Computational Modeling of the Staphylococcal Enterotoxins and Their Interaction with Natural Antitoxin Compounds
Abstract
:1. Introduction
2. Results and Discussion
2.1. Homology Modeling of SEA and SEB-Like Proteins
2.2. Homology Modeling of the 3-D Structures
2.3. Validation of the 3-D Structures
2.3.1. Molecular Dynamics Studies
2.3.2. Ramachandran Plot Analysis
2.3.3. Analysis of the SEA and SEB-Like 3-D Structures
2.4. Docking Study
3. Materials and Methods
3.1. Source of Data
3.2. Generation of the 3-D Structure Using Homology Modeling
3.3. Molecular Dynamics
3.4. Binding Site Identification
3.5. Substrate Docking
4. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
Abbreviations
3-D | Three-Dimensional |
atm | Atmospheric Pressure |
CASTp | Computer Atlas of Surface Topology of Proteins |
CHARMM | Chemistry at Harvard Macromolecular Mechanics |
FRED | Fast Rigid Exhaustive Docking |
K | Kelvin |
MS | Molecular Surface |
NAMD | NAnoscale Molecular Dynamics |
NCBI | National Center for Biotechnology Information |
PDB | Protein Data Bank |
PDFs | Probability Functions |
ps and fs | Pico- and Femtoseconds |
RCSB | Research Collaboratory for Structural Bioinformatics |
RMSD | Root-Mean-Square Deviation |
SEA | Staphylococcal Enterotoxin A |
SEB | Staphylococcal Enterotoxin B |
SEs | Staphylococcal Enterotoxins |
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Compound Name | PubChem CID | Molecular Formula | Molecular Weight (g/mol) | Compound Structure | Staphylococcal Enterotoxin (SE) in Interaction | Free Energy (kcal/mol) |
---|---|---|---|---|---|---|
Betulin | 72326 | C30H50O2 | 442.728 | | SEA | −147.39 |
SEB-like | −139.97 | |||||
28-Norolean-12-en-3-one | 101616676 | C29H46O | 410.686 | | SEA | −83.97 |
SEB-like | −88.20 |
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Kurjogi, M.; Satapute, P.; Jogaiah, S.; Abdelrahman, M.; Daddam, J.R.; Ramu, V.; Tran, L.-S.P. Computational Modeling of the Staphylococcal Enterotoxins and Their Interaction with Natural Antitoxin Compounds. Int. J. Mol. Sci. 2018, 19, 133. https://doi.org/10.3390/ijms19010133
Kurjogi M, Satapute P, Jogaiah S, Abdelrahman M, Daddam JR, Ramu V, Tran L-SP. Computational Modeling of the Staphylococcal Enterotoxins and Their Interaction with Natural Antitoxin Compounds. International Journal of Molecular Sciences. 2018; 19(1):133. https://doi.org/10.3390/ijms19010133
Chicago/Turabian StyleKurjogi, Mahantesh, Praveen Satapute, Sudisha Jogaiah, Mostafa Abdelrahman, Jayasimha Rayalu Daddam, Venkatesh Ramu, and Lam-Son Phan Tran. 2018. "Computational Modeling of the Staphylococcal Enterotoxins and Their Interaction with Natural Antitoxin Compounds" International Journal of Molecular Sciences 19, no. 1: 133. https://doi.org/10.3390/ijms19010133