The Effect of Monte Carlo, Molecular Dynamic and Langevin Dynamic

Journal of Cell and Molecular Research

Article 5, Volume 2, Issue 2 - Serial Number 4, January 0, Pages 93-102   

DOI: 10.22067/jcmr.v2i2.10764

Authors

Reihaneh Sabbaghzadeh^* ; Majid Monajjemi; Fatemeh Mollaamin; Shahrbano Oryan

Abstract

Insulin-like growth factor (IGF-1) is an anti-apoptosis factor in multiple cell types associated with various
cancers. Computational methods allow investigating the systems between 50–100 atoms in the frame of
quantum mechanics and up to 50,000 atoms with molecular dynamics. Since there are specific interactions
between the residues, the solvent could play an important role in the stability of the native structure. Therefore
it is useful to carry out such simulations at atomistic detail. MC, MD and LD simulations of the IGF-1 were
performed with the HyperChem7.0 program. The geometries, and the interaction energies, bonds, angles,
stretch-bends, electrostatic and the VDW Interactions were carried out in solution and gas phase. We have
computed the transition temperature for the IGF-1 molecule. Studying the changes occurred in the potential
energy of the three force fields showed that Amber force field is better than MM+ and OPLS force field and
also MD simulation, at least in this model, is more effective than MC and LD methods. After equilibration, the
MD simulation was very stable, and the difference between the relation coefficients R2=0.8173 in gas and
R2=0.7558 in water was compared. The Pearson correlation suggests that there is an inverse relationship (R=-
0.25) between in vitro temperature and stability of the IGF-1,

Keywords

AMBER; MM+; OPLS; MC; MD; LD