Amyloid as a ribbon-like micelle

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Ligation site in proteins recognized in silico

Recognition of a ligation site in a protein molecule is important for identifying its biological activity. The model for in silico recognition of ligation sites in proteins is presented. The idealized hydrophobic core stabilizing protein structure is represented by a three-dimensional Gaussian function. The experimentally observed distribution of hydrophobicity compared with the theoretical distribution reveals differences. The area of high differences indicates the ligation site

Chaperonin Structure – The Large Multi-Subunit Protein Complex

The multi sub-unit protein structure representing the chaperonins group is analyzed with respect to its hydrophobicity distribution. The proteins of this group assist protein folding supported by ATP. The specific axial symmetry GroEL structure (two rings of seven units stacked back to back - 524 aa each) and the GroES (single ring of seven units - 97 aa each) polypeptide chains are analyzed using the hydrophobicity distribution expressed as excess/deficiency all over the molecule to search for structure-to-function relationships. The empirically observed distribution of hydrophobic residues is confronted with the theoretical one representing the idealized hydrophobic core with hydrophilic residues exposure on the surface. The observed discrepancy between these two distributions seems to be aim-oriented, determining the structure-to-function relation. The hydrophobic force field structure generated by the chaperonin capsule is presented. Its possible influence on substrate folding is suggested

The Influence of Proteins Surface on the Ordering of Surrounded Water

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