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Related Experiment Video

Updated: Jun 14, 2026

Quantifying the Binding Interactions Between Cu(II) and Peptide Residues in the Presence and Absence of Chromophores
11:38

Quantifying the Binding Interactions Between Cu(II) and Peptide Residues in the Presence and Absence of Chromophores

Published on: April 5, 2022

Modeling Cu(II) binding to peptides using the extensible systematic force field.

Faina Ryvkin1, Frederick T Greenaway

  • 1Department of Chemistry, Emmanuel College, Boston, MA 02115, USA. ryvkin@emmanuel.edu

Bioinorganic Chemistry and Applications
|March 20, 2010
PubMed
Summary

The extensible systematic force field (ESFF) showed limitations in accurately modeling copper(II) binding to histidine residues in peptides. Caution is advised when using ESFF for copper complexes with covalent bonds or unconstrained ligands.

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Last Updated: Jun 14, 2026

Quantifying the Binding Interactions Between Cu(II) and Peptide Residues in the Presence and Absence of Chromophores
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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:

  • Computational chemistry
  • Biophysics
  • Metalloprotein modeling

Background:

  • Copper(II) ions are crucial in biological systems, often coordinated by histidine residues.
  • Lysyl oxidase utilizes a copper-binding site involving histidine residues.
  • Accurate computational models are needed to study metal-ligand interactions in proteins.

Purpose of the Study:

  • To evaluate the accuracy of the extensible systematic force field (ESFF) for modeling copper(II) binding to a peptide containing histidine residues.
  • To assess the suitability of ESFF for simulating the copper-binding site of lysyl oxidase.

Main Methods:

  • Distance geometry calculations were employed to pre-constrain copper-histidine interactions.
  • ESFF computations were performed using optimized starting structures.
  • Various copper geometries were modeled to assess their impact on results.

Main Results:

  • ESFF predicted a distorted square pyramidal geometry around copper(II).
  • Imidazole rings showed suboptimal orientation for copper ligation.
  • Calculated copper-nitrogen bond distances were found to be excessively long.

Conclusions:

  • The extensible systematic force field (ESFF) may not be suitable for accurately modeling copper(II) complexes with significant bond covalency.
  • ESFF requires caution when applied to systems with non-planar or geometrically unconstrained ligands.
  • Further refinement of force fields is needed for precise metalloprotein simulations.