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Related Concept Videos

Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Related Experiment Video

Updated: Jul 7, 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

Published on: December 16, 2013

Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement.

Jennifer R Calhoun1, Weixia Liu, Katrin Spiegel

  • 1Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Structure (London, England : 1993)
|February 16, 2008
PubMed
Summary

We refined the structure of a designed dimetal-binding protein, di-Zn(II) DFsc, using molecular dynamics. This improved the metal-ligand geometry, providing a more accurate protein structure and insight into metalloprotein active sites.

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Last Updated: Jul 7, 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

Published on: December 16, 2013

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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

Area of Science:

  • Biochemistry and Structural Biology
  • Computational Chemistry
  • Biophysics

Background:

  • Nuclear Magnetic Resonance (NMR) spectroscopy is crucial for determining protein structures.
  • Metalloproteins, such as DFsc, contain metal ions essential for their function.
  • Accurate modeling of metal-ligand interactions is challenging in structural biology.

Purpose of the Study:

  • To determine the solution NMR structure of the designed dimetal-binding protein, di-Zn(II) DFsc.
  • To refine the initial NMR structure using molecular dynamics (MD) for improved metal-ligand geometry.
  • To provide a more realistic structural description of the metalloprotein active site.

Main Methods:

  • Solution Nuclear Magnetic Resonance (NMR) spectroscopy.
  • Standard computational methods for initial NMR structural ensemble calculation.
  • Unrestrained molecular dynamics (MD) with nonbonded force fields.
  • Quantum mechanical/molecular mechanical (QM/MM) MD simulations.
  • Explicit solvent modeling.

Main Results:

  • Initial NMR structure exhibited distortions in metal-ligand geometries.
  • MD refinement successfully relaxed local frustrations at the dimetal site.
  • The refined MD model remained consistent with NMR restraints.
  • The final structure aligns with expected structural and functional properties of DF proteins.

Conclusions:

  • Molecular dynamics methods, including QM/MM, can refine NMR structures of metalloproteins.
  • This approach provides enhanced insight into the metal center's geometry.
  • The refined structure offers a more realistic description of di-Zn(II) DFsc.
  • This methodology is valuable for studying metalloprotein active sites.