4DZU: Complex of 3-alpha bound to gp41-5

We report a new method for preorganization of alpha/beta-peptide helices, based on the use of a dense array of acidic and basic side chains. Previously we have used cyclically constrained beta residues to promote alpha/beta-peptide helicity; here we show that an engineered ion pair array can be comparably effective, as indicated by mimicry of the CHR domain of HIV protein gp41. The new design is effective in biochemical and cell-based infectivity assays; however, the resulting alpha/beta-peptide is susceptible to proteolysis. This susceptibility was addressed via introduction of a few cyclic beta residues near the cleavage site, to produce the most stable, effective alpha/beta-peptide gp41 CHR analogue identified. Crystal structures of an alpha- and alpha/beta-peptide (each involved in a gp41-mimetic helix bundle) that contain the dense acid/base residue array manifest disorder in the ionic side chains, but there is little side-chain disorder in analogous alpha- and alpha/beta-peptide structures with a sparser ionic side-chain array. These observations suggest that dense arrays of complementary acidic and basic residues can provide conformational stabilization via Coulombic attractions that do not require entropically costly ordering of side chains.
PDB ID: 4DZUDownload
MMDB ID: 99252
PDB Deposition Date: 2012/3/1
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 2.1  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 4DZU: dimeric; determined by author and by software (PISA)
Molecular Components in 4DZU
Label Count Molecule
Proteins (2 molecules)
Molecule annotation
Molecule annotation
Chemical (1 molecule)
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Citing MMDB