Nimbalkar and colleagues conducted a research to increase the butanol concentration produced by the enzyme butanol dehydrogenase (BDH) (Nimbalkar et al.
2018). For this purpose, they added trace elements such as nickel chloride and
sodium selenite into the reaction mixture and investigated changes in the butanol
production efficiency of BDH.
They also performed homology modeling and molecular docking analysis to
investigate the correct placement and molecular interactions between trace elements,
NADH (cofactor), and substrate (butyryl aldehyde) with the 3D structure of butanol
dehydrogenase. Molecular docking analyses were instrumental in visualizing possible substrate-inhibitor interactions in the BDH enzyme.
In another study, a comparative sequence alignment, molecular modeling, and
molecular docking study was conducted to understand in detail the enzyme-substrate
interaction in cellulose hydrolysis and to find out the binding free energies of five
different microbial cellulase enzymes (three bacteria and two fungi) with β-D
glucose. Furthermore, using an in silico approach, the researchers designed and
validated the deleterious mutations (E133A and H98A) in cellulase enzyme from
Dickeya dadantii (Paul et al. 2020).
In the molecular docking analysis, it was found that Streptomyces
sp. Endoglucanase-1 interacted with β-D glucose through Val114, Ala255,
Val288, Val289, and Ser301 residues and displayed the most negative binding free
energy (À5.61 kcal/mol).
Dodda and coworkers using homology modeling modeled the structure of
cellobiohydrolases (CBHs) of Aspergillus fumigatus NITDGPKA3 to predict its
catalytic activity, and they applied molecular docking and molecular dynamics
simulation to reveal the structural and functional mechanism of the enzyme. As a
result of molecular docking analysis with cellulose, they reported that Gln248,
Pro287, Val236, Asn284, and Ala288 were the main residues in the hydrolysis of
glucose (Dodda et al. 2016).
Wickramasinghe and coworkers, to hydrolyze xylan into xylooligosaccharides,
genetically modified Pichia stipitis (a pentose sugar fermenting yeast species) via
cloning and heterologous extracellular expression of EXN1 gene from Trichoderma
virens species. For this purpose, the 3D structure of the recombinant protein encoded
by the EXN1 gene was designed by homology modeling. Furthermore, molecular
docking and molecular dynamics methods were also used to investigate EXN1-xylan
interactions (Wickramasinghe et al. 2017).
Based on molecular docking results, it was concluded that the presence of
glutamic and aspartic acid in the active site of the enzyme in question may mediate
catalytic activity by retaining or inverting mechanisms, and the molecular dynamics
simulations indicated a stable EXN1-xylan complex throughout a short 15-ns simulation time. Therefore, the researchers concluded that the enzyme-substrate association was stable, and the modeled EXN1 enzyme was realistic.
The cellulase enzyme breaks the β-1,4-glycosidic bonds and degrades the cellulose into glucose. Cellulases, which have the great potential, are among the third
widely used enzymes in ethanol production, and they also play a vital role in
degrading biomass. Selvam and coworkers performed docking analysis of
286
T. Karaytuğ et al.
2018). For this purpose, they added trace elements such as nickel chloride and
sodium selenite into the reaction mixture and investigated changes in the butanol
production efficiency of BDH.
They also performed homology modeling and molecular docking analysis to
investigate the correct placement and molecular interactions between trace elements,
NADH (cofactor), and substrate (butyryl aldehyde) with the 3D structure of butanol
dehydrogenase. Molecular docking analyses were instrumental in visualizing possible substrate-inhibitor interactions in the BDH enzyme.
In another study, a comparative sequence alignment, molecular modeling, and
molecular docking study was conducted to understand in detail the enzyme-substrate
interaction in cellulose hydrolysis and to find out the binding free energies of five
different microbial cellulase enzymes (three bacteria and two fungi) with β-D
glucose. Furthermore, using an in silico approach, the researchers designed and
validated the deleterious mutations (E133A and H98A) in cellulase enzyme from
Dickeya dadantii (Paul et al. 2020).
In the molecular docking analysis, it was found that Streptomyces
sp. Endoglucanase-1 interacted with β-D glucose through Val114, Ala255,
Val288, Val289, and Ser301 residues and displayed the most negative binding free
energy (À5.61 kcal/mol).
Dodda and coworkers using homology modeling modeled the structure of
cellobiohydrolases (CBHs) of Aspergillus fumigatus NITDGPKA3 to predict its
catalytic activity, and they applied molecular docking and molecular dynamics
simulation to reveal the structural and functional mechanism of the enzyme. As a
result of molecular docking analysis with cellulose, they reported that Gln248,
Pro287, Val236, Asn284, and Ala288 were the main residues in the hydrolysis of
glucose (Dodda et al. 2016).
Wickramasinghe and coworkers, to hydrolyze xylan into xylooligosaccharides,
genetically modified Pichia stipitis (a pentose sugar fermenting yeast species) via
cloning and heterologous extracellular expression of EXN1 gene from Trichoderma
virens species. For this purpose, the 3D structure of the recombinant protein encoded
by the EXN1 gene was designed by homology modeling. Furthermore, molecular
docking and molecular dynamics methods were also used to investigate EXN1-xylan
interactions (Wickramasinghe et al. 2017).
Based on molecular docking results, it was concluded that the presence of
glutamic and aspartic acid in the active site of the enzyme in question may mediate
catalytic activity by retaining or inverting mechanisms, and the molecular dynamics
simulations indicated a stable EXN1-xylan complex throughout a short 15-ns simulation time. Therefore, the researchers concluded that the enzyme-substrate association was stable, and the modeled EXN1 enzyme was realistic.
The cellulase enzyme breaks the β-1,4-glycosidic bonds and degrades the cellulose into glucose. Cellulases, which have the great potential, are among the third
widely used enzymes in ethanol production, and they also play a vital role in
degrading biomass. Selvam and coworkers performed docking analysis of
286
T. Karaytuğ et al.