AMIDE MODES OF THE ALPHA-HELIX - RAMAN-SPECTROSCOPY OF FILAMENTOUS VIRUS FD CONTAINING PEPTIDE C-13 AND H-2 LABELS IN COAT PROTEIN SUBUNITS

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.