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  • 1
    Language: English
    In: Journal of medicinal chemistry, 14 April 2011, Vol.54(7), pp.2095-101
    Description: A novel cationic peptide based on L-lysine and L-diaminobutyric acid was prepared for the first time by solid phase synthesis. After HPLC purification and ESI MS characterization, we studied by CD and IR spectroscopy the structural features of the novel basic peptide, which is able to form a β-turn-like structure. Furthermore, its interaction with DNA and RNA was investigated by CD and UV spectroscopy, which revealed a preferential RNA-binding ability of the sequential peptide, whereas its inhibitory activity toward HIV and Moloney murine leukemia virus (MMLV) reverse transcriptase action was evaluated by semiquantitative PCR. The cationic sequential peptide was able to inhibit the reverse transcriptase activity in both cases, even if our PCR data suggested a major activity in the case of HIV-RT, probably due to the stronger cationic peptide-protein interaction evidenced by UV spectroscopy.
    Keywords: Amino Acids -- Chemistry ; HIV -- Enzymology ; Moloney Murine Leukemia Virus -- Enzymology ; Peptides -- Metabolism ; RNA -- Metabolism ; RNA-Directed DNA Polymerase -- Metabolism
    ISSN: 00222623
    E-ISSN: 1520-4804
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  • 2
    Language: English
    In: PLoS ONE, 2012, Vol.7(5), p.e35774
    Description: Peptide Nucleic Acids (PNAs), nucleic acid analogues showing high stability to enzyme degradation and strong affinity and specificity of binding toward DNA and RNA are widely investigated as tools to interfere in gene expression. Several studies have been focused on PNA analogues with modifications on the backbone and bases in the attempt to overcome solubility, uptake and aggregation issues. γ PNAs, PNA derivatives having a substituent in the γ position of the backbone show interesting properties in terms of secondary structure and affinity of binding toward complementary nucleic acids. In this paper we illustrate our results obtained on new analogues, bearing a sulphate in the γ position of the backbone, developed to be more DNA-like in terms of polarity and charge. The synthesis of monomers and oligomers is described. NMR studies on the conformational properties of monomers and studies on the secondary structure of single strands and triplexes are reported. Furthermore the hybrid stability and the effect of mismatches on the stability have also been investigated. Finally, the ability of the new analogue to work as antigene, interfering with the transcription of the ErbB2 gene on a human cell line overexpressing ErbB2 (SKBR3), assessed by FACS and qPCR, is described.
    Keywords: Research Article ; Biology ; Chemistry ; Physics ; Genetics And Genomics ; Chemistry ; Molecular Biology ; Biotechnology ; Cell Biology ; Biophysics ; Physics
    E-ISSN: 1932-6203
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  • 3
    Language: English
    In: FEBS Letters, 24 March 2015, Vol.589(7), pp.798-804
    Description: A change in the conformational plasticity of α-Synuclein (α-Syn) is hypothesised to be a key step in the pathogenic mechanism of Parkinson’s disease (PD). Here, we report the study of extracellular α-Syn interaction with whole cells and membranes isolated from the neuronal SH-SY5Y cells, exploiting NMR and CD spectroscopies. In addition, the crosslinking agent DSG was used to freeze the conformational and oligomeric state of α-Syn in the presence of cells. These data, in a quasi-physiological environment, confirm the protein monomeric state with a propensity to adopt a transient alpha helical following interaction with biological membranes.
    Keywords: Alpha Synuclein ; NMR Spectroscopy ; CD Analyses ; Protein–Membranes Interaction ; Biology ; Chemistry ; Anatomy & Physiology
    ISSN: 0014-5793
    E-ISSN: 1873-3468
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  • 4
    Language: English
    In: PLoS ONE, 01 January 2015, Vol.10(5), p.e0126808
    Description: Cullin 3 (Cul3) recognition by BTB domains is a key process in protein ubiquitination. Among Cul3 binders, a great attention is currently devoted to KCTD proteins, which are implicated in fundamental biological processes. On the basis of the high similarity of BTB domains of these proteins,...
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 5
    Language: English
    In: PLoS ONE, 01 January 2014, Vol.9(9), p.e106441
    Description: αvβ3 integrin is an important tumor marker widely expressed on the surface of cancer cells. Recently, we reported some biological features of RGDechi-hCit, an αvβ3 selective peptide antagonist. In the present work, we mainly investigated the pro-apoptotic activity of the molecule and its ability...
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 6
    Language: English
    In: Chemistry – A European Journal, 02 January 2015, Vol.21(1), pp.91-95
    Description: In this study, the functional interaction of HPLW peptide with VEGFR2 (Vascular Endothelial Growth Factor Receptor 2) was determined by using fast N‐edited NMR spectroscopic experiments. To this aim, N uniformly labelled HPLW has been added to Porcine Aortic Endothelial Cells. The acquisition of isotope‐edited NMR spectroscopic experiments, including N relaxation measurements, allowed a precise characterization of the in‐cell HPLW epitope recognized by VEGFR2. and NMR spectroscopic relaxation measurements on living cells have been used to map the binding determinants of N‐labelled HPLW peptide, able to target VEGFR2 and to act as a VEGF agonist (see figure; VEGF=Vascular Endothelial Growth Factor).
