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harry prayoga
universitas lampung
Materials Science & Nanotechnology Physics

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ANALISIS DINAMIKA MOLEKUL PROTEIN LYSOZYME PUTIH TELUR DENGAN MODEL POTENSIAL LENNARD-JONES MENGGUNAKAN APLIKASI GROMACS harry prayoga; Yanti Yulianti; Agus Riyanto
Jurnal Teori dan Aplikasi Fisika Vol 6, No 2 (2018): Jurnal Teori dan Aplikasi Fisika
Publisher : Universitas Lampung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23960/jtaf.v6i2.1849

Abstract

The molecular dynamic analysis oflysozyme protein has been done using Gromacs application. Lysozyme protein filled by water in the cubic form with variation of temperature was 300 K, 325 K, and 350 K and calculatedpotential energy values used Lennard Jones equation. Structure protein on temperature was 300 K showed that pressure value was 2,54 barand density value was 997,54 kg/m3 then protein changed in  unfolded state on ARG21-CA and SER81-CAamino acid chain with potential energy was 2992,14 kJ/mol . Structure protein on temperature was 325 K showed that pressure value was 4,84 barand density value was 974 kg/m3 then protein changed in  unfolded state on ASP101-CA and GLN121-CAamino acid chainwith potential energy was 2994,55 kJ/mol.Structure protein on temperature was 350 K showed that pressure value was 0,82 barand density value was 948,747 kg/m3 then protein changed in  unfolded state on ARG21-CA amino acid chain and lost on GLN121-CA amino acid chainwith potential energy was 2994,55 kJ/mol. Root Mean Standard Deviation (RMSD) showed that the protein will be denaturated on  temperature 350 K caused bylost on GLN121-CA amino acid with distance was0.07 nm.
Co-Authors Agus Riyanto Yanti Yulianti