We report lectin microarray profile of the polysaccharide fraction derived from Sasa veitchii leaf that exhibits anti-influenza activity. This fraction showed higher reactivities with lectins known as binders to oligo-mannose, fucose, or galactose. Our findings along with previously reported monosaccharide components suggest that the polysaccharide can be cross-reactive with cell surface receptors involved in immune system, thereby exerting anti-influenza activity.

The filamentous bacteriophage Pf1, which infects strain PAK of Pseudomonas aeruginosa, is a flexible filament ( approximately 2000 x 6.5 nm) consisting of a covalently closed DNA loop of 7349 nucleotides sheathed by 7350 copies of a 46-residue alpha-helical subunit. The subunit alpha-helices, which are inclined at a small average angle ( approximately 16 degrees ) from the virion axis, are arranged compactly around the DNA core. Orientations of the Pf1 DNA nucleotides with respect to the filament axis are not known. In this work we report and interpret the polarized Raman spectra of oriented Pf1 filaments. We demonstrate that the polarizations of DNA Raman band intensities establish that the nucleotide bases of packaged Pf1 DNA are well ordered within the virion and that the base planes are positioned close to parallel to the filament axis. The present results are combined with a previously proposed projection of the intraviral path of Pf1 DNA [Liu, D. J., and Day, L. A. (1994) Science 265, 671-674] to develop a novel molecular model for the Pf1 assembly.

The Raman scattering of a molecule is generated by interactions of its electrons with incident light. The electric vector of the Raman scattered light is related to the electric vector of the incident light through a characteristic Raman tensor. A unique Raman tensor exists for each Raman-active molecular vibrational mode. In the case of biologically important macromolecules Raman tensors have been determined for a few hundred vibrational Raman bands. These include proteins and their amino acid constituents, as well as nucleic acids (DNA and RNA) and their nucleotide constituents. In this review Raman tensors for 39 representative vibrational Raman bands of biological molecules are considered. We present details of the Raman tensor determinations and discuss their application in structural studies of filamentous bacteriophages (fd, Pf1, Pf3 and PH75), fowl feather rachis and eyespots of the protists, Chlamydomonas and Euglena.

Preface. Introduction. 1. DNA Structures and Spectra. 1.1. DNA Structures. 1.2. Electronic Spectra. 1.3. Vibrational Spectra. 1.4. NMR Spectra. 1.5. Electron Spin Resonance Spectra. 1.6. X-Ray Crystallography. 1.7. Molecular Modeling an molecular Mechanics. 2. Intercalating Drugs. 2.1. Acridine Dyes. 2.2. Ethidium Bromide. 2.3. Aclacinomycin. 2.4. Sequence Preference. 2.5. Bis- and Tris- Intercalators. 3. Groove- Binding Drugs. 3.1. Netropsin and Distamycin. 3.2. Derivatives of Netropsin and Distamycin. 3.3. Hoechst 33258, SN6999, and their Derivatives. 3.4. Chromomycin, Mithramycin, and Other GC Binders. 3.5. Groove Binding and Intercalation. 4. Covalent Bonding Drugs. 4.1. (+) CC1065 and Related Drugs. 4.2. Anthramycin and Tomaymycin. 4.3. Ecteinascidins. 4.4. Mitomycins. 4.5. Intercalating Alkylators. 5. Strand-Breaking Drugs. 5.1. Bleomycins. 5.2. Enediyne Antibiotics. 6. Metal-Containing Drugs. 6.1. Cisplatin. 6.2. Cisplatin Derivatives. 6.3. Transplatin and Derivatives. 6.4. Monofunctional Platinum Complexes. 6.5. Polynuclear and High-valent Platinum Complexes. 6.6. Complexes Containing Other Metals. Appendixes. Index.

This chapter contains sections titled: Bleomycins Enediyne Antibiotics References

This chapter contains sections titled: DNA Structures Electronic Spectra Vibrational Spectra NMR Spectra Electron Spin Resonance Spectra X-Ray Crystallography Molecular Modeling and Molecular Mechanics References

This chapter contains sections titled: Netropsin and Distamycin Derivatives of Netropsin and Distamycin Hoechst 33258, SN6999, and Their Derivatives Chromomycin, Mithramycin, and Other GC Binders Groove Binding and Intercalation References

The title cobalt(III) complexes have been investigated by polarized absorption and Raman spectroscopies of the single crystals. The symmetry properties of the d-electron orbitals and of the vibrational modes attributable to the Raman bands of trans(Cl2)-[CoCl2(NH3)n(H2O)4−n]Cl complexes (n=2,3, or 4) were examined to elucidated the peculiar observation that ligand substitution causes no splitting of the 15200-cm−1 absorption band and the 250-cm−1 Raman band. Effects of replacing the NH3 ligand with H2O on the electronic structure, atom–atom force constants and vibrational modes of these complex ions are briefly described.

