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Stabilizing nonpolar/polar side-chain interactions in the alpha-helix.

C D Andrew1, S Penel, G R Jones

  • 1Department of Biomolecular Sciences, UMIST, P.O. Box 88, Manchester M60 1QD, United Kingdom. Andrew.Doig@umist.ac.uk

Proteins
|December 18, 2001
PubMed
Summary

Contrary to popular belief, nonpolar and polar amino acids can stabilize protein structures. Specific nonpolar/polar pairs, like Val-Lys, favorably interact in alpha-helices, enhancing protein stability.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Protein Science

Background:

  • Traditional models suggest amino acids of similar polarity interact, while dissimilar polarities repel.
  • The role of nonpolar/polar interactions in protein structure stabilization is often overlooked.

Purpose of the Study:

  • To investigate the stabilizing effect of nonpolar/polar amino acid interactions in alpha-helices.
  • To challenge the simplistic view of amino acid interactions based solely on polarity.

Main Methods:

  • Synthesis of partially helical peptides with specific nonpolar/polar residue pairs (Ile-Lys, Ile-Arg, Val-Lys) at i, i+4 spacing.
  • Circular dichroism spectroscopy to assess helical content.
  • Helix-coil theory to quantify interaction free energy (DeltaG).

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Main Results:

  • Nonpolar/polar pairs (Ile-Lys, Ile-Arg, Val-Lys) were observed more frequently than expected at i, i+4 positions in protein helices.
  • Peptides with i, i+4 spacing exhibited greater helical content compared to controls with i, i+5 spacing.
  • Calculated DeltaG values indicated favorable stabilization, ranging from -0.14 to -0.32 kcal x mol(-1).

Conclusions:

  • Nonpolar/polar interactions, specifically between Val/Ile and Lys/Arg, can be stabilizing in alpha-helices.
  • These interactions are primarily hydrophobic, involving contacts between nonpolar side chains and the alkyl groups of charged residues.
  • Charged residues like Lys and Arg can engage in favorable interactions with both polar and nonpolar amino acids, adding complexity to protein stability models.