A. Breda^1,2, D.S. Santos^2,3, L.A. Basso^2,3 and O. Norberto de Souza^1-4
1Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas, Faculdade de Informática, PUCRS, Porto Alegre, RS, Brasil
²Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, RS, Brasil
³Centro de Pesquisa em Biologia Molecular e Funcional, TECNOPUC, Porto Alegre, RS, Brasil
⁴Programa de Pós-Graduação em Ciência da Computação, PUCRS, Porto Alegre, RS, Brasil
Corresponding author: O. Norberto de Souza
E-mail: osmar.norberto@pucrs.br

Genet. Mol. Res. 6 (4): 901-910 (2007)
Received August 03, 2007
Accepted September 25, 2007
Published October 05, 2007

ABSTRACT. The rate at which knowledge about genomic sequences and their protein products is produced is increasing much faster than the rate of 3-dimensional protein structure determination by experimental methods, such as X-ray diffraction and nuclear magnetic resonance. One of the major challenges in structural bioinformatics is the conversion of genomic sequences into useful information, such as characterization of protein structure and function. Using molecular dynamics (MD) simulations, we predicted the 3-dimensional structure of an artificially designed three-α-helix bundle, called A3, from a fully extended initial conformation, based on its amino acid sequence. The MD protocol enabled us to obtain the secondary, in 1.0 ns, as well as the supersecondary and tertiary structures, in 4.0-10.0 ns, of A3, much faster than previously described for a similar protein system. The structure obtained at the end of the 10.0-ns MD simulation was topologically a three-α-helix bundle.

Key words: Ab initio prediction, Three-α-helix bundle, Molecular dynamics simulations, Protein 3-D structure