Local structural motifs in proteins

Detection and characterization of fragments inserted in helices

Nicole Balasco, Giovanni Smaldone, Alessia Ruggiero, Alfonso De Simone, Luigi Vitagliano

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

The global/local fold of protein structures is stabilized by a variety of specific interactions. A primary role in this context is played by hydrogen bonds. In order to identify novel motifs in proteins, we searched Protein Data Bank structures looking for backbone H-bonds formed by NH groups of two (or more) consecutive residues with consecutive CO groups of distant residues in the sequence. The present analysis unravels the occurrence of recurrent structural motifs that, to the best of our knowledge, had not been characterized in literature. Indeed, these H-bonding patterns are found (i) in a specific parallel β-sheet capping, (ii) in linking of β-hairpins to α-helices, and (iii) in α-helix insertions. Interestingly, structural analyses of these motifs indicate that Gly residues frequently occupy prominent positions. The formation of these motifs is likely favored by the limited propensity of Gly to be embodied in helices/sheets. Of particular interest is the motif corresponding to insertions in helices that was detected in 1% of analyzed structures. Inserted fragments may assume different structures and aminoacid compositions and usually display diversified evolutionary conservation. Since inserted regions are physically separated from the rest of the protein structure, they represent hot spots for ad-hoc protein functionalization.

Original languageEnglish
Pages (from-to)1924-1930
Number of pages7
JournalInternational Journal of Biological Macromolecules
Volume118
DOIs
Publication statusPublished - Oct 15 2018

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Amino Acid Motifs
Proteins
Carbon Monoxide
Hydrogen
Databases
Conservation
Hydrogen bonds
Chemical analysis

Keywords

  • Glycine residue
  • Helix insertion
  • Protein stability
  • Ramachandran space

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Cite this

Local structural motifs in proteins : Detection and characterization of fragments inserted in helices. / Balasco, Nicole; Smaldone, Giovanni; Ruggiero, Alessia; De Simone, Alfonso; Vitagliano, Luigi.

In: International Journal of Biological Macromolecules, Vol. 118, 15.10.2018, p. 1924-1930.

Research output: Contribution to journalArticle

Balasco, Nicole ; Smaldone, Giovanni ; Ruggiero, Alessia ; De Simone, Alfonso ; Vitagliano, Luigi. / Local structural motifs in proteins : Detection and characterization of fragments inserted in helices. In: International Journal of Biological Macromolecules. 2018 ; Vol. 118. pp. 1924-1930.
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