Title: Is the protein folding an aim-oriented process? Human haemoglobin as example

Authors: Michal Brylinski, Leszek Konieczny, Irena Roterman

Addresses: Department of Bioinformatics and Telemedicine, Collegium Medicum, Jagiellonian University, Kopernika 17, 31-501 Krakow, Poland; Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland. ' Institute of Medical Biochemistry, Collegium Medicum, Jagiellonian University, Kopernika 7, 31 034 Krakow, Poland. ' Department of Bioinformatics and Telemedicine, Collegium Medicum, Jagiellonian University, Kopernika 17, 31-501 Krakow, Poland; Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland

Abstract: The model for protein folding (in silico) simulation is presented. Three steps have been implemented: early stage folding based on the backbone conformation; hydrophobic collapse based on the fuzzy-oil-drop model; aim-oriented structure modification by the function-related ligand. The model has been verified taking α and β haemoglobin chains as examples to fold them in two different conditions: with and without haem being present in the folding environment. The presence of haem and its participation in the folding simulation led to the structure more similar to the crystal one. It suggests that the haem presence directs the folding process towards the function-related structure.

Keywords: hydrophobic collapse; protein folding; protein structure prediction; active sites; protein–protein complex; ligand binding; human haemoglobin; hydrophobic scale; fuzzy oil-drop model; ligand library; bioinformatics; simulation; haemoglobin chains.

DOI: 10.1504/IJBRA.2007.013605

International Journal of Bioinformatics Research and Applications, 2007 Vol.3 No.2, pp.234 - 260

Published online: 09 May 2007 *

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