1,721,059 research outputs found
Interatomic contacts in viral capsids
No full textSpherical viral capsids possess icosahedral symmetry and are made of a large number of densely- packed protein subunits, each consisting of thousands of atoms. Similarly, a large number of close interactions contribute to packing in crystals of virus particles. A computational method, based on the representation of the three-dimensional shape of the subunits in the icosahedral asymmetric unit as a binary map for the fast evaluation of all short interatomic contacts between subunits within the capsid as well as between particles in the crystal lattice is presented. This method might be useful in the examination of the spatial relations of three-dimensional objects. Its application to sesbania mosaic virus reveals subunit packing dominated by polar interactions, in consistence with observed properties
Contrasting features in the assembly of Sesbania mosaic virus and Physalis mottle virus
No full textViruses have served as excellent model systems for studies on the assembly/disassembly of macromolecular complexes. We have studied the structures and molecular mechanisms of assembly of two icosahedral ss-RNA plant viruses, Sesbania mosaic virus (SeMV) and Physalis mottle virus (PhMV). The expression of CP gene of these viruses in E. coli was shown to result in the assembly of T=3 virus-like particles (VLPs). In SeMV, the recombinant T=3 particles encapsidate E. coli 23s rRNA and CP mRNA. Deletion of 31 or more amino acids from the N-terminus resulted in the formation of T=1 particles. X-ray diffraction data of three recombinant T=3 capsids and five recombinant T=1 capsids were collected and their structures were solved. A unique structure called b-annulus is found at the icosahedral three-folds of SeMV and many other T=3 viruses. It has been suggested that this structure is essential for T=3 capsid assembly. The structures of recombinant rCP and CP-P53A capsids indicate that despite the differences in the nucleic acid that is encapsidated and the manipulation of the crucial proline at the â-annulus, the core of the CP and the interactions at various interfaces are nearly identical to those of wild type particles. Surprisingly, deletion of residues involved in the formation of b-annulus did not affect capsid assembly. X-ray structural studies have revealed that the b-annulus is indeed absent in these capsids. The structures of T=1 mutants retain accurately several key intersubunit interactions of the native virus. Metal-ion mediated inter-subunit interactions increase the stability of SeMV but are not crucial for the assembly. An arginine rich motif found at the N-terminus of SeMV coat protein has been shown to be essential for RNA encapsidation. These studies have allowed proposition of a plausible model for the assembly of SeMV. The structural, mutational and immunological analysis of PhMV assembly has shown that the N-terminal arm is dynamic and could mediate an early step in the disassembly/assembly of the virus. Several mutants that disrupt interfacial interactions have been generated and their stability and assembly have been investigated. The results show that the coat protein folding and assembly are concerted events in the assembly of PhMV
Comparison of the Nucleotide Sequences of Cucumber Mosaic Virus and Brome Mosaic Virus
No full textCucumber mosaic virus (CMV) and brome mosaic virus (BMV) are isometric plant viruses. Although biologically distinct, they share many common chemical properties. An analysis of the partial genomic RNA sequence available for these two viruses reveals that they are evolutionarily related. Different segments of the genome exhibit different evolutionary rates. The coat proteins, which serve as carriers of genetic material, possess little or no homology. In contrast, the 3a proteins show over 35% homology. The non-coding regions of the genome also exhibit extensive but variable homology suggesting the functional importance of the nucleic acid
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Analysis of the effects of amino-acid-sequence on the structure of proteins
No full textThe conformation of amino acid side chains as observed in well-determined structures of globular proteins has earlier been extensively investigated. In contrast, the structural features of the polypeptide backbone that result from the occurrence of specific amino acids along the polypeptide have not been analysed. In this article, we present the statistically significant features in the backbone geometry that appear to be a consequence of the occurrence of rotamers of different amino acid side chains by analysing 102 well-refined structures that form a random collection of proteins. It is found that the persistence of helical segments around each residue is influenced by the residue type. Several residues exert asymmetrical influence between the carboxyl and amino terminal polypeptide segments. The degree to which secondary structures depart from an average geometry also appears to depend on residue type. These departures are correlated to the corresponding Chou and Fasman parameters of amino acid residues. The frequency distribution of the side chain rotamers is influenced by polypeptide secondary structure. In turn, the rotamer conformation of side chain affects the extension of the secondary structure of the backbone. The strongest correlation is found between the occurrence of g+ conformation and helix propagation on the carboxyl side of many residues
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