Combining Ancestral Reconstruction with Folding-Landscape Simulations to Engineer Heterologous Protein Expression

Ancestral Sequence Reconstruction: From Chemical Paleogenetics to Maximum Likelihood Algorithms and Beyond

(2021) Avery G. A. Selberg et al.   JOURNAL OF MOLECULAR EVOLUTION

Engineering of Ancestors as a Tool to Elucidate Structure, Mechanism, and Specificity of Extant Terpene Cyclase

(2021) Karen Schriever et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A reconstructed common ancestor of the fatty acid photodecarboxylase clade shows photodecarboxylation activity and increased thermostability

(2021) Yue Sun et al.   CHEMBIOCHEM

Ancestral sequence reconstruction for protein engineers

(2021) Matthew A. Spence et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Setting the stage for evolution of a new enzyme

(2021) Shelley D. Copley   CURRENT OPINION IN STRUCTURAL BIOLOGY

Consensus Mutagenesis and Ancestral Reconstruction Provide Insight into the Substrate Specificity and Evolution of the Front-End Δ6-Desaturase Family

(2020) Dongdi Li et al.   BIOCHEMISTRY

Deracemization and Stereoinversion to Aromatic D-Amino Acid Derivatives with Ancestral L-Amino Acid Oxidase

(2019) Shogo Nakano et al.   ACS Catalysis

Non-conservation of folding rates in the thioredoxin family reveals degradation of ancestral unassisted-folding

(2019) Gloria Gamiz-Arco et al.   BIOCHEMICAL JOURNAL

Ancestral-sequence reconstruction unveils the structural basis of function in mammalian FMOs

(2019) Callum R. Nicoll et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Recent Developments in Bioprocessing of Recombinant Proteins: Expression Hosts and Process Development

(2019) Nagesh K. Tripathi et al.   Frontiers in Bioengineering and Biotechnology

Biotechnological and protein-engineering implications of ancestral protein resurrection

(2018) Valeria A Risso et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction

(2018) Luke W Koblan et al.   NATURE BIOTECHNOLOGY

Directed -in vitro- evolution of Precambrian and extant Rubiscos

(2018) Bernardo J. Gomez-Fernandez et al.   Scientific Reports

Kinetic and structural comparison of a protein’s cotranslational folding and refolding pathways

(2018) Avi J. Samelson et al.   Science Advances

Ancestral diterpene cyclases show increased thermostability and substrate acceptance

(2018) Natalie M. Hendrikse et al.   FEBS Journal

Mechanochemical evolution of the giant muscle protein titin as inferred from resurrected proteins

(2017) Aitor Manteca et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Fast folding and slow unfolding of a resurrected Precambrian protein

(2017) Adela M. Candel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanochemical evolution of the giant muscle protein titin as inferred from resurrected proteins

(2017) Aitor Manteca et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Engineering ancestral protein hyperstability

(2016) M. L. Romero-Romero et al.   BIOCHEMICAL JOURNAL

Exploring the past and the future of protein evolution with ancestral sequence reconstruction: the 'retro approach to protein engineering

(2016) Y. Gumulya et al.   BIOCHEMICAL JOURNAL

Genome Evolution in the Obligate but Environmentally Active Luminous Symbionts of Flashlight Fish

(2016) Tory A. Hendry et al.   Genome Biology and Evolution

Quantifying Protein Disorder through Measures of Excess Conformational Entropy

(2016) Nandakumar Rajasekaran et al.   JOURNAL OF PHYSICAL CHEMISTRY B

On the Potential Origins of the High Stability of Reconstructed Ancestral Proteins

(2016) Devin L. Trudeau et al.   MOLECULAR BIOLOGY AND EVOLUTION

Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability

(2016) Adi Goldenzweig et al.   MOLECULAR CELL

Enhancing the pharmaceutical properties of protein drugs by ancestral sequence reconstruction

(2016) Philip M Zakas et al.   NATURE BIOTECHNOLOGY

Selection for Protein Kinetic Stability Connects Denaturation Temperatures to Organismal Temperatures and Provides Clues to Archaean Life

(2016) M. Luisa Romero-Romero et al.   PLoS One

In vivo aspects of protein folding and quality control

(2016) D. Balchin et al.   SCIENCE

An experimental phylogeny to benchmark ancestral sequence reconstruction

(2016) Ryan N. Randall et al.   Nature Communications

Metagenomics for the discovery of pollutant degrading enzymes

(2015) Lisa Ufarté et al.   BIOTECHNOLOGY ADVANCES

Production of Biopharmaceuticals in E. coli: Current Scenario and Future Perspectives

(2015) Mohammed N. Baeshen et al.   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

Designed protein reveals structural determinants of extreme kinetic stability

(2015) Aron Broom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction

(2015) Jason H. Whitfield et al.   PROTEIN SCIENCE

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

Recombinant protein expression in Escherichia coli: advances and challenges

(2014) Germán L. Rosano et al.   Frontiers in Microbiology

Ancestral mutations as a tool for solubilizing proteins: The case of a hydrophobic phosphate-binding protein

(2014) Daniel Gonzalez et al.   FEBS Open Bio

Genomic signatures of obligate host dependence in the luminous bacterial symbiont of a vertebrate

(2013) Tory A. Hendry et al.   ENVIRONMENTAL MICROBIOLOGY

Hyperstability and Substrate Promiscuity in Laboratory Resurrections of Precambrian β-Lactamases

(2013) Valeria A. Risso et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

High-Resolution Comparative Modeling with RosettaCM

(2013) Yifan Song et al.   STRUCTURE

Conservation of Protein Structure over Four Billion Years

(2013) Alvaro Ingles-Prieto et al.   STRUCTURE

Phylogenetic divergence between the obligate luminous symbionts of flashlight fishes demonstrates specificity of bacteria to host genera

(2013) Tory A. Hendry et al.   Environmental Microbiology Reports

Predictions from an Ising-like Statistical Mechanical Model on the Dynamic and Thermodynamic Effects of Protein Surface Electrostatics

(2012) Athi N. Naganathan   Journal of Chemical Theory and Computation

Overview of theCCP4 suite and current developments

(2011) Martyn D. Winn et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

The uncultured luminous symbiont of Anomalops katoptron (Beryciformes: Anomalopidae) represents a new bacterial genus

(2011) Tory A. Hendry et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Single-molecule paleoenzymology probes the chemistry of resurrected enzymes

(2011) Raul Perez-Jimenez et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Ribosome Modulates Nascent Protein Folding

(2011) C. M. Kaiser et al.   SCIENCE

Modular Evolution and the Origins of Symmetry: Reconstruction of a Three-Fold Symmetric Globular Protein

(2011) Aron Broom et al.   STRUCTURE

XDS

(2010) Wolfgang Kabsch   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Post-translational modifications of protein biopharmaceuticals

(2010) Gary Walsh   DRUG DISCOVERY TODAY

Exploiting Models of Molecular Evolution to Efficiently Direct Protein Engineering

(2010) Megan F. Cole et al.   JOURNAL OF MOLECULAR EVOLUTION

Molecular replacement withMOLREP

(2009) Alexei Vagin et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Functional metagenomics for enzyme discovery: challenges to efficient screening

(2009) Taku Uchiyama et al.   CURRENT OPINION IN BIOTECHNOLOGY

Roles of β-turns in protein folding: From peptide models to protein engineering

(2008) Anna Marie C. Marcelino et al.   BIOPOLYMERS

Chemical, physical, and theoretical kinetics of an ultrafast folding protein

(2008) J. Kubelka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA