Structural Analysis of a Helical Peptide Unfolding Pathway

Diana, Donatella; Ziaco, Barbara; Scarabelli, Guido; Pedone, Carlo; Colombo, Giorgio; D’Andrea, Luca Domenico; Fattorusso, Roberto

doi:10.1002/chem.200903428

Cited by 29 publications

(22 citation statements)

References 46 publications

(45 reference statements)

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“…To deeply describe the conformational proprieties of the RGDechi peptide, we have analysed the chemical shifts that are reporters for the structural features around the corresponding nuclei and, therefore, for the conformations sampled by the peptide in solution . In particular, the backbone chemical shifts are sensitive probes of polypeptide secondary structure, representing an average of multiple populations and allowing the detection of minor contributions.…”

Section: Resultsmentioning

confidence: 99%

Conformational studies of RGDechi peptide by natural‐abundance NMR spectroscopy

Farina

Gatto

Comegna

et al. 2019

Journal of Peptide Science

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Integrins are heterodimeric cell-surface proteins that play important roles during developmental and pathological processes. Diverse human pathologies involve integrin adhesion including thrombotic diseases, inflammation, tumour progression, fibrosis, and infectious diseases. Although in the past decade, novel integrin-inhibitor drugs have been developed for integrin-based medical applications, the structural determinants modulating integrin-ligands recognition mechanisms are still poorly understood, reducing the number of integrin subtype exclusive antagonists. In this scenario, we have very recently showed, by means of chemical and biological assays, that a chimeric peptide (named RGDechi), containing a cyclic RGD motif linked to an echistatin C-terminal fragment, is able to interact with the components of integrin family with variable affinities, the highest for α v β3. Here, in order to understand the mechanistic details driving the molecular recognition mechanism of α v β 3 by RGDechi, we have performed a detailed structural and dynamics characterization of the free peptide by natural abundance nuclear magnetic resonance (NMR) spectroscopy. Our data indicate that RGDechi presents in solution an heterogeneous conformational ensemble characterized by a more constrained and rigid pentacyclic ring and a largely unstructured acyclic region. Moreover, we propose that the molecular recognition of α v β 3 integrin by RGDechi occurs by a combination of conformational selection and induced fit mechanisms. Finally, our study indicates that a detailed NMR characterization, by means of natural abundance 15 N and 13 C, of a mostly unstructured bioactive peptide may provide the molecular basis to get essential structural insights into the binding mechanism to the biological partner.

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Section: Resultsmentioning

confidence: 99%

Conformational studies of RGDechi peptide by natural‐abundance NMR spectroscopy

Farina

Gatto

Comegna

et al. 2019

Journal of Peptide Science

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“…Initially, we focused on the VEGF helix 17-25 (29). The designed 15-mer peptide assumes in water a well defined helical conformation and presents a remarkable thermal stability (30,31). It binds and activates VEGF receptors and shows VEGF-like activity in vitro (29) and in vivo (32,33).…”

Section: Discussionmentioning

confidence: 99%

β-Hairpin Peptide That Targets Vascular Endothelial Growth Factor (VEGF) Receptors

Diana

Basile

Rosa

et al. 2011

Journal of Biological Chemistry

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VEGF receptors have been the target of intense research aimed to develop molecules able to inhibit or stimulate angiogenesis. Based on the x-ray structure of the complex placental growth factor-VEGF receptor 1 D2 , we designed a VEGF receptor-binding peptide reproducing the placental growth factor ␤-hairpin region Gln 87 -Val 100 that is involved in receptor recognition. A conformational analysis showed that the designed peptide adopts the expected fold in pure water. Moreover, a combination of NMR interaction analysis and cell binding studies were used to demonstrate that the peptide targets VEGF receptors. The VEGF receptor 1 D2 -interacting residues were characterized at the molecular level, and they correspond to the residues recognizing the placental growth factor sequence Gln -Val 100. Finally, the peptide biological activity was characterized in vitro and in vivo, and it showed a VEGF-like behavior. Indeed, the peptide activated VEGF-dependent intracellular pathways, induced endothelial cell proliferation and rescue from apoptosis, and promoted angiogenesis in vivo. This compound is one of the few peptides known with proangiogenic activity, which makes it a candidate for the development of a novel peptide-based drug for medical applications in therapeutic angiogenesis.

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“…To describe the RGDechi15D conformational motions, we explored 15 N backbone dynamics on the picosecond (ps) to millisecond (ms) timescale of the peptide by natural-abundance NMR techniques, and we probed the nanosecond conformational flexibility of the peptide, by using MD simulations. In fact, this latter technique provides a detailed picture of the dynamics process occurring in peptides/proteins on different timescales, and thus represents a valuable tool that is complementary to the experimental data obtained by NMR spectroscopy [55] , [56] , [57] . First, we generated, as reported in the materials and methods section, the conformational ensemble reproducing the ns RGDechi15D intrinsic motions ( Fig.…”

Section: Resultsmentioning

confidence: 99%