In-silico Analysis and Molecular Dynamics Simulations of Lysozyme by GROMACS 2020.2

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Anil Panwar, Ashok Kumar


Since last few years, number of publicationsdescribing accurate and reliable all-atom molecular dynamics simulations got significantly hiked. Availability of faster computers, development of high precision and fast methods for calculating the long-range electrostatic interactions made it possible. With the advances in hardware and software, it has been demonstrated that molecular dynamics simulation is not only capable of mimicking the behavior of macro molecules, but also can also be used for bio molecular structure prediction and drug discovery.Proteins are highly dynamic structures and their dynamism contributes toward ligand binding properties.In-vivo analysis of protein dynamism is very complex, expensive and tedious task. Therefore scientific community has lots of hope with in-silio methods. Present study uses MD simulations to explore relation between Sequence conservation and dynamism of amino acids of Lysozyme. Three Dimensional Structures of Five Lysozyme were downloaded from RCSB PDB. Amino Acid Sequences of download PDB structures were aligned using CLUSTAL O. Newton’s equation of motion was solved by considering all atoms simulation method. GROMACS 2020.2 package was used to perform MD simulations and all atom OPLS force field was used. GROMACS module Pdb2gmx was used to generate the topology of protein. Simple point charge water model [SPC216] was used to solvate the protein. Protein was solvated to maintain the equilibrium. The equilibrated system was then minimized at maximum force of 1000.0 KJ/mol/nm by using 50,000 steps. The solvated and energy minimized systems were than equilibrated for 100ps under NVT and NPT ensemble processes. All the bonds were constrained by LINCS algorithm. Finally 1ns molecular dynamics simulation was run to observe the stability of proteins. The Root Mean Standard Fluctuation was calculated and their 2D graphs were than plotted with xmgrance software. Comparative Root Mean Square Fluctuation (RMSF) values were found to be least for the segment whichis largest reserve segment in the sequences under course of study. RMSF for Lysozyme class shows a reciprocal relation with sequence conservation length.

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Anil Panwar, Ashok Kumar. (2021). In-silico Analysis and Molecular Dynamics Simulations of Lysozyme by GROMACS 2020.2. Annals of the Romanian Society for Cell Biology, 25(6), 9679–9685. Retrieved from