Abstract
Helix formation in folding proteins is stabilized by binding of recurrent hydrophobic side chains in one longitudinal quadrant against the locally most hydrophobic region of the protein. To test this hypothesis, we fitted sequences of 247 alpha-helices of 55 proteins to the circular (infinite) template (symbol; see text) to maximize the strip-of-helix hydrophobicity index (the mean hydrophobicity of residues in (symbol; see text) positions). These template-predicted configurations closely matched crystallographic structures in 87% of four- or five-turn helices compared. We determined the longitudinal quadrant distributions of amino acids in the template-fitted, sheet projections of alpha-helices with respect to the best longitudinal, hydrophobic strip on each helix and to the N and C termini, interiors, and entire helices. Amino acids Leu, Ile, Val, and Phe were concentrated in one longitudinal quadrant (p less than 0.001). Lys, Arg, Asp, and Glu were not in the quadrant of Leu, Ile, Val, and Phe (p less than 0.001). Significant quadrant distributions for other amino acids and for termini of the helices were also found.
Highlights
Helix formation in foldingproteins is stabilized by binding of recurrent hydrophobic side chains in one longitudinal quadrant againstthelocally most hydrophobic region of theprotein
Amino acids Leu, Ile, Val, and Phe were concentrated in one longitudinal quadrant ( p < 0.001)
Cent cycles of a helix could be stabilized by the binding of recurrent hydrophobic residues along one longitudinal quadrant of the helix to a locally hydrophobic region
Summary
Ence is coiled as an a-helix [1]. Perutz et al [2] originally All sequences of a-helices were taken from the papers of Presta observed in the a-helices of hemoglobin the recurrence of and Rose [8]and Richardson and Richardson [9]. Nonpolar residues every 3.6 residues, on the aver- lations based on both methods because, for 13 proteins common to age, making the interiofraces of the helices nonpolar. Schiffer both studies, helices determined by Richardson and Richardson avand Edmundson [3] created the wheel projection t o identify such segments with helical potential. Acircular template for a helix with a longitudinal hydrophobic amphipathic moments to predict a-helices. On a-helices to promoftoelding against a hydrophobic surface This generic, helicaltemplate corresponded to a sheet projection with successive coils of the helix in slanting columns anwdith longitudinal.
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