Computational Study on Temperature Driven Structure–Function Relationship of Polysaccharide Producing Bacterial Glycosyl Transferase Enzyme
Abstract
:1. Introduction
2. Materials and Methods
2.1. Accession of Target Proteins
2.2. Primary Analysis of Physicochemical Parameters and Structure
2.3. Secondary Structure Assessment
2.4. Assessment of the Three Dimensional Structure, Modeling, and Validation
2.5. Functional Analyses of the Enzymes
2.6. Selection and Optimization of Ligand with the Target Proteins
2.7. Molecular Docking to Ensemble Protein Structure
3. Results and Discussion
3.1. Accession of Target Proteins
3.2. Primary Analysis of Physicochemical Parameters and Structure
3.3. Secondary Structure Assessment
3.4. Assessment of the Three Dimensional Structure, Modeling, and Validation
3.5. Functional Analyses of the Enzymes
3.6. Selection and Optimization of Ligand with the Target Proteins
3.7. Molecular Docking to Ensemble Protein Structure
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Serial No. | Bacterial Isolates | Physicochemical Characters | Quality Assessment Scores | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
No. of AA | Theoretical PI | MW (KDa) | II | AI | GRAVY | 3D-1D Score (%) | ERRAT Quality Factor | QMEAN Z- Score | AA in FR of Ramamchandran Plot (%) | ||
1 | Lactobacillus plantarum | 514 | 6.18 | 58.346 | 26.34 | 77.88 | −0.419 | 83.70 | 84.4898 | −4.01 | 89.7 |
2 | Rhodothermus marinus | 443 | 9.85 | 50.116 | 31.28 | 94.09 | −0.21 | 92.54 | 80.7786 | −4.98 | 83.4 |
3 | Thermus aquaticus | 396 | 9.04 | 44.256 | 40.53 | 88.21 | −0.223 | 87.53 | 85.0575 | −2.59 | 86.8 |
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González-Faune, P.; Sánchez-Arévalo, I.; Sarkar, S.; Majhi, K.; Bandopadhyay, R.; Cabrera-Barjas, G.; Gómez, A.; Banerjee, A. Computational Study on Temperature Driven Structure–Function Relationship of Polysaccharide Producing Bacterial Glycosyl Transferase Enzyme. Polymers 2021, 13, 1771. https://doi.org/10.3390/polym13111771
González-Faune P, Sánchez-Arévalo I, Sarkar S, Majhi K, Bandopadhyay R, Cabrera-Barjas G, Gómez A, Banerjee A. Computational Study on Temperature Driven Structure–Function Relationship of Polysaccharide Producing Bacterial Glycosyl Transferase Enzyme. Polymers. 2021; 13(11):1771. https://doi.org/10.3390/polym13111771
Chicago/Turabian StyleGonzález-Faune, Patricio, Ignacio Sánchez-Arévalo, Shrabana Sarkar, Krishnendu Majhi, Rajib Bandopadhyay, Gustavo Cabrera-Barjas, Aleydis Gómez, and Aparna Banerjee. 2021. "Computational Study on Temperature Driven Structure–Function Relationship of Polysaccharide Producing Bacterial Glycosyl Transferase Enzyme" Polymers 13, no. 11: 1771. https://doi.org/10.3390/polym13111771
APA StyleGonzález-Faune, P., Sánchez-Arévalo, I., Sarkar, S., Majhi, K., Bandopadhyay, R., Cabrera-Barjas, G., Gómez, A., & Banerjee, A. (2021). Computational Study on Temperature Driven Structure–Function Relationship of Polysaccharide Producing Bacterial Glycosyl Transferase Enzyme. Polymers, 13(11), 1771. https://doi.org/10.3390/polym13111771