Virus crystallography comes of age

Virus assembly occurs following a pH- or Ca2+-triggered switch in the thermodynamic attraction between structural protein capsomeres

Viral self-assembly is of tremendous virological and biomedical importance. Although theoretical and crystallographic considerations suggest that controlled conformational change is a fundamental regulatory mechanism in viral assembly, direct proof that switching alters the thermodynamic attraction of self-assembling components has not been provided. Using the VP1 protein of polyomavirus, we report a new method to quantitatively measure molecular interactions under conditions of rapid protein self-assembly. We show, for the first time, that triggering virus capsid assembly through biologically relevant changes in Ca(2+) concentration, or pH, is associated with a dramatic increase in the strength of protein molecular attraction as quantified by the second virial coefficient (B(22)). B(22) decreases from -2.3 x 10(-4) mol ml g(-2) (weak protein-protein attraction) to -2.4 x 10(-3) mol ml g(-2) (strong protein attraction) for metastable and Ca(2+)-triggered self-assembling capsomeres, respectively. An assembly-deficient mutant (VP1CDelta63) is conversely characterized by weak protein-protein repulsion independently of chemical change sufficient to cause VP1 assembly. Concomitant switching of both VP1 assembly and thermodynamic attraction was also achieved by in vitro changes in ammonium sulphate concentration, consistent with protein salting-out behaviour. The methods and findings reported here provide new insight into viral assembly, potentially facilitating the development of new antivirals and vaccines, and will open the way to a more fundamental physico-chemical description of complex protein self-assembly systems.

Evidence for pH-induced release of RNA from belladonna mottle virus and the stabilizing effect of polyamines and cations

The RNA of belladonna mottle virus (BDMV) is released from virions by increasing the pH to neutrality or above, leaving behind intact protein shells. In contrast, much harsher conditions are required to release the RNA from the closely related turnip yellow mosaic virus (TYMV). The heat-induced or pH-dependent escape of RNA from BDMV has been investigated by 31P NMR spectroscopy and ultracentrifugation. The methods show a transition pH near 6.8 at which the RNA undergoes a structural alteration probably caused by disruption of protein-RNA linkages. Addition of cations or polyamines to BDMV prevents the RNA loss at alkaline pH; the virions become stable to pH values up to 11.5 as observed for TYMV. We suggest that repulsion of the negatively charged phosphate groups of the nucleic acid provides the driving force for RNA release at pH values above the threshold point where protein-RNA interactions are broken. The polyamines effectively counter the phosphate charge in BDMV and thereby prevent RNA loss. Since TYMV is packaged with polyamines and BDMV is not (R. Virudachalam, K. Sitaraman, K. L. Heuss, P. Argos, and J. L. Markley, Virology 130, 360-371, 1983), the different conditions required for RNA escape from the two viruses are explained. Heating of BDMV virions at pH 7.0 to 40 degrees resulted in their partial disruption; the product some intact particles, empty capsids, and RNA fragments with a sedimentation coefficient of 5S.

Spectroscopic and Potentiometric Characterization of Oxovanadium(IV) Complexes Formed by 3-Hydroxy-4-Pyridinones. Rationalization of the Influence of Basicity and Electronic Structure of the Ligand on the Properties of VIVO Species in Aqueous Solution

Aqueous solution studies regarding the identification and characterization of complexes formed by the VIVO ion and 11 3-hydroxy-4-pyridinone derivatives have been performed using EPR and UV/vis spectroscopic techniques. For the three ligands (HL) adequately soluble in water (1-methyl-3-hydroxy-4-pyridinone, 1-methyl-2-ethyl-3-hydroxy-4-pyridinone, and 1,2-diethyl-3-hydroxy-4-pyridinone), potentiometric titrations were performed; the results are consistent with the formation of [V(IV)OL]+, [V(IV)OL2], [V(IV)OL2H(-1)]-, [(V(IV)O)2L2H(-2)], and [V(IV)L3]+ species. Bis chelated complexes are characterized by a cis-trans isomerism, the trans isomer being strongly favored with respect to the cis arrangement. Tris chelated non-oxo V(IV) species were prepared in CH3COOH; their spectroscopic features point to a d(z2) ground state and a geometry intermediate between an octahedron and a trigonal prism, related to the steric requirements of the substituent on the carbon atom in position 2 of the pyridinone ring. Four new solid derivatives, [V(IV)O(1,2-diethyl-3-hydroxy-4-pyridinonato)2], [V(IV)O(1-(p-tolyl)-2-ethyl-3-hydroxy-4-pyridinonato)2], [V(IV)O(1-(p-(n-butyl)phenyl)-2-ethyl-3-hydroxy-4-pyridinonato)2], and [V(IV)O(1-(p-(n-hexyl)phenyl)-2-ethyl-3-hydroxy-4-pyridinonato)2], were isolated and characterized; they exhibited a five-coordinate geometry close to square-pyramid. A criterion for establishing the degree of distortion toward the trigonal-bipyramid on the basis of the electronic absorption spectra is provided. Relationships between the pKa of the -OH group in position 3 of the ring and (i) log K of mono and bis chelated complexes, (ii) pK of the water molecule in cis-[V(IV)OL2(H2O)], (iii) log K of tris chelated species [V(IV)L3]+, and (iv) 51V hyperfine coupling constant (Az) have been established and discussed for a number of pyrone, pyridinone, and catechol ligands. The results are rationalized by assuming for pyridinones an electronic structure intermediate between that of pyrones and catechols. The relationships are valuable to the understanding of the behavior of VIVO species in aqueous solution.

