining phylogenetic and atomistic calculations
Jonathan Weinstein et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2020)
Alignment-Integrated Reconstruction of Ancestral Sequences Improves Accuracy
Kelsey Aadland et al.
GENOME BIOLOGY AND EVOLUTION (2020)
Ancestral sequence reconstruction produces thermally stable enzymes with mesophilic enzyme-like catalytic properties
Ryutaro Furukawa et al.
SCIENTIFIC REPORTS (2020)
Comment on Ancient origins of allosteric activation in a Ser-Thr kinase
Yeonwoo Park et al.
SCIENCE (2020)
Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids
Shogo Nakano et al.
COMMUNICATIONS CHEMISTRY (2020)
Utility of B-Factors in Protein Science: Interpreting Rigidity, Flexibility, and Internal Motion and Engineering Thermostability
Zhoutong Sun et al.
CHEMICAL REVIEWS (2019)
What has de novo protein design taught us about protein folding and biophysics?
David Baker
PROTEIN SCIENCE (2019)
Model selection may not be a mandatory step for phylogeny reconstruction
Shiran Abadi et al.
NATURE COMMUNICATIONS (2019)
Following the Evolutionary Track of a Highly Specific L-Arginine Oxidase by Reconstruction and Biochemical Analysis of Ancestral and Native Enzymes
Shogo Nakano et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2019)
Accounting for ambiguity in ancestral sequence reconstruction
A. Oliva et al.
BIOINFORMATICS (2019)
Light-Emitting Dehalogenases: Reconstruction of Multifunctional Biocatalysts
Radka Chaloupkova et al.
ACS CATALYSIS (2019)
Protein stability engineering insights revealed by domain-wide comprehensive mutagenesis
Alex Nisthal et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
Planktonic adaptive evolution to the sea surface temperature in the Neoproterozoic inferred from ancestral NDK of marine cyanobacteria
Mariko Harada et al.
EARTH AND PLANETARY SCIENCE LETTERS (2019)
Deracemization and Stereoinversion to Aromatic D-Amino Acid Derivatives with Ancestral L-Amino Acid Oxidase
Shogo Nakano et al.
ACS CATALYSIS (2019)
Structural, thermodynamic and catalytic characterization of an ancestral triosephosphate isomerase reveal early evolutionary coupling between monomer association and function
Mariana Schulte-Sasse et al.
FEBS JOURNAL (2019)
Resurrection of efficient Precambrian endoglucanases for lignocellulosic biomass hydrolysis
Nerea Barruetabena et al.
COMMUNICATIONS CHEMISTRY (2019)
Benchmark Analysis of Native and Artificial NAD+-Dependent Enzymes Generated by a Sequence-Based Design Method with or without Phylogenetic Data
Shogo Nakano et al.
BIOCHEMISTRY (2018)
Alignment Modulates Ancestral Sequence Reconstruction Accuracy
Ricardo Assuncao Vialle et al.
MOLECULAR BIOLOGY AND EVOLUTION (2018)
Evolution of chalcone isomerase from a noncatalytic ancestor
Miriam Kaltenbach et al.
NATURE CHEMICAL BIOLOGY (2018)
Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein
Ben E. Clifton et al.
NATURE CHEMICAL BIOLOGY (2018)
Structural and Dynamics Comparison of Thermostability in Ancient, Modern, and Consensus Elongation Factor Tus
C. Denise Okafor et al.
STRUCTURE (2018)
Directed -in vitro- evolution of Precambrian and extant Rubiscos
Bernardo J. Gomez-Fernandez et al.
SCIENTIFIC REPORTS (2018)
Ancestral diterpene cyclases show increased thermostability and substrate acceptance
Natalie M. Hendrikse et al.
FEBS JOURNAL (2018)
Reconstructing the evolutionary history of F-420-dependent dehydrogenases
M. Laura Mascotti et al.
SCIENTIFIC REPORTS (2018)
Engineering highly functional thermostable proteins using ancestral sequence reconstruction
Yosephin Gumulya et al.
NATURE CATALYSIS (2018)
Enhancing the pharmaceutical properties of protein drugs by ancestral sequence reconstruction
Philip M. Zakas et al.
NATURE BIOTECHNOLOGY (2017)
Evolutionary drivers of thermoadaptation in enzyme catalysis
Vy Nguyen et al.
SCIENCE (2017)
Reverse engineering: transaminase biocatalyst development using ancestral sequence reconstruction
Matthew Wilding et al.
GREEN CHEMISTRY (2017)
Reconstructed ancestral enzymes suggest long-term cooling of Earth's photic zone since the Archean
Amanda K. Garcia et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
Ancestral Haloalkane Dehalogenases Show Robustness and Unique Substrate Specificity
Petra Babkova et al.
