ORALS

SESSION: MedicineWedPM1-R2	Intl. Symp. on Technological Innovations in Medicine for Sustainable Development
Wed. 30 Nov. 2022 / Room: Ballroom A
Session Chairs: Shozo Yanagida; Esther Nachliel; Session Monitor: TBA

14:25: [MedicineWedPM106] OS
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;
Paper Id: 227 [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.

References:
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.

SESSION: MedicineWedPM1-R2	Intl. Symp. on Technological Innovations in Medicine for Sustainable Development
Wed. 30 Nov. 2022 / Room: Ballroom A
Session Chairs: Shozo Yanagida; Esther Nachliel; Session Monitor: TBA

14:50: [MedicineWedPM107] OS
Characterization of the nano scale heterogeneity at the solvent – interface of bio-structures
Esther Nachliel¹ ; Menachem Gutman² ; ¹Tel Aviv University, Tel Aviv, Israel; ²Tel Aviv University, Ramat Gan, Israel;
Paper Id: 232 [Abstract]

On the nm scale, cellular constituents are highly heterogeneous: the dielectric constant boundaries, the uneven dispersion of fixed and mobile charges, partial ordering of water molecules create an environment where the local chemical and physical properties differ from one site to another. The study of this ‘ensemble” requires a methodology that can discriminate among nm size sites, where a “gauging” particle will remain for not more than few ns. This requirement is readily met by proton pule experiments (1). The photo-excited state of certain aromatic compound are very acidic (pK*< 2) and by illumination ejects a proton to the solvent. The released proton diffuses within the immediate vicinity and may recombine with the excited anion (ϕO-*) in response to its electric field reforming the ϕOH* state. Altogether, the observation time is few ns and the distance the proton can disperse, before the molecule relaxes to its ground state, is ~2-4 nm, thus assuring a localized observation (2). Judicious insertion of the photo-acids, like pyranine, into a well-defined environment (3) enables quantitative evaluation of the physical-chemical properties of the immediate vicinity of the site. The various studies were spread over a large biological domains; like active site of proteins (Apomyiglobin, lac permease), or the water filled space of a Large-Pore Channel protein (PhoE) or the interface between solvent and carbohydrate molecule (cyclodextrine), the aquose phase between lipid bilayer (multilamentar) and the reverse micelles of different radiuses. The micro loci are characterized by a lower chemical activity of the water, modulated diffusion coefficient, enhanced electrostatic field and highly affected by the geometry of the local space.

References:
1. Time-resolved dynamics of proton transfer in proteinous systems; M. Gutman and E. Nachliel. Annu. Rev. Phys. Chem. 1997. 48:329–56
2. Elementary Steps in Excited-State Proton Transfer† Noam Agmon. J. Phys. Chem. A 2005, 109, 13-35.
3. Gauging of the PhoE Channel by a Single Freely Diffusing Proton Sharron Bransburg-Zabary, Esther Nachliel, and Menachem Gutman. Biophysical Journal Volume 83 December 2002 2987–3000.