Structure of RNA in satellite tobacco necrosis virus. A low resolution neutron diffraction study using 1H2O/2H2O solvent contrast variation

The crystal structure of satellite tobacco necrosis virus has been studied by neutron diffraction at 16 A resolution using the technique of 1H2O/2H2O solvent contrast variation to distinguish between the regions of protein and nucleic acid. The RNA density is essentially localized in a region just inside the protein coat, leading to a significant interaction between the two components. From the appearance of the RNA density we conclude that the protein coat imposes partial icosahedral symmetry on a significant proportion of the nucleic acid. The shape and dimensions of the major part of this density suggests that about 72% of the total RNA could be double-helical in structure. The most important interaction between the two components of the virus occurs between the N-terminal triple-helical arms of the protein subunits and those regions of the RNA density that could have a double-helical secondary structure.

Structure and assembly of haptoglobin polymers by electron microscopy

Haptoglobin (Hp) consists of light (L) and heavy (H) chains, the latter of which combine with hemoglobin alpha beta dimers to form a highly stable complex. Human haptoglobin assembles as HL units that occur in two allelic forms; HL1 , which is monovalent, and HL2 , which is divalent. As a result, three phenotypic forms exist in the human population: Hp1-1, the homozygous form in which the monovalent HL1 unit occurs as a dimer; Hp2-2, the homozygous form of the divalent HL2 unit, which gives a series of polymers; and the heterozygous Hp2-1 form, which gives a different series of polymers. We have investigated the structures and assembly properties of these two haptoglobin polymeric series in their complexes with hemoglobin using high-resolution scanning transmission electron microscopy. Polymers of complex are composed of ellipsoidal or bilobal head groups, which are the H alpha beta subunits connected by thin filament-like structures, which are the L chains. Polymers of size up to pentamers can be identified easily by counting the number of head groups in the molecule. Complex 2-1 and complex 2-2 trimers were studied extensively. The differences in detailed morphology show that while the 2-1 trimer is a linear polymer, the 2-2 trimer is a closed circular molecule. The micrograph images suggest that complex 2-2 tetramers and pentamers, and perhaps higher forms may also be cyclic. The structure of the L2 subunit of haptoglobin is shown to be composed of two domains, which may be similar in structure to the single domain of the monovalent L1 chain. The two L2 domains are connected by a hinge that has quite limited flexibility. Using these structural models, assembly characteristics and structural properties of the trimers and tetramers of complex 2-1 and complex 2-2 are described.

Assembly and packing of clathrin into coats

We present a model for the packing of clathrin molecules into the characteristic hexagons and pentagons covering coated pits and vesicles. The assembly unit is a symmetrical trimer with three extended legs. Polymerization of these units occurs in seconds under suitable conditions, giving empty polyhedral cages resembling the structures around coated vesicles. Images of small, negatively stained fragments of cages, assembled directly on electron microscope grids, reveal details of the structure, which correlate well with the predicted features of the model. There is one clathrin trimer at each polyhedral vertex, and each leg of the trimer extends along two neighboring polyhedral edges. Quasi-equivalent packing in pentagons and hexagons in polyhedra of different sizes requires a variable joint at the vertex of the molecule and a hinge in each leg. The construction of clathrin coats is remarkable for the extended fibrous contacts that each molecule makes with many others. Such contacts may confer mechanical strength combined with flexibility needed when a vesicle is pinched off from the membrane.

Polyoma virion and capsid crystal structures

X-ray diffraction shows that complete virus particles and empty capsids crystallize isomorphously. The surface morphology of the protein coat, as revealed by electron microscopy, is the dominant structural feature determining the intensity of x-ray reflections to a resolution of approximately 30 angstroms. The structure and variability of the viral chromatin core can now be analyzed by comparison of electron density maps.