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Related Concept Videos

Peptide Bonds02:43

Peptide Bonds

71.6K
A peptide bond covalently attaches amino acids through a dehydration reaction. One amino acid's carboxyl group and another amino acid's amino group combine, releasing a water molecule. The resulting bond is the peptide bond. The products that such linkages form are peptides. As more amino acids join this growing chain, the resulting chain is a polypeptide. Each polypeptide has a free amino group at one end. This end has the N-terminal, or the amino-terminal, and the other end has a free...
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Protein Folding01:25

Protein Folding

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Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
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Protein Modifications in the RER01:26

Protein Modifications in the RER

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Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
Broadly, these modifications can be categorized into four main categories — glycosylation, formation of disulfide bonds, assembly of protein subunits, and specific proteolytic cleavages like removal of signal...
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Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

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ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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Protein Organization01:24

Protein Organization

6.0K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
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Phosphodiester Linkages01:01

Phosphodiester Linkages

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Overview
Phosphodiester bond forms when a phosphoric acid molecule (H3PO4) links with two hydroxyl groups (–OH) of two other molecules, forming two ester bonds. Two water molecules are released in this process. The phosphodiester bond is commonly found in nucleic acids (DNA and RNA) and plays a critical role in their structure and function.
Phosphodiester Bonds Link Nucleotides Together
DNA and RNA are polynucleotides or long chains of nucleotides that are linked together. A nucleotide is...
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Updated: May 16, 2025

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides
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Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Published on: November 21, 2013

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Peptide bonds revisited.

Santosh Panjikar1, Manfred S Weiss2

  • 1ANSTO, Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia.

Iucrj
|March 31, 2025
PubMed
Summary
This summary is machine-generated.

Peptide bonds in alpha-helices and beta-strands exhibit distinct structural and chemical properties. These differences in bond angles, dihedral angles, and electron density impact protein structure refinement and understanding of protein dynamics.

Keywords:
enol-like peptidespeptide bondsprotonated carbonyl oxygen

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Synthesis of Information-bearing Peptoids and their Sequence-directed Dynamic Covalent Self-assembly
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Area of Science:

  • Structural biology
  • Biochemistry
  • Computational chemistry

Background:

  • Peptide bonds are fundamental units of protein structure.
  • Understanding peptide bond characteristics in secondary structures is crucial for protein folding, stability, and function.

Purpose of the Study:

  • To investigate and compare the structural and chemical properties of peptide bonds in alpha-helices versus beta-strands.
  • To elucidate the implications of these differences for protein structure refinement and dynamics.

Main Methods:

  • Analysis of a nonredundant dataset of 1024 high-resolution protein crystal structures from the Protein Data Bank (PDB).
  • Examination of peptide bond lengths, angles, dihedral angles, electron-density distributions, and hydrogen bonding.
  • Calculation of normalized mean atomic displacement parameters (ADPs).

Main Results:

  • While bond lengths are similar, bond angles (∠CNCα and ∠OCN) are larger in beta-strands than in alpha-helices.
  • Peptide dihedral angles (ω) show distinct distributions: sharp Gaussian in helices, wider in strands.
  • Helical peptide bonds exhibit lower electron density ratios and higher ADPs, suggesting increased flexibility and potential enol-like character.

Conclusions:

  • Peptide bonds in alpha-helices and beta-strands possess unique characteristics.
  • Helical peptide bonds may display more enol-like character, indicating a higher likelihood of protonation.
  • Findings necessitate adapting protein structure refinement protocols to account for these subtle geometric variations.