RESUMEN
Quadruple bonding is uncommon for main group elements and the identification of species forming such bonds is remarkably interesting particularly in diatomic anions for which there is a lack of information. Here, it is found that the MX- anions, TcN- , RuC- , RhB- , and PdBe- , present quadruple bonding, as do the corresponding MX neutrals, even though a different type of σ2 bond is involved in ∑+ states of neutral and anions. Specifically, the ground states (X2 Δ or X2 ∑+ ) of the four anions and their first excited states (A2 ∑+ or A2 Δ) of TcN- , RuC- , and RhB- present quadruple bonds consisting of two σ and two π bonds: (4dz2 - 2pz )2 , 5pz 0 â 2s2 , (4dxz - 2px )2 , and (4dyz - 2py )2 . Bond lengths, dissociation energies, spectroscopic data and electron affinities were calculated via high-level multireference and coupled-cluster methodology using the aug-cc-pV5ZX (-PP)M basis set. Strong bonding results in short bond lengths ranging from 1.602 (TcN- ) to 1.944 (PdBe- ) Å. Adiabatic (diabatic) binding energies reach up to 139 (184) kcal/mol. Electron affinities (EA) were calculated at 1.368 (TcN), 1.242 (RuC), 0.873 (RhB), 0.743 (PdBe) eV. Only for RhB has EA been measured experimentally at 0.961 eV, in good agreement with the value reported here.
RESUMEN
The dramatic increase in the number of protein sequences and structures deposited in biological databases has led to the development of many bioinformatics tools and programs to manage, validate, compare, and interpret this large volume of data. In addition, powerful tools are being developed to use this sequence and structural data to facilitate protein classification and infer biological function of newly identified proteins. This chapter covers freely available bioinformatics resources on the World Wide Web that are commonly used for protein structure analysis.
Asunto(s)
Biología Computacional/métodos , Modelos Moleculares , Conformación Proteica , Proteínas/química , Programas Informáticos , Bases de Datos de Proteínas , Ligandos , Unión Proteica , Reproducibilidad de los Resultados , Relación Estructura-Actividad , Interfaz Usuario-Computador , Navegador WebRESUMEN
Web-based protein structure databases come in a wide variety of types and levels of information content. Those having the most general interest are the various atlases that describe each experimentally determined protein structure and provide useful links, analyses, and schematic diagrams relating to its 3D structure and biological function. Also of great interest are the databases that classify 3D structures by their folds as these can reveal evolutionary relationships which may be hard to detect from sequence comparison alone. Related to these are the numerous servers that compare folds-particularly useful for newly solved structures, and especially those of unknown function. Beyond these are a vast number of databases for the more specialized user, dealing with specific families, diseases, structural features, and so on.
Asunto(s)
Bases de Datos de Proteínas , Proteínas/química , Sitios de Unión , Sistemas de Computación , Evolución Molecular , Internet , Modelos Moleculares , Unión Proteica , Conformación Proteica , Pliegue de ProteínaRESUMEN
The Protein Data Bank in Europe (PDBe) has developed web-based tools for the visualisation and analysis of 3D electron microscopy (3DEM) structures in the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB). The tools include: (1) a volume viewer for 3D visualisation of maps, tomograms and models, (2) a slice viewer for inspecting 2D slices of tomographic reconstructions, and (3) visual analysis pages to facilitate analysis and validation of maps, tomograms and models. These tools were designed to help non-experts and experts alike to get some insight into the content and assess the quality of 3DEM structures in EMDB and PDB without the need to install specialised software or to download large amounts of data from these archives. The technical challenges encountered in developing these tools, as well as the more general considerations when making archived data available to the user community through a web interface, are discussed.
Asunto(s)
Bases de Datos de Proteínas , Programas Informáticos , Tomografía con Microscopio Electrónico , Imagenología Tridimensional , Internet , Modelos Moleculares , Estructura Cuaternaria de Proteína , Proteínas/química , Proteínas/ultraestructuraRESUMEN
The history and the current state of the PDB and EMDB archives is briefly described, as well as some of the challenges that they face. It seems natural that the role of structural biology archives will change from being a pure repository of historic data into becoming an indispensable resource for the wider biomedical community. As part of this transformation, it will be necessary to validate the biomacromolecular structure data and ensure the highest possible quality for the archive holdings, to combine structural data from different spatial scales into a unified resource and to integrate structural data with functional, genetic and taxonomic data as well as other information available in bioinformatics resources. Some recent developments and plans to address these challenges at PDBe are presented.