Ancestral Sequence Reconstruction and Comprehensive Computational Simulations Unmask an Efficient PET Hydrolase with the Wobbled Catalytic Triad.
Sign Up to like & getrecommendations! Published in 2025 at "ChemSusChem"
DOI: 10.1002/cssc.202402614
Abstract: Beyond directed evolution, ancestral sequence reconstruction (ASR) has emerged as a powerful strategy for engineering proteins with superior functional properties. Herein, we harnessed ASR to uncover robust PET hydrolase variants, expanding the repertoire of PET-degrading… read more here.
Keywords: sequence; ancestral sequence; pet hydrolase; sequence reconstruction ... See more keywords
Ancestral Sequence Reconstruction of the Ethylene-Forming Enzyme
Sign Up to like & getrecommendations! Published in 2025 at "Biochemistry"
DOI: 10.1021/acs.biochem.5c00334
Abstract: The ethylene-forming enzyme (EFE) catalyzes two main reactions: the conversion of 2-oxoglutarate (2OG) to ethylene plus CO2 and the oxidative decarboxylation of 2OG coupled to the C5 hydroxylation of l-arginine (l-Arg). EFE also facilitates two… read more here.
Keywords: reconstruction ethylene; forming enzyme; ancestral sequence; arg ... See more keywords
Engineering the Thermostability of a d-Carbamoylase Based on Ancestral Sequence Reconstruction for the Efficient Synthesis of d-Tryptophan.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of agricultural and food chemistry"
DOI: 10.1021/acs.jafc.2c07781
Abstract: Employing ancestral sequence reconstruction and consensus sequence analysis, the thermostability of a novel d-carbamoylase derived from Nitratireductor indicus (NiHyuC) was engineered through greedy-oriented iterative combinatorial mutagenesis. A mutant S202P/E208D/R277L (M4Th3) was obtained with significantly elevated… read more here.
Keywords: ancestral sequence; carbamoylase; sequence; thermostability ... See more keywords
Unveiling Highly Active and Stable l-Glutaminase through Ancestral Sequence Reconstruction and Turnover Number Prediction.
Sign Up to like & getrecommendations! Published in 2025 at "Journal of agricultural and food chemistry"
DOI: 10.1021/acs.jafc.4c11502
Abstract: In our study, we employed ancestral sequence reconstruction and DLKcat analysis to engineer l-glutaminases with enhanced activity and thermal stability, using Bacillus subtilis 168 l-glutaminase (YbgJ) as the template. We identified two ancestral l-glutaminases, Anc165… read more here.
Keywords: anc165; sequence reconstruction; ancestral sequence; activity ... See more keywords
Stable and Promiscuous Galactose Oxidases Engineered by Directed Evolution, Atomistic Design, and Ancestral Sequence Reconstruction
Sign Up to like & getrecommendations! Published in 2024 at "ACS Synthetic Biology"
DOI: 10.1021/acssynbio.4c00653
Abstract: Galactose oxidase (GOase) is a versatile biocatalyst with a wide range of potential applications, ranging from synthetic chemistry to bioelectrochemical devices. Previous GOase engineering by directed evolution generated the M-RQW mutant, with unprecedented new-to-nature oxidation… read more here.
Keywords: chemistry; ancestral sequence; directed evolution; sequence reconstruction ... See more keywords
Evolutionary insights into the stereoselectivity of imine reductases based on ancestral sequence reconstruction
Sign Up to like & getrecommendations! Published in 2024 at "Nature Communications"
DOI: 10.1038/s41467-024-54613-3
Abstract: The stereoselectivity of enzymes plays a central role in asymmetric biocatalytic reactions, but there remains a dearth of evolution-driven biochemistry studies investigating the evolutionary trajectory of this vital property. Imine reductases (IREDs) are one such… read more here.
Keywords: evolution; ancestral sequence; imine reductases; biochemistry ... See more keywords
Deciphering the evolution of flavin-dependent monooxygenase stereoselectivity using ancestral sequence reconstruction.
Sign Up to like & getrecommendations! Published in 2023 at "Proceedings of the National Academy of Sciences of the United States of America"
DOI: 10.1073/pnas.2218248120
Abstract: Controlling the selectivity of a reaction is critical for target-oriented synthesis. Accessing complementary selectivity profiles enables divergent synthetic strategies, but is challenging to achieve in biocatalytic reactions given enzymes' innate preferences of a single selectivity.… read more here.
Keywords: flavin dependent; ancestral sequence; reaction; stereoselectivity ... See more keywords
Consequences of Substitution Model Selection on Protein Ancestral Sequence Reconstruction
Sign Up to like & getrecommendations! Published in 2022 at "Molecular Biology and Evolution"
DOI: 10.1093/molbev/msac144
Abstract: Abstract The selection of the best-fitting substitution model of molecular evolution is a traditional step for phylogenetic inferences, including ancestral sequence reconstruction (ASR). However, a few recent studies suggested that applying this procedure does not… read more here.
Keywords: substitution; substitution model; ancestral sequence; reconstruction ... See more keywords
ARPIP: Ancestral sequence Reconstruction with insertions and deletions under the Poisson Indel Process.
Sign Up to like & getrecommendations! Published in 2022 at "Systematic biology"
DOI: 10.1093/sysbio/syac050
Abstract: Modern phylogenetic methods allow inference of ancestral molecular sequences given an alignment and phylogeny relating present day sequences. This provides insight into the evolutionary history of molecules, helping to understand gene function and to study… read more here.
Keywords: insertions deletions; reconstruction insertions; ancestral sequence; poisson indel ... See more keywords
Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP)
Sign Up to like & getrecommendations! Published in 2022 at "PLOS Computational Biology"
DOI: 10.1101/2019.12.30.891457
Abstract: Ancestral sequence reconstruction is a technique that is gaining widespread use in molecular evolution studies and protein engineering. Accurate reconstruction requires the ability to handle appropriately large numbers of sequences, as well as insertion and… read more here.
Keywords: representation ancestral; indel; ancestral sequence; sequence ... See more keywords
Single-character insertion–deletion model preserves long indels in ancestral sequence reconstruction
Sign Up to like & getrecommendations! Published in 2024 at "BMC Bioinformatics"
DOI: 10.1186/s12859-024-05986-1
Abstract: Insertions and deletions (indels) play a significant role in genome evolution across species. Realistic modelling of indel evolution is challenging and is still an open research question. Several attempts have been made to explicitly model… read more here.
Keywords: deletion; long indels; ancestral sequence; reconstruction ... See more keywords