1. Modeling of solvent role in protein folding experiments : dissertationKnarik Yeritsyan, 2025, doctoral dissertation Abstract: 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.
Keywords: 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
Published in RUNG: 27.01.2025; Views: 1415; Downloads: 13
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2. Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteinsArtem Badasyan, Sh. A. Tonoyan, Matjaž Valant, Jože Grdadolnik, 2021, original scientific article Abstract: 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.
Keywords: protein folding, cold denaturation, water, Zimm-Bragg model
Published in RUNG: 06.05.2021; Views: 3742; Downloads: 17
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3. Developments of a new mirror technology for the Cherenkov Telescope ArrayJerzy Michałowski, Andrej Filipčič, Gašper Kukec Mezek, Samo Stanič, Serguei Vorobiov, Lili Yang, Gabrijela Zaharijas, Danilo Zavrtanik, Marko Zavrtanik, 2015, published scientific conference contribution Keywords: Cherenkov Telescope Array (CTA), mirror technology for CTA, cold-slumping, front reflecting aluminium-coated panel
Published in RUNG: 16.01.2017; Views: 5110; Downloads: 256
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4. Phenolic Contents and Postharvest Quality Changes of Norwegian ‘Mallard’ plums (Prunus domestica L.) as a Consequence of Delayed Time to Low Temperature Storage : /Branka Mozetič Vodopivec, Alena Gibalova, Eivind Vangdal, 2012, published scientific conference contribution Abstract: During the picking season in the Norwegian plum production areas, the
harvested plums are brought to cold storage in packing houses once or twice a day.
Plums picked late in the afternoon may even not be cooled properly until the next
day. The average time from picking until the plums are placed in a cold storage is
approximately 8 hours. Previous reports have shown that delayed cooling of sweet
cherries and apples reduced the fruits’ susceptibility to physiological or fungal
decay. An experiment was performed in order to evaluate the impact of different
delay-to-cold storage times (0, 5, 10, 15 and 25 hours) on quality and phenolic
contents changes of Norwegian ‘Mallard’ plums during cold storage, transport, and
retail in normal atmosphere (NA). The fruits (10 fruits in PE tray, n=3) were stored
for 14 days at 1°C, followed by 3 days at 7°C and then for 4 days at 20°C. Fruit
quality parameters (firmness, colour in CIE L, a*, b* colour space, weight, rot
occurrence (%)) and total phenol and anthocyanin content were determined.
Samples were analyzed just before cold storage and then after 14 days at 1°C, 3 days
at 7°C, or 4 days at 20°C. Evaluation of results has shown that delay of cooling has a
retarding effect on rot development during 20°C storage (post cold transport),
weight loss and stimulates anthocyanin accumulation and colour changes to some
extent. At the end of storage no effect on fruit firmness could be observed.
Keywords: anthocyanins, total phenols, colour, rot, firmness, postharvest, plums, cold
storage
Published in RUNG: 11.11.2016; Views: 6251; Downloads: 0
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5. WATER-POLYPEPTIDE INTERACTION IN CLASSICAL MODELS OF HELIX-COIL TRANSITIONKnarik Yeritsyan, 2016, undergraduate thesis Abstract: 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.
Keywords: Zimm-Bragg model, conformational transitions in biopolymers, cold denaturation
Published in RUNG: 28.09.2016; Views: 9999; Downloads: 284
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