Comprehensive structural analysis of designed incomplete polypeptide chains of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus

PLoS One. 2017 Jul 27;12(7):e0182132. doi: 10.1371/journal.pone.0182132. eCollection 2017.

Abstract

The cotranslational folding is recognized as a very cooperative process that occurs after the nearly completion of the polypeptide sequence of a domain. Here we investigated the challenges faced by polypeptide segments of a non-vectorial β-barrel fold. Besides the biological interest behind the SARS coronavirus non-structural protein 1 (nsp1, 117 amino acids), this study model has two structural features that motivated its use in this work: 1- its recombinant production is dependent on the temperature, with greater solubility when expressed at low temperatures. This is an indication of the cotranslational guidance to the native protein conformation. 2- Conversely, nsp1 has a six-stranded, mixed parallel/antiparallel β-barrel with intricate long-range interactions, indicating it will need the full-length protein to fold properly. We used non-denaturing purification conditions that allowed the characterization of polypeptide chains of different lengths, mimicking the landscape of the cotranslational fold of a β-barrel, and avoiding the major technical hindrances of working with the nascent polypeptide bound to the ribosome. Our results showed partially folded states formed as soon as the amino acids of the second β-strand were present (55 amino acids). These partially folded states are different based on the length of polypeptide chain. The native α-helix (amino acids 24-37) was identified as a transient structure (~20-30% propensity). We identified the presence of regular secondary structure after the fourth native β-strand is present (89 amino acids), in parallel to the collapse to a non-native 3D structure. Interestingly the polypeptide sequences of the native strands β2, β3 and β4 have characteristics of α-helices. Our comprehensive analyses support the idea that incomplete polypeptide chains, such as the ones of nascent proteins much earlier than the end of the translation, adopt an abundance of specific transient folds, instead of disordered conformations.

MeSH terms

  • Amino Acid Sequence
  • Circular Dichroism
  • Hydrophobic and Hydrophilic Interactions
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Peptides / chemistry*
  • Protein Biosynthesis
  • Protein Folding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Recombinant Fusion Proteins / chemistry
  • Scattering, Small Angle
  • Severe acute respiratory syndrome-related coronavirus / chemistry*
  • Viral Nonstructural Proteins / chemistry*
  • X-Ray Diffraction

Substances

  • Peptides
  • Recombinant Fusion Proteins
  • Viral Nonstructural Proteins
  • nonstructural protein, coronavirus

Grants and funding

This work was supported by Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro—www.faperj.br—Grant #: E-26/111.771/2012 and Conselho Nacional de Desenvolvimento Científico e Tecnológico—www.cnpq.br—Grant #: 470349/2012-3. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.