1. Entropic cost of folding and phase diagrams of polypeptides: Why are IDPs unfolded at room temperature?Artem Badasyan, predavanje na tuji univerzi Opis: 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 alphahelix 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 socalled Ramachandran map can be plotted, which is actually the phase space visualization for the helixcoil 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 Qvalues, 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. Najdeno v: ključnih besedah Povzetek najdenega: ...IDP, protein folding, phase diagram... Ključne besede: IDP, protein folding, phase diagram Objavljeno: 23.06.2016; Ogledov: 2466; Prenosov: 0 Polno besedilo (2,96 MB) Gradivo ima več datotek! Več...

2. Physics behind the Conformational Transitions in Biopolymers. Demystification of DNA melting and Protein FoldingArtem 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 biopolymers and constitutes the basis of Biophysics. During the talk I will report on the biophysical problems I have solved with numerical simulations (Langevinbased Molecular Dynamics of Golike protein folding model and Monte Carlo with WangLandau 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 noncommutative operators and decorated spin models will be elucidated. Najdeno v: ključnih besedah Ključne besede: Biophysics, protein folding, helixcoil transition, spin models Objavljeno: 13.12.2016; Ogledov: 3297; Prenosov: 0 Polno besedilo (136,69 KB) 
3. Water reveals nonArrhenius kinetics in protein folding experimentsArtem Badasyan, 2020, objavljeni povzetek znanstvenega prispevka na konferenci (vabljeno predavanje) Opis: Statistical theories describe systems in equilibrium, and cannot be used to study kinetics. However, the theo
ries are based on coarsegrained 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 ZimmBragg [1] theory to process folding
experiments, and discuss the reasons and consequences.
Studies of relaxation phenomena in glassforming 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 supercooled liquids as the
temperature is approaching[3]. The key idea of AdamGibbs 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 AdammGibbs temperature
shift into their simple analytical model of water to achieve the agreement with experimental data on the tem
perature dependence of selfdiffusion 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 superArrhenius relaxation region above the ”protein dynamic
transition” temperature [4]. Recently, Mallamace et al have used the AdamGibbs theory in their NMR meas
urements of protein foldingunfolding in water [4] and to rationalise the complicated pressuretemperature
diagrams in these glassforming 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 Najdeno v: ključnih besedah Ključne besede: water, protein folding, nonArrhenius kinetics Objavljeno: 20.07.2020; Ogledov: 544; Prenosov: 28 Polno besedilo (2,35 MB) 
4. The finite size effects and twostate paradigm of protein foldingVladimir N. Uversky, Jože Grdadolnik, Artem Badasyan, Matjaž Valant, 2021, izvirni znanstveni članek Opis: 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 coilglobule phase transition. Based on the pedantic derivation of the twostate 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 twostate 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 coilglobule phase transition. Moreover, these two measures are shown to describe different characteristics of protein folding Najdeno v: ključnih besedah Ključne besede: protein folding, twostate model, size scaling, thermodynamic cooperativity Objavljeno: 24.02.2021; Ogledov: 211; Prenosov: 7 Polno besedilo (0,00 KB) Gradivo ima več datotek! Več...

5. Implicit water model within the ZimmBragg approach to analyze experimental data for heat and cold denaturation of proteinsJože Grdadolnik, Matjaž Valant, Sh. A. Tonoyan, Artem Badasyan, 2021, izvirni znanstveni članek Opis: 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 ZimmBragg model we propose includes a simplified, yet
explicit model of waterpolypeptide 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 Hbonds, 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. Najdeno v: ključnih besedah Povzetek najdenega: ... protein folding, cold denaturation, water, ZimmBragg model... Ključne besede: protein folding, cold denaturation, water, ZimmBragg model Objavljeno: 06.05.2021; Ogledov: 56; Prenosov: 1 Polno besedilo (0,00 KB) Gradivo ima več datotek! Več...
