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1.
The generalized model of polypeptide chain describing the helix-coil transition in biopolymers
Artem V. Badasyan, Yevgeni S. Mamasakhlisov, Artem V. Tsarukyan, Arsen V. Grigoryan, Vladimir F. Morozov, 2005, končno poročilo o rezultatih raziskav

Najdeno v: ključnih besedah
Ključne besede: biopolymers, helix-coil transition, conformation
Objavljeno: 25.04.2014; Ogledov: 2186; Prenosov: 64
URL Polno besedilo (0,00 KB)

2.
Physics behind the Conformational Transitions in Biopolymers. Demystification of DNA melting and Protein Folding
Artem V. Badasyan, predavanje na tuji univerzi

Opis: Biophysics is the area of research, devoted to the studies of physical problems related to living systems. Animal cell is the smallest unit of an organism and mainly contains water solutions of structurally inhomogeneous polymers of biological origin: polypeptides (proteins) and polynucleotides (DNA, RNA). Statistical physics of macromolecules allows to describe the conformations of both synthetic and bio-polymers and constitutes the basis of Biophysics. During the talk I will report on the biophysical problems I have solved with numerical simulations (Langevin-based Molecular Dynamics of Go-like protein folding model and Monte Carlo with Wang-Landau sampling) and analytical studies of spin models (formula evaluation by hand, enforced with computer algebra systems). The direct connections with the theory of phase transitions, algebra of non-commutative operators and decorated spin models will be elucidated.
Najdeno v: ključnih besedah
Povzetek najdenega: ...Biophysics, protein folding, helix-coil transition, spin models...
Ključne besede: Biophysics, protein folding, helix-coil transition, spin models
Objavljeno: 13.12.2016; Ogledov: 1836; Prenosov: 0
.pdf Polno besedilo (136,69 KB)

3.
New method to process Circular Dichroism experimental data on heat and cold denaturation of polypeptides in water
Artem V. Badasyan, Matjaž Valant, 2018, objavljeni povzetek znanstvenega prispevka na konferenci

Opis: 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)
Najdeno v: ključnih besedah
Povzetek najdenega: ...Microscopic formulation of the Zimm-Bragg model for the helix-coil transition/Physical Review E, 81, 021921. [4] B. H.... ...essentially relies on theoretical approaches to conformational transitions in biopolymers [2]. However, the models that are...
Ključne besede: Biopolymers, Circular Dichroism, Zimm-Bragg model, helix-coil transition.
Objavljeno: 22.10.2018; Ogledov: 852; Prenosov: 0
.pdf Polno besedilo (83,24 KB)

4.
On spin description of water-biopolymer interactions: theory and experiment of reentrant order-disorder transition.
Artem V. 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.
Najdeno v: ključnih besedah
Povzetek najdenega: ... helix-coil transition, water-polypeptide interactions...
Ključne besede: helix-coil transition, water-polypeptide interactions
Objavljeno: 13.03.2019; Ogledov: 755; Prenosov: 0
.pdf Polno besedilo (78,48 KB)

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