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Ionomic and metabolomic changes in mercury and selenium exposed plants and animals by X - ray and FTIR spectrometry
Katarina Vogel-Mikuš, Iztok Arčon, Jože Grdadolnik, Petra Gregorič, Anja Kavčič, 2018, published scientific conference contribution abstract

Found in: osebi
Keywords: mercury, selenium, plants, animals
Published: 12.09.2018; Views: 1948; Downloads: 0
.pdf Fulltext (62,45 KB)

The finite size effects and two-state paradigm of protein folding
Vladimir N. Uversky, Jože Grdadolnik, Artem Badasyan, Matjaž Valant, 2021, original scientific article

Abstract: The coil to globule transition of the polypeptide chain is the physical phenomenon behind the folding of globular proteins. Globular proteins with a single domain usually consist of about 30 to 100 amino acid residues, and this finite size extends the transition interval of the coil-globule phase transition. Based on the pedantic derivation of the two-state model, we introduce the number of amino acid residues of a polypeptide chain as a parameter in the expressions for two cooperativity measures and reveal their physical significance. We conclude that the k2 measure, defined as the ratio of van ’t Hoff and calorimetric enthalpy is related to the degeneracy of the denatured state and describes the number of cooperative units involved in the transition; additionally, it is found that the widely discussed k2=1 is just the necessary condition to classify the protein as the two-state folder. We also find that Ωc, a quantity not limited from above and growing with system size, is simply proportional to the square of the transition interval. This fact allows us to perform the classical size scaling analysis of the coil-globule phase transition. Moreover, these two measures are shown to describe different characteristics of protein folding
Found in: osebi
Keywords: protein folding, two-state model, size scaling, thermodynamic cooperativity
Published: 24.02.2021; Views: 515; Downloads: 21
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Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins
Jože Grdadolnik, Matjaž Valant, Sh. A. Tonoyan, Artem Badasyan, 2021, original scientific article

Abstract: Studies of biopolymer conformations essentially rely on theoretical models that are routinely used to process and analyze experimental data. While modern experiments allow study of single molecules in vivo, corresponding theories date back to the early 1950s and require an essential update to include the recent significant progress in the description of water. The Hamiltonian formulation of the Zimm-Bragg model we propose includes a simplified, yet explicit model of water-polypeptide interactions that transforms into the equivalent implicit description after performing the summation of solvent degrees of freedom in the partition function. Here we show that our model fits very well to the circular dichroism experimental data for both heat and cold denaturation and provides the energies of inter- and intra- molecular H-bonds, unavailable with other processing methods. The revealed delicate balance between these energies determines the conditions for the existence of cold dena- turation and thus clarifies its absence in some proteins.
Found in: osebi
Keywords: protein folding, cold denaturation, water, Zimm-Bragg model
Published: 06.05.2021; Views: 402; Downloads: 2
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1,8-dihydroxy naphthalene (DHN) - melanin confers tolerance to cadmium in isolates of melanised dark septate endophytes
Marjana Regvar, Jože Grdadolnik, Iztok Arčon, Katarina Vogel-Mikuš, Matevž Likar, Mateja Potisek, 2021, original scientific article

Abstract: The contribution of 1,8-dihydroxy naphthalene (DHN) melanin to cadmium (Cd) tolerance in two dark septate endophytes (DSE) of the genus Cadophora with different melanin content was investigated in vitro. The DSE isolate Cad#148 with higher melanin content showed higher tolerance to Cd than the less melanised Cad#149. Melanin synthesis was significantly reduced by Cd in both isolates with uninhibited melanin synthesis, in a dosedependent manner. Inhibition of melanin synthesis by tricyclazole reduced the relative growth of Cad#148 exposed to Cd and did not affect Cad#149. Cd accumulation was not altered by tricyclazole in the two isolates, but it increased catalase and reduced glutathione reductase activity in more melanised Cad#148, indicating higher stress levels. In contrast, in Cad#149 the enzyme activity was less affected by tricyclazole, indicating a more pronounced role of melanin-independent Cd tolerance mechanisms. Cd ligand environment in fungal mycelia was analysed by extended EXAFS (X-ray absorption fine structure). It revealed that Cd was mainly bound to O- and S-ligands, including hydroxyl, carboxyl, phosphate and thiol groups. A similar proportion of S- and Oligands (~35% and ~65%) were found in both isolates with uninhibited melanin synthesis. Among O-ligands two types with Cd-O-C- and Cd-O-P- coordination were identified. Tricyclazole altered Cd-O- ligand environment in both fungal isolates by reducing the proportion of Cd-O-C- and increasing the proportion of Cd-O-P coordination. DHN-melanin, among other tolerance mechanisms, significantly contributes to Cd tolerance in more melanised DSE fungi by immobilising Cd to hydroxyl groups and maintaining the integrity of the fungal cell wall.
Found in: osebi
Keywords: DSE, melanin, Cd tolerance, inhibitor tricyclazole, antioxidant enzymes, EXAFS
Published: 13.07.2021; Views: 272; Downloads: 0
.pdf Fulltext (1,73 MB)

Finite size effects at protein folding from the two-state perspective
Vladimir N. Uversky, Jože Grdadolnik, Matjaž Valant, Artem Badasyan, 2021, published scientific conference contribution abstract

Found in: osebi
Keywords: protein folding, two-state model, finite size effects
Published: 27.09.2021; Views: 130; Downloads: 0
.pdf Fulltext (23,57 MB)

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