Identification of tunnels as in potato hydrolases.

Identification of tunnels as in potato hydrolases. Bioinformation. 2020;16(1):21-25 Authors: Banach M, Piotr F, Katarzyna S, Leszek K, Roterman I Abstract Enzymes with an active center hidden in the middle of the molecule in a tunnel-like cavity constitute an interesting object of analysis due to the highly specialized environment for the course of the catalytic reaction. Identifying the tunnel is a challenge in itself. Moreover, the structural conditioning for the course of the reaction provides information on the diversity of the environment, which must necessarily meet the conditions of high specificity. The use of a fuzzy oil drop model to identify residues constituting the walls of the tunnel located in the center of the protein seems highly justified. The fuzzy oil drop model, which assumes the highest concentration of hydrophobicity in the center of the molecule, in these enzymes shows a significant hydrophobicity deficit resulting from the absence of any residues in the central part of the molecule. Comparison of the expected distribution in consistent with the 3D Gaussian distribution where the observed distribution resulting from the interaction of residues in the protein shows significant differences precisely in the positions of residues located near the center of the molecule. The inside characteristics of the tunnel are the background for the enzymatic reaction. This environment additionally constitutes an external forc...
Source: Bioinformation - Category: Bioinformatics Authors: Tags: Bioinformation Source Type: research