Predicting the Assembly of the Transmembrane Domains of Viral Channel Forming Proteins and Peptide Drug Screening Using a Docking Approach
Abstract
:1. Introduction
2. Materials and Methods
2.1. Secondary Structure Prediction Programs
2.2. Prediction of Ion Channel Assembly (PICA), Assembly and Docking
2.3. MD Simulations
2.4. Data Analysis
2.5. Hardware Software
3. Results
3.1. Handedness
3.2. Docking
4. Discussion
4.1. Consideration on the Set-Up of the System
4.2. Handedness
4.3. Ligand Docking
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Acknowledgments
Conflicts of Interest
References
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Oligomer | AA | CG | AA-MD | |
---|---|---|---|---|
M2 | 4i | 1 * (1.29, L) [12.20] | 19 * (1.22, L) [6.36] | 4 * (1.66, L) [34.82] |
4e (L) [37.73 ± 0.24] | 1 * (0.42, L) [10.04] | 43 * (0.64, L) [13.29] | 20 * (1.56, L) [22.76] | |
E | 5p | 53 * (0.45, R) [32.24] | 9 * (0.83, R) [53.51] | 51 * (1.87, R) [40.68] |
5e (R) [21.69 ± 8.05] | 12 * (2.67, R) [24.31] | 45 * (2.33, R) [21.63] | - | |
6Kp | 6 | 1 | 59 | 1 |
SHp | 5 | 1 | 1 | 15 |
SHe | 5 | 1 | 1 | 1 |
Vpu32 | 4 | 7 | 2 | 244 |
5 | 3 | 1 | 145 | |
6 | 3 | 1 | 24 | |
Vpu28 | 4 | 14 | 1 | 67 |
5 | 14 | 1 | 4 | |
6 | 15 | 2 | 15 | |
Vpue | 4 | 6 | 1 | 41 |
5 | 19 | 1 | 2 | |
6 | 8 | 3 | 1 | |
Vpup | 4 | 1 | 2 | 5 |
5 | 2 | 16 | 12 | |
6 | 2 | 1 | 2 |
M2 | |||||
---|---|---|---|---|---|
Crystal Structure (L) [37.73 ± 0.24] | |||||
Rank 1 | Rank 2 | Rank 3 | Rank 4 | Rank 5 | |
PICA (M2e) | (1.29, L) [12.20] | (1.28, L) [12.11] | (1.30, L) [12.30] | (1.30, -) [3.99] | (1.35, -) [5.19] |
CF | (1.34, L) [30.87 ± 11.76] | (1.33, L) [24.32 ± 0.06] | (0.41, L) [30.53 ± 1.68] | (0.34, L) [27.49 ± 1.04] | (1.61, -) [88.83 ± 51.20] |
GH | (0.40, L) [28.15 ± 0.30] | (0.32, L) [33.68 ± 13.72] | (0.88, R) [5.52 ± 2.11] | (0.60, L) [26.69 ± 2.89] | (1.11, R) [27.42 ± 3.55] |
E | |||||
Crystal structure (R) [21.69 ± 8.05] | |||||
PICA (Ee) | (0.98, R) [48.10] | (1.22, L) [43.51] | (1.26, R) [54.51] | (1.29, L) [47.94] | (1.62, L) [54.16] |
Rank 53 (0.45, R) [32.24] | |||||
CF | (1.51, L) [1.07 ± 0.36] | (1.49, R) [3.02 ± 0.48] | (1.38, L) [7.29 ± 0.32] | (1.50, R) [7.48 ± 3.72] | (1.62, R) [23.68 ± 7.25] |
GH | (1. 14, L) [30.47 ± 1.44] | (1.11, L) [25.84 ± 5.63] | (1.56, R) [24.27 ± 1.55] | (0.72, R) [11.60 ± 2.53] | (0.62, R) [19.71 ± 0.86] |
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Huang, T.-C.; Fischer, W.B. Predicting the Assembly of the Transmembrane Domains of Viral Channel Forming Proteins and Peptide Drug Screening Using a Docking Approach. Biomolecules 2022, 12, 1844. https://doi.org/10.3390/biom12121844
Huang T-C, Fischer WB. Predicting the Assembly of the Transmembrane Domains of Viral Channel Forming Proteins and Peptide Drug Screening Using a Docking Approach. Biomolecules. 2022; 12(12):1844. https://doi.org/10.3390/biom12121844
Chicago/Turabian StyleHuang, Ta-Chou, and Wolfgang B. Fischer. 2022. "Predicting the Assembly of the Transmembrane Domains of Viral Channel Forming Proteins and Peptide Drug Screening Using a Docking Approach" Biomolecules 12, no. 12: 1844. https://doi.org/10.3390/biom12121844
APA StyleHuang, T.-C., & Fischer, W. B. (2022). Predicting the Assembly of the Transmembrane Domains of Viral Channel Forming Proteins and Peptide Drug Screening Using a Docking Approach. Biomolecules, 12(12), 1844. https://doi.org/10.3390/biom12121844