1. Modeling of solvent role in protein folding experiments : dissertationKnarik Yeritsyan, 2025, doktorska disertacija Opis: 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.
Ključne besede: 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
Objavljeno v RUNG: 27.01.2025; Ogledov: 719; Prenosov: 13
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2. Photoelectrochemical conversion of biomass alcohols using in-situ Sn-doped ▫$\alpha-Fe_2O_3$▫ thin filmsManel Machreki, Artem Badasyan, Dušan Žigon, Georgi Tyuliev, Saim Emin, 2025, izvirni znanstveni članek Opis: Transformation of biomass into value-added chemicals and fuels is considered an upcycling process that is beneficial to resource utilization. In this study, we used a photoelectrochemical (PEC) approach for selective oxidation of propane-1,2,3-triol to dihydroxyacetone (DHA) with high efficiency and selectivity (99%) using Sn-doped -Fe2O3 (Sn:-Fe2O3) thin films with intrinsic oxygen vacancies (OVs). DHA is an essential compound utilized in the cosmetic industry. In a similar manner, we conducted the first study of the PEC oxidation of 4-hydroxy-3-methoxybenzyl alcohol under visible light. A kinetic model has been formulated and solved to find the time-dependent generation of the products. Electrochemical impedance analyses and PEC experiments demonstrated a correlation between the concentration of molecules and the catalytic performance of Sn:-Fe2O3. Studies using scavengers indicate that the photogenerated holes (h+), singlet oxygen (1O2), hydroxyl radicals (•OH), and superoxide radicals (•O2–) play key roles in achieving high PEC activity. This work provided a new perspective on designing efficient PEC systems for biomass conversion into energy and value-added chemicals.
Ključne besede: Sn-doped alpha-Fe2O3, oxygen vacancies, photoelectrochemical oxidation, propane-1, 2, 3-triol, 4-hydroxy-3-methoxybenzyl alcohol
Objavljeno v RUNG: 08.01.2025; Ogledov: 630; Prenosov: 6
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4. Sequence disorder-induced first order phase transition in confined polyelectrolytesV. Stepanyan, Artem Badasyan, V. Morozov, Yevgeni S. Mamasakhlisov, Rudolf Podgornik, 2024, izvirni znanstveni članek Opis: We consider a statistical mechanical model of a generic flexible polyelectrolyte, comprised of identically charged monomers with long-range electrostatic interactions and short-range interactions quantified by a disorder field along the polymer contour sequence, which is randomly quenched. The free energy and the monomer density profile of the system for no electrolyte screening are calculated in the case of a system composed of two infinite planar bounding surfaces with an intervening oppositely charged polyelectrolyte chain. We show that the effect of the contour sequence disorder, mediated by short-range interactions, leads to an enhanced localization of the polyelectrolyte chain and a first order phase transition at a critical value of the inter-surface spacing. This phase transition results in an abrupt change of the pressure from negative to positive values, effectively eliminating polyelectrolyte mediated bridging attraction.
Ključne besede: polyelectrolyte, Anderson localization, Poisson-Boltzmann equation, phase transitions, electrostatics, polyelectrolytes, Edwards equation, nonlinear schrodinger equation, nucleic acids
Objavljeno v RUNG: 04.10.2024; Ogledov: 1034; Prenosov: 2
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6. Differential scanning calorimetry of proteins and Zimm–Bragg model in waterKnarik Yeritsyan, Artem Badasyan, 2019, izvirni znanstveni članek Opis: 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.
Ključne besede: protein folding, differential scanning calorimetry, heat capacity, two-state model, Hawley model
Objavljeno v RUNG: 26.08.2024; Ogledov: 1351; Prenosov: 4
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7. Origins of fine structure in DNA melting curvesArevik V. Asatryan, Albert S. Benight, Artem Badasyan, 2024, izvirni znanstveni članek Opis: With the help of the one-dimensional random Potts-like model, we study the origins of fine structures observed on differential melting profiles of double-stranded DNA. We theoretically assess the effects of sequence arrangement on DNA melting curves through the comparison of results for random, correlated, and block sequences. Our results re-confirm the smearing out of the fine structure with the increase in chain length for all types of sequence arrangements and suggest that the fine structure is a finite-size effect. We have found that the fine structures on melting curves of chains comprised of blocks with correlations in sequence are more persistent, probably because of increased sequence disorder the blocks introduce. Many natural DNAs show a well-expressed fine structure of melting profiles. Our results for block sequences may suggest the existence of such sequence motifs in natural DNA sequences.
Ključne besede: disordered systems, DNA melting, Potts model
Objavljeno v RUNG: 08.08.2024; Ogledov: 1513; Prenosov: 5
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