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Related Concept Videos

Termination of Translation01:44

Termination of Translation

The large ribosomal subunit has several important structures essential to translation. These include the peptidyl transferase center (PTC) - which is the site where the peptide bond is formed - and a large, internal, water-filled tube through which the nascent polypeptide moves. This latter structure is called the Peptide Exit Tunnel, and it begins at the PTC and spans the body of the large ribosomal subunit. During translation, as the nascent polypeptide chain is synthesized, it passes through...
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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.
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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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Microfluidic Mixers for Studying Protein Folding
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Published on: April 10, 2012

End-to-end vs interior loop formation kinetics in unfolded polypeptide chains.

Beat Fierz1, Thomas Kiefhaber

  • 1Division of Biophysical Chemistry, Biozentrum der Universität Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.

Journal of the American Chemical Society
|January 18, 2007
PubMed
Summary

Protein folding kinetics differ for loop types. Interior loops (type II and III) form slower than end-to-end loops (type I) due to reduced internal flexibility, impacting protein structure formation.

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Thermodynamics of Membrane Protein Folding Measured by Fluorescence Spectroscopy
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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Physical Chemistry

Background:

  • Protein folding involves intramolecular interactions and loop formation.
  • Previous studies focused on end-loop formation, but interior contacts are crucial.
  • Understanding loop formation kinetics is key to protein folding mechanisms.

Purpose of the Study:

  • To compare the kinetics of different loop formation types during protein folding.
  • To investigate the influence of loop position (end-to-end, end-to-interior, interior-to-interior) on folding rates.
  • To elucidate the role of internal chain flexibility and solvent interactions in loop formation.

Main Methods:

  • Utilized triplet-triplet energy transfer (xanthone to naphthylalanine) to measure loop formation kinetics.
  • Compared kinetics of type I (end-to-end), type II (end-to-interior), and type III (interior-to-interior) loops.
  • Analyzed the effect of loop size, amino acid sequence, and chain dimensions on rate constants.

Main Results:

  • Type II and type III loop formation is significantly slower than type I loops of comparable size and sequence.
  • Type II loop formation rate decreases with increasing chain dimensions, becoming ~2.5-fold slower than type I.
  • Type III loop formation is ~1.7-fold slower than type II, indicating coupled chain motions.

Conclusions:

  • Differences in loop formation kinetics are primarily attributed to variations in internal polypeptide chain flexibility.
  • Solvent interactions influence loop formation but do not explain the observed kinetic differences between loop types.
  • Internal chain flexibility dictates the distinct folding dynamics of different loop positions.