Cuban, a case study of selective binding: Structural details of the discrimination between ubiquitin and nedd8

Elena Santonico, Ridvan Nepravishta, Walter Mandaliti, Luisa Castagnoli, Gianni Cesareni, Maurizio Paci

Research output: Contribution to journalArticle

Abstract

The newly identified CUBAN (Cullin binding domain associating with NEDD8) domain recognizes both ubiquitin and the ubiquitin-like NEDD8. Despite the high similarity between the two molecules, CUBAN shows a clear preference for NEDD8, free and conjugated to cullins. We previously characterized the domain structure, both alone and in complex with NEDD8. The results here reported are addressed to investigate the determinants that drive the selective binding of CUBAN towards NEDD8 and ubiquitin. The 15 N HSQC NMR perturbation pattern of the labeled CUBAN domain, when combined with either NEDD8 or ubiquitin, shows a clear involvement of hydrophobic residues that characterize the early stages of these interactions. After a slow conformational selection step, hydrophobic and then neutral and polar interactions take place, which drive the correct orientation of the CUBAN domain, leading to differences in the recognition scheme of NEDD8 and ubiquitin. As a result, a cascade of induced fit steps seems to determine the structural preference shown for NEDD8 and therefore the basis of the selectivity of the CUBAN domain. Finally, molecular dynamics analysis was performed to determine by fluctuations the internal flexibility of the CUBAN/NEDD8 complex. We consider that our results, based on a structural investigation mainly focused on the early stages of the recognition, provide a fruitful opportunity to report the different behavior of the same protein with two highly similar binding partners.

Original languageEnglish
Article number1185
JournalInternational Journal of Molecular Sciences
Volume20
Issue number5
DOIs
Publication statusPublished - Mar 1 2019

Fingerprint

Cullin Proteins
Ubiquitin
Dynamic analysis
discrimination
Molecular dynamics
Nuclear magnetic resonance
Proteins
Molecules
Molecular Dynamics Simulation
determinants

Keywords

  • Biomolecular NMR
  • Biomolecular recognition
  • NEDD8
  • Protein–protein interactions
  • Ubiquitin

ASJC Scopus subject areas

  • Catalysis
  • Molecular Biology
  • Spectroscopy
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Inorganic Chemistry

Cite this

Cuban, a case study of selective binding : Structural details of the discrimination between ubiquitin and nedd8. / Santonico, Elena; Nepravishta, Ridvan; Mandaliti, Walter; Castagnoli, Luisa; Cesareni, Gianni; Paci, Maurizio.

In: International Journal of Molecular Sciences, Vol. 20, No. 5, 1185, 01.03.2019.

Research output: Contribution to journalArticle

Santonico, Elena ; Nepravishta, Ridvan ; Mandaliti, Walter ; Castagnoli, Luisa ; Cesareni, Gianni ; Paci, Maurizio. / Cuban, a case study of selective binding : Structural details of the discrimination between ubiquitin and nedd8. In: International Journal of Molecular Sciences. 2019 ; Vol. 20, No. 5.
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