Structural properties of the complex formed between genomic DNA and the intercalating drug ethidium bromide (EtBr) have been determined by use of a Raman microscope equipped with near-infrared laser excitation. The polarized spectra, which were obtained from oriented fibers of the EtBr:DNA complex, are interpreted in terms of the relative orientations of the phenanthridinium ring of EtBr and bases of DNA. Quantification of structure parameters of EtBr and DNA in the complex were assessed using Raman tensors obtained from polarized Raman analyses of oriented specimens of EtBr (single crystal) and DNA (hydrated fiber). We find that the phenanthridinium plane is tilted by 35±5° from the plane perpendicular to the fiber (DNA helix) axis. Assuming coplanarity of the phenanthridinium ring and its immediate base neighbors at the intercalation site, such bases would have a tilt angle closer to that of A-DNA (20°) than to that of B-DNA (6°). The average base tilt in stretches of DNA between intercalation sites remains that of B-DNA.

The amide I Raman tensor corresponding to the antiparallel beta-sheet structure in proteins has been determined by polarized Raman microspectroscopy of fowl feather rachis using polarized Raman spectra excited in the near-infrared (785 nm). For a Raman tensor principal axis system (XYZ), in which X is perpendicular to the plane of the pleated beta-sheet, Y is in the plane of the sheet and perpendicular to the direction of the polypeptide chain, and Z is parallel to the direction of the polypeptide chain, the principal tensor components (alpha(XX), alpha(YY), alpha(ZZ)) are found to satisfy the following relationships: R-1 = alpha(XX)/alpha(ZZ) = 0.32 and R-2 = alpha(YY)/alpha(ZZ) = 3.48. With this Raman tensor determination, we show that semiquantitative estimates of the total antiparallel beta-sheet content in beta-rich proteins can be extracted from polarized Raman intensity measurements on the amide I marker of the beta-sheet occurring near 1664 cm(-1). We demonstrate this approach for the beta-rich silk proteins of the silkworm and spider. Copyright (C) 2006 John Wiley & Sons, Ltd.

Many thin helical polymers, including bacterial pili and filamentous bacteriophage, have been seen as refractory to high-resolution studies by electron microscopy. Studies of the quaternary structure of such filaments have depended upon techniques such as modeling or X-ray fiber diffraction, given that direct visualization of the subunit organization has not been possible. We report the first image reconstruction of a filamentous virus, bacteriophage fd, by cryoelectron microscopy. Although these thin (similar to 70 angstrom in diameter) rather featureless filaments scatter weakly, we have been able to achieve a nominal resolution of similar to 8 A using an iterative helical reconstruction procedure. We show that two different conformations of the virus exist, and that in both states the subunits are packed differently than in conflicting models previously proposed on the basis of X-ray fiber diffraction or solid-state NMR studies. A significant fraction of the population of wild-type fd is either disordered or in multiple conformational states, while in the presence of the Y21M mutation, this heterogeneity is greatly reduced, consistent with previous observations. These results show that new computational approaches to helical reconstruction can greatly extend the ability to visualize heterogeneous protein polymers at a reasonably high resolution. (c) 2006 Elsevier Ltd. All rights reserved.

The filamentous virus PH75, which infects the thermophile Thermus thermophilus, consists of a closed DNA strand of 6500 nucleotides encapsidated by 2700 copies of a 46-residue coat subunit (pVIII). The PH75 virion is similar in composition to filamentous viruses infecting mesophilic bacteria but is distinguished by in vivo assembly at 70 degrees C and thermostability to at least 90 degrees C. Structural details of the PH75 assembly are not known, although a fiber X-ray diffraction based model suggests that capsid subunits are highly alpha-helical and organized with the same symmetry (class II) as in the mesophilic filamentous phages Pf1 and Pf3 [Pederson et al. (2001) J. Mol. Biol. 309, 401-421]. This is distinct from the symmetry (class I) of phages fd and M13. We have employed polarized Raman microspectroscopy to obtain further details of PH75 architecture. The spectra are interpreted in combination with known Raman tensors for modes of the pVIII main chain (amide I) and Trp and Tyr side chains to reveal the following structural features of PH75: (i) The average pVIII peptide group is oriented with greater displacement from the virion axis than peptide groups of fd, Pf1, or Pf3. The data correspond to an average helix tilt angle of 25 degrees in PH75 vs 16 degrees in fd, Pf1, and Pf3. (ii) The indolyl ring of Trp 37 in PH75 projects nearly equatorially from the subunit alpha-helix axis, in contrast to the more axial orientations for Trp 26 of fd and Trp 38 of Pf3. (iii) The phenolic rings of Tyr 15 and Tyr 39 project along the subunit helix axis, and one phenoxyl engages in hydrogen-bonding interaction that has no counterpart in either fd or Pf1 tyrosines. Also, in contrast to fd, Pf1, and Pf3, the packaged DNA genome of PH75 exhibits no Raman anisotropy, suggesting that DNA bases are not oriented unidirectionally within the nucleocapsid assembly. The structural findings are discussed in relation to intrasubunit and intersubunit interactions that may confer hyperthermostability to the PH75 virion. A refined molecular model is proposed for the PH75 capsid subunit.