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From polymers to proteins: the effect of side chains and broken symmetry on the formation of secondary structures within a Wang–Landau approach
2016, original scientific article

Abstract: We use a micro-canonical Wang–Landau technique to study the equilibrium properties of a single flexible homopolymer where consecutive monomers are represented by impenetrable hard spherical beads tangential to each other, and non-consecutive monomers interact via a square-well potential. To mimic the characteristics of a protein-like system, the model is then refined in two different directions. Firstly, by allowing partial overlap between consecutive beads, we break the spherical symmetry and thus provide a severe constraint on the possible conformations of the chain. Alternatively, we introduce additional spherical beads at specific positions in the direction normal to the backbone, to represent the steric hindrance of the side chains in real proteins. Finally, we consider also a combination of these two ingredients. In all three systems, we obtain the full phase diagram in the temperature-interaction range plane and find the presence of helicoidal structures at low temperatures in the intermediate range of interactions. The effect of the range of the square-well attraction is highlighted, and shown to play a role similar to that found in simple liquids and polymers. Perspectives in terms of protein folding are finally discussed.
Found in: ključnih besedah
Keywords: Wang-Landau approach, Monte-Carlo simulations, proteins, secondary structures
Published: 04.05.2016; Views: 3432; Downloads: 0
.pdf Fulltext (10,13 MB)

Biotinylated Vanadium and Chromium Sulfide Nanoparticles as Probes for Colocalization of Membrane Proteins
Saim Emin, Alexandre Loukanov, 2016, original scientific article

Abstract: ABSTRACT We report the microemulsion synthesis of vanadium and chromium sulfide nanoparticles (NPs) and their biological application as nanoprobes for colocalization of membrane proteins. Spherical V2S3 and Cr2S3 NPs were prepared in reverse microemulsion droplets, as nanoreactors, obtained by the surfactant sodium bis(2-ethylhexyl) sulfosuccinate (AOT) in nonpolar organic phase (heptane). Electron microscopic data indicated that the size distribution of the nanoparticles was uniform with an average diameter between 3 4 5 nm. The prepared hydrophobic nanocrystals were transferred in aqueous phase by surface cap exchange of AOT with biotindihydrolipoic ligands. This substitution allows the nanoparticles solubility in aqueous solutions and confer their bioactivity. In addition, we report the conjugation procedure between a-Lipoic acid (LA) and biotin (abbreviated as biotin-LA). The biotin-LA structure was characterized by 1D and 2D NMR spectroscopy. The biotinylated vanadium and chromium sulfide nanoparticles were tested as probes for colocalization of glutamate receptors on sodium-dodecyl-sulfate-digested replica prepared from rat hippocampus. The method suggests their high labeling efficiency for study of membrane biological macromolecules.
Found in: ključnih besedah
Keywords: biotin-dihydrolipoic conjugate, vanadium and chromium sulfide nanoparticles, membrane proteins
Published: 02.02.2017; Views: 4489; Downloads: 0
.pdf Fulltext (581,45 KB)

An extracellular polymeric substance quickly chelates mercury(II) with N-heterocyclic groups
Claudia Faleri, Dario Battistel, Salvatore Daniale, Michele Gallo, Franco Baldi, Alojz Kodre, Iztok Arčon, 2017, original scientific article

Abstract: A strain of Klebsiella oxytoca DSM 29614 is grown on sodium citrate in the presence of 50 mg l−1 of Hg as Hg(NO3)2. During growth, the strain produces an extracellular polymeric substance (EPS), constituted by a mixture of proteins and a specific exopolysaccharide. The protein components, derived from the outer membrane of cells, are co-extracted with the extracellular exopolysaccharide using ethanol. The extracted EPS contains 7.5% of Hg (total amount). This indicates that EPS is an excellent material for the biosorption of Hg2+, through chemical complexation with the EPS components. The binding capacity of these species towards Hg2+ is studied by cyclic voltammetry, and Hg L3-edge XANES and EXAFS spectroscopy. The results found indicate that Hg2+ is mainly bound to the nitrogen of the imidazole ring or other N-heterocycle compounds. The hydroxyl moities of sugars and/or the carboxyl groups of two glucuronic acids in the polysaccharide can also play an important role in sequestring Hg2+ ions. However, N-heterocyclic groups of proteins bind Hg2+ faster than hydroxyl and carboxyl groups of the polysaccharide.
Found in: ključnih besedah
Summary of found: ...substance (EPS), constituted by a mixture of proteins and a specific exopolysaccharide. The protein components,...
Keywords: Klebsiella oxytoca, Biosorption, Proteins, Polysaccharide, Cyclic voltammetry, EXAFS analysis
Published: 03.03.2017; Views: 3903; Downloads: 0
.pdf Fulltext (1,66 MB)

