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

• Main Authors: Irena Roterman, Mateusz Banach, Barbara Kalinowska, Leszek Konieczny
• Format: Article
• Language: English
• Published: MDPI AG 2016-09-01
• Series: Entropy
• Subjects: amyloid; prion; transthyretin; titin; bioinformatics; hydrophobic core; divergence entropy
• Online Access: http://www.mdpi.com/1099-4300/18/10/351

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.