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: 570; Downloads: 11
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2. Probing hadronic interactions using the latest data measured by the Pierre Auger ObservatoryCaterina Trimarelli, Andrej Filipčič, Jon Paul Lundquist, Shima Ujjani Shivashankara, Samo Stanič, Serguei Vorobiov, Danilo Zavrtanik, Marko Zavrtanik, Lukas Zehrer, 2022, published scientific conference contribution Abstract: The Pierre Auger Observatory is the world’s largest ultra-high energy cosmic ray observatory. Its hybrid detection technique combines the observation of the longitudinal development of extensive air showers and the lateral distribution of particles arriving at the ground. In this contribution, a review of the latest results on hadronic interactions using measurements from the Pierre Auger Observatory is given. In particular, we report on the self-consistency tests of the post-LHC models using measurements of the depth of the shower maximum and the main features of the muon component at the ground. The tensions between the model predictions and the data, considering different shower observables, are reviewed.
Keywords: ultra-high-energy cosmic rays, hadronic interactions, extensive air showers, maximum depth, EAS muon content, Pierre Auger Observatory, post-LHC hadronic interaction models
Published in RUNG: 04.10.2024; Views: 881; Downloads: 8
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3. Native agarose gels and contact blotting as means to optimize the protocols for the formation of antigen-ligand complexesClaudia D'Ercole, Ario De Marco, 2024, published scientific conference contribution abstract Abstract: Background. Protein complexes provide valuable biological information but can be difficult to handle [1]. Therefore, technical advancements designed to improve their manipulation are al-ways useful.
Methods. We investigated the opportunity to exploit native agarose gels and the contact bot method for the transfer of native proteins to membranes as means for optimizing the conditions for obtaining stable complexes [2]. As a simple model of protein-protein interactions, an anti-gen-ligand complex was used in which both proteins were fused to reporters.
Results. At each step, it was possible to visualize both the antigen, fused to a fluorescent pro-tein, and the ligand, fused to a monomeric ascorbate peroxidase (APEX) and, as such, a way to tune the protocol. The conditions for the complex formation were adapted by modifying the buffer conditions, the concentration of the proteins and of the cross-linkers.
Conclusions. The procedure is rapid, inexpensive, and the several detection opportunities al-lows for both the monitoring of complex stability and the preservation of the functionality of its components, which is critical for understanding their biomedical implications and supporting drug discovery. The overall protocol represents a handy alternative to gel filtration, uses very standard and ubiquitous equipment, and can be implemented rapidly and without specific train-ing.
References:
[1] O. Puig, F. Caspary, G. Rigaut, B. Rutz, E. Bouveret, E. Bragado-Nilsson, M. Wilm, B. Séraphin. The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods. (San Diego, Calif.), 24(3), 218–229
[2] C. Sakuma, M. Nakagawa, Y. Tomioka, T. Maruyama, K. Entzminger, J.K. Fleming, T. Shibata, Y. Kurosawa, C.J. Okumura, T. Arakawa, T. Akuta. Western blotting of native proteins from agarose gels. Biotechniques. 2022 May;72(5):207-218
Keywords: protein complexes, contact blotting, native agarose gels, protein interaction
Published in RUNG: 17.06.2024; Views: 1429; Downloads: 2
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4. The second knee in the cosmic ray spectrum observed with the surface detector of the Pierre Auger ObservatoryGabriel Brichetto Orquera, Andrej Filipčič, Jon Paul Lundquist, Shima Ujjani Shivashankara, Samo Stanič, Serguei Vorobiov, Danilo Zavrtanik, Marko Zavrtanik, 2023, published scientific conference contribution Abstract: The determination of the energy spectrum features with low systematic uncertainty is crucial for interpreting the nature of cosmic rays. In this study, we conducted a measurement of the energy spectrum at the Pierre Auger Observatory using a surface detector with a calorimetric
energy scale indirectly set by a fluorescence detector. The surface detector consists of an array of water-Cherenkov detectors that extends over 3000 km^2 with 1500m spacing. Additionally,
two nested arrays of the same kind with 750m and 433m spacing were utilized to lower the energy threshold of the measurements. This contribution presents, for the first time, the spectrum measured with the 433m array, which reduces the energy threshold down to 63 PeV, nearly half the energy at which we previously published a steepening using the 750m array. Our measurements include a characterization of the spectral features of the flux steepening around 230 PeV, known
as the second-knee. The study benefits from a nearly 100% duty cycle and geometrical exposure. Notably, this is the first simultaneous measurement of the second knee energy and spectral indexes before and after the break, using a surface detector with an energy scale predominantly independent of air shower simulations and assumptions regarding hadronic interaction models.
