Inside polyomavirus at 25-A resolution.

Empty capsids and complete virions of polyomavirus crystallize isomorphously. Here we use difference Fourier analysis of X-ray diffraction data at 25-A resolution from these crystals to obtain an electron-density map of the inside of the virion. The polyomavirus capsid is built from 72 pentamers of VP1 that form three different types of connections in the T = 7d icosahedral surface lattice. Self-assembly of purified recombinant VP1 into capsid-like aggregates has shown that switching of the bonding specificity to form the unanticipated non-equivalent connections is an inherent property of the VP1 pentamers. Our map of the inside of the virion displays 72 prongs of electron density extending from the core into the axial cavities of the VP1 pentamers. We identify these prongs with the VP2 and VP3 molecules, which may function to guide the assembly of the highly ordered capsid on the nucleohistone core. The atomic structure of the closely related simian virus-40 capsid has been determined from the high-resolution diffraction data. Our polyomavirus map, calculated using all the low-resolution diffraction data, shows no indication of regular order inside the spherical core.     

Structural disorder in plant proteins: where plasticity meets sessility

Plants are sessile organisms. This intriguing nature provokes the question of how they survive despite the continual perturbations caused by their constantly changing environment. The large amount of knowledge accumulated to date demonstrates the fascinating dynamic and plastic mechanisms, which underpin the diverse strategies selected in plants in response to the fluctuating environment. This phenotypic plasticity requires an efficient integration of external cues to their growth and developmental programs that can only be achieved through the dynamic and interactive coordination of various signaling networks. Given the versatility of intrinsic structural disorder within proteins, this feature appears as one of the leading characters of such complex functional circuits, critical for plant adaptation and survival in their wild habitats. In this review, we present information of those intrinsically disordered proteins (IDPs) from plants for which their high level of predicted structural disorder has been correlated with a particular function, or where there is experimental evidence linking this structural feature with its protein function. Using examples of plant IDPs involved in the control of cell cycle, metabolism, hormonal signaling and regulation of gene expression, development and responses to stress, we demonstrate the critical importance of IDPs throughout the life of the plant.     

Proxy evidence for an El Niño-like response to volcanic forcing

Past studies have suggested a statistical connection between explosive volcanic eruptions and subsequent El Ni?o climate events. This connection, however, has remained controversial. Here we present support for a response of the El Ni?o/Southern Oscillation (ENSO) phenomenon to forcing from explosive volcanism by using two different palaeoclimate reconstructions of El Ni?o activity and two independent, proxy-based chronologies of explosive volcanic activity from ad 1649 to the present. We demonstrate a significant, multi-year, El Ni?o-like response to explosive tropical volcanic forcing over the past several centuries. The results imply roughly a doubling of the probability of an El Ni?o event occurring in the winter following a volcanic eruption. Our empirical findings shed light on how the tropical Pacific ocean-atmosphere system may respond to exogenous (both natural and anthropogenic) radiative forcing.     

Spontaneous arterial dissection: phenotype and molecular pathogenesis

Arterial dissection (AD) is defined as the longitudinal splitting up of the arterial wall caused by intramural bleeding. It can occur as a spontaneous event in all large and medium sized arteries. The histological hallmark of AD is medial degeneration. Histological investigations, gene expression profiling and proteome studies of affected arteries reveal disturbances in many different biological processes including inflammation, proteolytic activity, cell proliferation, apoptosis and smooth muscle cell (SMC) contractile function. Medial degeneration can be caused by various rare dominant Mendelian disorders. Genetic linkage analysis lead to the identification of mutations in different disease-causing genes involved in the biosynthesis of the extracellular matrix (FBN1, COL3A1), in transforming growth factor (TGF) beta signaling (FBN1, TGFBR1, TGFBR2) and in the SMC contractile system (ACTA2, MYH11). Genome wide association studies suggest that the CDKN2A/CDKN2B locus plays a role in the etiology AD and other arterial diseases.     