Biotechnological applications of nanobody pre-immune libraries
Ario De Marco, invited lecture at foreign university

Found in: ključnih besedah
Keywords: nanobodies, pre-immune libraries, in vitro selection, biomarkers, recombinant proteins
Published: 16.05.2017; Views: 3245; Downloads: 0
.pdf Fulltext (331,92 KB)

Acting of folding effectors to improve recombinant protein yields and functional quality
Ario de Marco, 2017, independent scientific component part or a chapter in a monograph

Found in: ključnih besedah
Summary of found: ...recombinant proteins, chaperones, osmolytes, protein aggregation...
Keywords: recombinant proteins, chaperones, osmolytes, protein aggregation
Published: 24.05.2017; Views: 3618; Downloads: 0
.pdf Fulltext (9,50 MB)

Whole-cell biopanning with a synthetic phage display library of nanobodies enabled the recovery of follicle-stimulating hormone receptor inhibitors
Ronan Crepin, Gianluca Veggiani, Selma Djender, Anne Beugnet, Francois Planeix, Christophe Pichon, Sandrine Moutel, Sebastian Amigorena, Franck Pérez, Nicolae Ghinea, Ario De Marco, 2017, original scientific article

Abstract: Antibodies are essential reagents that are increasingly used in diagnostics and therapy. Their specificity and capacity to recognize their native antigen are critical characteristics for their in vivo application. Follicle-stimulating hormone receptor is a GPCR protein regulating ovarian follicular maturation and spermatogenesis. Recently, its potentiality as a cancer biomarker has been demonstrated but no antibody suitable for in vivo tumor targeting and treatment has been characterized so far. In this paper we describe the first successful attempt to recover recombinant antibodies against the FSHR and that: i) are directly panned from a pre-immune library using whole cells expressing the target receptor at their surface; ii) show inhibitory activity towards the FSH-induced cAMP accumulation; iii) do not share the same epitope with the natural binder FSH; iv) can be produced inexpensively as mono- or bivalent functional molecules in the bacterial cytoplasm. We expect that the proposed biopanning strategy will be profitable to identify useful functional antibodies for further members of the GPCR class.
Found in: ključnih besedah
Summary of found: ...nanobodies, GPCR proteins, FSHR, panning, pre-immune antibody library...
Keywords: nanobodies, GPCR proteins, FSHR, panning, pre-immune antibody library
Published: 19.10.2017; Views: 3308; Downloads: 0
.pdf Fulltext (982,69 KB)

A caccia di proteine usando gli anticorpi come esca
Ario de Marco, unpublished invited conference lecture

Found in: ključnih besedah
Summary of found: ...Fluorescent proteins, antibodies, microscopy, diagnostics...
Keywords: Fluorescent proteins, antibodies, microscopy, diagnostics
Published: 13.02.2018; Views: 2980; Downloads: 0
.pdf Fulltext (215,78 KB)

On the usage of classical nucleation theory in quantification of the impact of bacterial INP on weather and climate
Maher Sahyoun, Heike Wex, Ulrich Karlson Gosewinkel, Tina Šantl Temkiv, Niels Woetman Nielsen, Kai Finster, Jens H. Sørensen, Frank Stratmann, Ulrik S. Korsholm, 2016, original scientific article

Found in: ključnih besedah
Summary of found: ...Ice nucleation, Bacterial INP, Ice nucleation active proteins, Classical nucleation theory, Ice nucleation rate...
Keywords: Ice nucleation, Bacterial INP, Ice nucleation active proteins, Classical nucleation theory, Ice nucleation rate
Published: 04.01.2021; Views: 1902; Downloads: 0
.pdf Fulltext (1,34 MB)

Effects of Ice Nucleation Protein Repeat Number and Oligomerization Level on Ice Nucleation Activity
Meilee Ling, Heike Wex, Sarah Grawe, Jonas Jakobsson, Jakob Löndahl, Susan Hartmann, Kai Finster, Thomas Boesen, Tina Šantl Temkiv, 2018, original scientific article

Found in: ključnih besedah
Summary of found: ...biological ice nucleation, ice-nucleating proteins, ice-nucleation active bacteria...
Keywords: biological ice nucleation, ice-nucleating proteins, ice-nucleation active bacteria
Published: 04.01.2021; Views: 1610; Downloads: 58
.pdf Fulltext (943,44 KB)

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