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Related Concept Videos

Peptide Bonds02:43

Peptide Bonds

A peptide bond covalently attaches amino acids through a dehydration reaction. One amino acid's carboxyl group and another amino acid's amino group combine, releasing a water molecule. The resulting bond is the peptide bond. The products that such linkages form are peptides. As more amino acids join this growing chain, the resulting chain is a polypeptide. Each polypeptide has a free amino group at one end. This end has the N-terminal, or the amino-terminal, and the other end has a free...
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

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Related Experiment Video

Updated: May 8, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Sequence-specific Ni(II)-dependent peptide bond hydrolysis for protein engineering: active sequence optimization.

Anna Maria Protas1, Hanieh Hossein Nejad Ariani, Arkadiusz Bonna

  • 1Lodz Regional Park of Science and Technology Ltd., 114/116 Dubois Street, 93-465 Lodz, Poland.

Journal of Inorganic Biochemistry
|August 27, 2013
PubMed
Summary

Nickel(II) ions selectively cleave peptide bonds. This study identified a strong preference for aromatic amino acids at specific positions (Zaa and Baa) in peptide sequences, optimizing Ni(II)-catalyzed peptide bond cleavage for protein engineering.

Keywords:
Nickel(II) complexPeptide bond hydrolysisPeptide libraryRate constant

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Area of Science:

  • Biochemistry
  • Chemical Biology
  • Proteomics

Background:

  • Nickel(II) ions are known to hydrolytically cleave peptide bonds preceding serine (Ser) or threonine (Thr) residues.
  • Previous work identified preferences for bulky and aromatic residues at positions Xaa and Zaa in Ni(II)-catalyzed peptide cleavage.

Purpose of the Study:

  • To investigate the influence of the residue downstream of position Zaa on the reaction rate of Ni(II)-catalyzed peptide bond cleavage.
  • To identify optimal amino acid substitutions for enhancing Ni(II)-catalyzed peptide cleavage in protein engineering.

Main Methods:

  • Synthesis and screening of a peptide library (Ac-Gly-Ala-Ser-Arg-His-Zaa-Baa-Arg-Leu-NH2) with variations at Zaa and Baa positions.
  • Kinetic analysis of selected peptides to determine reaction rates.

Main Results:

  • A strong preference for aromatic residues was observed at both Zaa and Baa positions.
  • These findings significantly narrow down the useful substitutions for Xaa, Zaa, and Baa positions.

Conclusions:

  • The specific amino acid sequence surrounding the cleavage site, particularly aromatic residues at Zaa and Baa, critically influences the efficiency of Ni(II)-catalyzed peptide bond hydrolysis.
  • This knowledge facilitates the rational design of peptides and proteins for targeted cleavage applications in biotechnology and protein engineering.