STUDIES ON THE INACTIVATION OF TOBACCO MOSAIC VIRUS BY ULTRAVIOLET LIGHT*,‡,§

Abstract— The irradiation of TMV with u.v. light of 2537 Å wavelength results in the binding of protein subunits to the RNA. These bound subunits are stable towards warm sodium dodecyl-sulfate; however, the binding is not covalent since the subunits are removed by 66% acetic acid, guanidine hydrochloride, or phenol. Approximately one protein subunit is bound per lethal biological 'hit'. The virus and the nucleic acid extracted from irradiated virus show virtually identical rates of inactivation.     

STUDIES OF THE ROLE OF THE COAT PROTEIN IN THE U.V. PHOTOINACTIVATION OF U(1) AND U(2) STRAINS OF TMV*

Abstract— Two properties of the u.v. inactivation process in the u.v. sensitive U(2) strain have been investigated: (1) The increased binding of protein to RNA induced by irradiation of the virus at 254 nm; (2) The action spectrum for u.v. inactivation of U(2) between 250 nm and 285 nm. The extent of the u.v. induced binding of protein to RNA is similar to that previously found in the resistant U(1) strain, thereby eliminating the possibility that the capacity for this binding phenomenon bears any correlation to the difference in u.v. sensitivities of these two viruses at 254 nm. The results indicate that the radiation induced interaction of protein and RNA in U(1) and U(2) are probably similar. The action spectrum for U(2) resembles the absorption spectrum of the RNA between 250 nm and 285 nm implicating the RNA as the primary absorber leading to inactivation of the virus in this region of the spectrum. Quantum yields calculated for U(2) virus and free TMV-RNA irradiated at 254 nm reveal that the irradiated free RNA may be as much as 1–4 times more sensitive to inactivation at this wavelength than RNA in the intact virus. It is concluded that the coat protein of U(2) probably offers some protection to the enclosed RNA against u.v. damage at 254 nm, therefore, the difference in u.v. sensitivity between U(1) and U(2) TMV at this wavelength is a consequence of a difference in the degree of protection offered by the respective coat proteins to the enclosed RNA.     

Ultraviolet photoinactivation studies on hybrid viruses obtained by the cross-reconstitution of the protein and RNA components of U(1) and U(2) strains of TMV

The sensitivities of U(1) and U(2) TMV strains to inactivation by ultraviolet light at 253.7 nm were compared with those of hybrid viruses obtained by reconstituting the protein of either native strain with the RNA of the other. In each case, the hybrid virus was found to be virtually identical in sensitivity to the native strain which supplied the protein coat, indicating that the relative sensitivities of the two native strains to ultraviolet light are solely a function of their respective protein coats. Amino acid analysis of the U (2) protein reveals about thirteen or fourteen amino acid replacements compared with the U (1) strain, which is in agreement with earlier studies indicating that there are considerable differences in the protein subunits of the two proteins. Some of the ways in which the observed differences in proteins of the two strains may determine their respective ultraviolet sensitivities are discussed.     

Prevention of photoreactivation of tobacco mosaic virus-ribonucleic acid by reconstitution

Abstract— The photoreactivation of TMV–RNA? irradiated with either 253–7 mμ or 302 mμ light can be prevented by reconstitution of the virus from TMV–protein and the ultraviolet irradiated RNA. The prevention of photoreactivation by reconstitution is not irreversible as the RNA can be extracted from the reconstituted virus and is still capable of undergoing photoreactivation.     

The crystal structure of the CeNA:RNA hybrid ce(GCGTAGCG):r(CGCUACGC)

Cyclohexenyl nucleic acids (CeNA) are characterised by the carbon–carbon double bond replacing the O4′‐oxygen atom of the natural D ‐2′‐deoxyribose sugar ring in DNA. CeNAs exhibit a high conformational flexibility, are stable against nuclease activity and their hybridisation is RNA selective. Additionally, CeNA has been shown to induce an enhanced biological activity when incorporated in siRNA. This makes CeNA a good candidate for siRNA and synthetic aptamer applications. The crystal structure of the synthetic CeNA:RNA hybrid ce(GCGTAGCG):r(CGCUACGC) has been solved with a resolution of 2.50 Å. The CeNA:RNA duplex adopts an anti‐parallel, right‐handed double helix with standard Watson–Crick base pairing. Analyses of the helical parameters revealed the octamer to form an A‐like double helix. The cyclohexenyl rings mainly adopt the ³H₂ conformation, which resembles the C3′‐endo conformation of RNA ribose ring. This C3′‐endo ring puckering was found in most of the RNA residues and is typical for A‐family helices. The crystal structure is stabilised by the presence of hexahydrated magnesium ions. The fact that the CeNA:RNA hybrid adopts an A‐type double helical conformation confirms the high potential of CeNAs for the construction of efficient siRNAs which can be used for therapeutical applications.     

