1. Local climate and cultivation practice shape total protein and phenolic content of mulberry (morus sp.) leaves in sub-mediterranean and sub-pannonian regions of SloveniaŠpela Jelen, Martin Kozmos, Jan Senekovič, Danijel Ivajnšič, Silvia Cappellozza, Andreja Urbanek Krajnc, 2025, izvirni znanstveni članek Opis: Mulberry (Morus sp.) trees, traditionally cultivated for their leaves used in sericulture, have recently gained recognition for their adaptability and valuable ecosystem services. The biochemical composition of mulberry leaves varies both qualitatively and quantitatively, depending on genotype, environmental conditions, and cultivation practices. This study aimed to (1) identify differences in old local white (M. alba L.) and black mulberry (M. nigra L.) leaves, (2) perform a chemotype analysis of monitored local varieties, and (3) evaluate the influence of selected bioclimatic factors and pruning practices on the biochemical composition of leaves of white mulberry trees across Slovenian mesoregions. Black mulberry exhibited a higher phenolic content, particularly caffeoylquinic acid derivatives (16.05 mg/g dry weight (DW)), while white mulberry contained more quercetin glycosides (6.04 mg/g DW). Ward’s clustering identified three chemotypes, two of which had elevated protein and hydroxycinnamic acid levels, making them particularly suitable for silkworm feeding. Considering pruning practices of white mulberries, we determined significantly increased protein contents in yearly pruned trees (187.24 mg/g DW). Principal component analysis revealed interactions between bioclimatic, morphological, and biochemical factors, distinctly separating mulberries from the Sub-Mediterranean and Sub-Pannonian macroregions. White mulberries from Sub-Pannonian regions accumulated more caffeoylquinic acids in leaves under lower precipitation and total insolation, while those from Sub-Mediterranean regions exhibited higher kaempferol derivatives due to photo-thermal stress. These findings highlight the influence of climate and pruning on mulberry biochemical diversity and adaptation.
Ključne besede: mulberry, Morus alba, Morus nigra, local genetic resources, phenolics, protein, climatic effect, metabolite screening, pruning
Objavljeno v DKUM: 07.10.2025; Ogledov: 0; Prenosov: 2
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2. Unveiling polyphenol-protein interactions : a comprehensive computational analysisSamo Lešnik, Marko Jukič, Urban Bren, 2025, izvirni znanstveni članek Opis: Our study investigates polyphenol-protein interactions, analyzing their structural diversity and dynamic behavior. Analysis of the entire Protein Data Bank reveals diverse polyphenolic structures, engaging in various noncovalent interactions with proteins. Interactions observed across crystal structures among diverse polyphenolic classes reveal similarities, underscoring consistent patterns across a spectrum of structural motifs. On the other hand, molecular dynamics (MD) simulations of polyphenol-protein complexes unveil dynamic binding patterns, highlighting the influx of water molecules into the binding site and underscoring limitations of static crystal structures. Water-mediated interactions emerge as crucial in polyphenol-protein binding, leading to variable binding patterns observed in MD simulations. Comparison of high- and low-resolution crystal structures as starting points for MD simulations demonstrates their robustness, exhibiting consistent dynamics regardless of the quality of the initial structural data. Additionally, the impact of glycosylation on polyphenol binding is explored, revealing its role in modulating interactions with proteins. In contrast to synthetic drugs, polyphenol binding seems to exhibit heightened flexibility, driven by dynamic water-mediated interactions, which may also facilitate their promiscuous binding. Comprehensive dynamic studies are, therefore essential to understand polyphenol-protein recognition mechanisms. Overall, our study provides novel insights into polyphenol-protein interactions, informing future research for harnessing polyphenolic therapeutic potential through rational drug design.
Ključne besede: polyphenols, polyphenol-protein complexes, molecular dynamics simulations, noncovalent interactions, water-mediated interactions, glycosylation, dynamic behavior
Objavljeno v DKUM: 14.08.2025; Ogledov: 0; Prenosov: 3
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3. The effect of preconditioning strategies on the adsorption of model proteins onto screen-printed carbon electrodesTea Romih, Ivan Konjević, Lea Žibret, Ika Fazarinc, Ajda Beltram, David Majer, Matjaž Finšgar, Samo B. Hočevar, 2022, izvirni znanstveni članek Opis: The preconditioning and modification of the supporting electrode surface is an essential
step in every biosensor architecture. In particular, when using screen-printed carbon electrodes (SPEs)
as inexpensive and convenient disposable sensor substrates, their somewhat lower electrochemical
(surface) reproducibility might represent a complex hurdle. Herein, we investigated the effect of
selected preconditioning strategies, such as cyclic voltammetric pretreatment, in H2SO4 and H2O2
and plasma pretreatment with a positive and negative glow discharge, which all improved the electrochemical stability of the unmodified SPEs. Furthermore, we studied the influence of preconditioning
strategies on the adsorption kinetics of the two most commonly used building blocks for biosensor
preparation, i.e., bovine serum albumin (BSA) and protein A. We observed an advantageous effect
of all the examined preconditioning strategies for the modification of SPEs with protein A, being
the most effective the negative glow discharge. On the other hand, BSA exhibited a more complex
adsorption behavior, with the negative glow discharge as the only generally beneficial preconditioning strategy providing the highest electrochemical stability. Protein A revealed a more substantial
impact on the electrochemical signal attenuation than BSA considering their same concentrations in
the modification solutions. For both BSA and protein A, we showed that the concentrations of 5 and
10 µg mL−1 already suffice for an electrochemically satisfactorily stable electrode surface after 60 min
of incubation time, except for BSA at the positive-plasma-treated electrode.