CHEMBIOCHEM (2017)
Experimental recreation of the evolution of lignin-degrading enzymes from the Jurassic to date
Ivan Ayuso-Fernandez et al.
BIOTECHNOLOGY FOR BIOFUELS (2017)
Catalytic Promiscuity of Ancestral Esterases and Hydroxynitrile Lyases
Titu Devamani et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2016)
On the Potential Origins of the High Stability of Reconstructed Ancestral Proteins
Devin L. Trudeau et al.
MOLECULAR BIOLOGY AND EVOLUTION (2016)
Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability
Adi Goldenzweig et al.
MOLECULAR CELL (2016)
Why reinvent the wheel? Building new proteins based on ready-made parts
Olga Khersonsky et al.
PROTEIN SCIENCE (2016)
Gene Tree Discordance Causes Apparent Substitution Rate Variation
Fabio K. Mendes et al.
SYSTEMATIC BIOLOGY (2016)
Ancestral Reconstruction
Jeffrey B. Joy et al.
PLOS COMPUTATIONAL BIOLOGY (2016)
Protein thermostability engineering
H. Pezeshgi Modarres et al.
RSC ADVANCES (2016)
Robustness of predictions of extremely thermally stable proteins in ancient organisms
Satoshi Akanuma et al.
EVOLUTION (2015)
Assessing the prediction fidelity of ancestral reconstruction by a library approach
Hagit Bar-Rogovsky et al.
PROTEIN ENGINEERING DESIGN & SELECTION (2015)
Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction
Jason H. Whitfield et al.
PROTEIN SCIENCE (2015)
On the Origin of Protein Superfamilies and Superfolds
Abram Magner et al.
SCIENTIFIC REPORTS (2015)
Trends in substitution models of molecular evolution
Miguel Arenas
FRONTIERS IN GENETICS (2015)
Toward More Accurate Ancestral Protein Genotype-Phenotype Reconstructions with the Use of Species Tree-Aware Gene Trees
Mathieu Groussin et al.
MOLECULAR BIOLOGY AND EVOLUTION (2015)
Stability properties of an ancient plant peroxidase
N. B. Loughran et al.
BIOCHIMIE (2014)
Protein disulfide engineering
Alan A. Dombkowski et al.
FEBS LETTERS (2014)
Phenotypic comparisons of consensus variants versus laboratory resurrections of Precambrian proteins
Valeria A. Risso et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2014)
Thermodynamic System Drift in Protein Evolution
Kathryn M. Hart et al.
PLOS BIOLOGY (2014)
Stabilizing biocatalysts
Andreas S. Bommarius et al.
CHEMICAL SOCIETY REVIEWS (2013)
Structure- and sequence-analysis inspired engineering of proteins for enhanced thermostability
Hein J. Wijma et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2013)
Modulating protein stability - directed evolution strategies for improved protein function
Raymond D. Socha et al.
FEBS JOURNAL (2013)
Hyperstability and Substrate Promiscuity in Laboratory Resurrections of Precambrian β-Lactamases
Valeria A. Risso et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2013)
Navigating the protein fitness landscape with Gaussian processes
Philip A. Romero et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Experimental evidence for the thermophilicity of ancestral life
Satoshi Akanuma et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Hydrophobic environment is a key factor for the stability of thermophilic proteins
M. Michael Gromiha et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2013)
Conservation of Protein Structure over Four Billion Years
Alvaro Ingles-Prieto et al.
STRUCTURE (2013)
On the Origin and Evolution of Thermophily: Reconstruction of Functional Precambrian Enzymes from Ancestors of Bacillus
Joanne K. Hobbs et al.
MOLECULAR BIOLOGY AND EVOLUTION (2012)
Random Field Model Reveals Structure of the Protein Recombinational Landscape
Philip A. Romero et al.
PLOS COMPUTATIONAL BIOLOGY (2012)
Triosephosphate Isomerase by Consensus Design: Dramatic Differences in Physical Properties and Activity of Related Variants
Brandon J. Sullivan et al.
JOURNAL OF MOLECULAR BIOLOGY (2011)
Phylogeny-Based Design of a B-Subunit of DNA Gyrase and Its ATPase Domain Using a Small Set of Homologous Amino Acid Sequences
Satoshi Akanuma et al.
JOURNAL OF MOLECULAR BIOLOGY (2011)
Exploiting Models of Molecular Evolution to Efficiently Direct Protein Engineering
Megan F. Cole et al.
