Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Metal-Ligand Bonds02:51

Metal-Ligand Bonds

The hemoglobin in the blood, the chlorophyll in green plants, vitamin B-12, and the catalyst used in the manufacture of polyethylene all contain coordination compounds. Ions of the metals, especially the transition metals, are likely to form complexes.
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Metallic Solids02:37

Metallic Solids

Metallic solids such as crystals of copper, aluminum, and iron are formed by metal atoms. The structure of metallic crystals is often described as a uniform distribution of atomic nuclei within a “sea” of delocalized electrons. The atoms within such a metallic solid are held together by a unique force known as metallic bonding that gives rise to many useful and varied bulk properties.
All metallic solids exhibit high thermal and electrical conductivity, metallic luster, and malleability. Many...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Modeling CO<sub>2</sub> Hydrogenation to Methanol on an Ensemble of Inverse ZrO<sub>2</sub> on Cu Catalytic Sites: Mechanism, Reactivity, and Deactivation.

Angewandte Chemie (International ed. in English)·2026
Same author

Cation-Limited Hydroxide Anion Diffusion Drives Asymmetric Hydrogen Kinetics on Transition-Metal Decorated Platinum Surface.

Journal of the American Chemical Society·2026
Same author

What can Raman spectroscopy really say about the adsorbed CO on roughened Cu electrodes in CO<sub>2</sub> electroreduction conditions?

Faraday discussions·2026
Same author

A protein-based model of carbon monoxide dehydrogenase exhibits tunable covalency across cluster oxidation and ligand-bound states.

Chemical science·2026
Same author

Low-Temperature Non-Oxidative Coupling of Methane on Atomically Dispersed Titanium-Aluminum-Boron Nanopowder.

Journal of the American Chemical Society·2026
Same author

The Crucial Role of Hydrogen Ligation in the Stability of Single Atoms on Rutile TiO<sub>2</sub>: A First-Principles Study.

ACS applied materials & interfaces·2026
Same journal

Tau protein differentially affects Piezo1 and Kir2.1 channels in brain capillary endothelial cells.

Biophysical journal·2026
Same journal

Emergent Intercellular Junction Stability during Cyclic Tissue Loading.

Biophysical journal·2026
Same journal

Enhanced-Sampling Simulations Reveal Distinct Intermediates in SARS-CoV-2 FSE Pseudoknot Interconversion.

Biophysical journal·2026
Same journal

Structure-based simulations of the full Flock House virus capsid reveal pathways and energetics of an infection-critical peptide externalization event.

Biophysical journal·2026
Same journal

Quantifying the Peripheral Surface Information Entropy from Conformational Ensembles of Globular Protein-Peptide Complexes.

Biophysical journal·2026
Same journal

Anisotropic unbinding and location-dependent hovering of a kinesin motor head over microtubule.

Biophysical journal·2026
See all related articles

Related Experiment Video

Updated: May 19, 2026

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations
05:57

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations

Published on: April 26, 2024

Hybrid dynamics simulation engine for metalloproteins.

Manuel Sparta1, David Shirvanyants, Feng Ding

  • 1Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA.

Biophysical Journal
|September 6, 2012
PubMed
Summary
This summary is machine-generated.

We developed a new QM/DMD method for robust metalloprotein characterization. This efficient approach accurately describes metalloprotein structure, dynamics, and electronic properties, overcoming computational challenges.

More Related Videos

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry
11:37

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry

Published on: November 29, 2013

Designing Silk-silk Protein Alloy Materials for Biomedical Applications
11:14

Designing Silk-silk Protein Alloy Materials for Biomedical Applications

Published on: August 13, 2014

Related Experiment Videos

Last Updated: May 19, 2026

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations
05:57

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations

Published on: April 26, 2024

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry
11:37

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry

Published on: November 29, 2013

Designing Silk-silk Protein Alloy Materials for Biomedical Applications
11:14

Designing Silk-silk Protein Alloy Materials for Biomedical Applications

Published on: August 13, 2014

Area of Science:

  • Computational chemistry
  • Biophysics
  • Structural biology

Background:

  • Metalloproteins present significant computational challenges due to their complex dynamics and electronic structures across multiple scales.
  • Accurate computational models are crucial for understanding metalloprotein function and designing new ones.

Purpose of the Study:

  • To introduce an efficient and robust computational method for characterizing metalloproteins.
  • To enable accurate descriptions of metalloprotein structure, dynamics, and electronic properties.

Main Methods:

  • A hybrid quantum mechanical/discrete molecular dynamics (QM/DMD) approach.
  • QM describes the metal active site, while DMD captures extensive protein dynamics.
  • A dynamic quantum-classical boundary facilitates feedback between QM and DMD.

Main Results:

  • QM/DMD successfully characterized rubredoxin and its mutants, providing a balanced description of structure, dynamics, and electronic structure.
  • The method accurately predicted the inactive Ca(2+) form of catechol O-methyl transferase, revealing structural changes facilitating catalytic inactivity.

Conclusions:

  • QM/DMD offers a reliable and efficient computational solution for metalloprotein research.
  • This method provides crucial structural insights into metalloprotein function and dysfunction.