Ključne besede: screen-printed carbon electrode, SPE, electrochemical biosensor, adsorption, bovine serum albumin, protein A, glow discharge
Objavljeno v DKUM: 15.05.2025; Ogledov: 0; Prenosov: 2
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4. Protein stacking on the APTES-functionalized pyrochlore ▫$Bi_2Ru_2O_7$▫ clusters for ultrasensitive and selective immunosensingNikola Tasić, Nika Vranešič, Dino Metarapi, Kristina Mervič, Milan Žunić, Aleksandra Dapčević, Matjaž Finšgar, Samo B. Hočevar, 2025, izvirni znanstveni članek Opis: With their unique physicochemical properties, such as metallic-like conductivity, favorable (electro)catalytic properties, electrochemical stability, and ease of functionalization, pyrochlores have found applications in various fields such as solid oxide fuel cells, batteries, thick film resistors, and temperature sensors; however, there are no reports on their application in electrochemical immunosensing. In this study, we exploited the (electro)catalytic nature and stability of the pyrochlore Bi2Ru2O7 clusters silanized with (3-aminopropyl)triethoxysilane (APTES) to demonstrate their potential for the effective stacking of functional proteins. Characterization of the clusters by XPS disclosed a dual environment of Bi, also indicating the presence of Bi2O3 alongside APTES-Bi2Ru2O7 clusters and, importantly, the predominant involvement of pyrochlore moieties in subsequent protein stacking. After stacking protein A and antibodies, the immunosensor revealed a nearly interference-free operation, high sensitivity, a detection limit of 118 fM SARS-CoV-2 spike protein, and operation in a wide examined concentration range of 10−5−10−1 μg mL−1 with an r2 of 0.98. In combination with a short incubation time of 30 min, the pyrochlore-based immunosensor provides a solid platform for future point-of-need applications.
Ključne besede: Bi2Ru2O7 pyrochlore, APTES, SARS-CoV-2, spike protein, immunosensors, electrochemical
Objavljeno v DKUM: 23.04.2025; Ogledov: 0; Prenosov: 2
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5. Enhancing Martini3 for protein self-interaction simulationsJonas Binder, Matja Zalar, Martin Huelsmeyer, Michael Siedler, Robin Curtis, Wolfgang Frieß, 2025, izvirni znanstveni članek Opis: Coarse-grained molecular dynamics simulations are highly valuable for studying protein-protein interactions. Unfortunately, commonly used force fields often overestimate these interactions. Here, we investigate the performance of the Martini 3 force field in predicting the self-interaction behavior of lysozyme and subtilisin using Metadynamics. The original Martini 3, despite improvements over its predecessor, overestimates interaction strength. Through reparameterization of bead interactions, we achieve good agreement with experimental data of the second virial coefficient and the diffusion coefficient. The new, refined force field enables more accurate CG-MD simulations, with potential applications in understanding and prediction of protein stability, aggregation tendencies, and solubility, with the possibility to aid in the development of protein-based drugs.