    Keywords: 15 N Labelled Peptides ; Living Cells ; Nmr Spectroscopy ; Peptide–Protein Interaction ; Vegf Receptors
    ISSN: 0947-6539
    E-ISSN: 1521-3765
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  • 7
    Language: English
    In: BBA - Proteins and Proteomics, July 2014, Vol.1844(7), pp.1289-1298
    Description: Recent investigations have highlighted a key role of the proteins of the KCTD (K-potassium channel tetramerization domain containing proteins) family in several fundamental biological processes. Despite the growing importance of KCTDs, our current understanding of their biophysical and structural properties is very limited. Biochemical characterizations of these proteins have shown that most of them act as substrate adaptor in E3 ligases during protein ubiquitination. Here we present a characterization of the KCTD5-Cullin3 interactions which are mediated by the KCTD5 BTB domain. Isothermal titration calorimetry experiments reveal that KCTD5 avidly binds the Cullin3 (Cul3). The complex presents a 5:5 stoichiometry and a dissociation constant of 59 nM. Molecular modeling and molecular dynamics simulations clearly indicate that the two proteins form a stable (KCTD5–Cul3) pinwheel-shaped heterodecamer in which two distinct KCTD5 subunits cooperate in the binding of each cullin chain. Molecular dynamics simulations indicate that different types of interactions contribute to the stability of the assembly. Interestingly, residues involved in Cul3 recognitions are conserved in the KCTD5 orthologs and paralogs implicated in important biological processes. These residues are also rather well preserved in most of the other KCTD proteins. By using molecular modeling techniques, the entire ubiquitination system including the E3 ligase, the E2 conjugating enzyme and ubiquitin was generated. The analysis of the molecular architecture of this complex machinery provides insights into the ubiquitination processes which involve E3 ligases with a high structural complexity.
    Keywords: Molecular Dynamics ; Isothermal Titration Calorimetry ; Insomniac Protein ; Protein–Protein Interactions ; Chemistry ; Anatomy & Physiology
    ISSN: 1570-9639
    E-ISSN: 1878-1454
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  • 8
    Language: English
    In: Chemistry – A European Journal, 11 January 2016, Vol.22(2), pp.681-693
    Description: The critical role of integrins in tumor progression and metastasis has stimulated intense efforts to identify pharmacological agents that can modulate integrin function. In recent years, αβ and αβ integrin antagonists were demonstrated to be effective in blocking tumor progression. RGDechi‐hCit, a chimeric peptide containing a cyclic RGD motif linked to an echistatin C‐terminal fragment, is able to recognize selectively αβ integrin both in vitro and in vivo. High‐resolution molecular details of the selective αβ recognition of the peptide are certainly required, nonetheless RGDechi‐hCit internalization limited the use of classical in cell NMR experiments. To overcome such limitations, we used WM266 isolated cellular membranes to accomplish a detailed NMR interaction study that, combined with a computational analysis, provides significant structural insights into αβ molecular recognition by RGDechi‐hCit. Remarkably, on the basis of the identified molecular determinants, we design a RGDechi‐hCit mutant that is selective for αβ integrin. αβ : NMR data were combined with computational analysis to provide a three‐dimensional model of the RGDechi‐αβ complex, elucidating the molecular requirements for peptide‐specific recognition of the receptor (see figure).
    Keywords: Integrin ; Cell Membranes ; Molecular Docking ; Nmr Spectroscopy ; Rgd Ligand
    ISSN: 0947-6539
    E-ISSN: 1521-3765
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  • 9
    Language: English
    In: Chemistry – A European Journal, 06 August 2018, Vol.24(44), pp.11461-11466
    Description: QK peptide is a vascular endothelial growth factor (VEGF)‐mimetic molecule with significant proangiogenic activity. In particular, QK is able to bind and activate VEGF receptors (VEGFRs) to stimulate a functional response in endothelial cells. To characterize the peptide bioactivity and its molecular recognition properties, a detailed picture of the interaction between peptide QK and VEGF receptors is reported. By combining NMR spectroscopy studies in solution on the purified receptor and in the presence of intact endothelial cells, a molecular description of the binding interaction between peptide QK and VEGFR2 in the cellular context is obtained. These results reveal useful insights into the peptide biological mechanism, which opens the way to further optimization of this class of VEGF‐mimicking peptides. : The molecular details of the interaction between a vascular endothelial growth factor (VEGF)‐mimetic peptide and receptor VEGFR2 were determined by combining in vitro and cellular NMR spectroscopy experiments (see figure).
    Keywords: Angiogenesis ; Nmr Spectroscopy ; Noncovalent Interactions ; Peptides ; Receptors
    ISSN: 0947-6539
    E-ISSN: 1521-3765
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  • 10
    Language: English
    In: Chemistry – A European Journal, 09 September 2013, Vol.19(37), pp.12217-12220
    Description: : The C‐terminal third domain of h‐prune is largely unfolded and involved in relevant protein–protein interactions, particularly with Nm23‐H1 (see figure), GSK‐3β and gelsolin. This study shows that protein functions mediated by protein–protein interactions can be accurately followed in cell lysates by using fast NMR spectroscopy, which could be easily used for a very efficient NMR drug‐discovery strategy.
    Keywords: Human Cell Lysates ; Intrinsically Disordered Proteins ; Nmr Spectroscopy ; Protein–Protein Interactions ; Structure Elucidation
    ISSN: 0947-6539
    E-ISSN: 1521-3765
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