Three-dimensional structure of satellite tobacco mosaic virus at 2.9 A resolution.
ABSTRACT The crystal structure of satellite tobacco mosaic virus (STMV) has been solved by a combination of multiple isomorphous replacement and molecular replacement methods and refined at 2.9 A resolution to a conventional R-factor of 0.215. STMV, a T = 1 icosahedral virus, is the smallest whose structure has been determined. The coat protein is an eight-stranded "Swiss roll" beta-barrel with an amino-terminal strand that extends away from the beta-barrel by more than 60 A. This strand is primarily responsible for quaternary interactions within the capsid. The most arresting feature of the virus structure is the intimate association of each capsid protein dimer with a Watson-Crick base-paired segment of RNA double helix on the interior of the virion. The icosahedral 2-fold axis of each dimer pair is coincident with that of the central base-pair of each helical RNA segment whose helical axis is along the edge of the icosahedron. The helical RNA segments are seven base-pairs in length with a stacked base at each 3' end so that a total of 16 nucleotides is clearly visible. The character of the RNA helix is somewhat different than any of the canonical forms. Assuming full occupancy, then approximately 45% of the total RNA genome is present in the electron density map. The close association of capsid with highly structured nucleic acid suggests that assembly of STMV is likely to be a highly co-operative process involving both protein and RNA. The nucleic acid is distributed within the virion with a high degree of order. The capsid protein is a true double helical RNA binding protein and a number of prominent interactions between protein and RNA can be clearly seen.
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ABSTRACT: Agarose gel electrophoresis, circular dichroism and differential scanning calorimetry showed that single-stranded RNA from satellite tobacco mosaic virus transforms from a conformationally 'closed state' at 4°C to a more conformationally 'open state' at 65°C. The transition is reversible and shows no hysteresis. Atomic force microscopy (AFM) allowed visualization of the two states and indicated that the conformationally 'closed state' probably corresponds to the native encapsidated conformation, and that the 'open state' represents a conformation, characterized as short, thick chains of domains, as a consequence of the loss of tertiary interactions. Heating from 75°C to 85°C in the presence of EDTA was necessary to further unravel the 'open' conformation RNA into extended chains of lengths >280 nm. Virus exposed to low concentrations of phenol at 65°C, extruded RNA as distinctive 'pigtails' in a synchronous fashion, and these 'pigtails' then elongated, as the RNA was further discharged by the particles. Moderate concentrations of phenol at 65°C produced complete disruption of virions and only remains of decomposed particles and disordered RNA were evident. AFM images of RNA emerging from disrupted virions appear most consistent with linear arrangements of structural domains.Nucleic Acids Research 12/2010; 38(22):8284-94. · 8.28 Impact Factor
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ABSTRACT: The classical analytical method for gaseous carbonyl measurements based on solid sorbent coated with 2,4-dinitrophenylhydrazine (DNPH) and analysis by HPLC/UV suffers from limited resolution of carbonyls with similar molecular structures and high molecular weights. In this paper, we report the development of a sensitive and reliable analytical method for simultaneous determination of 21 airborne carbonyls within the C(1)-C(9) range. Carbonyls were collected on a sampling tube filled with 100mg Tenax TA (60-80 mesh) sorbent coated with 1 μmol pentafluorophenyl hydrazine (PFPH), followed by solvent desorption and analysis by gas chromatography (GC)/mass spectrometry (MS). Common carbonyl gases including formaldehyde, acetaldehyde, butyraldehyde, hexaldehyde and benzaldehyde at ppbv levels were collected with efficiency greater than 90% onto sampling tubes at a flow rate of 100 mL min(-1). The limits of detection (LODs, signal/noise=3) of the tested carbonyls were in the range of 0.08-0.20 ppbv for a sampled volume of 24.0 L. These limits are less than or comparable with those that can be obtained using the DNPH-HPLC method. The method has been field-tested both in ambient air of York and in diluted cigarette smoke. Comparing field tests with the classical DNPH-HPLC method, good agreement was displayed between the two methods for the same carbonyls, but with more carbonyl species detected by the PFPH-GC/MS method. The PFPH-GC/MS method provides better molecular separation for carbonyls with similar structures, is highly sensitivity and gives confirmation of identification by structures when detected using MS.Talanta 07/2011; 85(1):406-14. · 3.50 Impact Factor
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ABSTRACT: This study deals with O(2)(-) generation in corona discharge (CD) in point to plane geometry for single flow ion mobility spectrometry (IMS) with gas outlet located behind the ionization source. We have designed CD of special geometry in order to achieve the high O(2)(-) yield. Using this ion source we have achieved in zero air conditions that up to 74% all negative ions were O(2)(-) or O(2)(-)(H(2)O). It has been demonstrated that the non-electronegative nitrogen positively influences the efficiency of O(2)(-) generation in O(2)/N(2) mixtures. The reduced ion mobility of 2.27 cm(2)V(-1)s(-1) has been measured for O(2)(-)/O(2)(-)(H(2)O) ions in zero air. Additional ions detected in zero air (less than 200 ppb CO(2)) using the mass spectrometric and IMS technique were, NO(2)(-), N(2)O(2)(-) (2.37 cm(2)V(-1)s(-1)), NO(3)(-), N(2)O(3)(-) and N(2)O(3)(-)(H(2)O). The CO(3)(-) and CO(4)(-) ions have been detected after the introduction of 5 ppm CO(2) into zero air.Talanta 07/2011; 85(1):400-5. · 3.50 Impact Factor