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31.
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: 505; Downloads: 20
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32.
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: 391; Downloads: 2
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33.
Entropic cost of folding and phase diagrams of polypeptides: Why are IDPs unfolded at room temperature?
Artem Badasyan, invited lecture at foreign university

Abstract: In spin models, that are applied to describe the conformational transitions in polymers, the number of spin orientations, that correspond to the disordered conformation, can be estimated using fundamental definitions of Statistical Physics. For instance, when considering alpha-helix to coil transition in polypeptides, the role of generalized coordinates is played by pairs of torsional angle, and the repeating unit populates different regions of that 2D contour map, depending on conformation. By scanning over all possible torsional angles, that do not violate the obvious limitations due to the excluded volume, the so-called Ramachandran map can be plotted, which is actually the phase space visualization for the helix-coil transition problem. The region of phase space, corresponding to the ordered, helical conformations, is much more limited, than the one, corresponding to all other (allowed) conformations. We can calculate the areas of these regions as Γhelix and Γcoil , and construct the ratio Q = Γcoil . Naturally, it can be interpreted as log(Q) = Scoil − Shelix = ΔS, the entropic cost of helix with respect to coil. To illustrate the importance of the entropic price of ordered conformation we report our recent results, that allowed to explain the peculiarity of phase diagrams of Intrinsically Disordered Proteins (IDP) out of larger Q-values, as compared to globular counterparts. In particular, it has been shown, that due to larger Q, the phase diagram of IDP is shifted towards higher temperatures.
Found in: osebi
Keywords: IDP, protein folding, phase diagram
Published: 23.06.2016; Views: 2817; Downloads: 0
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34.
WATER-POLYPEPTIDE INTERACTION IN CLASSICAL MODELS OF HELIX-COIL TRANSITION
Knarik Yeritsyan, 2016, undergraduate thesis

Abstract: Zimm-Bragg model is the simplest to describe the conformational transitions in biopolymers and is regularly used for preocessing the experimental data. We review the model and its Hamiltonian definition with the goal to introduce the interaction with water into the picture. We show how modified ZB model with the account of water-polypeptide interactions allows to describe both cold denaturation and helix-coil transition and derive such the formula explicitly. The obtained theoretical expression for the helicity degree contains two independent parameters that can be fitted with the experimental data to determine the parameters of cold denaturation and helix-coil transition from a single fit and for a single set of experimental data.
Found in: osebi
Keywords: Zimm-Bragg model, conformational transitions in biopolymers, cold denaturation
Published: 28.09.2016; Views: 4528; Downloads: 193
.pdf Fulltext (1,70 MB)

35.
System size dependence in the Zimm-Bragg model
Artem Badasyan, 2021, original scientific article

Abstract: Within the recently developed Hamiltonian formulation of the Zimm and Bragg model we re-evaluate several size dependent approximations of model partition function. Our size analysis is based on the comparison of chain length N with the maximal correlation (persistence) length ξ of helical conformation. For the first time we re-derive the partition function of zipper model by taking the limits of the Zimm–Bragg eigenvalues. The critical consideration of applicability boundaries for the single-sequence (zipper) and the long chain approximations has shown a gap in description for the range of experimentally relevant chain lengths of 5–10 persistence lengths ξ. Correction to the helicity degree expression is reported. For the exact partition function we have additionally found, that: at N/ξ ≈ 10 the transition temperature T m reaches its asymptotic behavior of infinite N; the transition interval ∆T needs about a thousand persistence lengths to saturate at its asymptotic, infinite length value. Obtained results not only contribute to the development of the Zimm–Bragg model, but are also relevant for a wide range of Biotechnologies, including the Biosensing applications.
Found in: osebi
Keywords: Zimm-Bragg model, helix-coil transition, zipper model
Published: 17.06.2021; Views: 354; Downloads: 12
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36.
Least-square fit
Aleksander Đorđević, 2021, research project (high school)

Found in: osebi
Keywords: least-square fit, non-linear regression, Levenberg-Marquardt algorithm
Published: 28.06.2021; Views: 262; Downloads: 0
.pdf Fulltext (469,84 KB)

37.
Finite size effects in the Zimm-Bragg model
Artem Badasyan, 2021, invited lecture at foreign university

Found in: osebi
Published: 02.08.2021; Views: 239; Downloads: 20
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38.
Presentation of University of Nova Gorica and teaching numerical methods and modelling in environmental study programmes
Artem Badasyan, 2021, unpublished conference contribution

Found in: osebi
Published: 02.08.2021; Views: 270; Downloads: 0
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39.
System size dependence of the Zimm-Bragg model
Artem Badasyan, 2021, published scientific conference contribution abstract

Found in: osebi
Keywords: Zimm-Bragg model, final size effects
Published: 27.09.2021; Views: 87; Downloads: 0
.pdf Fulltext (23,57 MB)

40.
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: 113; Downloads: 0
.pdf Fulltext (23,57 MB)

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