Evolutionary coupling saturation mutagenesis: Coevolution‐guided identification of distant sites influencing Bacillus naganoensis pullulanase activity

X Wang, X Jing, Y Deng, Y Nie, F Xu, Y Xu… - FEBS …, 2020 - Wiley Online Library
Pullulanases are well‐known debranching enzymes hydrolyzing α‐1, 6‐glycosidic linkages.
To date, engineering of pullulanase is mainly focused on catalytic pocket or domain tailoring …

Thermostabilizing mechanisms of canonical single amino acid substitutions at a GH1 β‐glucosidase probed by multiple MD and computational approaches

REO Rocha, DCB Mariano, TS Almeida… - Proteins: Structure …, 2023 - Wiley Online Library
Abstract β‐glucosidases play a pivotal role in second‐generation biofuel (2G‐biofuel)
production. For this application, thermostable enzymes are essential due to the denaturing …

Glutantβase: a database for improving the rational design of glucose-tolerant β-glucosidases

D Mariano, N Pantuza, LH Santos, REO Rocha… - BMC Molecular and Cell …, 2020 - Springer
Β-glucosidases are key enzymes used in second-generation biofuel production. They act in
the last step of the lignocellulose saccharification, converting cellobiose in glucose …

VTR: a web tool for identifying analogous contacts on protein structures and their complexes

V Pimentel, D Mariano, LXS Cantão… - Frontiers in …, 2021 - frontiersin.org
Evolutionarily related proteins can present similar structures but very dissimilar sequences.
Hence, understanding the role of the inter-residues contacts for the protein structure has …

Using the amino acid network to modulate the hydrolytic activity of β-glycosidases

FK Tamaki, DP Souza, VP Souza, CM Ikegami… - PLoS …, 2016 - journals.plos.org
The active site residues in GH1 β-glycosidases are compartmentalized into 3 functional
regions, involved in catalysis or binding of glycone and aglycone motifs from substrate …

Computer-Aided Saturation Mutagenesis of Arabidopsis thaliana Ent-Copalyl Diphosphate Synthase

P Szymczyk, G Szymańska, A Lipert… - Interdisciplinary …, 2020 - Springer
Ent-copalyl diphosphate synthase controls the biosynthesis of gibberellin plant hormones,
which in turn coordinate the expression of numerous enzymes. Some gibberellin-dependent …

Loss of a conserved salt bridge in bacterial glycosyl hydrolase BgIM-G1 improves substrate binding in temperate environments

D Mhaindarkar, R Gasper, N Lupilov… - Communications …, 2018 - nature.com
Salt bridges are the strongest electrostatic interactions in proteins. They substantially
contribute to a protein's structural stability. Thus, mutations of salt bridges are typically …

Rational design of adenylate kinase thermostability through coevolution and sequence divergence analysis

J Chang, C Zhang, H Cheng, YW Tan - International Journal of Molecular …, 2021 - mdpi.com
Protein engineering is actively pursued in industrial and laboratory settings for high
thermostability. Among the many protein engineering methods, rational design by …

[HTML][HTML] A mutant β-glucosidase increases the rate of the cellulose enzymatic hydrolysis

FK Tamaki, ÉM Araujo, R Rozenberg… - … and biophysics reports, 2016 - Elsevier
The enzymatic hydrolysis of cellulose and lignocellulosic materials is marked by a rate
decrease along the reaction time. Cellobiohydrolase slow dissociation from the substrate …

VTR: an algorithm for identifying analogous contacts on protein structures and their complexes

V Pimentel, D Mariano, LXS Cantão, LL Bastos… - 2020 - researchsquare.com
Evolutionarily related proteins can present similar structures but very dissimilar sequences.
Hence, understanding the role of the inter-residues contacts for the protein structure has …