References
- Abraham, M., Murtola, T., Schulz, R., Páll, S., Smith, J., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
- Antonucci, A., Kupis-Rozmysłowicz, J., & Boghossian, A. (2017). Noncovalent protein and peptide functionalization of single-walled carbon nanotubes for bio-delivery and optical sensing applications. ACS Applied Materials & Interfaces, 9(13), 11321–11331. https://doi.org/10.1021/acsami.7b00810
- Beqa, L., Fan, Z., Singh, A., Senapati, D., & Ray, P. (2011). Gold nano-popcorn attached SWCNT hybrid nanomaterial for targeted diagnosis and photothermal therapy of human breast cancer cells. ACS Applied Materials & Interfaces, 3(9), 3316–3324. https://doi.org/10.1021/am2004366
- Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/10.1063/1.448118
- Bussi, G., Donadio, D., & Parrinello, M. (2007). Canonical sampling through velocity rescaling. Journal of Chemical Physics. 126(1), 014101.
- Byléhn, F., Menéndez, C. A., Perez-Lemus, G. R., Alvarado, W., & de Pablo, J. J. (2021). Modeling the binding mechanism of remdesivir, favilavir, and ribavirin to SARS-CoV-2 RNA-Dependent RNA Polymeras. ACS Central Science, 7(1), 164–174. https://doi.org/10.1021/acscentsci.0c01242
- Calvaresi, M., & Zerbetto, F. (2013). The devil and holy water: Protein and carbon nanotube hybrids. Accounts of Chemical Research, 46(11), 2454–2463. https://doi.org/10.1021/ar300347d
- Chen, M., Zeng, G., Xu, P., Yan, M., Xiong, W., & Zhou, S. (2017). Interaction of carbon nanotubes with microbial enzymes: Conformational transitions and potential toxicity. Environmental Science, 4, 1954–1960.
- Chien, M., Anderson, T., Jockusch, S., Tao, C., Li, X., Kumar, S., Russo, J., Kirchdoerfer, R., & Ju, J. (2020). Nucleotide analogues as inhibitors of SARS-CoV-2 polymerase, a key drug target for COVID-19. Journal of Proteome Research, 19(11), 4690–4697. https://doi.org/10.1021/acs.jproteome.0c00392
- Cui, X., Xu, S., Wang, S., & Chen, C. (2018). The nano-bio interaction and biomedical applications of carbon nanomaterials. Carbon, 138, 436–450. https://doi.org/10.1016/j.carbon.2018.07.069
- Dallakyan, S., & Olson, A. (2016). Small-Molecule library screening by docking with PyRx. methods. Molecular Biology, 1263, 243–250.
- Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
- Delano, W. (2019). The PyMOL Molecular Graphics System. Schrödinger.
- Elfiky, A. (2021). SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: An in silico perspective. Journal of Biomolecular Structure & Dynamics, 39(9), 3204–3212. https://doi.org/10.1080/07391102.2020.1761882
- Gao, Y., Yan, L., Huang, Y., Liu, F., Zhao, Y., Cao, L., Wang, T., Sun, Q., Ming, Z., Zhang, L., Ge, J., Zheng, L., Zhang, Y., Wang, H., Zhu, Y., Zhu, C., Hu, T., Hua, T., Zhang, B., … Rao, Z. (2020). Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science, 368(6492), 779–782. https://doi.org/10.1126/science.abb7498
- Gethard, K., Sae-Khow, O., & Mitra, S. (2011). Water desalination using carbon-nanotube-enhanced membrane distillation. ACS Applied Materials & Interfaces, 3(2), 110–114. https://doi.org/10.1021/am100981s
- Grant, B., Rodrigues, A., Elsawy, K., Mccammon, J., & Caves, L. (2006). Bio3d: An R package for the comparative analysis of protein structures. Bioinformatics, 22(21), 2695–2696. https://doi.org/10.1093/bioinformatics/btl461
- Guex, N., & Peitsch, M. (1997). SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis, 18(15), 2714–2723. https://doi.org/10.1002/elps.1150181505
- Han, D., Guo, Z., Zeng, R., Kim, C., Meng, Y., & Liu, H. (2009). Multiwalled carbon nanotube-supported Pt/Sn and Pt/Sn/PMo12 electrocatalysts for methanol electro-oxidation. International Journal of Hydrogen Energy, 34(5), 2426–2434. https://doi.org/10.1016/j.ijhydene.2008.12.073
