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1.
Numerical calculations of the kinetic model of a potentiometric enzymatic sensor
Karen Simonyan, Artem Badasyan, 2023, published scientific conference contribution abstract

Keywords: Michaelis-Menten kinetics, steady state, potentiometric enzymatic sensor, urease sensor
Published in RUNG: 09.07.2024; Views: 197; Downloads: 0
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2.
Processing CD and DSC data on protein folding with Zimm-Bragg model in water
Artem Badasyan, Knarik Yeritsyan, 2024, published scientific conference contribution abstract

Abstract: Circular Dichroism (CD) and Differential Scanning Calorimetry (DSC) data are processed with a novel model incorporating water effects and inter-/intra-molecular hydrogen bonding energies to better fit experimental data on protein folding as compared to the two-state approach.
Keywords: protein folding, circular dichroism, differential scanning calorimetry, water-protein interactions
Published in RUNG: 10.06.2024; Views: 330; Downloads: 0
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3.
Differential scanning calorimetry of proteins and the two-state model : comparison of two formulas
Knarik Yeritsyan, Artem Badasyan, 2024, original scientific article

Abstract: Differential Scanning Calorimetry (DSC) is a regular and powerful tool to measure the specific heat profile of various materials. In order to connect the measured profile to the properties of a particular protein, a model is required to fit. We discuss here the application of an exact two-state formula with its approximation and process the DSC experimental data on protein folding in water. The approximate formula relies on the smallness of the transition interval, which is different for each protein. With an example of the set of 33 different proteins, we show the practical validity of the approximation and the equivalence of exact and approximate two-state formulas for processing DSC data.
Keywords: protein folding, differential scanning calorimetry, heat capacity, two-state model, Hawley model
Published in RUNG: 21.05.2024; Views: 589; Downloads: 3
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Modelling water for calorimetry of proteins
Knarik Yeritsyan, Artem Badasyan, 2023, published scientific conference contribution abstract

Abstract: Differential Scanning Calorimetry (DSC) is a powerful technique used to study the thermal stability and unfolding of proteins. DSC provides the excess heat capacity profile and is used to study the thermodynamics of a given protein. By fitting DSC data to the model, researchers can obtain valuable information about the thermodynamics of protein folding and unfolding, which can help them better understand protein structure, stability, and function. Based on Hamiltonian representation of ZB model and using the solvent effects we derived an expression for heat capacity in proteins and successfuly fit it to experimental data. As we show, our model provides a better fit to experimental data, as compared to the 2-state model. The model we propose takes into account also water effects and we show that it fits better to experimental data giving inter- and intra-molecular H-bonding energies instead of reporting only one total enthalpy.
Keywords: Zimm-Bragg model, water model, helix-coil transition, protein folding, differential scanning calorimetry
Published in RUNG: 18.10.2023; Views: 1155; Downloads: 0
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7.
The polyelectrolyte with a disorder over short-range interactions
Yevgeni S. Mamasakhlisov, Artem Badasyan, V. Stepanyan, 2023, published scientific conference contribution abstract (invited lecture)

Keywords: polyelectrolytes, short-range interactions
Published in RUNG: 04.09.2023; Views: 1028; Downloads: 0
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8.
Spin model of water and post-processing of protein folding experiments
Artem Badasyan, Knarik Yeritsyan, 2023, published scientific conference contribution abstract

Abstract: The presence of several distinct minima in nearest-neighbor potentials in polymers makes it possible to describe polymer conformations in terms of discrete isomeric states, naturally leading to spin language. Using this general approach, a decade ago we have suggested the Hamiltonian formulation for the Zimm and Bragg model of protein conformations [1,2]. Later we have augmented the model by an oversimplified spin model for water, resulting in both cold and hot denaturations [3]. We construct the Statistical Mechanics for the model and get access to its Thermodynamics. Resulting order parameter and specific heat expressions are successfully fit to available experimental data [4]. Thanks to solid and traceable theoretical foundations, the procedure provides better quality fits as compared to the state-of-the-art two-state model, routinely used to process protein folding experiments.
Keywords: spin model, water, protein folding
Published in RUNG: 04.09.2023; Views: 1176; Downloads: 7
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9.
Potts spins, protein conformations and implicit water model
Artem Badasyan, 2023, published scientific conference contribution abstract (invited lecture)

Abstract: I will summarize past and current achievements in the field of spin model applications to protein conformations. Using classical Statistical Mechanics scheme and 1D many-body Hamiltonian, exact partition function can be estimated, giving access to the free energy, order parameter and specific heat. I will introduce a simplified water model as an additive term at the level of Hamiltonian, and will show how the solvent degrees of freedom can be summed out. The suggested procedure results in the effective Hamiltonian with the temperature dependent hydrogen bonding energy. If the many-body range is reduced to the nearest neighbour, the approach reduces to the Zimm-Bragg model. Obtained expressions for the order parameter and the specific heat nicely fit to the corresponding experiments for protein folding, providing an alternative or complementary scheme for the processing of experimental data.
Keywords: protein folding, Zimm-Bragg, protein-water interactions
Published in RUNG: 19.06.2023; Views: 1479; Downloads: 7
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10.
University of Nova Gorica: organization structure and general description : lecture at the University of Gabes, Gabes, Tunisia, 9th of May, 2023
Artem Badasyan, 2023, invited lecture at foreign university

Published in RUNG: 15.05.2023; Views: 1288; Downloads: 0
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