Ultraviolet-resonance Raman spectroscopy of the filamentous virus Pf3: Interactions of Trp 38 specific to the assembled virion subunit

The class a filamentous virus Pf3 packages a circular single-stranded DNA g enome of similar to 6300 nucleotides within a cylindrical capsid constructe d from similar to 2630 copies of a 44 residue alpha-helical subunit. The si ngle tryptophan residue (Trp 38) of the capsid subunit is located within a basic C-terminal sequence (...R(+)WIK(+)AQFF). The local environment of Trp 38 in the native Pf3 assembly has been investigated using 229 nm excited u ltraviolet-resonance Raman (UVRR) spectroscopy and fluorescence spectroscop y. Trp 38 exhibits an anomalous UVRR signature in Pf3, including structure- diagnostic Raman bands (763, 1228, 1370, and 1773 cm(-1)) that are greatly displaced from corresponding Raman markers observed in either detergent-dis assembled Pf3, class I filamentous viruses, most globular proteins, or aque ous L-Trp. An unusual and highly quenched fluorescence spectrum is also obs erved fur Trp 38, These distinctive UVRR and fluorescence signatures togeth er reflect interactions of the Trp 38 side chain that are specific to the n ative Pf3 assembly. The experimental results on Pf3 and supporting spectros copic data from other proteins of known three-dimensional structure favor a model in which pi electrons of the Trp 38 indolyl ring interact specifical ly with a basic side chain of the subunit C-terminal sequence. Residues Arg 37 and Lys 40 are plausible candidates for the proposed cation-pi interact ion of Trp 38. The present study suggests that Raman spectroscopy may be a generally useful probe of interactions between the indolyl pi-electron syst em of tryptophan and electropositive groups in proteins and their assemblie s.