Molecular Dynamics Simulations to Study the Role of Temperature on Carbon Nanotube and Protein Interactions

Sandeep Kumar; Dwij Mehta; Sunita Negi

doi:10.17485/IJST/v16i28.607

Article

Molecular Dynamics Simulations to Study the Role of Temperature on Carbon Nanotube and Protein Interactions

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Indian Journal of Science and Technology

DOI: 10.17485/IJST/v16i28.607

Year: 2023, Volume: 16, Issue: 28, Pages: 2153-2159

Original Article

Molecular Dynamics Simulations to Study the Role of Temperature on Carbon Nanotube and Protein Interactions

Sandeep Kumar¹, Dwij Mehta², Sunita Negi^1*

¹School of Engineering and Sciences, G. D Goenka University, Sohna, Gurugram, Haryana, India
²P.D. Patel Institute of Applied Sciences, Charusat University, Changa, Anand, Gujrat, India

*Corresponding Author
Email: [email protected]

Received Date:11 April 2023, Accepted Date:26 June 2023, Published Date:26 July 2023

This work is licensed under a Creative Commons Attribution 4.0 International License.

Abstract

Background/Objectives: Almost all chemical reactions within our bodies are catalysed by proteins. The calcium signalling inside the eukaryotic cell structure is significantly influenced by the calcium modulated protein (3CLN). On the other hand, carbon nanotubes are an excellent choice for the aim of targeted drug delivery. Therefore, it is crucial to research how these two elements interact. Methods: In this work, we perform extensive molecular dynamics (MD) simulations of 100 ns each to study the interaction of 3CLN protein with a carbon nanotube (CNT) at 320 K, 420 K, 520 K, 590 K, and 660 K temperature ranges. The conformational changes in the calmodulin protein are studied with MD simulations at different temperature ranges using open-source software, VMD and NAMD. Findings: A significant dependence of the temperature is observed on the overall conformation change of the protein around the carbon nanotube. The quantitative comparison of the simulation data with complete studies shows the different aspects of the folding process. It can also give detailed structural results for the experimental observations as well as physical results for theoretical concepts without actual experimentation. Novelty: The protein is seen to form a stable corona structure around the CNT at a temperature of 520 K, as previously reported by the other researchers. While this stability is lost at higher temperatures. This interaction study can be used to investigate the impact of environmental factors on the dynamics of a particular protein in conjunction with a nanomaterial. It will open up new avenues for future research.

Keywords: Carbon Nanotube; Calmodulin Protein; Eukaryotic Cell; NanoMolecular Dynamics (NAMD); Simulation; Visual Molecular Dynamics (VMD)

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© 2023 Kumar et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Published By Indian Society for Education and Environment (iSee)