RNA—PROTEIN CROSSLINK AND RNA CHAIN BREAK FORMATION ON UV-IRRADIATION OF TOBACCO MOSAIC VIRUS

Abstract— The ability of UV-irradiation (254 nm) to induce formation of RNA-protein crosslinks in tobacco mosaic virus (TMV) particles have been studied by Cs₂SO₄ density gradient centrifugation, analytical centrifugation, nitrocellulose filter binding and two-dimensional peptide mapping. RNA-protein crosslinks were found to be formed on UV-irradiation of TMV, but the parallel process of UV-induced RNA chain breakage complicated their quantitation. Using speciall devised equations, the quantum yield of RNA-protein crosslink formation was found to be 0.65 × 10⁻⁵ and that of RNA chain break formation 0.95 × 10⁻⁵.     

Pyrene-stacked nanostructures constructed in the recombinant tobacco mosaic virus rod scaffold

The effect of pyrenes introduced into a tobacco mosaic virus (TMV) coat protein monomer on the formation and stability of the TMV assembly was investigated. The possible arrangement of the pyrenes in the inner cavity of the TMV rod was also estimated. The pyrene derivative was introduced to four specific amino acids in the cavity of the TMV rod structure. Rod-structure formation was examined by atomic force microscopy (AFM). Two pyrene-attached mutants (positions 99 and 100) assembled to increase the length of the rod structures by 2.5 microm at pH 5.5. The interaction of the pyrene moieties in the TMV cavity was investigated by steady-state and time-resolved spectroscopic analysis. Strong excimer emission with significantly short wavelength (465 nm) was observed from the two mutants mentioned above. Excitation and UV-visible spectra indicate that the pyrene moieties form pi-stacked structures in the TMV cavity. Details of the pyrene interaction were investigated by analyzing the fluorescence lifetime of the excimer. Results suggest that the pyrenes formed preassociated rigid structures with partially overlapped geometry in the restricted space of the TMV cavity. The pyrenes effectively stabilize the TMV rod through a pi-stacking interaction in a well-ordered way, and the single pyrene moiety introduced into the monomer affects the overall formation of the TMV rod structure.     

Product bound structures of the soluble methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath): protein motion in the alpha-subunit

The soluble methane monooxygenase hydroxylase (MMOH) alpha-subunit contains a series of cavities that delineate the route of substrate entrance to and product egress from the buried carboxylate-bridged diiron center. The presence of discrete cavities is a major structural difference between MMOH, which can hydroxylate methane, and toluene/o-xylene monooxygenase hydroxylase (ToMOH), which cannot. To understand better the functions of the cavities and to investigate how an enzyme designed for methane hydroxylation can also accommodate larger substrates such as octane, methylcubane, and trans-1-methyl-2-phenylcyclopropane, MMOH crystals were soaked with an assortment of different alcohols and their X-ray structures were solved to 1.8-2.4 A resolution. The product analogues localize to cavities 1-3 and delineate a path of product exit and/or substrate entrance from the active site to the surface of the protein. The binding of the alcohols to a position bridging the two iron atoms in cavity 1 extends and validates previous crystallographic, spectroscopic, and computational work indicating this site to be where substrates are hydroxylated and products form. The presence of these alcohols induces perturbations in the amino acid side-chain gates linking pairs of cavities, allowing for the formation of a channel similar to one observed in ToMOH. Upon binding of 6-bromohexan-1-ol, the pi helix formed by residues 202-211 in helix E of the alpha-subunit is extended through residue 216, changing the orientations of several amino acid residues in the active site cavity. This remarkable secondary structure rearrangement in the four-helix bundle has several mechanistic implications for substrate accommodation and the function of the effector protein, MMOB.     

