Repository of University of Nova Gorica

Search the repository
A+ | A- | Help | SLO | ENG

Query: search in
search in
search in
search in
* old and bologna study programme

Options:
  Reset


1 - 6 / 6
First pagePrevious page1Next pageLast page
1.
Modeling of solvent role in protein folding experiments : dissertation
Knarik Yeritsyan, 2025, doctoral dissertation

Abstract: The Zimm-Bragg (ZB) model serves as a fundamental framework for elucidating conformational transitions in biopolymers, offering simplicity and efficacy in processing experimental data. This study provides a comprehensive review of the Zimm-Bragg model and its Hamiltonian formulation, with particular emphasis on incorporating water interactions and chain size effects into the computational framework. We propose a modified ZB model that accounts for water-polypeptide interactions, demonstrating its ability to describe phenomena such as cold denaturation and helix-coil transitions. In the realm of NanoBioTechnologies, the manipulation of short polypeptide chains is commonplace. Experimental investigation of these chains in vitro often relies on techniques like Circular Dichroism (CD) and timeresolved infrared spectroscopy. Determining interaction parameters necessitates processing the temperature dependence of the normalized degree of helicity through model fitting. Leveraging recent advancements in the Hamiltonian formulation of the Zimm and Bragg model, we explicitly incorporate chain length and solvent effects into the theoretical description. The resulting expression for helicity degree adeptly fits experimental data, yielding hydrogen bonding energies and nucleation parameter values consistent with field standards. Differential Scanning Calorimetry (DSC) stands as a potent tool for measuring the specific heat profile of materials, including proteins. However, relating the measured profile to microscopic properties requires a suitable model for fitting. We propose a novel algorithm for processing DSC experimental data based on the ZB theory of protein folding in water. This approach complements the classical two-state paradigm and provides insights into protein-water and intraprotein hydrogen bonding energies. An analytical expression for heat capacity, considering water interaction, is derived and successfully applied to fit numerous DSC experimental datasets reported in the literature. Additionally, we compare this approach with the classical two-state model, demonstrating its efficacy in fitting DSC data. Furthermore, we have developed and launched a free online tool for processing CD and DSC experimental data related to protein folding, aiming to support scientific research.
Keywords: Zimm-Bragg model, conformational transitions, helix-coil transitions, cold denaturation, circular dichroism, differential scanning calorimetry, protein folding, water-protein interaction, hydrogen bonding energy, degree of helicity, short polypeptide chains, protein heat capacity, protein data analysis, dissertations
Published in RUNG: 27.01.2025; Views: 312; Downloads: 10
.pdf Full text (5,12 MB)

2.
Differential scanning calorimetry of proteins and Zimm–Bragg model in water
Knarik Yeritsyan, Artem Badasyan, 2019, original scientific article

Abstract: Differential Scanning Calorimetry (DSC) is a regular and powerful tool to measure the specific heat profile of various materials. Hydrogen bonds play a crucial role in stabilizing the three-dimensional structure of proteins. Naturally, information about the strength of hydrogen bonds is contained in the measured DSC profiles. Despite its obvious importance, there is no approach that would allow the extraction of such information from the heat capacity measurements. In order to connect the measured profile to microscopic properties of a polypeptide chain, a proper model is required to fit. Using recent advances in the Zimm–Bragg (ZB) theory of protein folding in water, we propose a new and efficient algorithm to process the DSC experimental data and to extract the H-bonding energy among other relevant constants. Thus, for the randomly picked set of 33 proteins, we have found a quite narrow distribution of hydrogen bonding energies from 1 to 8 kJ/mol with the average energy of intra-protein hydrogen bonds kJ/mol and the average energy of water–protein bonds as kJ/mol. This is an important illustration of a tiny disbalance between the water–protein and intraprotein hydrogen bonds. Fitted values of the nucleation parameter belong to the range from 0.001 to 0.01, as expected. The reported method can be considered as complementary to the classical two-state approach and together with other parameters provides the protein–water and intraprotein H-bonding energies, not accessible within the two-state paradigm.
Keywords: protein folding, differential scanning calorimetry, heat capacity, two-state model, Hawley model
Published in RUNG: 26.08.2024; Views: 1054; Downloads: 4
.pdf Full text (645,94 KB)
This document has many files! More...

3.
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: 1183; Downloads: 4
URL Link to file
This document has many files! More...

4.
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: 1470; Downloads: 10
.pdf Full text (380,96 KB)
This document has many files! More...

5.
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: 2323; Downloads: 0
This document has many files! More...

6.
Temperature induced de-agglomeration of the polysilane macromolecules
Andraž Mavrič, Artem Badasyan, Mattia Fanetti, Matjaž Valant, 2016, published scientific conference contribution abstract

Keywords: polysilane, de-agglomeration, dynamic light scattering, differential scanning calorimetry
Published in RUNG: 05.10.2016; Views: 6408; Downloads: 0
This document has many files! More...

Search done in 0.03 sec.
Back to top