Keywords: ultra-high energy cosmic rays, Pierre Auger Observatory, hadronic interaction model, water-Cherenkov detectors
Published in RUNG: 23.01.2024; Views: 1850; Downloads: 5
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5. Measurement of the Proton-Air Cross Section with Telescope Arrays Black Rock, Long Ridge, and Surface Array in Hybrid Mode.R. Abbasi, Jon Paul Lundquist, 2022, published scientific conference contribution Abstract: Ultra High Energy Cosmic Ray (UHECR) detectors have been reporting on the proton-air cross section measurement beyond the capability of particle accelerators since 1984. The knowledge of this fundamental particle property is vital for our understanding of high energy particle interactions and could possibly hold the key to new physics. The data used in this work was collected over eight years using the hybrid events of Black Rock (BR) and Long Ridge (LR) fluorescence detectors as well as the Telescope Array Surface Detector (TASD). The proton-air cross section is determined at s√=73~TeV by fitting the exponential tail of the Xmax distribution of these events. The proton-air cross section is then inferred from the exponential tail fit and from the most updated high energy interaction models. σ^inel_p−air is observed to be 520.1±35.8 [Stat.] +25.3−42.9 [Sys.] mb. This is the second proton-air cross section work reported by the Telescope Array collaboration.
Keywords: Telescope Array, indirect detection, hybrid detection, ground array, fluorescence detection, ultra-high energy, cosmic rays, Xmax, proton-air cross-section, high energy particle interaction
Published in RUNG: 04.10.2023; Views: 2076; Downloads: 5
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6. Measurement of the fluctuations in the number of muons in extensive air showers with the Pierre Auger ObservatoryA. Aab, Andrej Filipčič, Gašper Kukec Mezek, Jon Paul Lundquist, Samo Stanič, Marta Trini, Serguei Vorobiov, Danilo Zavrtanik, Marko Zavrtanik, Lukas Zehrer, 2021, original scientific article Keywords: ultra-high energy cosmic rays, extensive air showers (EAS), EAS muonic component, hadronic interaction models, Pierre Auger Observatory
Published in RUNG: 29.04.2021; Views: 3197; Downloads: 0
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7. podMAST / Jenny Brockmann : Leaving the audience unsatisfied through unstable systems, to create communication about urgent questions in societyPeter Purg, Lange Teena, radio or television broadcast, podcast, interview, press conference Keywords: Experiment, inbetween, balance, architecture, speculative, transdisciplinary, embodiment, knowledge sharing, conversation, unsatisfied audience, process based, shaping interaction spaces, encounter, care, integrity., inbetween, balance, architecture, speculative, transdisciplinary, embodiment, knowledge sharing, conversation, unsatisfied audience, process based, shaping interaction spaces, encounter, care, integrity.
