Abnormal filamentous aggregates formed by tangled tau protein turn out to be classic amyloid fibrils, meeting all criteria defined under the fuzzy oil drop model in the context of amyloid characterization. The model recognizes amyloids as linear structures where local hydrophobicity minima and maxima propagate in an alternating manner along the fibril’s long axis. This distribution of hydrophobicity differs greatly from the classic monocentric hydrophobic core observed in globular proteins. Rather than becoming a globule, the amyloid instead forms a ribbonlike (or cylindrical) structure, which can be thought of as a distorted spherical micelle, which in limit form appears to be the ribbon-like micelle.

The main problem discussed in this paper concerns the importance of the presence of a hydrophobic core in β-sandwich supersecondary structures. The aim of this research is to propose an alternative structural classification of the relationship between sequence and spatial structure. The set of analyzed proteins contains very diverse examples (taking into consideration source organisms, chain length, domain composition, ligand and metal complexation, quaternary structure), allowing for generalization of conclusions. The biological function of the proteins in question is also fundamentally different. The only common feature of these proteins is the presence of a β-sandwich or β-sandwich-like domain. The data base is taken from alternative classification of secondary and supersecordary of sandwich-like domains. The results show that the secondary and supersecondary

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Protein folding remains not satisfactory understood process. Considering the critical importance of water for proteins and other biologically active molecules, analysis of water-protein interactions should play a central role in studies concerning the folding process and biological activity of proteins. Folding simulations should acknowledge the aqueous solvent as an active partner which determines the final conformation of a protein. In the fuzzy oil drop model (which is applied in the presented analysis), the solvent is treated as a continuum-an external force field guiding the folding process. This interaction goes both ways: (1) the solvent shapes the protein and (2) the presence of a natively folded protein also alters the structure of the solvent (the structure of water has not heretofore been sufficiently studied-except for the solid state). This work focuses on this second reverse relationship, that is, the influence of proteins upon the structuralization of water. We formulate a hypothesis which is based on the fuzzy oil drop model. The ordering of the hydrophobic core which resides inside the protein and may include local discordances is analyzed from the point of view of its external effects. In accordance to the fuzzy oil drop model, the solvent is expected to "react" to local differentiation in the properties of the molecular surface. Our hypothesis remains speculative, since experimental studies have not yet yielded sufficient evidence to either prove or disprove it. The presented analysis bases on the assumption that a protein is nothing more than a tool engineered to perform a specific task. Thus, the protein's structure must encode its intended use and the inter-molecular communication system. Our study focuses on antifreeze proteins, which are particularly interesting since their function involves altering the properties of the solvent-specifically, preventing the formation of ice crystals.