Conformational Design and Characterisation of a Truncated Diamine Oxidase from Arthrobacter globiformis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Homology Modelling of Diamine Oxidase
2.2. Analysing the Diamine Oxidase Domains
2.3. Molecular Dynamics (MD) Simulation and Ligand Docking Analysis
2.4. Cloning and Expression of Mini DAO
2.5. Purification of Mini DAO
2.6. Measurement of Mini DAO Activity and Stability
3. Results and Discussion
3.1. Molecular Analysis of Mini Diamine Oxidase from A. globiformis
3.2. Homology Modelling of Mini Diamine Oxidase
3.3. Molecular Dynamic Simulation and Protein Docking Analysis
3.4. Expressing of Recombinant Mini DAO in E. coli Cells
3.5. Purification of Fusion Mini DAO
3.6. Characterisation of Mini DAO
4. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
DAO | Diamine Oxidase |
DNA | Deoxyribonucleic acid |
YASARA | Yet Another Scientific Artificial Reality Application |
PDB | Protein Data Bank |
3D | Three-dimensional |
MD | Molecular dynamics |
NVT | (constant number of particles, volume, and temperature |
SDF | Structure Data Format |
OD | Optical Density |
IPTG | isopropyl-β-d-1-thiogalactopyranoside |
PAGE | polyacrylamide gel electrophoresis |
SDS-PAGE | sodium dodecyl sulphate polyacrylamide gel electrophoresis |
ODA | Dianisidine |
NMR | Nuclear magnetic resonance |
AGAO | Arhrobacter globiformis |
hDAO | Human diamine oxidase |
CDD | Conserved domain database |
RMSD | Root-Mean-Square deviation |
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Protein | Number of Residues in Favoured Region (98.0% Expected) | Number of Residues in Allowed Region (~2.0% Expected) | Number of Residues in Outlier Region |
---|---|---|---|
HDAO | 97.7 | 2.3 | 0 |
AGAO | 96.4 | 3.5 | 0 |
D4 | 96.7 | 3.3 | 0 |
Mini DAO | 98.0 | 2.0 | 1 |
Substrates | Natives | D04 | D03 | D02 | Mini DAO |
---|---|---|---|---|---|
Histamine | 8.92 | 7.45 | 4.11 | 3.66 | 8.13 |
Putresine | 7.04 | 6.42 | 4.82 | 4.04 | 6.92 |
Cadaverine | 6.04 | 5.56 | 6.39 | 3.92 | 5.99 |
Spermidine | 5.92 | 5.46 | 4.52 | 3.64 | 5.99 |
Spermine | 5.16 | 4.60 | 4.36 | 3.50 | 5.13 |
Purification Step | Total Protein (mg) | Total Activity (U) | Specific Activity (U/mg) | Fold | Yield (%) |
---|---|---|---|---|---|
Crude | 19.613 | 438.929 | 22.380 | 1 | 100 |
Ni2+-Sepharose | 11.872 | 498.265 | 41.970 | 1.875 | 88 |
Properties | Native DAO | Mini DAO |
---|---|---|
Molecular weight (SDS-PAGE) | ~74 kDa | ~24 kDa (32% smaller) |
Temperature | 35 °C | 40 °C |
pH | 7 | 7 |
Substrate specificity | Histamine (C5) | Histamine (C5), Spermidine (C7) |
Half-life | 50 min at 37 °C, no activity at 50 °C | 80 min at 50 °C |
Km Value | 0.274 mM | 1.3 mM |
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Razali, N.N.; Hashim, N.H.; Leow, A.T.C.; Salleh, A.B. Conformational Design and Characterisation of a Truncated Diamine Oxidase from Arthrobacter globiformis. High-Throughput 2018, 7, 21. https://doi.org/10.3390/ht7030021
Razali NN, Hashim NH, Leow ATC, Salleh AB. Conformational Design and Characterisation of a Truncated Diamine Oxidase from Arthrobacter globiformis. High-Throughput. 2018; 7(3):21. https://doi.org/10.3390/ht7030021
Chicago/Turabian StyleRazali, Nur Nadia, Nur Hafizah Hashim, Adam Thean Chor Leow, and Abu Bakar Salleh. 2018. "Conformational Design and Characterisation of a Truncated Diamine Oxidase from Arthrobacter globiformis" High-Throughput 7, no. 3: 21. https://doi.org/10.3390/ht7030021
APA StyleRazali, N. N., Hashim, N. H., Leow, A. T. C., & Salleh, A. B. (2018). Conformational Design and Characterisation of a Truncated Diamine Oxidase from Arthrobacter globiformis. High-Throughput, 7(3), 21. https://doi.org/10.3390/ht7030021