2022-Sustainable Industrial Processing Summit
SIPS2022 Volume 19 Intl. Symp on Technological Innovations in Medicine and Covid19 and Infectious Diseases
| Editors: | F. Kongoli, F. Murad, T. Yoshikawa, S. Waldman, J. Ribas, S. Hirano, D. Joseph, R. Guerrant, W. Petri, H. Inufusa, H. Yedoyan, S. Heysell. |
| Publisher: | Flogen Star OUTREACH |
| Publication Year: | 2022 |
| Pages: | 130 pages |
| ISBN: | 978-1-989820-70-4(CD) |
| ISSN: | 2291-1227 (Metals and Materials Processing in a Clean Environment Series) |
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Computational Reconstruction of Multi-Step Reactions
Menachem Gutman1; Esther Nachliel2; Eran Bosis3;1TEL AVIV UNIVERSITY, Ramat Gan, Israel; 2TEL AVIV UNIVERSITY, RAmat Hasharon, Israel; 3DEPARTMENT OF BIOTECHNOLOGY ENGINEERING, ORT BRAUDE COLLEGE OF ENGINEERING,, Karmiel 2161002, Israel, Israel;
Type of Paper: Regular
Id Paper: 227
Topic: 65
Abstract:
Metabolic pathways are summation of many simultaneous parallel reactions with numerous interactions between the reactants. Here, a general mode capable of treating a large number of linked processes as a set of coupled kinetic equations is described, where all forward and backward reactions are expressed. The analysis is capable of considering multi component processes with high precision; determining the rate constants of partial reactions without neglecting any event, providing an insight into parameters like the local viscosity, the energy barrier, the diffusivity of the reactants in the reaction space and identify redundant pathways that are not essential for the process. The input for the analysis are time resolved signals generated by brief perturbation of the system; the analysis is carried out by integration of the differential rate equations that reconstruct the observed signals. The analysis was first implemented for experiments, where acid-base equilibria were perturbed by sub-nanosecond increments of the H+ concentration (1). The analysis was extended to study biological multi-equilibria systems like the interaction of Calmodulin with bio-membranes (2), the quality control of protein synthesis (3), proton-ion exchange between aqueous phases separated by a bio-membrane impregnated by a diffusing carrier (4), the sequential reactions involving the release of signaling small molecules by the pre-synaptic membrane, or the evaluation of the heterogeneous reactivity of the Syntaxin molecules on the inner leaflet of the plasma membrane (5). This chapter will discuss both the theoretical framework and as well as the methodology in order to make it applicable for diverged biochemical and chemical processes.
Keywords:
biocomputational sciences; kinetic analysis, multi-equilibria, perturbation of equilibrium, dynamics of coupled reactions, coupled nonlinear ordinary differential rate equations, genetic algorithm, modelingReferences:
1. Gutman M, Nachliel E. Time-resolved dynamics of proton transfer in proteinous systems. Annu Rev Phys Chem. 1997;48:329-56.2. Sengupta P, Bosis E, Nachliel E, et al. EGFR juxtamembrane domain, membranes, and calmodulin: kinetics of their interaction. Biophys J. 2009;96(12):4887-95.
3. Bosis E, Nachliel E, Cohen T, et al. Endoplasmic reticulum glucosidase II is inhibited by its end products. Biochemistry. 2008;47(41):10970-80.
4. Bosis E, Nachliel E, Cohen T, et al. Endoplasmic reticulum glucosidase II is inhibited by its end products. Biochemistry. 2008;47(41):10970-80.
5. Bar-On D, Gutman M, Mezer A, Ashery U, Lang T, Nachliel E. Evaluation of the heterogeneous reactivity of the syntaxin molecules on the inner leaflet of the plasma membrane. J Neurosci. 2009;29(39):12292-301.