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Title:Self-organization of enzyme-catalyzed reactions studied by the maximum entropy production principle
Authors:ID Dobovišek, Andrej (Author)
ID Vitas, Marko (Author)
ID Blaževič, Tina (Author)
ID Markovič, Rene (Author)
ID Marhl, Marko (Author)
ID Fajmut, Aleš (Author)
Files:.pdf RAZ_Dobovisek_Andrej_2023.pdf (2,57 MB)
MD5: DCACFD4480BE2894159EFF2B0C3B8E19
 
URL https://www.mdpi.com/1422-0067/24/10/8734
 
Language:English
Work type:Article
Typology:1.01 - Original Scientific Article
Organization:FNM - Faculty of Natural Sciences and Mathematics
MF - Faculty of Medicine
PEF - Faculty of Education
FZV - Faculty of Health Sciences
Abstract:The self-organization of open reaction systems is closely related to specific mechanisms that allow the export of internally generated entropy from systems to their environment. According to the second law of thermodynamics, systems with effective entropy export to the environment are better internally organized. Therefore, they are in thermodynamic states with low entropy. In this context, we study how self-organization in enzymatic reactions depends on their kinetic reaction mechanisms. Enzymatic reactions in an open system are considered to operate in a non-equilibrium steady state, which is achieved by satisfying the principle of maximum entropy production (MEPP). The latter is a general theoretical framework for our theoretical analysis. Detailed theoretical studies and comparisons of the linear irreversible kinetic schemes of an enzyme reaction in two and three states are performed. In both cases, in the optimal and statistically most probable thermodynamic steady state, a diffusion-limited flux is predicted by MEPP. Several thermodynamic quantities and enzymatic kinetic parameters, such as the entropy production rate, the Shannon information entropy, reaction stability, sensitivity, and specificity constants, are predicted. Our results show that the optimal enzyme performance may strongly depend on the number of reaction steps when linear reaction mechanisms are considered. Simple reaction mechanisms with a smaller number of intermediate reaction steps could be better organized internally and could allow fast and stable catalysis. These could be features of the evolutionary mechanisms of highly specialized enzymes.
Keywords:enzymes, kinetic data analysis, steady state, self-organization, maximum entropy production
Publication status:Published
Publication version:Version of Record
Submitted for review:31.03.2023
Article acceptance date:12.05.2023
Publication date:13.05.2023
Year of publishing:2023
Number of pages:21 str.
Numbering:Vol. 24, iss. 10
PID:20.500.12556/DKUM-88180 New window
UDC:536.75
ISSN on article:1422-0067
COBISS.SI-ID:152729603 New window
DOI:10.3390/ijms24108734 New window
Publication date in DKUM:08.05.2024
Views:234
Downloads:11
Metadata:XML DC-XML DC-RDF
Categories:Misc.
:
DOBOVIŠEK, Andrej, VITAS, Marko, BLAŽEVIČ, Tina, MARKOVIČ, Rene, MARHL, Marko and FAJMUT, Aleš, 2023, Self-organization of enzyme-catalyzed reactions studied by the maximum entropy production principle. International journal of molecular sciences [online]. 2023. Vol. 24, no. 10. [Accessed 27 April 2025]. DOI 10.3390/ijms24108734. Retrieved from: https://dk.um.si/IzpisGradiva.php?lang=eng&id=88180
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Record is a part of a journal

Title:International journal of molecular sciences
Shortened title:Int. j. mol. sci.
Publisher:MDPI
ISSN:1422-0067
COBISS.SI-ID:2779162 New window

Document is financed by a project

Funder:ARIS - Slovenian Research and Innovation Agency
Project number:P1-0055-2022
Name:Biofizika polimerov, membran, gelov, koloidov in celic
Funder:ARIS - Slovenian Research and Innovation Agency
Project number:J3-3077-2021
Name:Analiza kolektivne celične aktivnosti v normalnih in diabetičnih pankreatičnih otočkih s principi večplastnih mrež

Licences

License:CC BY 4.0, Creative Commons Attribution 4.0 International
Link:http://creativecommons.org/licenses/by/4.0/
Description:This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

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