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Related Concept Videos

Peptide Bonds02:43

Peptide Bonds

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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 Organization01:24

Protein Organization

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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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What are Proteins?01:28

What are Proteins?

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Proteins are polymers of amino acids linked together by peptide bonds. Proteins and polypeptides are interchangeably used to refer to long chains of amino acids. However, polypeptides have a molecular weight of fewer than 10,000 daltons, while proteins have greater molecular weight.  Polypeptides with less than 20 amino acids are called oligopeptides or simply peptides. Interactions among the constituent amino acid side chains of proteins help them fold into a stable 3-dimensional...
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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 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.
A protein's shape is critical to its function. For example, an enzyme...
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Updated: May 10, 2025

Constructing Cyclic Peptides Using an On-Tether Sulfonium Center
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Constructing Cyclic Peptides Using an On-Tether Sulfonium Center

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Peptide bonds strike back.

Ashwin Chari1

  • 1Research Group for Structural Biochemistry and Mechanisms, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany.

Iucrj
|April 25, 2025
PubMed
Summary
This summary is machine-generated.

Structural biology remains vital, as experimental methods reveal crucial peptide bond properties missed by computational protein design and structure prediction. These overlooked features are key for understanding protein function.

Keywords:
keto–enol tautomerismpeptide bondsprotein designprotein structure prediction

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Recent advances in protein design and structure prediction challenge the necessity of experimental structural biology.
  • Computational methods have largely overlooked specific peptide bond properties.

Purpose of the Study:

  • To investigate the continued relevance of experimental structural biology in light of computational advances.
  • To identify and highlight overlooked peptide bond properties potentially important for protein function.

Main Methods:

  • Review and analysis of existing literature on protein design, structure prediction, and experimental structural biology.
  • Identification of specific peptide bond characteristics often absent in computational models.

Main Results:

  • Experimental structural biology retains a crucial role, particularly in uncovering subtle molecular details.
  • Several key peptide bond properties, vital for protein function, are frequently omitted in current protein design and prediction models.
  • These overlooked properties have not been a primary focus for the broader structural biology community.

Conclusions:

  • Experimental structural biology is indispensable for a complete understanding of protein structure-function relationships.
  • Future protein design and prediction efforts should incorporate the detailed peptide bond properties identified.
  • A renewed focus on these overlooked aspects is necessary for advancing the field of structural biology.