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2.
Coil-globule transition of a homopolymer chain in a square-well potential
Artem V. Badasyan, Achille Giacometti, Rudolf Podgornik, Trinh Xuan Hoang, 2012, other component parts

Found in: ključnih besedah
Summary of found: ...Monte Carlo simulation, biopolymers, coil-globule transition, Wang-Landau sampling, ...
Keywords: Monte Carlo simulation, biopolymers, coil-globule transition, Wang-Landau sampling
Published: 25.04.2014; Views: 1965; Downloads: 6
URL Fulltext (0,00 KB)

3.
Do we really need water models in full, when it comes to studies of biopolymer conformations?
Artem V. Badasyan, 2014, published scientific conference contribution abstract

Found in: ključnih besedah
Summary of found: ...water, biopolymers, cold denaturation, ...
Keywords: water, biopolymers, cold denaturation
Published: 22.01.2015; Views: 1830; Downloads: 9
URL Fulltext (0,00 KB)

4.
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: ključnih besedah
Summary of found: ...simplest to describe the conformational transitions in biopolymers and is regularly used for preocessing the...
Keywords: Zimm-Bragg model, conformational transitions in biopolymers, cold denaturation
Published: 28.09.2016; Views: 2679; Downloads: 132
.pdf Fulltext (1,70 MB)

5.
New method to process Circular Dichroism experimental data on heat and cold denaturation of polypeptides in water
Artem V. Badasyan, Matjaž Valant, 2018, published scientific conference contribution abstract

Abstract: During the past decade the experimental studies of biopolymer conformations have reached an unprecedented level of detailization and allow 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. References [1] I. König, A. Zarrine-Afsar, M. Aznauryan, A. Soranno, B. Wunderlich, F. Dingfelder, J. C. Stüber, A. Plückthun, D. Nettels, B. Schuler, (2015), Single-molecule spectroscopy of protein conformational dynamics in live eukaryotic cells/Nature Methods, 12, 773-779. [2] J. Seelig, H.-J. Schönfeld, (2016), Thermal protein unfolding by differential scanning calorimetry and circular dichroism spectroscopy. Two-state model versus sequential unfolding/Quarterly Reviews of Biophysics, 49, e9, 1-24. [3] A.V. Badasyan, A. Giacometti, Y. Sh. Mamasakhlisov, V. F. Morozov, A. S. Benight, (2010), Microscopic formulation of the Zimm-Bragg model for the helix-coil transition/Physical Review E, 81, 021921. [4] B. H. Zimm, J. K. Bragg, (1959), Theory of the Phase Transition between Helix and Random Coil in Polypeptide Chains/Journal of Chemical Physics, 31, 526. [5] A. Badasyan, Sh.A. Tonoyan, A. Giacometti, R. Podgornik, V.A. Parsegian, Y.Sh. Mamasakhlisov, V.F. Morozov, (2014), Unified description of solvent effects in the helix-coil transition/Physical Review E, 89, 022723. Corresponding author: Artem Badasyan (artem.badasyan@ung.si)
Found in: ključnih besedah
Summary of found: ...relies on theoretical approaches to conformational transitions in biopolymers [2]. However, the models that are currently...
Keywords: Biopolymers, Circular Dichroism, Zimm-Bragg model, helix-coil transition.
Published: 22.10.2018; Views: 481; Downloads: 0
.pdf Fulltext (83,24 KB)

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