Structural comparison in solution of a native and retro peptide derived from the third helix of Staphylococcus aureus protein A, domain B: retro peptides, a useful tool for the discrimination of helix stabilization factors dependent on the peptide chain orientation.
A peptide fragment corresponding to the third helix of Staphylococcus Aureus protein A, domain B, was chosen to study the effect of the main-chain direction upon secondary structure formation and stability, applying the retro-enantio concept. For this purpose, two peptides consisting of the native (Ln) and reversed (Lr) sequences were synthesized and their conformational preferences analysed by CD and NMR spectroscopy. A combination of CD and NMR data, such as molar ellipcitity. NOE connectivities, H alpha and NH chemical shifts, 3J alpha N coupling constants and amide temperature coefficients indicated the presence of nascent helices for both Ln and Lr in water, stabilized upon addition of the fluorinated solvents TFE and HFIP. Helix formation and stabilization appeared to be very similar in both normal and retro peptides, despite the unfavourable charge-macrodipole interactions and bad N-capping in the retro peptide. Thus, these helix stabilization factors are not a secondary structure as determined for this specific peptide. In general, the synthesis and confirmational analysis of peptide pairs with opposite main-chain directions, normal and retro peptides, could be useful in the determination of secondary structure stabilization factors dependent on the direction.
Haack
T
T
Department of Organic Chemistry, University of Barcelona, Spain.
Sánchez
Y M
YM
González
M J
MJ
Giralt
E
E
D000595:Amino Acid Sequence; D002942:Circular Dichroism; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry; D017433:Protein Structure, Secondary; D012996:Solutions; D013205:Staphylococcal Protein A / Q000737:chemistry*; D014867:Water / Q000737:chemistry
D010446:Peptide Fragments; D012996:Solutions; D013205:Staphylococcal Protein A; D014867:Water