2021
DOI: 10.1080/07391102.2021.1898469
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Active site dynamics and catalytic mechanism in arabinan hydrolysis catalyzed by GH43 endo-arabinanase from QM/MM molecular dynamics simulation and potential energy surface

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Cited by 9 publications
(8 citation statements)
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“…Since metformin is highly hydrophilic and relies on transporters to move through membranes, we assumed that hydrogen bonding (Hbonding), a very frequent mechanism of interaction between proteins and ligands and proteins and proteins, is involved. We turned to hydrogen bond (HB) analysis to quantify the observations from the video.…”
Section: Results and Discussionmentioning
confidence: 99%
“…Since metformin is highly hydrophilic and relies on transporters to move through membranes, we assumed that hydrogen bonding (Hbonding), a very frequent mechanism of interaction between proteins and ligands and proteins and proteins, is involved. We turned to hydrogen bond (HB) analysis to quantify the observations from the video.…”
Section: Results and Discussionmentioning
confidence: 99%
“…The SCC–DFTB method is a fast semi-empirical density functional approach that has been extensively applied in the QM/MM studies of carbohydrate-active enzymes. ,, The remaining atoms beyond the QM region (i.e., the protein and solvent) were incorporated via MM with the CHARMM27 force field . We opted to use CHARMM27 and SCC–DFTB since we have a good experience with this combination, as it was used successfully by us before to tackle similar questions. ,, Furthermore, this SCC–DFTB/CHARMM27 method is well validated for carbohydrate description and could reproduce the X-ray structures (Figures S5–S6).…”
Section: Computational Detailsmentioning
confidence: 99%
“…Finally, the weighted histogram analysis method (WHAM) was used to obtain the final PMF. Thereafter, corrected PMFs were obtained at the ωB97XD full QM level with the 6-31+G(d,p) basis set using our energy correction scheme, , a procedure that has been used to generate the correction free-energy profiles based on the following equation normalΔ G PMF , corr ( protein ) = normalΔ G PMF , SCC DFTB ( protein ) + [ E DFT false( model false) E SCC DFTB false( model false) ] where E DFT (model) – E SCC–DFTB (model) corresponds to the difference in the energies of the stationary points that were obtained using SCC–DFTB and ωB97XD. To use this, we assume that the QM/MM interaction energy does not change significantly at both levels of theory and that the thermal and zero-point energy corrections are small enough to be negligible.…”
Section: Computational Detailsmentioning
confidence: 99%
“…Because of its simplicity, a limited number of reported investigations are reported for inverting enzymes (Figure ). One dealing with endoglucanase from GH8 was investigated with the DFT QM/MM method. Another group characterized the nature of the reaction’s transition state and the conformations adopted by the glycan xylopyranosyl ring along the reaction pathway under the action of an inverting β-xylosidase. , A series of articles have been reported describing the application of computational methods in retaining glycosidases. …”
Section: Protein Carbohydrate Interactionsmentioning
confidence: 99%