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A survey of left-handed polyproline II helices
1Kentucky Center for Structural Biology, Department of Biochemistry, University of Kentucky, Lexington 40536-0298, USA.
Protein Science : a Publication of the Protein Society
|March 26, 1999
Summary
Left-handed polyproline II helices (PPII) are rare but found in most proteins. Proline, glutamine, and charged residues are favored in these structures, which exhibit threefold rotational symmetry.
Area of Science:
- Protein structure and bioinformatics
Background:
- Polyproline II (PPII) helices are a distinct protein secondary structure.
- PPII helices play roles in structural proteins, unfolded states, and protein signaling.
Purpose of the Study:
- To survey known protein structures for the occurrence and characteristics of PPII helices.
- To identify amino acid preferences and structural properties of PPII helices.
Main Methods:
- Analysis of 274 nonhomologous polypeptide chains from proteins with known structures.
- Identification and characterization of contiguous regions forming PPII helices.
Main Results:
- PPII helices are uncommon but present in most proteins, typically shorter than five residues.
- Proline, glutamine (Gln), and positively charged residues are favored.
- Gln's prevalence is linked to hydrogen bonding stabilizing PPII conformation.
- PPII helices are solvent-exposed, disfavoring apolar residues.
- Significant correlation between hydrophobicity at i and i+3 positions indicates amphipathic nature.
Conclusions:
- PPII helices are a significant, albeit rare, structural motif in proteins.
- Specific amino acid propensities and stabilizing interactions dictate PPII helix formation.
- The amphipathic nature of PPII helices in globular proteins suggests functional roles in protein-protein interactions or solvent exposure.