journal article·2024-03-01Open access

Dynamic behavior of enzyme kinetics cooperative chemical reactions

Akhtar Jan, Rehan Ali Shah, Hijaz Ahmad, Hazrat Bilal, Bandar Almohsen

AIP Advances· Volume 14· Issue 3

Abstract

This article uses computational mathematics to investigate the dynamics of cooperative occurrences in chemical reactions inside living organisms. We study the dynamics of complex systems using mathematical models based on ordinary differential equations, paying special attention to chemical equilibrium and reaction speed. Explanations of cooperation, non-cooperation, and positive cooperation are presented in our study. We analyze the stabilities of equilibrium points by a systematic analysis that makes use of the Jacobian matrix and the threshold parameter R0. We next extend our investigation to evaluate global stability and the probability of the model. Variations in k3 have a notable effect on substrate concentration probabilities, indicating that it plays an important role in reaction kinetics. Reducing k3 highlights the substrate's critical contribution to the system by extending its presence in the concentration. We find that different results were obtained for cooperative behavior: higher reaction rates at different binding sites are correlated with positive cooperativity, while slower reactions are induced by negative cooperativity. The Adams–Bashforth method is used to show numerical and graphical solutions with the help of MATLAB. Tables and graphs are used to further explain the effects of the parameters. This study underlines how well ordinary differential equations may represent the complicated system dynamics found in chemical reactions. It also provides elusive insights into cooperative occurrences, which develops our understanding of the phenomenon and serves as a foundation for future research.
Source: crossref · Quality: baseline

Research context

OpenAlex topics: Mathematical and Theoretical Epidemiology and Ecology Models · Evolution and Genetic Dynamics · Nonlinear Dynamics and Pattern Formation

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

Affiliations

Department of Basic Sciences and Islamiat University of Engineering and Technology 1 , Peshawar 25120, Pakistan

Section of Mathematics, International Telematic University Uninettuno 2 , Corso Vittorio Emanuele II, 39,00186 Roma, Italy

Near East University, Operational Research Center in Healthcare, TRNC Mersin 10, Nicosia, 99138 3 , Türkiye

Department of Computer Science and Mathematics, Lebanese American University, Beirut 4 , Lebanon

Department of Mathematics, College of Science, King Saud University 5 , P.O. Box 2455 Riyadh 11451, Saudi Arabia

Funding

King Saud University

References (23)

Show source-provided references
1. Optimal control of a fractional-order enzyme kinetic model
2. E. Reznik , D.Segre, and W. E.Sherwood, “The quasi-steady state assumption in an enzymatically open system,” arXiv:1103.1200 (2011).
3. New types of experimental data shape the use of enzyme kinetics for dynamic network modeling10.1111/febs.12525 ↗
4. Mathematical modelling of enzyme kinetics reaction mechanisms and analytical solutions of non-linear reaction equations10.1007/s10910-009-9659-5 ↗
5. Cooperativity and specificity in enzyme kinetics: A single-molecule time-based perspective10.1529/biophysj.108.131771 ↗
6. The role of cooperativity in a p53-miR34 dynamical mathematical model10.1016/j.jtbi.2020.110252 ↗
7. Die kinetik der invertinwirkung
8. Theoretical analysis of the relationship between positive/negative cooperativity and enzyme activation/inhibition10.1007/s12539-009-0013-1 ↗
9. Asymptotics and numerical analysis for enzymatic auxiliary reactions10.1007/s00161-020-00962-5 ↗
10. Sensitivity amplification in the phosphorylation-dephosphorylation cycle: Nonequilibrium steady states, chemical master equation, and temporal cooperativity10.1063/1.2948965 ↗
11. S. Özöğür , “Mathematical modelling of enzymatic reactions, simulation and parameter estimation,” Master’s thesis, Middle East Technical University, 2005.
12. Fractal soliton solutions for the fractal-fractional shallow water wave equation arising in ocean engineering10.1016/j.aej.2022.10.024 ↗
13. Polyvalent interactions in biological systems: Implications for design and use of multivalent ligands and inhibitors10.1002/(sici)1521-3773(19981102)37:20<2754::aid-anie2754>3.3.co;2-v ↗
14. Novel traveling wave solutions for the fractal Zakharov–Kuznetsov–Benjamin–Bona–Mahony model10.1142/s0218348x22501705 ↗
15. Ultrasensitivity in biochemical systems controlled by covalent modification. interplay between zero-order and multistep effects10.1016/s0021-9258(17)42619-6 ↗
16. New perspective on fractional Hamiltonian amplitude equation10.1007/s11082-023-05309-3 ↗
17. 2000
18. Toward molecular cooperation by de novo peptides10.1007/s11084-021-09603-6 ↗
19. On the analysis of Caputo fractional order dynamics of Middle East Lungs Coronavirus (MERS-CoV) model10.1016/j.aej.2021.10.016 ↗
20. Qualitative analysis of an ode model of a class of enzymatic reactions10.1007/s11538-017-0360-8 ↗
21. 2004
22. 2007
23. A stochastic analysis of co-infection model in a finite carrying capacity population10.1142/s1793524523500833 ↗