Carbohydrate–protein interactions: Molecular modeling insights
S Perez, I Tvaroška - Advances in carbohydrate chemistry and biochemistry, 2014 - Elsevier
The article reviews the significant contributions to, and the present status of, applications of
computational methods for the characterization and prediction of protein–carbohydrate …
computational methods for the characterization and prediction of protein–carbohydrate …
A reoptimized GROMOS force field for hexopyranose‐based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers …
HS Hansen, PH Hünenberger - Journal of computational …, 2011 - Wiley Online Library
This article presents a reoptimization of the GROMOS 53A6 force field for hexopyranose‐
based carbohydrates (nearly equivalent to 45A4 for pure carbohydrate systems) into a new …
based carbohydrates (nearly equivalent to 45A4 for pure carbohydrate systems) into a new …
Revision of the GROMOS 56A6CARBO force field: Improving the description of ring‐conformational equilibria in hexopyranose‐based carbohydrates chains
W Plazinski, A Lonardi… - Journal of computational …, 2016 - Wiley Online Library
This article describes a revised version 56A6CARBO_R of the GROMOS 56A6CARBO force
field for hexopyranose‐based carbohydrates. The simulated properties of unfunctionalized …
field for hexopyranose‐based carbohydrates. The simulated properties of unfunctionalized …
Molecular mechanism of the glycosylation step catalyzed by Golgi α-mannosidase II: a QM/MM metadynamics investigation
L Petersen, A Ardevol, C Rovira… - Journal of the American …, 2010 - ACS Publications
Golgi α-mannosidase II (GMII), a member of glycoside hydrolase family 38, cleaves two
mannosyl residues from GlcNAcMan5GlcNAc2 as part of the N-linked glycosylation …
mannosyl residues from GlcNAcMan5GlcNAc2 as part of the N-linked glycosylation …
Quantum mechanics/molecular mechanics modeling of substrate-assisted catalysis in family 18 chitinases: conformational changes and the role of Asp142 in catalysis …
Family 18 chitinases catalyze the hydrolysis of β-1, 4-glycosidic bonds in chitin. The
mechanism has been proposed to involve the formation of an oxazolinium ion intermediate …
mechanism has been proposed to involve the formation of an oxazolinium ion intermediate …
Insight into the catalytic mechanism of GH11 xylanase: computational analysis of substrate distortion based on a neutron structure
The reaction mechanism of biomass decomposition by xylanases remains the subject of
debate. To clarify the mechanism we investigated the glycosylation step of GH11 xylanase …
debate. To clarify the mechanism we investigated the glycosylation step of GH11 xylanase …
Probing the active site chemistry of β-glucosidases along the hydrolysis reaction pathway
β-Glucosidases (EC 3.2. 1.21) can be found in all domains of living organisms, where they
play essential roles in the removal of terminal glucosyl residues from nonreducing ends of …
play essential roles in the removal of terminal glucosyl residues from nonreducing ends of …
A critical survey of average distances between catalytic carboxyl groups in glycoside hydrolases
Published X‐ray crystallographic structures for glycoside hydrolases (GHs) from 39 different
families are surveyed according to some rigorous selection criteria, and the distances …
families are surveyed according to some rigorous selection criteria, and the distances …
An in-silico layer-by-layer adsorption study of the interaction between Rebaudioside A and the T1R2 human sweet taste receptor: modelling and biosensing …
The human sweet taste receptor (T1R2) monomer—a member of the G-protein coupled
receptor family that detects a wide variety of chemically and structurally diverse sweet tasting …
receptor family that detects a wide variety of chemically and structurally diverse sweet tasting …
Dynamics of the thumb-finger regions in a GH11 xylanase Bacillus circulans: comparison between the Michaelis and covalent intermediate
The structure and dynamics of B. circulans β-1, 4-xylanase (BCX) were comparatively
studied utilizing molecular dynamics. Simulations of the free enzyme, non-covalently bound …
studied utilizing molecular dynamics. Simulations of the free enzyme, non-covalently bound …