Summer Research Fellowship Programme of India's Science Academies

Molecular Dynamic Simulation using NAMD

Vemuri. Harika Sai

Department of Biochemistry & Bioinformatics, GITAM Deemed to be University, Visakhapatnam.

Dr. Deva Priyakumar U

CCNSB, International Institute of Information Technology, Hyderabad.


Molecular Dynamics (MD) simulation is a computer simulation technique to study a system by integrating Newton’s laws of motion. Molecular dynamics simulations aid our understanding of biochemical processes and give a dynamic dimension to structural data. The current study involves performing MD simulations on HIV1 Protease (subtype C) mutated and wild-type protease. Protease enzyme is responsible to produce structural proteins and enzymes of the virus. Its active site resembles that of other aspartic proteases and contains the conserved triad, Asp-Thr-Gly, at positions 25–27. MD simulations were subjected to wild type protease and the mutant protein in combination with Nelfinavir, which helped in identifying the dynamic properties and the differences between mutated protein and wild type protein. The obtained results can pave the way to know that protease inhibitors can help in blocking the activity of protease. It can also be assumed that the Protease inhibitors help to reduce the risk of HIV until and unless the virus alters its structure.

Keywords: C-SA PR, E35D↑G↑S, insertion mutations, protease, autocatalysis.

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