Satellite tobacco mosaic virus RNA: structure and implications for assembly

Larson, Steven B.; McPherson, Alexander

doi:10.1016/s0959-440x(00)00166-4

Cited by 70 publications

(105 citation statements)

References 18 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Frequently, however, bits and pieces, and occasionally large segments of nucleic acid are visible in electron density maps of spherical viruses where the RNA or DNA does, through virion design, appear systematically consistent with the icosahedral symmetry (see Larson & McPherson for examples). 28 No discrete elements of nucleic acid, however, were apparent in this BMV structure. This is, perhaps, not surprising.…”

Section: Protein-nucleic Acid Interactions and Assemblymentioning

confidence: 82%

“…20,28 No such interactions are seen in BMV. Mechanism (3) is characterized by rigorous protein-protein interactions and the in vivo formation of empty capsids.…”

Section: Protein-nucleic Acid Interactions and Assemblymentioning

confidence: 99%

“…This was proposed for satellite tobacco mosaic virus (STMV). 28 Another means (2) is where the RNA folds independently into some roughly spherical core structure, purely as a consequence of secondary and tertiary nucleic acid interactions, and the protein shell then forms around it by virtue of non-speci®c charge interactions involving positively charged subunits and negatively charged phosphate groups. A third possibility (3) which might be operable, and is likely in the case of the tymoviruses, 4 is that a nearly complete capsid forms entirely through protein-protein interactions, and the RNA is then drawn into the capsid, again, probably through charge interactions.…”

Section: Protein-nucleic Acid Interactions and Assemblymentioning

confidence: 99%

See 2 more Smart Citations

The crystallographic structure of brome mosaic virus

Lucas

Larson

McPherson

2002

Journal of Molecular Biology

Self Cite

136

181

View full text Add to dashboard Cite

The structure of brome mosaic virus (BMV), the type member of the bromoviridae family, has been determined from a single rhombohedral crystal by X-ray diffraction, and re®ned to an R value of 0.237 for data in the range 3.4-40.0 A Ê . The structure, which represents the native, compact form at pH 5.2 in the presence of 0.1 M Mg 2 , was solved by molecular replacement using the model of cowpea chlorotic mottle virus (CCMV), which BMV closely resembles. The BMV model contains amino acid residues 41-189 for the pentameric capsid A subunits, and residues 25-189 and 1-189 for the B and C subunits, respectively, which compose the hexameric capsomeres. In the model there are two Mg ions and one molecule of polyethylene glycol (PEG). The ®rst 25 amino acid residues of the C subunit are modeled as polyalanine. The coat protein has the canonical``jellyroll'' b-barrel topology with extended amino-terminal polypeptides as seen in other icosahedral plant viruses. Mass spectrometry shows that in native BMV virions, a signi®cant fraction of the amino-terminal peptides are apparently cleaved. No recognizable nucleic acid residue is visible in the electron density maps except at low resolution where it appears to exhibit a layered arrangement in the virion interior. It is juxtaposed closely with the interior surface of the capsid but does not interpenetrate. The protein subunits forming hexameric capsomeres, and particularly dimers, appear to interact extensively, but the subunits otherwise contact one another sparsely about the 5-fold and quasi 3-fold axes. Thus, the virion appears to be an assembly of loosely associated hexameric capsomeres, which may be the basis for the swelling and dissociation that occurs at neutral pH and elevated salt concentration. A Mg ion is observed to lie exactly on the quasi-3-fold axis and is closely coordinated by side-chains of three quasi-symmetry-related residues glutamates 84, with possible participation of side-chains from threonines 145, and asparagines 148. A presumptive Mg 2 is also present on the 5-fold axis where there is a concentration of negatively charged side-chains, but the precise coordination is unclear. In both cases these cations appear to be essential for maintenance of virion stability. Density that is contiguous with the viral interior is present on the 3-fold axis at the center of the hexameric capsomere, where there is a pore of about 6 A Ê diameter. The density cannot be attributed to cations and it was modeled as a PEG molecule.

show abstract

Section: Protein-nucleic Acid Interactions and Assemblymentioning

confidence: 82%

“…20,28 No such interactions are seen in BMV. Mechanism (3) is characterized by rigorous protein-protein interactions and the in vivo formation of empty capsids.…”

