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Related Concept Videos

Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as 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...
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...

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Updated: May 14, 2026

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English
14:34

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

Single vs. multiple ligand pathways in globins: a computational view.

M Fátima Lucas1, Víctor Guallar

  • 1Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain.

Biochimica Et Biophysica Acta
|February 8, 2013
PubMed
Summary
This summary is machine-generated.

Computational simulations reveal distinct ligand entry pathways in myoglobin and mini-hemoglobin. This study clarifies ligand migration, offering insights into protein dynamics for researchers.

Keywords:
Cerebratulus lacteusGlobinLigand migrationMyoglobinPELE

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Modeling Ligands into Maps Derived from Electron Cryomicroscopy
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Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Area of Science:

  • Biochemistry
  • Computational Biology
  • Structural Biology

Background:

  • Diatomic ligand migration in globins is extensively studied, yet ligand entrance pathways remain unclear.
  • Computational simulations often predict multiple pathways, causing concern among experimental researchers.
  • Modeling unbiased ligand entrance using conventional molecular dynamics is challenging and resource-intensive.

Purpose of the Study:

  • To investigate and compare diatomic ligand entrance pathways in myoglobin (Mb) and the mini-hemoglobin from Cerebratulus lacteus (CerHb).
  • To demonstrate the utility of a novel Monte Carlo methodology for mapping ligand diffusion and rare events.
  • To provide computationally inexpensive and accessible simulation data for non-profit researchers.

Main Methods:

  • Utilized a Monte Carlo methodology within the PELE (Protein-Environment HEat LEakage Estimation) framework.
  • Simulated ligand diffusion and rare events for myoglobin and Cerebratulus lacteus mini-hemoglobin.
  • Analyzed ligand entrance pathways and identified key gating mechanisms.

Main Results:

  • Simulations demonstrated system-specific ligand entrance pathways, aligning with experimental expectations.
  • Myoglobin exhibited multiple entrance pathways, including known xenon cavities, with 64% of trajectories gated by the distal histidine.
  • Cerebratulus lacteus mini-hemoglobin showed a single, exclusive apolar channel for ligand entry.

Conclusions:

  • The Monte Carlo approach accurately models system-specific ligand migration in globins.
  • Distinct ligand entrance mechanisms in Mb and CerHb highlight the importance of protein structure in ligand dynamics.
  • The PELE algorithms offer a computationally efficient and accessible tool for studying protein-ligand interactions.