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Related Concept Videos

Structure of Cadherins01:25

Structure of Cadherins

The cadherins were one of the first cell adhesion molecules discovered; the term “cadherins”   is based on their calcium-dependent adhering properties. The first cadherins discovered on the epithelial, neuronal, and placental cells were named E-cadherin, P-cadherin, and N-cadherin, respectively. These classical cadherins share sequence and structural similarities. Other cadherins, including those involved in cell signaling, are grouped into non-classical cadherins. This diversity of cadherins...
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...
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...
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.
Crystal Field Theory - Octahedral Complexes02:58

Crystal Field Theory - Octahedral Complexes

Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...

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Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
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Pattern prediction and coordination geometry analysis from cadmium-binding proteins: a computational approach.

R Jesu Jaya Sudan1, C Sudandiradoss

  • 1Bioinformatics Division, VIT University, Vellore 632 014, India.

Acta Crystallographica. Section D, Biological Crystallography
|September 21, 2012
PubMed
Summary

Computational analysis of cadmium binding revealed specific protein motifs. These structure-based motifs can aid in developing chelators for effective cadmium removal from the body.

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Published on: November 3, 2011

Area of Science:

  • Biochemistry and Molecular Biology
  • Computational Chemistry
  • Toxicology

Background:

  • Cadmium toxicity poses significant health risks, including carcinogenicity, respiratory, kidney, liver, and neurological damage.
  • Understanding cadmium's interaction with biomolecules is crucial for predicting disease susceptibility.

Purpose of the Study:

  • To computationally investigate cadmium-binding characteristics in proteins.
  • To identify and characterize cadmium-binding motifs for potential therapeutic applications.

Main Methods:

  • Analysis of approximately 140 cadmium-bound protein structures and 34 cadmium-binding sequences.
  • Examination of metal-coordinating architecture, including chelate loops, residue arrangements, secondary structures, distances, and angles.
  • Prediction of binding patterns based on residue occurrence probabilities and sequence patterns.

Main Results:

  • Identification of 56 distinct chelate loops involved in cadmium binding.
  • Derivation of four short-length, structure-based cadmium-binding motifs: Y-X-G-X-G, Q-X(9)-E, E-X(2)-E-X(2)-E, and T-X(5)-E-X(2)-E.
  • These motifs were found within conserved regions of cadmium-binding proteins, though surrounding residue conservation varied.

Conclusions:

  • The identified structure-based motifs provide insights into cadmium-protein interactions.
  • These motifs are proposed as effective tools for designing chelators to remove cadmium toxicity.