Structural Biology

Biography

Biography: Christophe Guyeux

Abstract

In our first theoretical studies about folded self-avoiding walks, we have raised raises several questions regarding the protein structure prediction problem and the current ways to solve it. In one category of PSP software, the protein is supposed to be synthesized first as a straight line of amino acids, and then this line of a.a. is folded out until reaching a conformation that optimizes a given scoring function. The second category consider that, as the protein is already in the aqueous solvent, it does not wait the end of the synthesis to take its 3D conformation. So they consider SAWs whose number of steps increases until the number of amino acids of the targeted protein and, at each step, the current walk is stretched (one amino acid is added to the protein) in such a way that the pivot k  placed in the position that optimizes the scoring function. We have proven that the two sets of possible conformations are different. So these two kinds of PSP software cannot predict the same kind of conformations.

We have proven too that the folding process G in the 2D model is chaotic according to Devaney. A consequence of this theorem is that this process is highly sensitive to its initial condition. If the 2D model can accurately describe the natural process, then this theorem implies that even a minute difference on an intermediate conformation of the protein, in forces that act in the folding process, or in the position of an atom, can lead to enormous differences in its final conformation. In particular, it seems very difficult to predict, in this 2D model, the structure of a given protein by using the knowledge of the structure of similar proteins. Let us remark that the whole 3D folding process with real torsion angles is obviously more complex. And finally, that chaos refers to our incapacity to make good prediction, it does not mean that the biological process is a random one.

References:

1. Christophe Guyeux, Nicod J M, Philippe L, and Bahi J (2015) The study of unfoldable self-avoiding walks: Application to protein structure prediction software. Journal of Bioinformatics and Computational Biology 13(4): 1550009.

2. Christophe Guyeux, Côté N-L, Bienia W and Bahi J (2013) Is protein folding problem really a NP-complete one? First investigations. Journal of Bioinformatics and Computational Biology 12(1): 24.

3. Christophe Guyeux, Bahi J, Mazouzi K, and Philippe L (2013) Computational investigations of folded self-avoiding walks related to protein folding. Computational Biology and Chemistry 47: 246-256.

4. Christophe Guyeux, Bahi J, Côté N and Salomon M (2012) Protein folding in the 2D hydrophobic-hydrophilic (HP) square lattice model is chaotic. Cognitive Computation 4(1): 98-114.