JOURNAL OF MOLECULAR EVOLUTION (2011)
Single-molecule paleoenzymology probes the chemistry of resurrected enzymes
Raul Perez-Jimenez et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2011)
Robustness of Ancestral Sequence Reconstruction to Phylogenetic Uncertainty
Victor Hanson-Smith et al.
MOLECULAR BIOLOGY AND EVOLUTION (2010)
Improvement of Bacillus circulans β-amylase activity attained using the ancestral mutation method
Kan Yamashiro et al.
PROTEIN ENGINEERING DESIGN & SELECTION (2010)
Stability effects of mutations and protein evolvability
Nobuhiko Tokuriki et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2009)
Directed evolution of an extremely stable fluorescent protein
Csaba Kiss et al.
PROTEIN ENGINEERING DESIGN & SELECTION (2009)
Intense neutral drifts yield robust and evolvable consensus proteins
Shimon Bershtein et al.
JOURNAL OF MOLECULAR BIOLOGY (2008)
An improved general amino acid replacement matrix
Si Quang Le et al.
MOLECULAR BIOLOGY AND EVOLUTION (2008)
Parallel adaptations to high temperatures in the Archaean eon
Bastien Boussau et al.
NATURE (2008)
Palaeotemperature trend for Precambrian life inferred from resurrected proteins
Eric A. Gaucher et al.
NATURE (2008)
Extremely thermophilic translation system in the common ancestor commonote:: Ancestral mutants of glycyl-tRNA synthetase from the extreme thermophile Thermus thermophilus
Hideaki Shimizu et al.
JOURNAL OF MOLECULAR BIOLOGY (2007)
The effects of multiple ancestral residues on the Thermus thermophilus 3-isopropylmalate dehydrogenase
Keiko Watanabe et al.
FEBS LETTERS (2006)
Lessons in stability from thermophilic proteins
Abbas Razvi et al.
PROTEIN SCIENCE (2006)
Assessing the accuracy of ancestral protein reconstruction methods
Paul D. Williams et al.
PLOS COMPUTATIONAL BIOLOGY (2006)
Simple and accurate estimation of ancestral protein sequences
BG Hall
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Designing thermostable proteins: Ancestral mutants of 3-isopropylmalate dehydrogenase designed by using a phylogenetic tree
K Watanabe et al.
JOURNAL OF MOLECULAR BIOLOGY (2006)
Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability
Manfred T. Reetz et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2006)
Directed evolution of enzyme stability
VGH Eijsink et al.
BIOMOLECULAR ENGINEERING (2005)
Thermostability of ancestral mutants of Caldococcus noboribetus isocitrate dehydrogenase
H Iwabata et al.
FEMS MICROBIOLOGY LETTERS (2005)
Functional evolution and structural conservation in chimeric cytochromes P450: Calibrating a structure-guided approach
CR Otey et al.
CHEMISTRY & BIOLOGY (2004)
Rational engineering of enzyme stability
VGH Eijsink et al.
JOURNAL OF BIOTECHNOLOGY (2004)
Reconstruction of ancestral protein sequences and its applications
W Cai et al.
BMC EVOLUTIONARY BIOLOGY (2004)
Protein tolerance to random amino acid change
HH Guo et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
Construction of stabilized proteins by combinatorial consensus mutagenesis
N Amin et al.
PROTEIN ENGINEERING DESIGN & SELECTION (2004)
The relationship between conservation, thermodynamic stability, and function in the SH3 domain hydrophobic core
AA Di Nardo et al.
JOURNAL OF MOLECULAR BIOLOGY (2003)
Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins
EA Gaucher et al.
NATURE (2003)
Designed to be stable:: Crystal structure of a consensus ankyrin repeat protein
A Kohl et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
The consensus concept for thermostability engineering of proteins: further proof of concept
M Lehmann et al.
PROTEIN ENGINEERING (2002)
The search for the ideal biocatalyst
SG Burton et al.
NATURE BIOTECHNOLOGY (2002)
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
S Whelan et al.
MOLECULAR BIOLOGY AND EVOLUTION (2001)
Ancestral residues stabilizing 3-isopropylmalate dehydrogenase of an extreme thermophile: Experimental evidence supporting the thermophilic common ancestor hypothesis
J Miyazaki et al.
JOURNAL OF BIOCHEMISTRY (2001)
The consensus concept for thermostability engineering of proteins
M Lehmann et al.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEIN STRUCTURE AND MOLECULAR ENZYMOLOGY (2000)
The design of a hyperstable mutant of the Abp1p SH3 domain by sequence alignment analysis
A Rath et al.
PROTEIN SCIENCE (2000)
A fast algorithm for joint reconstruction of ancestral amino acid sequences
T Pupko et al.
MOLECULAR BIOLOGY AND EVOLUTION (2000)