Structural properties of the truncated and wild types of Taka-amylase: A molecular dynamics simulation and docking study

Housaindokht, Mohammad Reza; Bozorgmehr, Mohammad Reza; Eshtiagh‐Hosseini, Hossein; Jalal, Razieh; Asoodeh, Ahmad; Saberi, Mahin; Haratipour, Zeinab; Monhemi, Hassan

doi:10.1016/j.molcatb.2013.05.011

Cited by 13 publications

(7 citation statements)

References 43 publications

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“…D206, E230, and D297 (shown in sticks) in the binding site interacted with ligand. These residues coincided with the proposed catalytic triad of α-amylase in experimental and simulation studies [ 29 , 47 – 48 ]. It was clearly seen that the binding site of maltotriose concerning AmyB exposed more polar contact number with ligand than AmyA ( Fig 5 ).…”

Section: Resultssupporting

confidence: 79%

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Aspergillus Oryzae S2 α-Amylase Domain C Involvement in Activity and Specificity: In Vivo Proteolysis, Molecular and Docking Studies

et al. 2016

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We previously reported that Aspergillus oryzae strain S2 had produced two α-amylase isoforms named AmyA and AmyB. The apparent molecular masses revealed by SDS-PAGE were 50 and 42 kDa, respectively. Yet AmyB has a higher catalytic efficiency. Based on a monitoring study of the α-amylase production in both the presence and absence of different protease inhibitors, a chymotrypsin proteolysis process was detected in vivo generating AmyB. A. oryzae S2 α-amylase gene was amplified, cloned and sequenced. The sequence analysis revealed nine exons, eight introns and an encoding open reading frame of 1500 bp corresponding to AmyA isoform. The amino-acid sequence analysis revealed aY371 potential chymotrypsin cleaving site, likely to be the AmyB C-Terminal end and two other potential sites at Y359, and F379. A zymogram with a high acrylamide concentration was used. It highlighted two other closed apparent molecular mass α-amylases termed AmyB1 and AmyB2 reaching40 kDa and 43 kDa. These isoforms could be possibly generated fromY359, and F379secondary cut, respectively. The molecular modeling study showed that AmyB preserved the (β/α)8 barrel domain and the domain B but lacked the C-terminal domain C. The contact map analysis and the docking studies strongly suggested a higher activity and substrate binding affinity for AmyB than AmyA which was previously experimentally exhibited. This could be explained by the easy catalytic cleft accessibility.

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Section: Resultssupporting

confidence: 79%

“…was used in order to visualize the constructed model structures and to generate graphical figures. The maltotriose which is a frequently-used ligand in the study of the ligand–α-amylase interaction [ 29 ] was docked into AmyA and AmyB. The contact maps of the AmyA and AmyB isoforms were visualized using CMView-1.1.1 program.…”

Section: Methodsmentioning

confidence: 99%

Aspergillus Oryzae S2 α-Amylase Domain C Involvement in Activity and Specificity: In Vivo Proteolysis, Molecular and Docking Studies

et al. 2016

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“…The authors mentioned that the number and strength of hydrogen binding between amino acid residues and PCs have to be carefully considered, because the strongest binding affinity and the highest inhibitory activity are directly related to them [ 81 ]. The use of different and innovative modeling software, such as molecular dynamic simulation would provide information about the possible flexibility of PCs–enzyme complexes and their stability, by truncation fitting to experimental data [ 106 , 107 ]. The truncation step means to eliminate, in silico, one or a few amino acids from the protein, and compare the binding of ligands with both enzymes (native and truncated) structures [ 106 ].…”

Section: Resultsmentioning

confidence: 99%

“…The use of different and innovative modeling software, such as molecular dynamic simulation would provide information about the possible flexibility of PCs–enzyme complexes and their stability, by truncation fitting to experimental data [ 106 , 107 ]. The truncation step means to eliminate, in silico, one or a few amino acids from the protein, and compare the binding of ligands with both enzymes (native and truncated) structures [ 106 ].…”

