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Intermediates in the Protein Folding Process: A Computational Model
Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland
Chair of Medical Biochemistry, Medical College, Jagiellonian University, Kopernika 7, 31-034 Krakow, Poland
Faculty of Physics, Astronomy, Applied Computer Science, Jagiellonian University, Reymonta 4, 30-059 Krakow, Poland
* Author to whom correspondence should be addressed.
Received: 7 April 2011; in revised form: 7 June 2011 / Accepted: 25 July 2011 / Published: 29 July 2011
Abstract: The paper presents a model for simulating the protein folding process in silico. The two-step model (which consists of the early stage—ES and the late stage—LS) is verified using two proteins, one of which is treated (according to experimental observations) as the early stage and the second as an example of the LS step. The early stage is based solely on backbone structural preferences, while the LS model takes into account the water environment, treated as an external hydrophobic force field and represented by a 3D Gauss function. The characteristics of 1ZTR (the ES intermediate, as compared with 1ENH, which is the LS intermediate) confirm the link between the gradual disappearance of ES characteristics in LS structural forms and the simultaneous emergence of LS properties in the 1ENH protein. Positive verification of ES and LS characteristics in these two proteins (1ZTR and 1ENH respectively) suggest potential applicability of the presented model to in silico protein folding simulations.
Keywords: protein structure; hydrophobicity; divergence entropy; intermediates in protein folding
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Roterman, I.; Konieczny, L.; Banach, M.; Jurkowski, W. Intermediates in the Protein Folding Process: A Computational Model. Int. J. Mol. Sci. 2011, 12, 4850-4860.
Roterman I, Konieczny L, Banach M, Jurkowski W. Intermediates in the Protein Folding Process: A Computational Model. International Journal of Molecular Sciences. 2011; 12(8):4850-4860.
Roterman, Irena; Konieczny, Leszek; Banach, Mateusz; Jurkowski, Wiktor. 2011. "Intermediates in the Protein Folding Process: A Computational Model." Int. J. Mol. Sci. 12, no. 8: 4850-4860.