Study of the diffusion coefficient in protein folding

• Grant number: 07/04647-8
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: November 01, 2007
• End date: July 31, 2011
• Field of knowledge: Biological Sciences - Biophysics - Molecular Biophysics
• Principal Investigator: Vitor Barbanti Pereira Leite
• Grantee: Ronaldo Júnio de Oliveira
• Host Institution: Instituto de Biociências, Letras e Ciências Exatas (IBILCE). Universidade Estadual Paulista (UNESP). Campus de São José do Rio Preto. São José do Rio Preto , SP, Brazil

Abstract

The development of models and theoretical/computational ideas that predict the protein native structure from its primary sequence has been one of the motivations for folding experimental studies. The folding process is, in general, mapped through an equation of diffusion applied throughout the coordinate of reaction Q, that describes the degree of similarity of a determined configuration with the protein native state. The folding times can be calculated from effective potentials and of the diffusion coefficient D. In literature, D is assumed constant during this process. Using lattice model, we calculated, in the master degree work, the diffusion coefficient of one heteropolymer in function of Q getting folding times more precisely than in literature. In this project, we intend to study the diffusion coefficient in function of Q and Z, this last one is the number of total contacts present in a determined conformation. With this approach, we will also study the influence of the hydrophobicity degree and temperature in folding. We intend to get more detail insight on the folding as a diffusive process. We will use a lattice model for the computational simulations and the diffusion calculations. Also, improving the level of resolution of simulation, we will use the C-alpha model in which we will compare the obtained results by Go model simulations with the experimental results described in literature. The use of these models, although minimalist and reasonable level of resolution, will allow to study the folding of small globular proteins aiming to better understand its complex mechanism that takes them to its native and functional structure. (AU)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

OLIVEIRA, Ronaldo Júnio de. Estudo do coeficiente de difusão no enovelamento de proteína. 2011. Doctoral Thesis - Universidade Estadual Paulista (Unesp). Instituto de Biociências Letras e Ciências Exatas. São José do Rio Preto São José do Rio Preto.