Ancestral sequence reconstruction for protein engineers

Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase

(2021) Gloria Gamiz-Arco et al.   Nature Communications

Were Ancestral Proteins Less Specific?

(2021) Lucas C Wheeler et al.   MOLECULAR BIOLOGY AND EVOLUTION

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Origin of complexity in haemoglobin evolution

(2020) Arvind S. Pillai et al.   NATURE

Evolution of multifunctionality through a pleiotropic substitution in the innate immune protein S100A9

(2020) Joseph L Harman et al.   eLife

Alignment-Integrated Reconstruction of Ancestral Sequences Improves Accuracy

(2020) Kelsey Aadland et al.   Genome Biology and Evolution

A hydrophobic ratchet entrenches molecular complexes

(2020) Georg K. A. Hochberg et al.   NATURE

Altered conformational sampling along an evolutionary trajectory changes the catalytic activity of an enzyme

(2020) Joe A. Kaczmarski et al.   Nature Communications

Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids

(2020) Shogo Nakano et al.   Communications Chemistry

Model selection may not be a mandatory step for phylogeny reconstruction

(2019) Shiran Abadi et al.   Nature Communications

Accounting for ambiguity in ancestral sequence reconstruction

(2019) A Oliva et al.   BIOINFORMATICS

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

(2019) Alexey M Kozlov et al.   BIOINFORMATICS

Modelling structural constraints on protein evolution via side-chain conformational states

(2019) Umberto Perron et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios

(2019) Sohta A Ishikawa et al.   MOLECULAR BIOLOGY AND EVOLUTION

Consensus sequence design as a general strategy to create hyperstable, biologically active proteins

(2019) Matt Sternke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2019) Shogo Nakano et al.   ACS Catalysis

Higher-order epistasis shapes the fitness landscape of a xenobiotic-degrading enzyme

(2019) Gloria Yang et al.   Nature Chemical Biology

ASPEN, a methodology for reconstructing protein evolution with improved accuracy using ensemble models

(2019) Roman Sloutsky et al.   eLife

Protein engineers turned evolutionists—the quest for the optimal starting point

(2019) Devin L Trudeau et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

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

Biotechnological and protein-engineering implications of ancestral protein resurrection

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

Alignment Modulates Ancestral Sequence Reconstruction Accuracy

(2018) Ricardo Assunção Vialle et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2018) Luke W Koblan et al.   NATURE BIOTECHNOLOGY

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

Pervasive contingency and entrenchment in a billion years of Hsp90 evolution

(2018) Tyler N. Starr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural and Dynamics Comparison of Thermostability in Ancient, Modern, and Consensus Elongation Factor Tus

(2018) C. Denise Okafor et al.   STRUCTURE

Coevolution of the Toll-Like Receptor 4 Complex with Calgranulins and Lipopolysaccharide

(2018) Andrea N. Loes et al.   Frontiers in Immunology

Tracing a protein's folding pathway over evolutionary time using ancestral sequence reconstruction and hydrogen exchange

(2018) Shion An Lim et al.   eLife

Ancestral sequence reconstruction: accounting for structural information by averaging over replacement matrices

(2018) Asher Moshe et al.   BIOINFORMATICS

Ancestral diterpene cyclases show increased thermostability and substrate acceptance

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

Ancient mechanisms for the evolution of the bicoid homeodomain's function in fly development

(2018) Qinwen Liu et al.   eLife

Structure and dynamics conspire in the evolution of affinity between intrinsically disordered proteins

(2018) Per Jemth et al.   Science Advances

Reverse engineering: transaminase biocatalyst development using ancestral sequence reconstruction

(2017) Matthew Wilding et al.   GREEN CHEMISTRY

De novo active sites for resurrected Precambrian enzymes

(2017) Valeria A. Risso et al.   Nature Communications

Emergence and evolution of an interaction between intrinsically disordered proteins

(2017) Greta Hultqvist et al.   eLife

The thermostability and specificity of ancient proteins

(2016) Lucas C Wheeler et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

Enhancing the pharmaceutical properties of protein drugs by ancestral sequence reconstruction

(2016) Philip M Zakas et al.   NATURE BIOTECHNOLOGY

Ancestral Reconstruction

(2016) Jeffrey B. Joy et al.   PLoS Computational Biology

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

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

The Evolutionary Origins of Detoxifying Enzymes

(2013) Hagit Bar-Rogovsky et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

On the Origin and Evolution of Thermophily: Reconstruction of Functional Precambrian Enzymes from Ancestors of Bacillus

(2011) J. K. Hobbs et al.   MOLECULAR BIOLOGY AND EVOLUTION

Enzyme Promiscuity: A Mechanistic and Evolutionary Perspective

(2010) Olga Khersonsky and Dan S. Tawfik   Annual Review of Biochemistry