Intensity of the polarized Raman band at 1340-1345 cm-1 as an indicator of protein alpha-helix orientation: application to Pf1 filamentous virus.
Raman spectra of oriented alpha-helical protein molecules exhibit a prominent band near 1340-1345 cm(-)(1), the intensity of which is highly sensitive to molecular orientation. Polarization of the 1340-1345 cm(-)(1) marker is evident in Raman spectra of alpha-helical poly-L-alanine (alphaPLA) and alpha-helical poly-gamma-benzyl-L-glutamate (alphaPBLG). Corresponding polarization is also observed in Raman spectra of the filamentous virus Pf1, which is an assembly of alpha-helical coat protein molecules. In alphaPLA and alphaPBLG, we assign the band to a normal mode of symmetry type E(2) and specifically to a vibration localized in the (O=C)-C(alpha)-H linkages of the main chain peptide group. Although strict helical symmetry does not apply to coat subunits of filamentous viruses, an approximate E(2)-type mode may be presumed to account for a corresponding Raman band of Pf1 and fd filamentous viruses. Spectroscopic studies of N-methylacetamide and isotopically-edited fd viruses support the present assignment of the 1340-1345 cm(-)(1) band. Polarization anisotropy indicates that this band may be exploited as a novel indicator of protein alpha-helix orientation. Application of this approach to the polarized Raman spectrum of Pf1 suggests that, on average, the axis of the alpha-helical coat protein subunit in the native virion structure forms an angle of 20 +/- 10 degrees with respect to the virion axis.
Tsuboi
M
M
Department of Fundamental Science, Iwaki-Meisei University, Iwaki, Fukushima 970, Japan.
Suzuki
M
M
Overman
S A
SA
Thomas
G J
GJ
D000409:Alanine / Q000737:chemistry; D000577:Amides / Q000737:chemistry; D002138:Calibration; D002213:Capsid / Q000737:chemistry* / Q000592:standards; D002247:Carbon Isotopes; D017912:Inovirus / Q000737:chemistry*; D008956:Models, Chemical; D010446:Peptide Fragments / Q000737:chemistry; D010455:Peptides / Q000737:chemistry; D011099:Polyglutamic Acid / Q000031:analogs & derivatives / Q000737:chemistry / Q000592:standards; D017433:Protein Structure, Secondary; D013059:Spectrum Analysis, Raman / Q000379:methods / Q000592:standards; D014771:Virion / Q000737:chemistry
D000577:Amides; D002247:Carbon Isotopes; D010446:Peptide Fragments; D010455:Peptides; C003172:poly-gamma-benzyl-L-glutamate; C019529:polyalanine; D011099:Polyglutamic Acid; D000409:Alanine