Molecular Dynamics and Monte Carlo Method applied to in silico Protein Folding

FQ02

Dal Molin, J.P.¹; Faccioli, R.A. ^1,2; Soares, R.O.S. ¹; Caliri, A¹.

¹Faculdade de Ciências Farmacêuticas de Ribeirão Preto

²Escola de Engenharia de São Carlos

With the aid of computational simulation, it is possible to assess the structures and processes concerning polymers, like their stabilities, folding pathways and techniques of developing de novo molecular designs. Nowadays, among several known biopolymer classes, the proteins are particularly the most studied through in silico modeling. Among numerous available computational methods, basically two of them are widely employed to the task: the molecular dynamics and Monte Carlo. The first one is substantiated in classics Newtonian dynamics, through movement equations. With given initial conditions and the proper force field, it is possible to follow the temporal evolution from all atoms in the system.   The second one, the Monte Carlo Method, is capable to drive this temporal evolution by stochastic means, for that, it hands over resources as random generator of numbers along with the Metropolis criteria. The minimalist models are a useful analytical tool to focus specific aspects of the protein folding problem. These models are based on the application of a methodological reductionism, whose minimizes the number of possible variables of the system. We adopt those approach because it’s produces a model as simple as possible, but not simpler.  Moreover, the minimalist models preserve at last an analogy with particular aspects of original problem. Our model is concerned on the essential physics of the problem and connected with experimental observables for a target protein. The essential ingredients used are: hydrophobic effect and stereo-chemical potential. We employed the Monte Carlo method for simulation of model. Since the founding of the Biological Physics Area within the Pharmaceutical Sciences Graduation Program from the Faculty of Pharmaceutical Sciences of Ribeirão Preto, the in silico study of protein folding is being developed as one of the group's priorities.