Structural studies of tobacco mosaic virus and its components by laser Raman spectroscopy

A transition to sustainable ocean governance

Human wellbeing relies on the Biosphere, including natural resources provided by ocean ecosystems. As multiple demands and stressors threaten the ocean, transformative change in ocean governance is required to maintain the contributions of the ocean to people. Here we illustrate how transition theory can be applied to ocean governance. We demonstrate how current economic and social systems can adapt to existing pressures and shift towards ocean stewardship through incorporation of niche innovations within and across economic sectors and stakeholder communities. These novel approaches support an emergent but purposeful transition and suggest a clear path to a thriving and vibrant relationship between humans and the ocean. Oceans provide important natural resources, but the management and governance of the ocean is complex and the ecosystem is suffering as a result. The authors discuss current barriers to sustainable ocean governance and suggest pathways forward.

Oceans provide important natural resources, but the management and governance of the ocean is complex and the ecosystem is suffering as a result. The authors discuss current barriers to sustainable ocean governance and suggest pathways forward.

Hemispherical platinum : silver core : shell nanoparticles for miRNA detection

Novel electrochemical detection based on regioselective functionalised electrocatalytic nanoparticles suitable for the detection of low-abundance molecular biomarkers, miR-132 of neuroblastoma.

Competition between Co(NH(3)(6)3+ and inner sphere Mg2+ ions in the HDV ribozyme

Divalent cations play critical structural and functional roles in many RNAs. While the hepatitis delta virus (HDV) ribozyme can undergo self-cleavage in the presence of molar concentrations of monovalent cations, divalent cations such as Mg(2+) are required for efficient catalysis under physiological conditions. Moreover, the cleavage reaction can be inhibited with Co(NH(3))(6)(3+), an analogue of Mg(H(2)O)(6)(2+). Here, the binding of Mg(2+) and Co(NH(3))(6)(3+) to the HDV ribozyme is studied by Raman microscopic analysis of crystals. Raman difference spectra acquired at different metal ion conditions reveal changes in the ribozyme. When Mg(2+) alone is introduced to the ribozyme, inner sphere coordination of Mg(H(2)O)(x)(2+) (x </= 5) to nonbridging PO(2)(-) oxygen and changes in base stretches and phosphodiester group conformation are observed. In addition, binding of Mg(2+) induces deprotonation of a cytosine assigned to the general acid C75, consistent with solution studies. When Co(NH(3))(6)(3+) alone is introduced, deprotonation of C75 is again observed, as are distinctive changes in base vibrational ring modes and phosphodiester backbone conformation. In contrast to Mg(2+) binding, Co(NH(3))(6)(3+) binding does not perturb PO(2)(-) group vibrations, consistent with its ability to make only outer sphere contacts. Surprisingly, competitive binding studies reveal that Co(NH(3))(6)(3+) ions displace some inner sphere-coordinated magnesium species, including ions coordinated to PO(2)(-) groups or the N7 of a guanine, likely G1 at the active site. These observations contrast with the tenet that Co(NH(3))(6)(3+) ions displace only outer sphere magnesium ions. Overall, our data support two classes of inner sphere Mg(2+)-PO(2)(-) binding sites: sites that Co(NH(3))(6)(3+) can displace and others it cannot.

Raman and Raman optical activity (ROA) analysis of RNA structural motifs in Domain I of the EMCV IRES

Raman and Raman optical activity (ROA) spectra were collected for four RNA oligonucleotides based on the EMCV IRES Domain I to assess the contributions of helix, GNRA tetraloop, U.C mismatch base pair and pyrimidine-rich bulge structures to each. Both Raman and ROA spectra show overall similarities for all oligonucleotides, reflecting the presence of the same base paired helical regions and GNRA tetraloop in each. Specific bands are sensitive to the effect of the mismatch and asymmetric bulge on the structure of the RNA. Raman band changes are observed that reflect the structural contexts of adenine residues, disruption of A-form helical structure, and incorporation of pyrimidine bases in non-helical regions. The ROA spectra are also sensitive to conformational mobility of ribose sugars, and verify a decrease in A-type helix content upon introduction of the pyrimidine-rich bulge. Several Raman and ROA bands also clearly show cooperative effects between the mismatch and pyrimidine-rich bulge motifs on the structure of the RNA. The complementary nature of Raman and ROA spectra provides detailed and highly sensitive information about the local environments of bases, and secondary and tertiary structures, and has the potential to yield spectral signatures for a wide range of RNA structural motifs.

A Raman scattering study of the helix-destabilizing gene-5 protein with adenine-containing nucleotides

Raman spectra of gp5 and complexes of gp5 with poly(rA) and poly(dA) have been determined and analysed. From a fit of the amide I-band with model spectra it follows that the secondary structure of gp5 contains 52% beta-sheet, 28% undefined conformation and 19% alpha-helix. The band at 1032 cm-1 due to phenylalanine has an anomalous intensity both in the spectra of the complexes and the free protein. This possibly indicates a stacked structure present in the protein. Binding of gp5 to poly(rA) and poly(dA) influences the intensity of bands near 1338 and 1480 cm-1 which are considered to be marker-bands for the phosphate-sugar-base conformer. A change in conformation of the nucleotides is also reflected by vibrations originating in the phosphate- and sugar-residues of the backbone. In the spectrum of complexed poly(rA) the intensity of the conformation sensitive band at 813 cm-1, which is due to the phosphodiester group, is zero. It seems that gp5 forces poly(rA) and poly(dA) to a similar conformation. A marker band for stacking interaction in poly(rA) indicates that stacking interactions in the complex have increased.

