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Bhattacharyya, Debasish
- Molecular Modelling Approaches for Designing Inhibitors of L-Amino Acid Oxidase from Crotalus adamanteus Venom
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PDF Views:80
Authors
Affiliations
1 Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mallick Road, Jadavpur, Kolkata 700 032, IN
1 Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mallick Road, Jadavpur, Kolkata 700 032, IN
Source
Current Science, Vol 108, No 6 (2015), Pagination: 1086-1096Abstract
L-amino acid oxidase (LAAO) from snake venom induces diverse toxicity into the victims, which is attributed to H2O2 generated during the catalytic conversion of L-amino acids. In this study, homology model of LAAO from Crotalus adamanteus has been compared with the crystal structure of LAAO from Calloselasma rhodostoma. The ischolar_main mean square deviations obtained from superposition of the FADbinding, substrate-binding and helical domains of LAAO from Crotalus adamanteus with those of LAAO from Calloselasma rhodostoma crystal structure confirmed a high degree of structural similarity between them. Based on the interactions of the substrate, L-phenylalanine and the reversible inhibitor, o-aminobenzoic acid with the catalytic residues of LAAO from Calloselasma rhodostoma, five probable inhibitors were designed. AutoDock Vina program was employed to perform automated molecular docking of these probable inhibitors. Two of them emerged as reversible inhibitors with IC50 values of 1.6 and 3.3 μM respectively.Keywords
Docking, Molecular Modelling, Snake Venom Toxins, Suicide Substrate, L-Amino Acid Oxidase.Full Text
- Application of Transverse Urea Gradient Zymography for Structural and Functional Characterization of Proteolytic Enzymes
Abstract Views :270 |
PDF Views:82
Authors
Affiliations
1 Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata 700 0032, IN
1 Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata 700 0032, IN
Source
Current Science, Vol 111, No 8 (2016), Pagination: 1340-1348Abstract
Inactivation of an enzyme as it begins to unfold, along with the conformational perturbations which follow, can provide an insight into dynamics of the unfolding pathway. Urea gradient electrophoresis combined with zymography is a sensitive technique which provides a continuous visual profile of a proteolytic enzyme undergoing denaturation and inactivation simultaneously. Trypsin has been used as a reference protease to validate and standardize the method by correlating inactivation profile generated in zymography with a solution state assay. Stem bromelain, a cysteine endopeptidase was used as a case study to evaluate this methodology. The method highlighted the effect rendered by the substrate on the stability of the proteolytic domain of the enzyme, as it undergoes urea-induced unfolding. Transverse urea gradient zymography combined with molecular modelling of stem bromelain, where the disulphide bonds have been reduced, indicated that the evolutionary retention of Cys23-Cys63 could be attributed to localized stabilization imparted by this bond to the catalytic site. This method encompasses various dimensions to extend the understanding of structure-function relationship in denaturant-induced unfolding pathways of proteases.Keywords
Protein Unfolding, Stem Bromelain, Urea Gradient, Zymography.Full Text
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- Degraded Products of Stem Bromelain Destabilize Aggregates of β-Amyloid Peptides Involved in Alzheimer’s Disease
Abstract Views :211 |
PDF Views:67
Authors
Debratna Mukherjee
1,
Payel Bhattacharjee
1,
Reema Bhattacharya
1,
Alok K. Dutta
1,
Debasish Bhattacharyya
1
Affiliations
1 Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology 4, Raja S.C. Mallick Road, Jadavpur, Kolkata 700 032, IN
1 Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology 4, Raja S.C. Mallick Road, Jadavpur, Kolkata 700 032, IN
Source
Current Science, Vol 115, No 11 (2018), Pagination: 2133-2141Abstract
Deposition of fibrils originating from monomeric β- amyloid (Aβ) peptide in brain cells is responsible for progressive neuronal damages in Alzheimer’s disease. Peptides from bromelain, a cysteine protease from Ananas comosus (pineapple), were generated after digestion with proteases under conditions similar to human gastrointestinal tract. These peptides not only inhibit the growth of Aβ-amyloid aggregates, but also irreversibly destabilize the preformed aggregates. Gel filtration followed by mass spectrometric analysis identified a pool of peptides of <700 Da in the digest. Probable composition of the peptides interacting with Aβ-peptide was predicted from homology alignment between Aβ-peptide and bromelain using bioinformatics tools. Corresponding synthetic peptides can also destabilize the preformed aggregates as observed from thioflavin T assay, transmission electron microscopy and atomic force microscopy. Aβ aggregates that were preincubated with the bromelain-derived peptides did not exert appreciable toxicity on human neuroblastoma cells (SH-SY5Y) cultured in vitro.Keywords
Alzheimer’s Disease, Aβ Peptide, Disaggregation, Stem Bromelain.Full Text
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