BION-2: Predicting Positions of Non-Specifically Bound Ions on Protein Surface by a Gaussian-Based Treatment of Electrostatics
Abstract
:1. Introduction
2. Results and Discussion
2.1. The Visual Example Section Outlines Two Cases
2.2. Benchmarking of BION-2 Performance
2.2.1. BION-2 vs. VMD
2.2.2. BION-2 vs. FoldX
2.2.3. Computational Efficiency
2.2.4. BION-2 Webserver
3. Materials and Methods
3.1. Database of Protein Structures
3.2. Ions’ Treatment in the Framework of Gaussian-Based Smooth Dielectric Function
3.3. Electrostatic Potential Map Calculations
3.4. Algorithm for Predicting Ion’s Position
3.5. Using VMD to Place Ions
3.6. Using FoldX to Predict Ions’ Positions
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
BION | bound ion prediction method |
Zeta | Zeta potential |
PDB | Protein data bank |
DelPhi | Poisson–Boltzmann solver |
VMD | visual molecular dynamics |
PBE | Poisson–Boltzmann equation |
vdW | van der Waals |
PQR | position, charge, radius format |
NMR | nucleic magnetic resonance |
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PDB | FoldX(s) | BION-2 (s) | No. of Residues | Ion Type |
---|---|---|---|---|
1L9A | 5.0 | 3.0 | 87 | Mg+2 |
1QGW | 33.0 | 9.0 | 176 | Mg+2 |
1E2D | 23.0 | 6.0 | 215 | Mg+2 |
1NG1 | 19.0 | 14.0 | 294 | Mg+2 |
1LR0 | 9.0 | 6.7 | 125 | Zn+2 |
2CEI | 27.7 | 9.3 | 183 | Zn+2 |
2AS9 | 72.7 | 12.0 | 210 | Zn+2 |
1ET5 | 54.0 | 16.0 | 341 | Zn+2 |
1TY3 | 22.0 | 14.0 | 357 | Zn+2 |
3HK5 | 205.0 | 65.0 | 427 | Zn+2 |
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Shashikala, H.B.M.; Chakravorty, A.; Panday, S.K.; Alexov, E. BION-2: Predicting Positions of Non-Specifically Bound Ions on Protein Surface by a Gaussian-Based Treatment of Electrostatics. Int. J. Mol. Sci. 2021, 22, 272. https://doi.org/10.3390/ijms22010272
Shashikala HBM, Chakravorty A, Panday SK, Alexov E. BION-2: Predicting Positions of Non-Specifically Bound Ions on Protein Surface by a Gaussian-Based Treatment of Electrostatics. International Journal of Molecular Sciences. 2021; 22(1):272. https://doi.org/10.3390/ijms22010272
Chicago/Turabian StyleShashikala, H. B. Mihiri, Arghya Chakravorty, Shailesh Kumar Panday, and Emil Alexov. 2021. "BION-2: Predicting Positions of Non-Specifically Bound Ions on Protein Surface by a Gaussian-Based Treatment of Electrostatics" International Journal of Molecular Sciences 22, no. 1: 272. https://doi.org/10.3390/ijms22010272