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

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...
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...
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 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...
Coordination Number and Geometry02:57

Coordination Number and Geometry

For transition metal complexes, the coordination number determines the geometry around the central metal ion. Table 1 compares coordination numbers to molecular geometry. The most common structures of the complexes in coordination compounds are octahedral, tetrahedral, and square planar.
Valence Bond Theory02:42

Valence Bond Theory

Coordination compounds and complexes exhibit different colors, geometries, and magnetic behavior, depending on the metal atom/ion and ligands from which they are composed. In an attempt to explain the bonding and structure of coordination complexes, Linus Pauling proposed the valence bond theory, or VBT, using the concepts of hybridization and the overlapping of the atomic orbitals. According to VBT, the central metal atom or ion (Lewis acid) hybridizes to provide empty orbitals of suitable...

You might also read

Related Articles

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

Sort by
Same author

Transcriptomic and Metabolomic Analyses Reveal Mechanisms of Sexual Differentiation and Dimorphism in <i>Morus macroura</i>.

Plants (Basel, Switzerland)·2026
Same author

Effects of prophylactic infusion of equivalent doses of metaraminol and norepinephrine for preventing spinal anesthesia-induced hypotension during cesarean delivery on fetal and maternal outcomes: a dual-center, non-inferiority randomized clinical trial.

International journal of surgery (London, England)·2025
Same author

Stoichiometric homeostasis of <i>Morus alba</i> in the dry-hot valley.

Frontiers in plant science·2025
Same author

Organellular imaging <i>in vivo</i> reveals a depletion of endoplasmic reticular calcium during post-ictal cortical spreading depolarization.

bioRxiv : the preprint server for biology·2024
Same author

Molecular regulation of calcium-sensing receptor (CaSR)-mediated signaling.

Chronic diseases and translational medicine·2024
Same author

Depletion of Activated Hepatic Stellate Cells and Capillarized Liver Sinusoidal Endothelial Cells Using a Rationally Designed Protein for Nonalcoholic Steatohepatitis and Alcoholic Hepatitis Treatment.

International journal of molecular sciences·2024

Related Experiment Video

Updated: Jun 28, 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

Towards predicting Ca2+-binding sites with different coordination numbers in proteins with atomic resolution.

Xue Wang1, Michael Kirberger, Fasheng Qiu

  • 1Department of Computer Science, Georgia State University, Atlanta, Georgia 30303, USA.

Proteins
|November 13, 2008
PubMed
Summary

A new algorithm, MUG, accurately predicts calcium-binding sites in proteins, including challenging low-coordination and cofactor sites. This tool enhances understanding of diverse calcium-binding site geometries and functions.

More Related Videos

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Related Experiment Videos

Last Updated: Jun 28, 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

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Calcium-binding sites in proteins display diverse geometries crucial for various biological functions.
  • While EF-Hand motifs are well-studied, non-EF-Hand sites present structural diversity, complicating Ca(2+) site prediction.
  • Previous graph-theory-based algorithms identified Ca(2+) sites by oxygen clusters on a sphere.

Purpose of the Study:

  • To introduce a novel algorithm, MUG (MUltiple Geometries), for predicting Ca(2+)-binding sites in proteins with atomic resolution.
  • To improve the accuracy and scope of Ca(2+) site prediction, especially for non-EF-Hand and low-coordination sites.
  • To provide a flexible tool capable of incorporating water molecules and cofactors for enhanced prediction.

Main Methods:

  • Developed the MUG algorithm to identify potential Ca(2+) binding sites by finding maximal cliques of oxygen atoms.
  • Located a calcium center (CC) for each cluster, optimizing its position to regularize the cluster-CC structure.
  • Employed geometric filters and recursive refinement to qualify potential Ca(2+) sites, determining ligand coordination.

Main Results:

  • MUG successfully predicted over 90% of documented Ca(2+)-binding sites across three diverse protein structure datasets with 0.22–0.49 Å accuracy.
  • The algorithm accurately predicted all multiple-binding sites and half of the low-coordination sites.
  • MUG identified 14 out of 16 cofactor-coordinating sites and demonstrated flexibility in incorporating water and cofactors.

Conclusions:

  • The MUG algorithm offers a significant advancement in predicting Ca(2+)-binding sites with high accuracy and atomic resolution.
  • MUG's ability to handle diverse geometries and incorporate auxiliary molecules enhances its utility for studying calcium's biological roles.
  • This tool facilitates a deeper understanding of protein-calcium interactions and their associated biological functions.