Porphyrin light-harvesting arrays constructed in the recombinant tobacco mosaic virus scaffold

We have demonstrated the construction of multiple porphyrin arrays in the tobacco mosaic virus (TMV) supramolecular structures by self-assembly of recombinant TMV coat protein (TMVCP) monomers, in which Zn-coordinated porphyrin (ZnP) and free-base porphyrin (FbP) were site-selectively incorporated. The photophysical properties of porphyrin moieties incorporated in the TMV assemblies were also characterized. TMV-porphyrin conjugates employed as building blocks self-assembled into unique disk and rod structures under the proper conditions as similar to native TMV assemblies. The mixture of a ZnP donor and an FbP acceptor was packed in the TMV assembly and showed energy transfer and light-harvesting activity. The detailed photophysical properties of the arrayed porphyrins in the TMV assemblies were examined by time-resolved fluorescence spectroscopy, and the energy transfer rates were determined to be 3.1-6.4x10(9) s(-1). The results indicate that the porphyrins are placed at the expected positions in the TMV assemblies.     

烟草花叶病毒的特定位点改性及应用

病毒是自然界中已知结构最简单却侵染能力极强的生物,作为一种典型的一维棒状植物病毒,烟草花叶病毒(TMV)具有单分散的形貌与尺寸(18nm×300nm)、明确的空间结构、丰富的表面化学基团,且对哺乳动物不具有致病性,已广泛应用于电子器件、传感、成像、生物医用材料的研究。本文简述了对TMV进行基因工程或化学改性的多种方法及应用进展,并主要介绍了烟草花叶病毒在生物医用材料领域的潜在应用。     

Interfacially Bridging Covalent Network Yields Hyperstable and Ultralong Virus‐Based Fibers for Engineering Functional Materials

We present a strategy of interfacially bridging covalent network within tobacco mosaic virus (TMV) virus‐like particles (VLPs). We arranged T103C cysteine to laterally conjugate adjacent subunits. In the axis direction, we set A74C mutation and systematically investigated candidate from E50C to P54C as the other thiol function site, for forming longitudinal disulfide bond chains. Significantly, the T103C‐TMV‐E50C‐A74C shows the highest robustness in assembly capability and structural stability with the largest length, for TMV VLP to date. The fibers with lengths from several to a dozen of micrometers even survive under pH 13. The robust nature of this TMV VLP allows for reducer‐free synthesis of excellent electrocatalysts for application in harshly alkaline hydrogen evolution.     

Structural investigation of the GlmS ribozyme bound to Its catalytic cofactor

The GlmS riboswitch is located in the 5'-untranslated region of the gene encoding glucosamine-6-phosphate (GlcN6P) synthetase. The GlmS riboswitch is a ribozyme with activity triggered by binding of the metabolite GlcN6P. Presented here is the structure of the GlmS ribozyme (2.5 A resolution) with GlcN6P bound in the active site. The GlmS ribozyme adopts a compact double pseudoknot tertiary structure, with two closely packed helical stacks. Recognition of GlcN6P is achieved through coordination of the phosphate moiety by two hydrated magnesium ions as well as specific nucleobase contacts to the GlcN6P sugar ring. Comparison of this activator bound and the previously published apoenzyme complex supports a model in which GlcN6P does not induce a conformational change in the RNA, as is typical of other riboswitches, but instead functions as a catalytic cofactor for the reaction. This demonstrates that RNA, like protein enzymes, can employ the chemical diversity of small molecules to promote catalytic activity.     

Communication between the active site and the allosteric site in class A beta-lactamases

Bacterial production of beta-lactamases, which hydrolyze beta-lactam type antibiotics, is a common antibiotic resistance mechanism. Antibiotic resistance is a high priority intervention area and one strategy to overcome resistance is to administer antibiotics with beta-lactamase inhibitors in the treatment of infectious diseases. Unfortunately, beta-lactamases are evolving at a rapid pace with new inhibitor resistant mutants emerging every day, driving the design and development of novel beta-lactamase inhibitors. Here, we examined the inhibitor recognition mechanism of two common beta-lactamases using molecular dynamics simulations. Binding of beta-lactamase inhibitor protein (BLIP) caused changes in the flexibility of regions away from the binding site. One of these regions was the H10 helix, which was previously identified to form a lid over an allosteric inhibitor binding site. Closer examination of the H10 helix using sequence and structure comparisons with other beta-lactamases revealed the presence of a highly conserved Trp229 residue, which forms a stacking interaction with two conserved proline residues. Molecular dynamics simulations on the Trp229Ala mutants of TEM-1 and SHV-1 resulted in decreased stability in the apo form, possibly due to loss of the stacking interaction as a result of the mutation. The mutant TEM-1 beta-lactamase had higher H10 fluctuations in the presence of BLIP, higher affinity to BLIP and higher cross-correlations with BLIP. Our results suggest that the H10 helix and specifically W229 are important modulators of the allosteric communication between the active site and the allosteric site.     

