posted on 2000-06-14, 00:00authored byNatalia Carulla, Clare Woodward, George Barany
A new strategy for the design and construction of peptide fragments that can achieve defined,
nativelike secondary structure is presented. The strategy is based upon the hypothesis that ‘core elements'
of a protein, synthesized in a single polypeptide molecule, will favor nativelike structure, and that by
incorporating a cross-link, nativelike core structure will dominate the ensemble as the more extended
conformations are excluded. ‘Core elements' are the elements of packed secondary structure that contain
the slowest exchanging backbone amide protons in the native protein. The ‘core elements' in bovine
pancreatic trypsin inhibitor (BPTI) are the two long strands of antiparallel β-sheet (residues 18−24 and
29−35) and the small β-bridge (residues 43−44). To test the design strategy, we synthesized an ‘oxidized
core module', which contains the antiparallel strands connected by a modified reverse turn (A27 replaced
by D), a natural disulfide cross-link at the open end of the hairpin, and N- and C-termini blocking groups.
A peptide with identical sequence but lacking the disulfide cross-link at the open end was used as the
‘reduced core module' control. The conformational behavior of both peptides was examined using 1H
NMR spectroscopy. Chemical shift dispersion, chemical shift deviation from random coil values, sequential
and long-range NOEs, and H/D amide exchange rates were compared for the two peptides. We conclude
that the ensemble of oxidized and reduced core module conformations samples both nativelike 4:4 and
non-native 3:5 β-hairpin structure, and that the oxidized module samples nativelike structure for a greater
fraction of the time than the reduced module.