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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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Updated: Jun 15, 2026

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
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Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Published on: December 16, 2013

Precise structural determination of weakly binding peptides by utilizing dihedral angle constraints.

Yumiko Mizukoshi1, Michiko Nagasu, Ichio Shimada

  • 1Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Aomi 2-41-6, Koto-ku, Tokyo, 135-0064, Japan.

Journal of Biomolecular NMR
|March 16, 2010
PubMed
Summary

Precise peptide structure determination is crucial for drug design. New methods using dihedral angle constraints improve structural accuracy for weakly binding peptides, aiding ligand optimization.

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Last Updated: Jun 15, 2026

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
14:44

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Biochemistry
  • Structural Biology
  • Medicinal Chemistry

Background:

  • Determining peptide conformations bound to targets is vital for peptide ligand optimization and peptide-mimetic design.
  • Transferred nuclear Overhauser effect (TrNOE) is common for studying weakly binding ligands but yields limited distance constraints, especially for extended conformations.
  • Precise structural determination of weakly binding peptides necessitates additional structural constraints beyond TrNOE.

Purpose of the Study:

  • To present a novel strategy for introducing dihedral angle constraints to enhance peptide structure determination.
  • To demonstrate the effectiveness of this strategy for precisely determining the structures of weakly binding peptides.
  • To enable the definition of core binding motifs for peptide ligands.

Main Methods:

  • Systematic introduction of dihedral angle constraints.
  • Utilizing multiple transferred cross-correlated relaxation experiments.
  • Structural determination of phage-derived peptide ligands.

Main Results:

  • Achieved precise structural determination of weakly binding peptides.
  • Successfully obtained additional structural constraints.
  • Demonstrated the ability to define core binding motifs of peptide ligands.

Conclusions:

  • The developed strategy effectively enhances the precision of peptide structure determination.
  • This approach is valuable for optimizing peptide ligands and designing peptide-mimetics.
  • The method allows for the identification of critical binding elements in peptide ligands.