Three-dimensional electron cryomicroscopy of ribosomes

Single particle electron cryomicroscopy is nowadays routinely used to generate three-dimensional structural information of ribosomal complexes without the need of crystallization. A large number of structures of functional important ribosomal complexes have thus been determined using this technique. In E. coli 70S ribosomes all three tRNA binding sites could be localized. The ternary complex of EF-TutRNAGTP that delivers the tRNA to the ribosome was directly visualized in a ribosomal complex blocked by the antibiotic kirromycin. Three different functional states of translocation have been studied and the respective EF-G binding sites have been mapped. The level of resolution achievable with electron cryomicroscopy allows conformational changes in the domain structures of elongation factors to be modelled in terms of rigid body movements. Structural information on eukaryotic ribosomes is also available for yeast and mammalian 80S ribosomes. The structural differences between rabbit 80S and E. coli 70S ribosomes could be interpreted in terms of ribosomal RNA expansion segments in the 18S and 23S RNA. The EF-G homologue EF2 was mapped analysing the structure of an 80SEF2sodarin complex and most recently the binding of a hepatitis C virus IRES element to a yeast 40S subunit has been studied. The first electron cryomicroscopical 3D reconstructions have further been used to overcome the initial phasing problems in X-ray crystallographic studies of the ribosome facilitating structure determination of the recent atomic resolution structures of the 30S and 50S ribosomal subunits. In turn, the knowledge of the atomic structure of the ribosome makes detailed interpretations of cryo-EM maps possible at approximately 20 A resolution.     

A triple helix of double helicates: three hierarchical levels of self-assembly in a single structure

The bis-bidentate bridging ligand L reacts with Ag(I) ions to form a conventional dinuclear [Ag(2)L(2)](2+) double helicate; individual double helicate units assemble via Ag···Ag interactions into infinite chains, three of which wrap around a central spine of anions to give a triple helical braid, which is therefore an infinite triple helix composed of molecular double helicate subunits.     

Two Histidines in an α‐Helix: A Rigid Co2+‐Binding Motif for PCS Measurements by NMR Spectroscopy

Pseudocontact shifts (PCS) generated by paramagnetic metal ions present valuable long‐range information in the study of protein structural biology by nuclear magnetic resonance (NMR) spectroscopy. Faithful interpretation of PCSs, however, requires complete immobilization of the metal ion relative to the protein, which is difficult to achieve with synthetic metal tags. We show that two histidine residues in sequential turns of an α‐helix provide a binding site for a Co²⁺ ion, which positions the metal ion in a uniquely well‐defined and predictable location. Exchange between the bound and free cobalt is slow on the timescale defined by chemical shifts, but the NMR resonance assignments are nonetheless readily transferred from the diamagnetic to the paramagnetic NMR spectrum by an I_zS_z‐exchange experiment. The double‐histidine‐Co²⁺ motif offers a straightforward, inexpensive, and convenient way of generating precision PCSs in proteins.     

Interfacially Bridging Covalent Network Yields Hyperstable and Ultralong Virus-Based Fibers for Engineering Functional Materials

We present a strategy of interfacially bridging covalent network within tobacco mosaic virus (TMV) virus-like particles (VLPs). We arranged T103C cysteine to laterally conjugate adjacent subunits. In the axis direction, we set A74C mutation and systematically investigated candidate from E50C to P54C as the other thiol function site, for forming longitudinal disulfide bond chains. Significantly, the T103C-TMV-E50C-A74C shows the highest robustness in assembly capability and structural stability with the largest length, for TMV VLP to date. The fibers with lengths from several to a dozen of micrometers even survive under pH 13. The robust nature of this TMV VLP allows for reducer-free synthesis of excellent electrocatalysts for application in harshly alkaline hydrogen evolution.