Polyoma virus capsid structure at 22.5 A resolution

X-ray diffraction data from polyoma capsid crystals were phased by refinement of low-resolution starting models to obtain a self-consistent structural solution. The unexpected result that the hexavalent morphological unit is a pentamer shows that specificity of bonding is not conserved among the protein subunits in the icosahedrally symmetric capsid.     

Site-directed mutation affecting polyomavirus capsid self-assembly in vitro

Nonequivalent bonding of identical protein subunits occurs in the polyomavirus capsid were identical pentameric capsomeres occupy both hexavalent and pentavalent positions in the icosahedral surface lattice. The polyomavirus major capsid protein VP1, purified after expression of the recombinant gene in Escherichia coli, has been isolated as capsomeres that self-assemble into capsid-like structures in vitro. The ability to switch bonding specificity in different symmetry environments therefore must be intrinsic to the VP1 molecule. In vitro self-assembly provides an assay for VP1 mutations affecting capsomere and capsid formation. We report here that a directed mutation in the VP1 expression vector, leading to a protein truncated at the carboxy terminus, results in a mutant VP1 that forms capsomeres, but not capsids, in the in vitro assembly assay. The carboxy terminus of VP1 therefore appears to be involved in the specific bonding responsible for the non-equivalent association of capsomeres.     

Liquid-like movements in crystalline insulin

Diffuse X-ray scattering from protein crystals provides information about molecular flexibility and packing irregularities. Here we analyse diffraction patterns from insulin crystals that show two types of scattering related to disorder: very diffuse, liquid-like diffraction, and haloes around the Bragg reflections. The haloes are due to coupled displacements of neighbouring molecules in the lattice, and the very diffuse scattering results from variations in atomic positions that are only locally correlated within each molecule. The measured intensity was digitally separated into three components: the Bragg reflections and associated haloes; the water and Compton scattering; and the scattering attributed to internal protein movements. We extend methods used to analyse disorder in membrane structures to simulate the diffuse scattering from crystalline insulin in terms of (1) the Patterson (autocorrelation) function of the ideal, ordered crystal structure, (2) the root-mean-square (r.m.s.) amplitude of the atomic movements, and (3) the mean distance over which these displacements are coupled. Movements of the atoms within the molecules, with r.m.s. amplitudes of 0.4-0.45 A, appear to be coupled over a range of approximately 6 A, as in a liquid. These locally coupled movements account for most of the disorder in the crystal. Also, the protein molecules, as a whole, jiggle in the lattice with r.m.s. amplitudes of approximately 0.25 A that appear to be significantly correlated only between nearest neighbours.     

Polyoma virus 'hexamer' tubes consist of paired pentamers

The discovery that the 72 capsomeres of the icosahedrally symmetric polyoma virus capsid are all pentamers shows that the expected quasi-equivalent bonding specificity is not conserved in the assembly of this virus coat protein. Tubular particles produced by polyoma and other papovaviruses seem to be polymorphic aggregates of capsomeres that may arise through variation in switching of the bonding specificity. Electron micrographs of wide and narrow classes of tubes were analysed by Kiselev and Klug using optical diffraction and optical filtering methods. The wide type were called 'hexamer' tubes because they consist of approximately hexagonally arrayed capsomeres that were assumed to be hexamers, in accord with the quasi-equivalence theory of icosahedral virus particle construction. The narrow type were called 'pentamer' tubes because the capsomeres are arrayed in a particular 'pentagonal tesselation' which arises from the pairing of pentamers across 2-fold axes of the surface lattice. Our reexamination of negatively-stained polyoma virus tubes by digital image processing of low-irradiation electron micrographs shows that all tubes are assemblies of paired pentameric capsomeres. We report here that the packing arrangement of the pentamers in the hexamer tubes is simply related to the pentagonal tessellation respresenting the packing in the narrow pentamer tubes. In all the tube structures examined, at least one pairwise contact between neighbouring pentamers closely resembles the contact between the pentavalent and hexavalent capsomeres in the icosahedral capsid.