- Huang, S., Grinter, S., & Zou, X. (2010). Scoring functions and their evaluation methods for protein − Ligand docking: Recent advances and future directions. Physical Chemistry Chemical Physics: PCCP, 12(40), 12899–12908. https://doi.org/10.1039/c0cp00151a
- Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
- Jang, Y., Moon, J., Lee, C., Lee, S., Kim, H., Song, G., Spinks, G., Wallace, G., & Kim, S. (2022). A coiled carbon canotube yarn-integrated surface electromyography system to monitor isotonic and isometric movements. ACS Applied Materials & Interfaces, 14(40), 45149–45155. https://doi.org/10.1021/acsami.2c11811
- Kim, H., Fábián, B., & Hummer, G. (2023). Neighbor list artifacts in molecular dynamics simulations. ChemRxiv, https://doi.org/10.26434/chemrxiv-2023-zbj6j
- Li, D., Ahmed, M., Khan, A., Xu, L., Walters, A., Ballesteros, B., & Al-Jamal, K. (2021). Tailoring the architecture of cationic polymer brush-modified carbon nanotubes for efficient siRNA delivery in cancer Immunotherapy. ACS Applied Materials & Interfaces, 13(26), 30284–30294. https://doi.org/10.1021/acsami.1c02627
- Li, J. (2022). Gmxtools. Zenodo, 2022, 973. https://doi.org/10.5281/zenodo.6408973.
- Luo, X., Wang, X., Yao, Y., Gao, X., & Zhang, L. (2022). Unveiling the “Template-Dependent” inhibition on the viral transcription of SARS-CoV-2. The Journal of Physical Chemistry Letters, 13(31), 7197–7205. https://doi.org/10.1021/acs.jpclett.2c01314
- Ma, J., Wang, G., Ding, X., Wang, F., Zhu, C., & Rong, Y. (2023). Carbon-Based nanomaterials as drug delivery agents for colorectal cancer: Clinical preface to colorectal cancer citing their markers and existing theranostic approaches. ACS Omega, 8(12), 10656–10668. https://doi.org/10.1021/acsomega.2c06242
- Maier, J., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K., & Simmerling, C. (2015). ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. https://doi.org/10.1021/acs.jctc.5b00255
- Marchesan, S., & Prato, M. (2015). Under the lens: Carbon nanotube and protein interaction at the nanoscale. Chemical Communications, 51(21), 4347–4359. https://doi.org/10.1039/c4cc09173f
- Meher, B., & Wang, Y. (2012). Binding of single walled carbon nanotube to WT and mutant HIV-1 proteases: Analysis of flap dynamics and binding mechanism. Journal of Molecular Graphics & Modelling, 38, 430–445. https://doi.org/10.1016/j.jmgm.2012.10.001
- Nguyen, H., Thai, N., Truong, D., & Li, M. (2020). Remdesivir strongly binds to both RNA-dependent RNA polymerase and main protease of SARS-CoV-2: Evidence from molecular simulations. The Journal of Physical Chemistry. B, 124(50), 11337–11348. https://doi.org/10.1021/acs.jpcb.0c07312
- Nosé, S., & Klein, M. (1983). Constant pressure molecular dynamics for molecular systems. Molecular Physics. 50(5), 1055–1076. https://doi.org/10.1080/00268978300102851
- Padhi, A., Rath, S., & Tripathi, T. (2021). Accelerating COVID-19 research using molecular dynamics simulation. The Journal of Physical Chemistry. B, 125(32), 9078–9091. https://doi.org/10.1021/acs.jpcb.1c04556
- Pettersen, E., Goddard, T., Huang, C., Couch, G., Greenblatt, D., Meng, E., & Ferrin, T. (2004). UCSF Chimera – A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
- Prussia, A., & Chennamadhavuni, S. (2021). Biostructural models for the binding of nucleoside analogs to SARS-CoV-2 RNA-dependent RNA polymerase. Journal of Chemical Information and Modeling, 61(3), 1402–1411. https://doi.org/10.1021/acs.jcim.0c01277
- Sharma, S. (2019). Molecular dynamics simulation of nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs. Elsevier. https://www.sciencedirect.com/science/book/978 0128169544.