Ključne besede: coarse-grained molecular dynamics, Martini 3 force field, protein-protein interactions, B22, reparameterization, NMR, diffusion coefficient
Objavljeno v DKUM: 20.03.2025; Ogledov: 0; Prenosov: 7
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6. Alginate coatings suppress unspecific protein adhesion on PVCMatej Bračič, Alenka Vesel, Lidija Fras Zemljič, 2025, izvirni znanstveni članek Opis: This study involved oxygen plasma activation of PVC and its effect on alginate coating adhesion, analyzed using a quartz crystal microbalance with dissipation (QCM-D). The results demonstrated improved adhesion of alginate on plasma-activated PVC due to an increase of oxidized functional groups. Wettability measurements, conducted using optical contact angle goniometry and QCM-D, showed a significant increase in the wettability of PVC after alginate coating, with contact angles decreasing from 81.4 ± 1.1◦ to 37.3 ± 3.1◦ 3D-profilometry mapping revealed a uniform distribution of alginate on the PVC film. Real-time antifouling studies using QCM-D with two model proteins, bovine serum albumin and bovine fibrinogen, were performed to elucidate the surface interactions involved in protein inhibition. The results indicated a substantial reduction in protein adhesion on alginate-coated PVC. This reduction in protein adhesion is attributed to the high hydrophilicity of the alginate coatings and partial removal of the alginate, which together contribute to poor protein adhesion. This comprehensive approach advances the development of effective solutions for mitigating biofilm-related issues on PVC-based medical devices, offering significant implications for improving patient outcomes.
Ključne besede: alginate, coatings, polyvinyl chloride, biofouling, quartz crystal microbalance, protein adhesion
Objavljeno v DKUM: 10.03.2025; Ogledov: 0; Prenosov: 10
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7. Why? - Successful Pseudomonas aeruginosa clones with a focus on clone CChanghan Lee, Jens Klockgether, Sebastian Fischer, Janja Trček, Burkhard Tümmler, Ute Römling, 2020, pregledni znanstveni članek Opis: The environmental species Pseudomonas aeruginosa thrives in a variety of habitats. Within the epidemic population structure of P. aeruginosa, occassionally highly successful clones that are equally capable to succeed in the environment and the human host arise. Framed by a highly conserved core genome, individual members of successful clones are characterized by a high variability in their accessory genome. The abundance of successful clones might be funded in specific features of the core genome or, although not mutually exclusive, in the variability of the accessory genome. In clone C, one of the most predominant clones, the plasmid pKLC102 and the PACGI-1 genomic island are two ubiquitous accessory genetic elements. The conserved transmissible locus of protein quality control (TLPQC) at the border of PACGI-1 is a unique horizontally transferred compository element, which codes predominantly for stress-related cargo gene products such as involved in protein homeostasis. As a hallmark, most TLPQC xenologues possess a core genome equivalent. With elevated temperature tolerance as a characteristic of clone C strains, the unique P. aeruginosa and clone C specific disaggregase ClpG is a major contributor to tolerance. As other successful clones, such as PA14, do not encode the TLPQC locus, ubiquitous denominators of success, if existing, need to be identified.
Ključne besede: disaggregase, FtsH, genomic island, protein homeostasis, pulsed field gel electrophoresis, whole genome sequencing
Objavljeno v DKUM: 28.01.2025; Ogledov: 0; Prenosov: 5
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8. Discovery of novel biomarkers with extended non-coding RNA interactor networks from genetic and protein biomarkersGregor Jezernik, Damjan Glavač, Pavel Skok, Martina Krušič, Uroš Potočnik, Mario Gorenjak, 2024, izvirni znanstveni članek Opis: Curated online interaction databases and gene ontology tools have streamlined the analysis of highly complex gene/protein networks. However, understanding of disease pathogenesis has gradually shifted from a protein-based core to complex interactive networks where non-coding RNA (ncRNA) is thought to play an essential role. As current gene ontology is based predominantly on protein-level information, there is a growing need to analyze networks with ncRNA. In this study, we propose a gene ontology workflow integrating ncRNA using the NPInter V5.0 database. To validate the proposed workflow, we analyzed our previously published curated biomarker datasets for hidden disease susceptibility processes and pharmacogenomics. Our results show a novel involvement of melanogenesis in psoriasis response to biological drugs in general. Hyperpigmentation has been previously observed in psoriasis following treatment with currently indicated biological drugs, thus calling attention to melanogenesis research as a response biomarker in psoriasis. Moreover, our proposed workflow highlights the need to critically evaluate computed ncRNA interactions within databases and a demand for gene ontology analysis of large miRNA blocks.
