Role of Temperature Variation on the Dynamics of Carbon Nanotube and Protein Interactions

EasyChair Preprint no. 7311

Abstract

3CLN (Calcium Modulated Protein) protein plays important role in the calcium signaling inside the eukaryotic cell structure. Temperature dependent conformation changes in the Calmodulin protein are studied with detailed molecular dynamics simulations by using VMD and NAMD software. The quantitative comparison of the simulation data with analysis probing different aspects of the folding process can facilitate with accuracy of the calculations. It can also provide a detailed structural interpretation for the experimental observations as well as physical interpretation for theoretical concept without actual experimentation. Earlier these kinds of studies also performed experimentally using fluorescence measurements as in. The transition temperature was observed to depend on the calcium ion concentration of the protein. Leap-dynamics approach was used earlier to study the temperature dependent conformation change of Calmodulin. At 310 K, both the N- and C-lobes were stable, at 500 K slightly more deviation than deviation at 310K. In this work, we perform molecular dynamics simulations of 100 ns each for the temperatures 310 K, 500 K, 550K, 600K and at 650K. A remarkable dependence of the temperature is observed on the overall dynamics of protein as reported in our earlier study. A carbon nanotube (CNT) has a cylindrical structure with a nanoscale diameter and appears like a rolled graphene sheet. Interaction between a carbon nanotube and 3CLN (Calmodulin) protein was studied with the help of software VMD and NAMD. This interaction will be helpful in drug delivery. Need of this interaction will give a pathway for further research also it will help to study the role of environmental conditions on a specified protein. As observed by VMD software, that a large deviation seen with 3CLN molecule at high temperature

Keyphrases: 3CLN, CNT, NAMD, protein, VMD

@Booklet{EasyChair:7311,
  author = {Sandeep Kumar and Dwij Mehta and Sunita Negi},
  title = {Role of Temperature Variation on the Dynamics of Carbon Nanotube and Protein Interactions},
  howpublished = {EasyChair Preprint no. 7311},

  year = {EasyChair, 2022}}