- Skjærven, L., Jariwala, S., Yao, X., & Grant, B. (2016). Online interactive analysis of protein structure ensembles with Bio3d-web. Bioinformatics, 32(22), 3510–3512. https://doi.org/10.1093/bioinformatics/btw482
- Sousa Da Silva, A., & Vranken, W. (2012). ACPYPE – AnteChamber PYthon Parser InterfacE. BMC Research Notes, 5, 367.
- Sun, X., Wang, Q., Zhan, J., Yang, T., Zhao, Y., Sun, C., Aisha, M., Guo, M., Tang, S., Zhao, H., Wang, L., & Liu, J. (2023). Superhydrophobic conductive suede fabrics based on carboxylated multiwalled carbon nanotubes and polydopamine for wearable pressure sensors. ACS Applied Nano Materials, 6(12), 10746–10757. https://doi.org/10.1021/acsanm.3c01667
- Tanimoto, S., Itoh, S., & Okumura, H. (2022). State-of-the-Art molecular dynamics simulation studies of RNA-dependent RNA polymerase of SARS-CoV-2. International Journal of Molecular Sciences, 23(18), 10358. https://doi.org/10.3390/ijms231810358
- Tavernelli, I., Cotesta, S., & Iorio, E. (2003). Protein dynamics, thermal stability, and free-energy landscapes: A molecular dynamics investigation. Biophysical Journal, 85(4), 2641–2649. https://doi.org/10.1016/S0006-3495(03)74687-6
- Volder, M., Tawfick, S., Baughman, R., & Hart, A. (2013). Carbon nanotubes: Present and future commercial applications. Science, 339(6119), 535–539. https://doi.org/10.1126/science.1222453
- Wakchaure, P., Ghosh, S., & Ganguly, B. (2020). Revealing the inhibition mechanism of RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 by remdesivir and nucleotide analogues: A molecular dynamics simulation study. The Journal of Physical Chemistry. B, 124(47), 10641–10652. https://doi.org/10.1021/acs.jpcb.0c06747
- Wang, E., Sun, H., Wang, J., Wang, Z., Liu, H., Zhang, John, Z. H., & Hou, T. (2019). End-Point binding free energy calculation with MM/PBSA and MM/GBSA: Strategies and applications in drug design. Chemical Reviews, 119(16), 9478–9508. https://doi.org/10.1021/acs.chemrev.9b00055
- Wang, J., Wolf, R., Caldwell, J., Kollman, P., & Case, D. (2004). Development and testing of a general Amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. https://doi.org/10.1002/jcc.20035
- Wu, E., Coppens, M., & Garde, S. (2015). Role of arginine in mediating protein-carbon nanotube interactions. Langmuir, 31(5), 1683–1692. https://doi.org/10.1021/la5043553
- Xu, Y., Jiang, X., Zhou, Z., Ferguson, T., Obliosca, J., Luo, C., Chan, K., Kong, X., & Tison, C. (2022). Mucosal delivery of HIV-1 glycoprotein vaccine candidate enabled by short carbon nanotubes. Particle and Particle Systems Characterization. 39, 2200011.
- Yang, D., Castellano, R., Silvy, R., Lageshetty, S., Praino, R., Fornasiero, F., & Shan, J. (2023). Fast water transport through subnanometer diameter vertically aligned carbon nanotube membranes. Nano Letters, 23(11), 4956–4964. https://doi.org/10.1021/acs.nanolett.3c00797
- Yu, H., & Dalby, P. (2018). Coupled molecular dynamics mediate long- and short-range epistasis between mutations that affect stability and aggregation kinetics. Proceedings of the National Academy of Sciences of the United States of America, 115(47), E11043–E11052. https://doi.org/10.1073/pnas.1810324115
- Zhang, L., & Zhou, R. (2020). Structural basis of the potential binding mechanism of remdesivir to SARS-CoV-2 RNA-dependent RNA polymerase. The Journal of Physical Chemistry. B, 124(32), 6955–6962. https://doi.org/10.1021/acs.jpcb.0c04198
- Zhang, Z., Wang, B., Wan, B., Yu, L., & Huang, Q. (2013). Molecular dynamics study of carbon nanotube as a potential dual-functional inhibitor of HIV-1 integrase. Biochemical and Biophysical Research Communications, 436(4), 650–654. https://doi.org/10.1016/j.bbrc.2013.06.009