A CD determination of the α‐helix contents of the coat proteins of four filamentous bacteriophages: fd, IKe, Pf1, and Pf3

Abstract

The CD spectra of four filamentous bacteriophages--fd, IKe, Pf1, and Pf3--were analyzed to determine the alpha-helix contents of their major coat proteins. Measured spectra included the 192-nm band so that analyses could be carried out over the full wavelength range of the reference spectra for protein secondary structures available (a) from globular proteins [J.T. Yang, C.S.C. Wu, and H.M. Martinez (1986) Methods in Enzymology 130, 208-269] and (b) from poly(L-lysine) [N. Greenfield and G.D. Fasman (1960) Biochemistry 8, 4108-4116]. Extended analyses were also performed with the addition of the spectrum of a model beta-turn to the Greenfield and Fasman reference set, with the spectrum of a short alpha-helix in the Yang et al. reference set, and with an estimate of the spectrum of Trp added to both reference sets. The reference set based on the simple poly(L-lysine) polypeptide, plus a spectrum of a model beta-turn or of Trp, gave reasonably good fits to the measured spectra for all four phages and yielded the largest percentages of alpha-helix. The class I phages--fd and IKe--had large percentages of alpha-helix of 98 +/- 2 and 97 +/- 5%, respectively, while the two class II phages--Pf1 and Pf3--had similar but smaller alpha-helix contents of 83 +/- 6 and 84 +/- 2, respectively. While these alpha-helix contents were within the ranges previously reported from CD spectra of these phages in solution, they were more precise, and they indicated that the coat proteins of the intact phages have CD spectra that are probably modeled better by the reference spectra of polypeptides than by those of globular proteins.

Molecular models and structural comparisons of native and mutant class I filamentous bacteriophages

“…The protein model that we use here is 100% a-helix, consistent with some spectroscopic experiments (Clack & Gray, 1989), but some variations in the secondary structure may appear as further evidence is accumulated. The last few residues at either end might have i to i + 3 or i + 5 rather than a-helix (i to i + 4) hydrogen-bonding patterns, as sometimes found in globular proteins (Baker & Hubbard, 1984).…”

Structure of the coat protein in fd filamentous bacteriophage particles determined by solid-state NMR spectroscopy

“…There have been numerous x-ray fiber diffraction studies of filamentous bacteriophages (3,(13)(14)(15)(16)(17), and although the resulting protein structures have relatively low resolution, these studies provide crucial information about the symmetry and packing of the coat protein subunits (15,18). Other spectroscopic investigations (19)(20)(21), as well as our earlier solid-state NMR studies (22)(23)(24)(25)(26), demonstrate that the coat protein is nearly all ␣-helix, its positively charged C-terminal residues are buried on the interior of the particle where they interact with the DNA, and the N-terminal residues are mobile (26) and exposed on the exterior of the virus particles.…”

Aromatic and Cystine Side-Chain Circular Dichroism in Proteins

“…8a), with the 222-nm band about 1.4 to 1.5 times more intense than the shoulder at 208 nm (Ikehara et al, 1975;Nozaki et al, 1976;Day and Wiseman, 1978;Clack and Gray, 1989;Arnold et al, 1992;Roberts and Dunker, 1993). Oxidation with N-bromosuccinimide (NBS) suggested that the one tryptophan out of 50 residues of the major coat protein was responsible for the atypical CD spectrum (Day and Wiseman, 1978).…”