1. Sequence disorder-induced first order phase transition in confined polyelectrolytesV. Stepanyan, Artem Badasyan, V. Morozov, Yevgeni S. Mamasakhlisov, Rudolf Podgornik, 2024, original scientific article Abstract: 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.
Keywords: polyelectrolyte, Anderson localization, Poisson-Boltzmann equation, phase transitions, electrostatics, polyelectrolytes, Edwards equation, nonlinear schrodinger equation, nucleic acids
Published in RUNG: 04.10.2024; Views: 438; Downloads: 2
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3. Differential scanning calorimetry of proteins and Zimm–Bragg model in waterKnarik 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: 755; Downloads: 4
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4. Origins of fine structure in DNA melting curvesArevik V. Asatryan, Albert S. Benight, Artem Badasyan, 2024, original scientific article Abstract: 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.
Keywords: disordered systems, DNA melting, Potts model
Published in RUNG: 08.08.2024; Views: 913; Downloads: 3
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8. Differential scanning calorimetry of proteins and the two-state model : comparison of two formulasKnarik 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: 1219; Downloads: 7
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