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Protein and Protein Structure02:15

Protein and Protein Structure

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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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Chirality is most prevalent in carbon-based tetrahedral compounds, but this important facet of molecular symmetry extends to sp3-hybridized nitrogen, phosphorus and sulfur centers, including trivalent molecules with lone pairs. Here, the lone pair behaves as a functional group in addition to the other three substituents to form an analogous tetrahedral center that can be chiral.
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Complexation Equilibria: The Chelate Effect01:19

Complexation Equilibria: The Chelate Effect

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In complexation reactions, metal atoms or cations interact with ligands to form donor-acceptor adducts called metal complexes. Ligands that bind through one donor site are monodentate, ligands with two donor sites are bidentate, and those with more than two donor sites are polydentate ligands. For example, ethylene diamine is a bidentate ligand that binds through two nitrogen donor atoms, forming a five-membered ring. EDTA is a polydentate ligand that binds through four oxygen and two nitrogen...
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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.
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Sulfides are the sulfur analog of ethers, just as thiols are the sulfur analog of alcohol. Like ethers, sulfides also consist of two hydrocarbon groups bonded to the central sulfur atom. Depending upon the type of groups present, sulfides can be symmetrical or asymmetrical. Symmetrical sulfides can be prepared via an SN2 reaction between 2 equivalents of an alkyl halide and one equivalent of sodium sulfide.
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Structural Isomerism02:34

Structural Isomerism

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Isomerism in Complexes
Isomers are different chemical species that have the same chemical formula. Structural isomerism of coordination compounds can be divided into two subcategories, the linkage isomers and coordination-sphere isomers.
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Chalcogen Bonds Involving Selenium in Protein Structures.

Oliviero Carugo1, Giuseppe Resnati2, Pierangelo Metrangolo2

  • 1Department of Chemistry, University of Pavia, 27100 Pavia, Italy.

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|September 3, 2021
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Selenium (Se) forms common chalcogen bonds with oxygen in proteins, revealing its underappreciated role in biomolecules. This discovery aids in designing functional peptides and understanding selenium

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Area of Science:

  • Biochemistry and Structural Biology
  • Chemical Bonding and Molecular Interactions

Background:

  • Chalcogen bonds, interactions involving Group 16 elements as electrophilic sites, are crucial in molecular recognition.
  • The role of chalcogen atoms, particularly sulfur (S), in biomolecular interactions is increasingly recognized, yet understudied.
  • Previous research has primarily focused on sulfur-mediated interactions, leaving other chalcogens less explored.

Purpose of the Study:

  • To statistically analyze the prevalence and characteristics of selenium-oxygen (Se···O) chalcogen bonds in protein structures.
  • To investigate the underappreciated role of selenium as a 'sticky site' in biological macromolecules.
  • To provide insights for the future design of functional peptides and understanding selenium's biological functions.

Main Methods:

  • Conducted a comprehensive statistical analysis of 3562 protein structures obtained from the Protein Data Bank (PDB).
  • Examined a dataset comprising 18,266 instances of selenomethionine residues within these protein structures.
  • Identified and quantified the occurrence of Se···O chalcogen bonds across the analyzed protein structures.

Main Results:

  • Selenium-oxygen (Se···O) chalcogen bonds were found to be a common feature in the analyzed protein structures.
  • The statistical analysis confirmed the widespread presence of these specific interactions involving selenium.
  • This prevalence suggests a significant, yet often overlooked, role for selenium in stabilizing protein structures.

Conclusions:

  • Selenium-oxygen chalcogen bonds are commonplace in protein structures, highlighting selenium's importance in biomolecular interactions.
  • These findings underscore the need to consider selenium's role beyond its known biochemical functions.
  • The study provides a foundation for designing novel peptides and understanding the biological significance of selenium.