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1.
Processing CD and DSC data on protein folding with Zimm-Bragg model in water
Artem Badasyan, Knarik Yeritsyan, 2024, objavljeni povzetek znanstvenega prispevka na konferenci

Opis: 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.
Ključne besede: protein folding, circular dichroism, differential scanning calorimetry, water-protein interactions
Objavljeno v RUNG: 10.06.2024; Ogledov: 148; Prenosov: 0
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2.
Differential scanning calorimetry of proteins and the two-state model : comparison of two formulas
Knarik Yeritsyan, Artem Badasyan, 2024, izvirni znanstveni članek

Opis: 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.
Ključne besede: protein folding, differential scanning calorimetry, heat capacity, two-state model, Hawley model
Objavljeno v RUNG: 21.05.2024; Ogledov: 356; Prenosov: 3
.pdf Celotno besedilo (380,96 KB)
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Modelling water for calorimetry of proteins
Knarik Yeritsyan, Artem Badasyan, 2023, objavljeni povzetek znanstvenega prispevka na konferenci

Opis: 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.
Ključne besede: Zimm-Bragg model, water model, helix-coil transition, protein folding, differential scanning calorimetry
Objavljeno v RUNG: 18.10.2023; Ogledov: 949; Prenosov: 0
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6.
The polyelectrolyte with a disorder over short-range interactions
Yevgeni S. Mamasakhlisov, Artem Badasyan, V. Stepanyan, 2023, objavljeni povzetek znanstvenega prispevka na konferenci

Ključne besede: polyelectrolytes, short-range interactions
Objavljeno v RUNG: 04.09.2023; Ogledov: 905; Prenosov: 0
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7.
Spin model of water and post-processing of protein folding experiments
Artem Badasyan, Knarik Yeritsyan, 2023, objavljeni povzetek znanstvenega prispevka na konferenci

Opis: 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.
Ključne besede: spin model, water, protein folding
Objavljeno v RUNG: 04.09.2023; Ogledov: 1002; Prenosov: 7
.pdf Celotno besedilo (1,47 MB)
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8.
Potts spins, protein conformations and implicit water model
Artem Badasyan, 2023, objavljeni povzetek znanstvenega prispevka na konferenci (vabljeno predavanje)

Opis: 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.
Ključne besede: protein folding, Zimm-Bragg, protein-water interactions
Objavljeno v RUNG: 19.06.2023; Ogledov: 1289; Prenosov: 7
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9.
University of Nova Gorica: organization structure and general description : lecture at the University of Gabes, Gabes, Tunisia, 9th of May, 2023
Artem Badasyan, 2023, predavanje na tuji univerzi

Objavljeno v RUNG: 15.05.2023; Ogledov: 1153; Prenosov: 0
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10.
Spin Model of Protein Conformations in water: Theory vs Experiment.
Artem Badasyan, Knarik Yeritsyan, objavljeni povzetek znanstvenega prispevka na konferenci (vabljeno predavanje)

Opis: Background (approx. 70 words) I will overview the application of spin models of Statistical Mechanics to describe polypeptide conformations. Zimm and Bragg model is one of the most successful examples of such approach [1]. In 2010 we have suggested the microscopic formulation of the model [2], which was later augmented by including the interactions with water [3]. Adding the solvent opened doors for the direct comparisons with UV-vis, Circular Dichroism (CD) and Differential Scanning Calorimetry (DSC) experiments. Aim (approx. 30 words) Based on a statistical Potts-like spin model of protein folding we provide formulas for experimentally measurable quantities and report a perfect fit. Our approach suggest a new method to process the results of protein folding experiments. Method (approx. 100 words) We start from the microscopic Hamiltonian formulation of the polypeptide model in water and use the usual Statistical Mechanics route from the model to partition function and the thermodynamics. Using Mayer expansion and summation over the solvent degrees of freedom, the problem is shown to be equivalent to in vacuo model with some effective, temperature dependent interaction energy. Estimated partition function leads to the expressions for the thermodynamic potentials and order parameter averages. The comparison (least-square fit) with the experimental data points from CD and DSC experiments on protein folding allows to extract the information on hydrogen bonding strengths, not available with the classical approach. Results & Discussion (approx 200 words, or less if you paste an image or insert a table ) Proposed model allows for the cold denaturation under certain well-defined conditions. The agreement between the theoretical curves and data points is excellent, and the values of fitted parameters are within the expected ranges. The limitations of the approach are naturally related to the limitations of the Zimm-Bragg original model, intended to describe the changes of the secondary structure elements only. Taking into account that the so-called “two-state” model widely used nowadays to process the experiment does not contain any info regarding the hydrogen bonding energies, the method we suggest provides a promising alternative. Conclusion (70 words approximately) The proposed approach does what it is intended to do: processing of the experimental data on protein folding. However the model contains the very same serious limitations, as the two-state model: it is oversimplified in many respects. Whether the currently available experimental methods need a better model than already suggested ones or not, is an open question. References: [1] Zimm, B.H.; Bragg, J.K.; J. Chem. Phys. 31:526–535 (1959). [2] Badasyan, A.V. et al., Phys. Rev. E 81:021921 (2010). [3] Badasyan, A.V. et al., Phys. Rev. E 89:022723 (2014). [4] Badasyan, A. et al.; Eur.Phys. J. E 36:1–9 (2013).
Ključne besede: Protein folding, CD, DSC, Zimm-Bragg
Objavljeno v RUNG: 15.05.2023; Ogledov: 1514; Prenosov: 0
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