"Protein Folding – Quantification of Protein Complexity, Robustness and Amino Acid Participation"

Abstract

The QCT (Quantitative Complexity Theory) algorithm has been applied to the analysis of the folding process of a protein composed of 435 atoms, monitoring its complexity at each step thereof. The folding has been simulated using Molecular Dynamics Simulation. The analysis has revealed that, while in the native state, the protein's configuration minimizes its energy, its complexity reaches a maximum. This result is interesting in that, according to the QCT, complexity is information that is encoded in structure. It is conjectured that the native state of a protein is a minimum energy-maximum information state. Moreover, QCT allows us to determine the footprint of each constituent amino acid in the dynamics, information content and robustness of a protein's structure. The application of QCT on proteins generates data and information about structure, complexity, special arrangements, etc., of proteins. The knowledge about the biological functions of such proteins derived from the above -which is crucial e.g., for designing new drugs -will have to be generated in collaboration with specialists from pharmaceutical R&D.