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NMR-based homology model for the solution structure of the C-terminal globular domain of EMILIN1

Journal of Biomolecular NMR volume 43, Article number: 79 (2009) Cite this article

Abstract

EMILIN1 is a glycoprotein of elastic tissues that has been recently linked to the pathogenesis of hypertension. The protein is formed by different independently folded structural domains whose role has been partially elucidated. In this paper the solution structure, inferred from NMR-based homology modelling of the C-terminal trimeric globular C1q domain (gC1q) of EMILIN1, is reported. The high molecular weight and the homotrimeric structure of the protein required the combined use of highly deuterated 15N, 13C-labelled samples and TROSY experiments. Starting from a homology model, the protein structure was refined using heteronuclear residual dipolar couplings, chemical shift patterns, NOEs and H-exchange data. Analysis of the gC1q domain structure of EMILIN1 shows that each protomer of the trimer adopts a nine-stranded β sandwich folding topology which is related to the conformation observed for other proteins of the family. Distinguishing features, however, include a missing edge-strand and an unstructured 19-residue loop. Although the current data do not allow this loop to be precisely defined, the available evidence is consistent with a flexible segment that protrudes from each subunit of the globular trimeric assembly and plays a key role in inter-molecular interactions between the EMILIN1 gC1q homotrimer and its integrin receptor α4β1.

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Abbreviations

ACRP30:

Adipocyte complement-related protein of 30 kDa

CSA:

Chemical shift anisotropy

DD:

Dipole–dipole

EMILIN1:

Elastin microfibril interface located protein 1

EMILIN2:

Elastin microfibril interface located protein 2

gC1q:

Globular C1q domain

IPAP:

In-phase anti-phase

NOE:

Nuclear overhauser effect

RDC:

Residual dipolar couplings

TGF:

Tumor growth factor

TNF:

Tumor necrosis factor

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Acknowledgments

This work was supported by Italian Ministry of Education (MIUR) funding (PRIN and FIRB N. RBRN07BMCT). The assistance of Dr. A. Makek is acknowledged. IDC and SAC were supported by the Wellcome Trust, GV was supported also by EMBO. Finally we wish to acknowledge the contribution of Dr. Anatoly Sharipo (ASLA Ltd.) who untimely passed away recently. His generous commitment was essential to start this and many other projects.

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Author notes

  1. Giuliana Verdone

    Present address: Istituto Biochimico Italiano ‘G. Lorenzini’, 04011, Aprilia, LT, Italy

Affiliations

  1. Dipartimento di Scienze e Tecnologie Biomediche – MATI Centre of Excellence, Università di Udine, P. le Kolbe, 4-33100, Udine, Italy

    Giuliana Verdone, Alessandra Corazza, Federico Fogolari, Paolo Viglino, Alfonso Colombatti & Gennaro Esposito

  2. INBB, Viale Medaglie d’Oro, 305, Rome, Italy

    Alessandra Corazza, Federico Fogolari, Paolo Viglino & Gennaro Esposito

  3. Department of Biochemistry, University of Oxford, Oxford, UK

    Simon A. Colebrooke, Jonathan Boyd & Iain D. Campbell

  4. Dipartimento di Chimica, Università di Tor Vergata, Rome, Italy

    Daniel Cicero & Tommaso Eliseo

  5. Divisione di Oncologia Sperimentale 2, Centro di Riferimento Oncologico di Aviano, Aviano, PN, Italy

    Roberto Doliana & Alfonso Colombatti

Authors
  1. Giuliana Verdone
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  2. Alessandra Corazza
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  12. Gennaro Esposito
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Correspondence to Gennaro Esposito.

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10858_2008_9290_MOESM1_ESM.pdf

MOESM1 The online version of this article contains “Supplementary material”, which is available to authorized users. Additional details are given of the assignment strategy, gel sample preparation and RDC measurement, together with the specific literature references and a list of the RDC values employed for the structure determination. Figures to illustrate the TROSY spectra quality, some details of the intersubunit interface, a graph of calculated versus experimental RDC values and the sequence alignment of C1q family are reported. PDF 229 kb)

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Verdone, G., Corazza, A., Colebrooke, S.A. et al. NMR-based homology model for the solution structure of the C-terminal globular domain of EMILIN1. J Biomol NMR 43, 79 (2009). https://doi.org/10.1007/s10858-008-9290-y

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Keywords

  • Elastic fibres
  • EMILIN1
  • Globular C1q domain
  • Homotrimeric proteins
  • Large system NMR
  • Partially deuterated proteins