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1.
Modeling of solvent role in protein folding experiments : dissertation
Knarik Yeritsyan, 2025, doktorska disertacija

Opis: The Zimm-Bragg (ZB) model serves as a fundamental framework for elucidating conformational transitions in biopolymers, offering simplicity and efficacy in processing experimental data. This study provides a comprehensive review of the Zimm-Bragg model and its Hamiltonian formulation, with particular emphasis on incorporating water interactions and chain size effects into the computational framework. We propose a modified ZB model that accounts for water-polypeptide interactions, demonstrating its ability to describe phenomena such as cold denaturation and helix-coil transitions. In the realm of NanoBioTechnologies, the manipulation of short polypeptide chains is commonplace. Experimental investigation of these chains in vitro often relies on techniques like Circular Dichroism (CD) and timeresolved infrared spectroscopy. Determining interaction parameters necessitates processing the temperature dependence of the normalized degree of helicity through model fitting. Leveraging recent advancements in the Hamiltonian formulation of the Zimm and Bragg model, we explicitly incorporate chain length and solvent effects into the theoretical description. The resulting expression for helicity degree adeptly fits experimental data, yielding hydrogen bonding energies and nucleation parameter values consistent with field standards. Differential Scanning Calorimetry (DSC) stands as a potent tool for measuring the specific heat profile of materials, including proteins. However, relating the measured profile to microscopic properties requires a suitable model for fitting. We propose a novel algorithm for processing DSC experimental data based on the ZB theory of protein folding in water. This approach complements the classical two-state paradigm and provides insights into protein-water and intraprotein hydrogen bonding energies. An analytical expression for heat capacity, considering water interaction, is derived and successfully applied to fit numerous DSC experimental datasets reported in the literature. Additionally, we compare this approach with the classical two-state model, demonstrating its efficacy in fitting DSC data. Furthermore, we have developed and launched a free online tool for processing CD and DSC experimental data related to protein folding, aiming to support scientific research.
Ključne besede: Zimm-Bragg model, conformational transitions, helix-coil transitions, cold denaturation, circular dichroism, differential scanning calorimetry, protein folding, water-protein interaction, hydrogen bonding energy, degree of helicity, short polypeptide chains, protein heat capacity, protein data analysis, dissertations
Objavljeno v RUNG: 27.01.2025; Ogledov: 830; Prenosov: 13
.pdf Celotno besedilo (5,12 MB)

2.
Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins
Artem Badasyan, Sh. A. Tonoyan, Matjaž Valant, Jože Grdadolnik, 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.
Ključne besede: protein folding, cold denaturation, water, Zimm-Bragg model
Objavljeno v RUNG: 06.05.2021; Ogledov: 3611; Prenosov: 17
URL Povezava na celotno besedilo
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3.
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.
Ključne besede: Zimm-Bragg model, conformational transitions in biopolymers, cold denaturation
Objavljeno v RUNG: 28.09.2016; Ogledov: 9619; Prenosov: 284
.pdf Celotno besedilo (1,70 MB)

4.
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: 6580; Prenosov: 36
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