Powered by OpenAIRE graph
Found an issue? Give us feedback
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Bioinformationarrow_drop_down
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
Bioinformation
Article . 2020 . Peer-reviewed
Data sources: Crossref
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
Bioinformation
Article
License: CC BY
Data sources: UnpayWall
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
Bioinformation
Other literature type
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
PubMed Central
Other literature type . 2020
License: CC BY
Data sources: PubMed Central
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
versions View all 5 versions
addClaim

This Research product is the result of merged Research products in OpenAIRE.

You have already added 0 works in your ORCID record related to the merged Research product.

Identification of tunnels as in potato hydrolases

Authors: Banach, Mateusz; Fabian, Piotr; Stapor, Katarzyna; Konieczny, Leszek; Roterman-Konieczna, Irena;

Identification of tunnels as in potato hydrolases

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 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).

Keywords

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, 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, Editorial, which assumes the highest concentration of hydrophobicity in the center of the molecule, the structural conditioning for the course of the reaction provides information on the diversity of the environment, 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)., 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

  • BIP!
    Impact byBIP!
    citations
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    1
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Average
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Average
Powered by OpenAIRE graph
Found an issue? Give us feedback
citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
1
Average
Average
Average
Green
gold