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1.
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: ključnih besedah
Summary of found: ...IDP, protein folding, phase diagram...
Keywords: IDP, protein folding, phase diagram
Published: 23.06.2016; Views: 1963; Downloads: 0
.pdf Fulltext (2,96 MB)
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2.
Physics behind the Conformational Transitions in Biopolymers. Demystification of DNA melting and Protein Folding
Artem V. Badasyan, invited lecture at foreign university

Abstract: 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.
Found in: ključnih besedah
Keywords: Biophysics, protein folding, helix-coil transition, spin models
Published: 13.12.2016; Views: 1803; Downloads: 0
.pdf Fulltext (136,69 KB)

3.
Water reveals non-Arrhenius kinetics in protein folding experiments
Artem V. Badasyan, 2020, published scientific conference contribution abstract (invited lecture)

Abstract: Statistical theories describe systems in equilibrium, and cannot be used to study kinetics. However, the theo- ries are based on coarse-grained parameters, that include assumptions regarding the underlying kinetics. If such assumptions are incorrect, the theoretical expressions, used to process the experimental data, will not fit. I report on one such case we have met within the application of Zimm-Bragg [1] theory to process folding experiments, and discuss the reasons and consequences. Studies of relaxation phenomena in glass-forming liquids by default account for the shift in temperature by some value, corresponding to the glass formation temperature, .In particular, temperature shift appears in hydrated proteins because of the presence of partially glassy states giving rise to non- Arrhenius relaxation times log τ ~ [2]. A phenomenological approach was suggested by Adam and Gibbs as early as in 1965 to describe the sudden increase of viscosity and the slowing down of the collective modes in super-cooled liquids as the temperature is approaching[3]. The key idea of Adam-Gibbs theory was to consider the supercooled liquid as a set of clusters (cooperatively rearranging regions) of different sizes that change with temperature, giving rise to the shift in re- laxation time. The temperature shift factor is present in many theories describing properties of water. Thus, Truskett and Dill had to include the Adamm-Gibbs temperature shift into their simple analytical model of water to achieve the agreement with experimental data on the tem- perature dependence of self-diffusion coefficient [4]. Later, Schiro and Weik have summarised recent in vitro and in silico experimental results regarding the role of hydration water in the onset of protein structural dy- namics, and have reported the presence of super-Arrhenius relaxation region above the ”protein dynamic transition” temperature [4]. Recently, Mallamace et al have used the Adam-Gibbs theory in their NMR meas- urements of protein folding-unfolding in water [4] and to rationalise the complicated pressure-temperature diagrams in these glass-forming systems. Motivated by the considerations above, and taking into account the relationship between the unimolecular rate of folding in water and the relaxation time 45 , we introduce the tem- perature shift into the formulas used to fit experimental data on hydrated polypeptides. By doing so we resolve the paradox and complete the new method of processing the Circular Dichroism ex- perimental data on protein folding
Found in: ključnih besedah
Keywords: water, protein folding, non-Arrhenius kinetics
Published: 20.07.2020; Views: 91; Downloads: 6
.pdf Fulltext (2,35 MB)

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