Computational SNP Analysis and Molecular Simulation Revealed the Most Deleterious Missense Variants in the NBD1 Domain of Human ABCA1 Transporter
Abstract
:1. Introduction
2. Results
2.1. Dataset Selection and Screening
2.2. Identification of Most Deleterious nsSNPs
2.3. Evolutionary Conservancy
2.4. Molecular Dynamics (MD) Simulation
2.4.1. Effects of Variants on Conformational Dynamics
2.4.2. Effects of Variants on Protein Dynamics
2.4.3. Effect of Variants on Intra-Protein Communication
2.4.4. Effect of Variants in Protein Secondary Structure Elements
2.4.5. Free Energy Landscapes (FELs)
3. Discussion
4. Materials and Methods
4.1. Data Retrieval and In Silico Deleterious nsSNP Prediction
4.2. Conservation Analysis
4.3. Molecular Dynamic Simulation
4.3.1. Preparation of Simulation System
4.3.2. Dynamic Cross-Correlation Map (DCCM) and Principle Component Analysis (PCA)
4.3.3. Dynamic Residue Network Analysis
4.3.4. Free Energy Landscape (FEL) Analysis
4.4. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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rs ID | Substitution | SIFT | PolyPhen 2 | MAPP | PANTHER | SNP & Go | PhD-SNP | PredictSNP | PROVEAN | I-Mutant 3 | |
---|---|---|---|---|---|---|---|---|---|---|---|
HumDiv | HumVar | ||||||||||
rs762112742 | S741C | 0.05 * | 1 * | 0.996 * | - | 0.663 * | 0.761 * | 0.803 * | D * | −4.265 * | −1.01 * |
rs1461682152 | Y793C | 0.05 * | 0.994 * | 0.964 * | - | 0.654 * | - | 0.607 * | D * | −6.46 * | −0.86 * |
rs985622413 | G1050V | 0 * | 1 * | 0.999 * | - | 0.568 * | - | 0.733 * | D * | −6.192 * | −0.58 * |
rs1394779021 | S1067C | 0 * | 0.999 * | 0.954 * | - | 0.671 * | - | 0.858 * | D * | −3.494 * | −0.58 * |
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Dash, R.; Ali, M.C.; Rana, M.L.; Munni, Y.A.; Barua, L.; Jahan, I.; Haque, M.F.; Hannan, M.A.; Moon, I.S. Computational SNP Analysis and Molecular Simulation Revealed the Most Deleterious Missense Variants in the NBD1 Domain of Human ABCA1 Transporter. Int. J. Mol. Sci. 2020, 21, 7606. https://doi.org/10.3390/ijms21207606
Dash R, Ali MC, Rana ML, Munni YA, Barua L, Jahan I, Haque MF, Hannan MA, Moon IS. Computational SNP Analysis and Molecular Simulation Revealed the Most Deleterious Missense Variants in the NBD1 Domain of Human ABCA1 Transporter. International Journal of Molecular Sciences. 2020; 21(20):7606. https://doi.org/10.3390/ijms21207606
Chicago/Turabian StyleDash, Raju, Md. Chayan Ali, Md. Liton Rana, Yeasmin Akter Munni, Largess Barua, Israt Jahan, Mst. Fatema Haque, Md. Abdul Hannan, and Il Soo Moon. 2020. "Computational SNP Analysis and Molecular Simulation Revealed the Most Deleterious Missense Variants in the NBD1 Domain of Human ABCA1 Transporter" International Journal of Molecular Sciences 21, no. 20: 7606. https://doi.org/10.3390/ijms21207606