Published in RUNG: 06.11.2020; Views: 3508; Downloads: 73
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8. Structural and functional determinants of TDP-43 aggregation : DissertationSanja Škaro, 2019, doctoral dissertation Abstract: TDP-43 (TAR DNA-binding protein) is an hnRNP that was identified as the main component of the brain inclusions characteristically found in patients suffering of Amyotrophic Lateral Sclerosis and Frontotemporal Lobar Degeneration. As an hnRNP protein, TDP-43 fulfills diverse roles in mRNA metabolism, localization and transport. Structurally, TDP-43 is composed of a well conserved N terminal domain (NTD), two RRM domains of which RRM1 is necessary for recognizing and binding to its target, UG rich RNA sequences, and the C-terminal domain (CTD) which is a Glycine rich domain. The CTD also contains a Q/N rich region that plays a key role in protein aggregation and interaction with another hnRNP proteins and polyglutamine repeats. This thesis focus on the structural determinants involved in the different TDP-43 interactions with itself and with other hnRNPs. Both the carboxyl and amino terminal domains are involved in these interactions. We have mapped the regions more relevant for the function of TDP-43 and for the aggregation process characteristic of the pathological pathway leading to neurodegeneration. We have started to further study the N-terminal domain. Previous results in our laboratory using a cellular aggregation model have shown that the N-terminal domain is also necessary for sequestering the endogenous TDP-43 into the aggregates. In particular, the intact NTD, specifically residues 1 to 77, have been shown to be needed to efficiently recruit TDP-43 monomers into these aggregates. We have extended our knowledge of NTD structure and function, by assessing the behavior of a series of proteins in which key structural features (α-helix and β-sheets) were modified and TDP-43 splicing function together with structure via NMR were analyzed. It was found that by disrupting protein secondary structure in the NTD (mutation in α-helix NTD-31V/R-32T/R) the capacity of the aggregates to sequester enough TDP-43 to induce loss of function was lost.In fact, this protein is also unable to recovery TDP-43 functionality when it is disrupted due to sequestration of the endogenous TDP-43 in add back experiments. Disturbing protein stability through substitution of residues in α-helix also affects its ability to form an active conformation. On the other hand, synthesis of hybrid peptides containing certain NTD and CTD segments was performed in order to see if they are capable to bind to the TDP-43 aggregates. However, it has been shown that these synthetic peptides have a greater ability to induce TDP-43 aggregation than to bind to them, probably due to specific functional characteristics of NTD and CTD segments used for their synthesis.The main focus of the thesis was on the C-terminal domain sequences involved in protein-protein interaction, misfolding and aggregation.A comparison of human, mouse, zebrafish, Annelida, flatworms and Drosophila showed a very strong conservation of the NTD and RRMs, but the C terminal regions of human and other TDP-43 orthologues are very different.I have studied Human and Drosophila melanogaster orthologues, because Drosophila orthologue contains different paralogs of TDP-43.Through a series of deletions and mutations it was shown that the shorter paralog of Drosophila TDP-43 (TBPH-RA) is more active than the longer one (TBPH-RC), and that this is due to a combination of two factors: 1. TBPH-RC by itself aggregates more than TBPH-RA, 2. The functionality of TBPH-RC is downregulated by intramolecular interactions in the C terminal domain. Apparently there is a cation-π interaction involving Tryptophan and Arginine in TBPH-RC that has a high relevance to the protein function and is lacking in the TBPH-RA.Overall this data has identified structural features essential for the proper function of TDP-43.In addition, we have also identified sequences that are critical in the pathological aggregation process of TDP-43 that lead to the characteristic brain inclusions in ALS and FTLD and to the loss of functionality
Keywords: TDP-43 structural determinants, hybrid peptides, protein-protein interactions, intramolecular interaction, cation-π interaction, Drosophila orthologues.
Published in RUNG: 22.07.2019; Views: 4636; Downloads: 196
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10. Shower universality reconstruction of data from the Pierre Auger Observatory and validations with hadronic interaction modelsAriel Bridgeman, Andrej Filipčič, Gašper Kukec Mezek, Ahmed Saleh, Samo Stanič, Marta Trini, Serguei Vorobiov, Lili Yang, Danilo Zavrtanik, Marko Zavrtanik, 2017, published scientific conference contribution Keywords: Pierre Auger Observatory, shower universality reconstruction, hadronic interaction models
Published in RUNG: 16.02.2018; Views: 4492; Downloads: 153
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