Background: As an approach to understanding the role of local sequence in determining protein tertiary structure, we have examined the conformation of a 23-residue peptide fragment corresponding to the structurally conserved helix-Schellman motif-helix (H-Sm-H) domain (residue 10-32) of cellular retinoic acid binding protein, along with variants designed to probe the contributions of the helix-terminating Gly23 and the hydrophobic interactions between Leu 19 and Val24 in stabilizing the Schellman motif and hence helix termination.
Results: In aqueous solution, NMR data for the H-Sm-H peptide show that it samples a largely helical conformation with a break in the helix at the point of the turn in the protein. The data also establish the presence of local hydrophobic interactions and intramolecular hydrogen bonds characteristic of a Schellman motif. Absence of helix termination in trifluoroethanol, a solvent known to disrupt hydrophobic interactions, along with an analysis of H alpha chemical shifts and NOEs in the variant peptides, suggest a major role for glycine in terminating the helix, with local hydrophobic interactions further stabilizing the Schellman motif.
Conclusions: The presence of a Schellman motif in this isolated fragment in water is governed by local interactions and specifies the interspatial arrangement of the helices. This observation underlines the structure predictive value of folding motifs. As proposed for a Schellman motif, helix termination in this fragment is dictated by the local distribution of polar/apolar residues, which is reminiscent of the binary code for protein folding.