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Related Concept Videos

Protein Folding01:22

Protein Folding

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Protein Folding01:25

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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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The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
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Noncovalent Attractions in Biomolecules02:35

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Related Experiment Video

Updated: Jun 20, 2026

Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions
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How strong are side chain interactions in the folding intermediate?

Ekaterina N Samatova1, Natalia S Katina, Vitaly A Balobanov

  • 1Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation.

Protein Science : a Publication of the Protein Society
|August 21, 2009
PubMed
Summary

This study investigated how hydrophobic amino acids in apomyoglobin affect protein stability. Conserved residues contribute significantly to the intermediate state

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Area of Science:

  • Biochemistry
  • Protein Folding
  • Biophysics

Background:

  • Apomyoglobin's hydrophobic core plays a crucial role in its stability and folding.
  • Understanding the contribution of specific amino acid residues to protein structure is essential.

Purpose of the Study:

  • To investigate the influence of 12 nonpolar amino acid residues in apomyoglobin's hydrophobic core on its native state and folding intermediate stability.
  • To differentiate the roles of conserved versus nonconserved hydrophobic residues in protein folding.

Main Methods:

  • Site-directed mutagenesis to substitute 12 nonpolar residues with alanine.
  • Equilibrium pH-induced transitions studied using circular dichroism and fluorescent spectroscopy.
  • Estimation of free energy changes during intermediate state formation.

Main Results:

  • Conserved hydrophobic residues contribute 15-50% to the side chain interaction strength in the apomyoglobin intermediate state compared to the native state.
  • Nonconserved hydrophobic residues contribute minimally (near 0%) to the intermediate state's stability.
  • Identified specific contributions of conserved and nonconserved residues to protein folding stages.

Conclusions:

  • Conserved hydrophobic residues are critical for stabilizing the apomyoglobin intermediate state.
  • Nonconserved hydrophobic residues have a limited role in the intermediate state's stability.
  • These findings enhance understanding of residue involvement in protein folding dynamics.