Section: Protein-nucleic Acid Interactions and Assemblymentioning

confidence: 99%

Section: Protein-nucleic Acid Interactions and Assemblymentioning

confidence: 99%

See 1 more Smart Citation

The crystallographic structure of brome mosaic virus

Lucas

Larson

McPherson

2002

Journal of Molecular Biology

Self Cite

136

181

View full text Add to dashboard Cite

show abstract

“…5,6 X-ray crystallographic analyses of some viruses from both plants and insects have demonstrated the presence of helical RNA within capsids. 1,7 In those cases, only the RNA elements that were consistent with icosahedral symmetry could be visualized; hence, it is likely that these were underestimates of all that might be present. Even so, in satellite tobacco mosaic virus (STMV), for example, about 45% of the RNA is seen to form double-helical elements, 4,8,9 in bean pod mottle virus about 20% exists in trefoil arrangements, 10 in turnip yellow mosaic virus (TYMV) roughly 40% is helical, 11 and in Flock house virus around 20%.…”

Section: Introductionmentioning

confidence: 99%

“…There is evidence that the RNA in other small icosahedral viruses may be arranged as linear sequences of stem-loop clusters distributed among the capsomeres with approximate icosahedral symmetry. 1,7 RNA regularity is, presumably, a consequence of its interaction with the symmetrically organized coat proteins.…”

Section: Introductionmentioning

confidence: 99%

Atomic Force Microscopy Analysis of Icosahedral Virus RNA

Kuznetsov

Daijogo

Zhou

et al. 2005

Journal of Molecular Biology

View full text Add to dashboard Cite

Single-stranded genomic RNAs from four icosahedral viruses (poliovirus, turnip yellow mosaic virus (TYMV), brome mosaic virus (BMV), and satellite tobacco mosaic virus (STMV)) along with the RNA from the helical tobacco mosaic virus (TMV) were extracted using phenol/chloroform. The RNAs were imaged using atomic force microscopy (AFM) under dynamic conditions in which the RNA was observed to unfold. RNAs from the four icosahedral viruses initially exhibited highly condensed, uniform spherical shapes with diameters consistent with those expected from the interiors of their respective capsids. Upon incubation at 26 8C, poliovirus RNA gradually transformed into chains of globular domains having the appearance of thick, irregularly segmented fibers. These ultimately unwound further to reveal segmented portions of the fibers connected by single strands of RNA of 0.5-1 nm thickness. Virtually the same transformations were shown by TYMV and BMV RNA, and with heating, the RNA from STMV. Upon cooling, the chains of domains of poliovirus RNA and STMV RNA condensed and re-formed their original spherical shapes. TMV RNAs initially appeared as single-stranded threads of 0.5-1.0 nm diameter but took on the structure of the multidomain chains upon further incubation at room temperature. These ultimately condensed into short, thick chains of larger domains. Our observations suggest that classical extraction of RNA from icosahedral virions produces little effect on overall conformation. As tertiary structure is lost however, it is evident that secondary structural elements are arranged in a sequential, linear fashion along the polynucleotide chain. At least in the case of poliovirus and STMV, the process of tertiary structure re-formation from the linear chain of secondary structural domains proceeds in the absence of protein. RNA base sequence, therefore, may be sufficient to encode the conformation of the encapsidated RNA even in the absence of coat proteins.

show abstract

Accelerating molecular modeling applications with graphics processors

et al. 2007

View full text Add to dashboard Cite

Molecular mechanics simulations offer a computational approach to study the behavior of biomolecules at atomic detail, but such simulations are limited in size and timescale by the available computing resources. Stateof-the-art graphics processing units (GPUs) can perform over 500 billion arithmetic operations per second, a tremendous computational resource that can now be utilized for general purpose computing as a result of recent advances in GPU hardware and software architecture. In this article, an overview of recent advances in programmable GPUs is presented, with an emphasis on their application to molecular mechanics simulations and the programming techniques required to obtain optimal performance in these cases. We demonstrate the use of GPUs for the calculation of long-range electrostatics and nonbonded forces for molecular dynamics simulations, where GPU-based calculations are typically 10-100 times faster than heavily optimized CPU-based implementations. The application of GPU acceleration to biomolecular simulation is also demonstrated through the use of GPU-accelerated Coulomb-based ion placement and calculation of time-averaged potentials from molecular dynamics trajectories. A novel approximation to Coulomb potential calculation, the multilevel summation method, is introduced and compared with direct Coulomb summation. In light of the performance obtained for this set of calculations, future applications of graphics processors to molecular dynamics simulations are discussed.

show abstract

Satellite tobacco mosaic virus RNA: structure and implications for assembly

Cited by 70 publications

References 18 publications

The crystallographic structure of brome mosaic virus

The crystallographic structure of brome mosaic virus

Atomic Force Microscopy Analysis of Icosahedral Virus RNA

Accelerating molecular modeling applications with graphics processors

Contact Info

Product

Resources

About