Ključne besede: gene ontology, non-coding RNA, ncRNA, disease pathogenesis, gene networks, protein networks, tools, psoriasis
Objavljeno v DKUM: 06.12.2024; Ogledov: 0; Prenosov: 13
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9. Določevanje vpliva multivalentnih fosfatnih in sulfonatnih pomožnih snovi na agregacijo proteinov za uporabo v biofarmacevtskih izdelkih : diplomsko delo univerzitetnega študijskega programa I. stopnjeTjaša Krepek, 2024, diplomsko delo Opis: V zadnjih desetletjih se je biofarmacevtska industrija osredotočila na razvoj bioloških zdravil. Večinoma gre za kompleksne beljakovinske molekule, ki so zahtevne in drage za izdelavo ter imajo omejen rok uporabe, ki je posledica nestabilnosti samih beljakovin. Na nestabilnost proteinov in agregacijo lahko vplivamo z dodatkom malih molekul in pomožnih snovi kot so površinsko aktivne snovi, pufri, sladkorji, soli itd., ki se na protein neposredno vežejo in ga tako stabilizirajo. Dosedanje raziskave so že preučile vpliv adenozin tripolifosfata in tripoli fosfata na agregacijo biofarmacevtskih proteinov, zato smo v diplomskem delu preučili še vpliv petih drugih že priznanih fosfatnih ionov in za primerjavo izbrali še deset ATP- ju podobnih sulfonatnih spojin, saj so polifosfati nagnjeni k hidrolizi in posledično niso primerni za uporabo kot pomožne snovi. Uporabili smo modelni protein lizocim kokošjega beljaka ter preverjali vpliv pomožnih snovi pri različnih koncentracijah na kinetiko agregacije proteina, ki smo jo spremljali z UV- Vis spektrometrijo. S pomočjo UV-Vis spektrometrije smo opravili tudi presejalni test pomožnih snovi na agregacijo proteina in izračunali delež monomernega proteina. Ugotovili smo, da fosfatne pomožne snovi in večina sulfonatnih učinkovito zaščitijo in stabilizirajo protein in ga tako zaščitijo pred agregacijo kot je ta podvržen temperaturnemu stresu ter ga zaščitijo pred agregacijo v daljšem časovnem obdobju, prav tako tudi zmanjšajo delež monomernega proteina v vzorcu. Preverili smo tudi vpliv pomožnih snovi na agregacijo delno razvitih beljakovin, kar smo dosegli z dodatkom ditiotreitola ali DTT, ki cepi disulfidne mostičke v beljakovini. V povprečju se je izkazalo, da dajejo boljše rezultate fosfatne pomožne snovi in ne sulfonatne. Najboljše rezultate sta med pomožnimi snovmi dala ATP in TPP, preostale pomožne snovi pa dale primerljive rezultate.
Ključne besede: protein, agregacija, pomožne snovi, fosfati, sulfonati, fazni diagram
Objavljeno v DKUM: 01.10.2024; Ogledov: 0; Prenosov: 37
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10. Preučevanje interakcij med tanini in lizocimom : diplomsko delo univerzitetnega študijskega programa I. stopnjeAnja Zaverla, 2024, diplomsko delo Opis: Razvoj odpornosti bakterij na antibiotike je eden izmed večjih izzivov človeštva, ki zahtevajo tako iskanje novih protibakterijskih učinkovin, kot tudi izboljšanih načinov uporabe protibakterijskih sredstev. Raziskovalci nove protibakterijske učinkovine iščejo tudi med naravnimi spojinami s protimikrobnimi in protibakterijskimi učinki. Rastline vsebujejo tanine, ki so polifenolni sekundarni metaboliti, ki jih raziskujemo zaradi njihovih številnih potencialnih za zdravje ugodnih učinkov. Glede na njihovo kemijsko strukturo jih delimo na proantocianidine (kondenzirane tanine) in hidrolizirajoče tanine. Slednji se nadalje razdelijo na dve glavni podskupini (galotanin in elagitanini).
V diplomskem delu smo proučevali vezavo elagitaninov na lizocim – modelni protein. Po dializi v pufru s pH = 5 smo lizocim titrirali z galno kislino, metil galatom in veskalaginom. Opazovali smo, kako prisotnost elagitaninov vpliva na fluorescenco lizocima. Vpliv dodatka taninov na sekundarno strukturo lizocima smo opazovali s cirkularnim dikroizmom (CD-spektroskopija), medtem ko smo termodinamiko vezave opazovali z izotermno titracijsko kalorimetrijo (ITC). Z opazovanjem temperaturne odvisnosti fluorescenčnega spektra lizocima smo ugotovili, da prisotnost taninov ne vpliva na temperaturo tališča proteina. S pomočjo Stern-Volmerjeve enačbe ob upoštevanju učinka notranjega filtra smo poskusili pridobiti konstante vezave taninov na lizocim. S CD-spektroskopijo smo ugotovili, da ima veskalagin večji vpliv na denaturacijo proteina, kot metil galat in galna kislina. Ugotovili smo, da je interakcija veskalagina in lizocima mnogo bolj eksotermna, kot interakcija metil galata ali galne kisline z lizocimom. Poleg tega smo z ITC-jem potrdili, da gre pri interakcijah taninov z lizocimom za razmeroma šibke interakcije.
Ključne besede: elagitanini, protein, konstanta vezave, sekundarna struktura, spektroskopija, termodinamični parametri vezave
Objavljeno v DKUM: 17.09.2024; Ogledov: 0; Prenosov: 87
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