RNA-protein interactions and secondary structures of cowpea chlorotic mottle virus for in vitro assembly

Laser Raman spectroscopy of the cowpea chlorotic mottle virus (CCMV) in native (pH 5.0) and partially swollen (pH 7.5) states reveals the presence of small percentages of protonated adenine (less than 15%) and cytosine (less than 7%) bases in the encapsidated RNA molecule of the native virion. The protonated bases are titrated with pH-induced swelling of the virus. Titration of putative COOH groups of aspartic and glutamic side chains of the virion subunit cannot be detected over the same pH range, which suggests that carboxyl anions (CO-2) and protonated bases are both available at pH 5 to stabilize the ribonucleoprotein particles by electrostatic interactions. The highly (95%) ordered secondary structure of encapsidated RNA may undergo a small additional increase (less than 3%) in ordered structure with release from the virion, suggesting at most a marginal structure-distorting influence from protein contacts in the native particle. The Raman spectra of the virion are also compared by difference spectroscopy with spectra of capsids (empty shells devoid of RNA), subunit dimers, and protein-free RNA. The results indicate that the subunit structure is altered by the release of RNA from the virion, as well as by the swelling of the virion. Amino acid residues and protein secondary structures that are affected in these in vitro assembly and disassembly processes are identified from their characteristic Raman lines. Two classes of cysteinyl SH groups, solvent exposed and solvent protected, are revealed for the capsid and virion subunit.(ABSTRACT TRUNCATED AT 250 WORDS)

Calcium ion binding by isolated tobacco mosaic virus coat protein

Calcium ion titrations were performed on solutions of tobacco mosaic virus coat protein using a calcium-specific ion-exchange electrode. Isolated coat protein was found incapable of binding calcium ions under equilibrium conditions at pH values above its iso-ionic point (pH 4.3 to 4.6). However, calcium ions were found to bind to coat protein under non-equilibrium conditions, which suggests that the isolated coat protein has the proper conformation to bind calcium ions at the iso-ionic point.

Structure similarity, difference and variability in the filamentous viruses fd, If1, IKe, Pf1 and Xf. Investigation by laser Raman spectroscopy

The filamentous bacteriophages fd, If1, IKe, Pf1, Xf and Pf3 in aqueous solutions of low, moderate and high ionic strength have been investigated as a function of temperature by laser Raman difference spectroscopy. By analogy with Raman spectra of model compounds and viruses of known structure, the data reveal the following structural features: the predominant secondary structure of the coat protein subunit in each virus is the alpha-helix, but the amount of alpha-helix differs from one virus to another, ranging from an estimated high of 100% in Pf1 to a low of approximately 50% in Xf. The molecular environment and intermolecular interactions of tyrosine, tryptophan and phenylalanine residues differ among the different viruses, as do the conformations of aliphatic amino acid side-chains. The foregoing features of coat protein structure are highly sensitive to changes in Na+ concentration, temperature or both. The backbones of A-DNA and B-DNA structures do not occur in any of the viruses, and unusual DNA structures are indicated for all six viruses. The alpha-helical protein subunits of Pf1, like those of Pf3 and Xf, can undergo reversible transitions to beta-sheet structures while retaining their association with DNA; yet fd, IKe and If1 do not undergo such transitions. Raman intensity changes with ionic strength or temperature suggest that transgauche rotations of aliphatic amino acid side-chains and stacking of aromatic side-chains are important structural variables in each virus.

Structural studies of P22 phage, precursor particles, and proteins by laser Raman spectroscopy

For the study of the protein--protein and protein--nucleic acid interactions in the assembly of virus particles, laser Raman spectra have been obtained in H2O and D2O solutions and as a function of temperature for the following Salmonella phage P22 components: mature phage particles, isolated mature phage DNA, mature protein shells empty of DNA, precursor protein shells (procapsids), and purified coat, scaffolding and tail-spike proteins. The spectra confirm that the condensed DNA within the phage capsid assumes the B-form secondary structure similar to aqueous DNA and reveal no evidence of specific molecular interactions between subgroups of DNA and protein subunits of the phage capsid. No differences were detected in the highly irregular secondary structure of the major capsid protein in mature capsids, empty capsids (lacking DNA), procapsids, and empty procapsids (lacking scaffolding protein). Features of both primary and secondary structures of the viral scaffolding and tail-spike proteins are also revealed by the spectra. Differences in thermal stability of tyrosyl side-chain interactions were observed between scaffolding protein extracted from the procapsid and within the procapsid. These differences correspond to different hydrogen bonding configurations of p-hydroxyphenyl groups and provide indirect evidence for the participation of the scaffolding proteins in specific macromolecular interactions within the procapsid.