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Entropy 2016, 18(10), 351; doi:10.3390/e18100351

Influence of the Aqueous Environment on Protein Structure—A Plausible Hypothesis Concerning the Mechanism of Amyloidogenesis

1
Department of Bioinformatics and Telemedicine, Collegium Medium, Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland
2
Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, 30-059 Krakow, Poland
3
Chair of Medical Biochemistry, Collegium Medicum, Jagiellonian University, Kopernika 7, 31-034 Krakow, Poland
*
Author to whom correspondence should be addressed.
Academic Editor: Raúl Alcaraz Martínez
Received: 28 July 2016 / Revised: 13 September 2016 / Accepted: 19 September 2016 / Published: 28 September 2016
(This article belongs to the Section Information Theory)
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Abstract

The aqueous environment is a pervasive factor which, in many ways, determines the protein folding process and consequently the activity of proteins. Proteins are unable to perform their function unless immersed in water (membrane proteins excluded from this statement). Tertiary conformational stabilization is dependent on the presence of internal force fields (nonbonding interactions between atoms), as well as an external force field generated by water. The hitherto the unknown structuralization of water as the aqueous environment may be elucidated by analyzing its effects on protein structure and function. Our study is based on the fuzzy oil drop model—a mechanism which describes the formation of a hydrophobic core and attempts to explain the emergence of amyloid-like fibrils. A set of proteins which vary with respect to their fuzzy oil drop status (including titin, transthyretin and a prion protein) have been selected for in-depth analysis to suggest the plausible mechanism of amyloidogenesis. View Full-Text
Keywords: amyloid; prion; transthyretin; titin; bioinformatics; hydrophobic core; divergence entropy amyloid; prion; transthyretin; titin; bioinformatics; hydrophobic core; divergence entropy
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Roterman, I.; Banach, M.; Kalinowska, B.; Konieczny, L. Influence of the Aqueous Environment on Protein Structure—A Plausible Hypothesis Concerning the Mechanism of Amyloidogenesis. Entropy 2016, 18, 351.

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