Sa. Overman et Gj. Thomas, AMIDE MODES OF THE ALPHA-HELIX - RAMAN-SPECTROSCOPY OF FILAMENTOUS VIRUS FD CONTAINING PEPTIDE C-13 AND H-2 LABELS IN COAT PROTEIN SUBUNITS, Biochemistry, 37(16), 1998, pp. 5654-5665
The filamentous virus fd consists of a single-stranded DNA genome shea
thed by 2700 copies of a 50-residue alpha-helical subunit (protein pVI
II) and serves as a model assembly of alpha-helices. To advance vibrat
ional assignments for the alpha-helix, we have investigated Raman spec
tra of fd virions containing C-13 and H-2 (deuterium) labels at variou
s main-chain sites of the pVIII subunits. C-13 was introduced at speci
fic peptide carbonyls, while deuterium was introduced at selected alph
a-carbon (C-alpha) and amide nitrogen positions. Interpretation of the
Raman spectra reveals a previously unrecognized alpha-helix band in t
he spectral interval 730-745 cm(-1), tentatively assigned to a carbony
l in-plane bending mode (amide IV). Experimental evidence has also bee
n obtained for a distinctive alpha-helix marker near 1345 cm(-1), assi
gned to a coupled C-alpha-H bending and C-alpha-C stretching mode. The
fd virions containing C-13-labeled carbonyls exhibit unexpectedly com
plex amide I profiles, consisting of multiple band components. Amide I
splitting resulting from C-13 substitution of carbonyls is attributed
to decoupling of transition-dipole interactions normally occurring in
the extended pVIII helix. The present study identifies novel conforma
tion-dependent Raman bands in a native alpha-helix assembly, confirms
amide I and amide III assignments proposed previously for filamentous
viruses, and facilitates new Raman assignments for the packaged ssDNA.
The alpha-helix markers identified here should also be useful in conf
ormation analyses of other proteins by Raman spectroscopy.