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Temperature induced de-agglomeration of the polysilane macromolecules
Andraž Mavrič, Artem Badasyan, Mattia Fanetti, Matjaž Valant, 2016, objavljeni povzetek znanstvenega prispevka na konferenci

Ključne besede: polysilane, de-agglomeration, dynamic light scattering, differential scanning calorimetry
Objavljeno v RUNG: 05.10.2016; Ogledov: 5509; Prenosov: 0
Gradivo ima več datotek! Več...

Knarik Yeritsyan, 2016, diplomsko delo

Opis: 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.
Ključne besede: Zimm-Bragg model, conformational transitions in biopolymers, cold denaturation
Objavljeno v RUNG: 28.09.2016; Ogledov: 7926; Prenosov: 272
.pdf Celotno besedilo (1,70 MB)

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 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.
Ključne besede: IDP, protein folding, phase diagram
Objavljeno v RUNG: 23.06.2016; Ogledov: 4924; Prenosov: 0
Gradivo ima več datotek! Več...

Do we really need water models in full, when it comes to studies of biopolymer conformations?
Artem Badasyan, 2014, objavljeni povzetek znanstvenega prispevka na konferenci

Ključne besede: water, biopolymers, cold denaturation
Objavljeno v RUNG: 22.01.2015; Ogledov: 5552; Prenosov: 33
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