LOCAL INTERACTIONS IN A SCHELLMAN MOTIF DICTATE INTERHELICAL ARRANGEMENT IN A PROTEIN-FRAGMENT

Background: As an approach to understanding the role of local sequence in determining protein tertiary structure, we have examined the confo rmation of a 23-residue peptide fragment corresponding to the structur ally conserved helix-Schellman motif-helix (H-Sm-H) domain (residues 1 0-32) of cellular retinoic acid binding protein, along with variants d esigned to probe the contributions of the helix-terminating Gly23 and the hydrophobic interactions between Leu19 and Val24 in stabilizing th e Schellman motif and hence helix termination. Results: In aqueous sol ution, 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 tur n in the protein. The data also establish the presence of local hydrop hobic 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 ana lysis of H alpha chemical shifts and NOEs in the variant peptides, sug gest a major role for glycine in terminating the helix, with local hyd rophobic interactions further stabilizing the Schellman motif. Conclus ions: The presence of a Schellman motif in this isolated fragment in w ater 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 distribut ion of polar/apolar residues, which is reminiscent of the binary code for protein folding.