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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: 334; Prenosov: 0
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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: 1491; Prenosov: 7
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Non-covalent ligand-oxide interaction promotes oxygen evolution
Qianbao Wu, Junwu Liang, Mengjun Xiao, Chang Long, Lei Li, Zhenhua Zeng, Andraž Mavrič, Xia Zheng, Jing Zhu, Matjaž Valant, 2023, izvirni znanstveni članek

Opis: Strategies to generate high-valence metal species capable of oxidizing water often employ composition and coordination tuning of oxide-based catalysts, where strong covalent interactions with metal sites are crucial. However, it remains unexplored whether a relatively weak “non-bonding” interaction between ligands and oxides can mediate the electronic states of metal sites in oxides. Here we present an unusual non-covalent phenanthroline-CoO2 interaction that substantially elevates the population of Co4+ sites for improved water oxidation. We find that phenanthroline only coordinates with Co2+ forming soluble Co(phenanthroline)2(OH)2 complex in alkaline electrolytes, which can be deposited as amorphous CoOxHy film containing non-bonding phenanthroline upon oxidation of Co2+ to Co3+/4+. This in situ deposited catalyst demonstrates a low overpotential of 216 mV at 10 mA cm−2 and sustainable activity over 1600 h with Faradaic efficiency above 97%. Density functional theory calculations reveal that the presence of phenanthroline can stabilize CoO2 through the non-covalent interaction and generate polaron-like electronic states at the Co-Co center.
Ključne besede: water oxidation, cobalt hydroxide, ligand-metal interactions
Objavljeno v RUNG: 23.02.2023; Ogledov: 1925; Prenosov: 15
.pdf Celotno besedilo (1,77 MB)

On spin description of water-biopolymer interactions: theory and experiment of reentrant order-disorder transition.
Artem Badasyan, predavanje na tuji univerzi

Opis: The experimental studies of biopolymer conformations have reached an unprecedented level of detailization during the past decade and allow now to study single molecules in vivo [1]. Processing of experimental data essentially relies on theoretical approaches to conformational transitions in biopolymers [2]. However, the models that are currently used, originate from the early 1960's and contain several unjustified assumptions, widely accepted at that time. Thus, the view on the conformational transitions in the polypeptides as a two-state process has very limited applicability because the all-or-none transition mechanism takes place only in short polypeptides with sizes comparable to the spatial correlation length; the original formulation of Zimm-Bragg model is phenomenological and does not allow for a microscopic model for water; the implicit consideration of the water-polypeptide interactions through the ansatz about the quadratic dependence of free energy difference on temperature can only be justified through the assumption of an ideal gas with a constant heat capacity. To get rid of these deficiencies, we augment the Hamiltonian formulation [3] of the Zimm-Bragg model [4] with the term describing the water-polypeptide interactions [5]. The analytical solution of the model results in a formula, ready to be fit to Circular Dichroism (CD) data for both heat and cold denaturation. On the example of several sets of experimental data we show, that our formula results in a significantly better fit, as compared to the existing approaches. Moreover, the application of our procedure allows to compare the strengths of inter- and intra-molecular H-bonds, an information, inaccessible before.
Ključne besede: helix-coil transition, water-polypeptide interactions
Objavljeno v RUNG: 13.03.2019; Ogledov: 3464; Prenosov: 0
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