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Related Concept Videos

Protein Folding01:22

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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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Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
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Thermodynamics of Membrane Protein Folding Measured by Fluorescence Spectroscopy
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How the hydrophobic factor drives protein folding.

Robert L Baldwin1, George D Rose2

  • 1Department of Biochemistry, Stanford University Medical Center, Beckman Center, School of Medicine, Stanford, CA 94305-5307; baldwinb@stanford.edu.

Proceedings of the National Academy of Sciences of the United States of America
|November 3, 2016
PubMed
Summary

Hydrophobicity drives protein folding through distinct mechanisms for rare gases and alkanes. Alkanes exhibit special hydration shells, crucial for protein folding, unlike rare gases.

Keywords:
hydration shellshydrophobic effecthydrophobicityprotein foldingsolvent shells

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Area of Science:

  • Biochemistry and Physical Chemistry
  • Protein Folding Dynamics
  • Hydrophobicity Studies

Background:

  • Hydrophobicity (HY) is a key driver of protein folding.
  • The traditional Nozaki-Tanford method for measuring HY has limitations.
  • Understanding the nuances of HY is critical for protein science.

Purpose of the Study:

  • To modify the Nozaki-Tanford method for easier HY measurement using gases.
  • To differentiate and characterize two types of hydrophobicity: intrinsic and extrinsic.
  • To investigate the role of hydration shells in alkane hydrophobicity and protein folding.

Main Methods:

  • Modification of the Nozaki-Tanford method using gases as solutes.
  • Measurement of hydrophobicity values for rare gases and alkanes.
  • Analysis of transfer energetics of alkanes to cyclohexane.
  • Development of a space-filling model for alkane hydration shells.

Main Results:

  • A modified, user-friendly method for measuring hydrophobicity was developed.
  • Rare gases exhibit intrinsic HY proportional to solvent-accessible surface area (ASA).
  • Alkanes show extrinsic HY dependent on special hydration shells stabilized by van der Waals interactions.
  • Evidence supports the presence of these shells and their role in protein folding.

Conclusions:

  • Two distinct types of hydrophobicity (intrinsic and extrinsic) were identified.
  • Extrinsic hydrophobicity in alkanes is driven by specific hydration shells, supporting Kauzmann's protein folding mechanism.
  • The short lifetime of van der Waals interactions likely explains the difficulty in detecting alkane hydration shells via NMR.