2O0S

LPS-bound structure of a designed peptide

Summary for 2O0S

• Entry DOI: 10.2210/pdb2o0s/pdb
• Descriptor: YW12 (1 entity in total)
• Functional Keywords: lps, peptide design, de novo protein
• Total number of polymer chains: 1
• Total formula weight: 1657.12

Authors

Bhattacharjya, S. (deposition date: 2006-11-28, release date: 2007-05-15, Last modification date: 2023-12-27)

Primary citation

Bhattacharjya, S.,Domadia, P.N.,Bhunia, A.,Malladi, S.,David, S.A.
High-Resolution Solution Structure of a Designed Peptide Bound to Lipopolysaccharide: Transferred Nuclear Overhauser Effects, Micelle Selectivity, and Anti-Endotoxic Activity
Biochemistry, 46:5864-5874, 2007

PubMed Abstract: Designing peptides that would interact with lipopolysaccharides (LPS) and acquire a specific folded conformation can generate useful structural insights toward the development of anti-sepsis agents. In this work, we have constructed a 12-residue linear peptide, YW12, rich in aromatic and aliphatic amino acid residues with a centrally located stretch of four consecutive positively charged (KRKR) residues. In absence of LPS, YW12 is predominantly unstructured in aqueous solution. Using transferred nuclear Overhauser effect (Tr-NOE) spectroscopy, we demonstrate that YW12 adopts a well-folded structure as a complex with LPS. Structure calculations reveal that YW12 assumes an extended conformation at the N-terminus followed by two consecutive beta-turns at its C-terminus. A hydrophobic core is formed by extensive packing between number of aromatic and nonpolar residues, whereas the positively charged residues are segregated out to a separate region essentially stabilizing an amphipathic structure. In an in vitro LPS neutralization assay using NF-kappaB induction as the readout, YW12 shows moderate activity with an IC50 value of approximately 10 microM. As would be expected, tryptophan fluorescence studies demonstrate that YW12 shows selective interactions only with the negatively charged lipid micelles including sodium dodecyl sulfate (SDS), 1-palmitoyl-2-oleoylphosphatidyl-dl-glycerol (POPG), and LPS, and no significant interactions are detected with zwitterionic lipid micelles such as dodecyl-phosphocholine (DPC). Far-UV CD studies indicate the presence of beta-turns or beta-sheet-like conformations of the peptide in negatively charged micelles, whereas no structural transitions are apparent in DPC micelles. These results suggest that structural features of YW12 could be utilized to develop nontoxic antisepsis compounds.

PubMed: 17469802
DOI: 10.1021/bi6025159

Experimental method

SOLUTION NMR