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1.
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

Najdeno v: ključnih besedah
Povzetek najdenega: ...water, biopolymers, cold denaturation, ...
Ključne besede: water, biopolymers, cold denaturation
Objavljeno: 22.01.2015; Ogledov: 2726; Prenosov: 16
URL Polno besedilo (0,00 KB)

2.
WATER-POLYPEPTIDE INTERACTION IN CLASSICAL MODELS OF HELIX-COIL TRANSITION
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.
Najdeno v: ključnih besedah
Povzetek najdenega: ...of water-polypeptide interactions allows to describe both cold denaturation and helix-coil transition and derive such...
Ključne besede: Zimm-Bragg model, conformational transitions in biopolymers, cold denaturation
Objavljeno: 28.09.2016; Ogledov: 4013; Prenosov: 177
.pdf Polno besedilo (1,70 MB)

3.
Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins
Jože 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 Zimm-Bragg model we propose includes a simplified, yet explicit model of water-polypeptide 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 H-bonds, 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
Ključne besede: protein folding, cold denaturation, water, Zimm-Bragg model
Objavljeno: 06.05.2021; Ogledov: 0; Prenosov: 0
URL Polno besedilo (0,00 KB)
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