Section: Resultsmentioning

confidence: 99%

Polyphenolic Compounds and Digestive Enzymes: In Vitro Non-Covalent Interactions

et al. 2017

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The digestive enzymes–polyphenolic compounds (PCs) interactions behind the inhibition of these enzymes have not been completely studied. The existing studies have mainly analyzed polyphenolic extracts and reported inhibition percentages of catalytic activities determined by UV-Vis spectroscopy techniques. Recently, pure PCs and new methods such as isothermal titration calorimetry and circular dichroism have been applied to describe these interactions. The present review focuses on PCs structural characteristics behind the inhibition of digestive enzymes, and progress of the used methods. Some characteristics such as molecular weight, number and position of substitution, and glycosylation of flavonoids seem to be related to the inhibitory effect of PCs; also, this effect seems to be different for carbohydrate-hydrolyzing enzymes and proteases. The digestive enzyme–PCs molecular interactions have shown that non-covalent binding, mostly by van der Waals forces, hydrogen binding, hydrophobic binding, and other electrostatic forces regulate them. These interactions were mainly associated to non-competitive type inhibitions of the enzymatic activities. The present review emphasizes on the digestive enzymes such as α-glycosidase (AG), α-amylase (PA), lipase (PL), pepsin (PE), trypsin (TP), and chymotrypsin (CT). Existing studies conducted in vitro allow one to elucidate the characteristics of the structure–function relationships, where differences between the structures of PCs might be the reason for different in vivo effects.

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“…The smaller size and simpler protein structure of human recombinant COX-2 protein has permitted its effective expression in prokaryotic expression systems ( 20 – 23 , 36 , 37 ). Information from the crystal structure of COX-2 has revealed that key active residues (Tyr-385, Phe-381, Val-523, Glu-524 and Ser-530) are found in the catalytic domain within the C-terminus.…”

Section: Discussionmentioning

confidence: 99%

Prokaryotic expression, purification and characterization of human cyclooxygenase-2

Liao

Wang

Fan

et al. 2017

International Journal of Molecular Medicine

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Cyclooxygenase-2 (COX-2) is a key enzyme which catalyzes the conversion of arachidonic acid (AA) into prostaglandins (PGs). It plays an important role in pathophysiological processes, such as tumorigenesis, angiogenesis, inflammation and tumor cell drug resistance. Therefore, COX-2 has been viewed as an important target for cancer therapy. The preparation of COX-2 protein is an important initial step for the subsequent development of COX-2 inhibitors. In this study, we report a strategy to heterologously express truncated human COX-2 (trCOX-2) in Escherichia coli (E. coli) BL21(DE3) host cells. Following denaturation, purification and renaturation, we successfully obtained enzymatically active trCOX-2 containing 257 residues of the C-terminus. Homology modeling and molecular docking analyses revealed that trCOX-2 retained the predicted 3D catalytic domain structure and AA could still bind to its hydrophobic groove. Western blot analysis and ELISA indicated that the trCOX-2 still retained its characteristic antigenicity and binding activity, while COX assays revealed that trCOX-2 maintained its enzyme activity. On the whole, in this study, we provided a novel method to isolate trCOX-2 possessing AA binding and catalytic activities. This study thus lays a foundation to facilitate further investigations of COX-2 and offers a valuable method with which to achieve the prokaryotic expression of a eukaryotic membrane protein.

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Structural properties of the truncated and wild types of Taka-amylase: A molecular dynamics simulation and docking study

Cited by 13 publications

References 43 publications

Aspergillus Oryzae S2 α-Amylase Domain C Involvement in Activity and Specificity: In Vivo Proteolysis, Molecular and Docking Studies

Aspergillus Oryzae S2 α-Amylase Domain C Involvement in Activity and Specificity: In Vivo Proteolysis, Molecular and Docking Studies

Polyphenolic Compounds and Digestive Enzymes: In Vitro Non-Covalent Interactions

Prokaryotic expression, purification and characterization of human cyclooxygenase-2

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