Protein Science, Vol 3, Issue 10 1741-1745, Copyright © 1994 by Cold Spring Harbor Laboratory Press

ARTICLE

Sequence determinants of the capping box, a stabilizing motif at the N-termini of {alpha}-helices

J. W. SEALE, R. SRINIVASAN and G. D. ROSE
Present address: Department of Biochemistry, University of Texas Health Sciences Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78284.

The capping box, a recurrent hydrogen bonded motif at the N-termini of {alpha}-helices, caps 2 of the initial 4 backbone amide hydrogen donors of the helix (Harper ET, Rose GD, 1993, Biochemistry 32:7605-7609). In detail, the side chain of the first helical residue forms a hydrogen bond with the backbone of the fourth helical residue and, reciprocally, the side chain of the fourth residue forms a hydrogen bond with the backbone of the first residue. We now enlarge the earlier definition of this motif to include an accompanying hydrophobic interaction between residues that bracket the capping box sequence on either side. The expanded box motif -- in which 2 hydrogen bonds and a hydrophobic interaction are localized within 6 consecutive residues -- resembles a glycine-based capping motif found at helix C-termini (Aurora R, Srinivasan R, Rose GD, 1994, Science 264:1126-1130).
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