Amide modes of the alpha-helix: Raman spectroscopy of filamentous virus fd containing peptide C-13 and H-2 labels in coat protein subunits

摘要

The filamentous virus fd consists of a single-stranded DNA genome sheathed by 2700 copies of a 50-residue alpha-helical subunit (protein pVIII) and serves as a model assembly of alpha-helices. To advance vibrational assignments for the alpha-helix, we have investigated Raman spectra of fd virions containing C-13 and H-2 (deuterium) labels at various main-chain sites of the pVIII subunits. C-13 was introduced at specific peptide carbonyls, while deuterium was introduced at selected alpha-carbon (C-alpha) and amide nitrogen positions. Interpretation of the Raman spectra reveals a previously unrecognized alpha-helix band in the spectral interval 730-745 cm(-1), tentatively assigned to a carbonyl in-plane bending mode (amide IV). Experimental evidence has also been obtained for a distinctive alpha-helix marker near 1345 cm(-1), assigned to a coupled C-alpha-H bending and C-alpha-C stretching mode. The fd virions containing C-13-labeled carbonyls exhibit unexpectedly complex 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 conformation-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 conformation analyses of other proteins by Raman spectroscopy. [References: 60]