Int. J. Mol. Sci. 2011, 12(8), 4850-4860; doi:10.3390/ijms11084850
Article

Intermediates in the Protein Folding Process: A Computational Model

1 Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland 2 Chair of Medical Biochemistry, Medical College, Jagiellonian University, Kopernika 7, 31-034 Krakow, Poland 3 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
(This article belongs to the Special Issue Protein Folding 2011)
PDF Full-text Download PDF Full-Text [648 KB, uploaded 29 July 2011 14:07 CEST]
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

Article Statistics

Load and display the download statistics.

Citations to this Article

Cite This Article

MDPI and ACS Style

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.

AMA Style

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.

Chicago/Turabian Style

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.

Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert