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Identification of tunnel as in potato hydrolase



1Mateusz Banach, 2Fabian Piotr, 2Stapor Katarzyna, 3Konieczny Leszek, 1,*Irena Roterman



1Department of bioinformatics and Telemedicine, Jagiellonian University - Medical College, Lazarza 16, 31-530 Krakow, Poland; 2SilesianTechnical University, Institute of Computer Science, 44-100 Gliwice, Akademicka 16 Poland; 3Chair of Medical Biochemistry, Jagiellonian University - Medical College 31-034 Kraków Kopernika 7, Poland



Irena Roterman – E-mail: myroterm@cyf-kr.edu.pl; *Corresponding author.


Article Type




Received January 2, 2020; Accepted January 7, 2020; Published January 15, 2020



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 force field, which creates favorable conditions for carrying out the catalytic process. The use of fuzzy oil drop model has been verified using the potato (solanum tuberosum) epoxide hydrolase I. This forms the preliminary basis for testing the fuzzy oil drop model. The data presented here provides an impetus for a large scale analysis of all proteins containing tunnels in enzyme structures available in the Protein Data Bank (PDB).



hydrophobicity, tunnels in proteins, submerged active center



Banach et al. Bioinformation 16(1): 21-25 (2020)


Edited by

P Kangueane






Biomedical Informatics



This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.