1,355,694 research outputs found
Particle filters for the magnetoencephalography inverse problem: Increasing the efficiency through a semi-analytic approach (Rao-Blackwellization)
No full textA Rao-Blackwellized particle filter for magnetoencephalography
No full textA Rao-Blackwellized particle filter for the tracking of neural sources from biomagnetic data is described. A comparison with a Sampling Importance Re-sampling particle filter performed in the case of both simulated and real data shows that the use of Rao-Blackwellization is highly recommended since it produces more accurate reconstructions within a lower computational effor
A databank (3D_ALI) collecting related protein sequences and structures
No full textAn updated version of the 3D_ali databank (Pascarella and
Argos, 1992) was constructed to incorporate new protein
structural and sequence data acquired since the original release
in 1992. The databank has proved useful in many research
fields, such as protein sequence and structure analysis and
comparison, protein folding, engineering and design, evolution,
and the like. The collection enhances present protein structural
knowledge by merging information from proteins having a
similar main-chain fold with homologous primary structures
taken from large databases of known sequences. However, the
construction philosophy of the databank has been modified.
Originally, the Protein Data Bank (PDB; Bernstein et al,
1977) of known 3-D structures was exhaustively scanned for
fold redundancy, and all the possible unique structures were
incorporated either in multiple structural alignment files or in
those containing only one structure where no relatives could
be detected. The tertiary structural superpositioning of the
backbones, which yielded spatial and topological Co atom
equivalencing and thus corresponding sequence alignments,
was mostly taken from the literature, but was sometimes
determined by the authors using the Rossman-Argos superposition
technique (Argos and Rossmann, 1979). In the updated
3D_ali databank, only published alignments based on superpositioning
by the authors of the tertiary structures were
collected and only folds with more than one sample structure
were considered. Different literature alignments were also
merged if they included common folds. As in the former
release, only full coordinate sets with assigned side chains
were included, while NMR structures, excluded in the 1992
release, are now incorporated
Cofactor binding as protein stability determinant in psychrophilic SHMT
No full textCofactor binding as protein stability determinant in psychrophilic SHMT
Sebastiana Angelaccio, Angela di Bello and Stefano Pascarella
Department of Biochemical Sciences “A. Rossi-Fanelli”, “La Sapienza”-University of Rome
[email protected]
Serine hydroxymethyltransferase (SHMT) is a pyridoxal-5’-phosphate (PLP)-dependent enzyme, which belongs to the fold type I superfamily and catalyzes the reversible conversion of L-serine and tetrahydropteroylglutamate (H4PteGlu) to glycine and 5,10-methylenetetrahydropteroylglutamate (5,10-CH2-H4PteGlu). This enzyme represents a good model for analyzing the intricate relationships between activity and stability, since it is ubiquitous in nature and is structurally conserved because of its critical metabolic role. The SHMT from the psychrophilic bacterium Psychromonas ingrahamii (piSHMT) was recently purified, characterized and its apo form crystallized. This enzyme displays interesting catalytic and stability properties similar to those often found in psychrophilic enzymes. The piSHMT is a more efficient biocatalyst compared to E. coli SHMT (eSHMT), in particular for the side reactions where many substrates, tipically -hydroxy--amino acids, represent important compounds in pharmaceuticals, agrochemicals and food additives. piSHMT activity is heat labile and the apparent melting temperature of the protein is 62 °C, lower than of the eSHMT. Interestingly, the difference of the apparent Tm values between the apoenzyme and the holoenzyme is about 20 degrees. Comparative analysis between the structure of the apo form and the homology modelled holo form suggests possible explanations of the strong cofactor stabilization effect on the structure of the piSHMT
Particle filtering, beamforming and multiple signal classification for the analysis of magnetoencephalography time series: A comparison of algorithms
No full text(Communicated by the associate editor name) Abstract. We present a comparison of three methods for the solution of the magnetoencephalography inverse problem. The methods are: a linearly con-strained minimum variance beamformer, an algorithm implementing multiple signal classification with recursively applied projection and a particle filter for Bayesian tracking. Synthetic data with neurophysiological significance are an-alyzed by the three methods to recover position, orientation and amplitude of the active sources. Finally, a real data set evoked by a simple auditory stimulus is considered. 1
Structural analysis of toxic volkensin, a type 2 ribosome inactivating protein from Adenia volkensii Harm (kilyambiti plant): Molecular modeling and surface analysis by computational methods and limited proteolysis
No full textVolkensin, isolated from Adenia volkensii, is one of the most toxic type 2 ribosome-inactivating protein (RIP), exerting its biological function by inhibiting protein synthesis. Despite the high sequence identity with type 2 RIPs, including ricin, volkensin shows interesting peculiar properties. In this work a computational model building of volkensin was performed. The volkensin electrostatic potential charge distribution, the hydrophobic profile and the surface topology analyses were also carried out to aid the understanding of structure-function relationships of this potent toxin. Volkensin surface topology was probed by applying a limited proteolysis approach with the aim to gain insights into volkensin conformational features. (C) 2009 Elsevier B.V. All rights reserved
Computational classification of MocR transcriptional regulators into subgroups as a support for experimental and functional characterization
No full textMocR bacterial transcriptional regulators are a subfamily within the GntR family. The MocR proteins possess an N-terminal domain containing the winged Helix-Turn-Helix (wHTH) motif and a C-terminal domain whose architecture is homologous to the fold type-I pyridoxal 5'-phosphate (PLP) dependent enzymes whose archetypical protein is aspartate amino transferase (AAT). The ancestor of the fold type-I PLP dependent super-family is considered one of the earliest enzymes. The members of this super-family are the product of evolution which resulted in a diversified protein population able to catalyze a set of reactions on substrates often containing amino groups. The MocR regulators are activators or repressors of gene control within many metabolic pathways often involving PLP enzymes. This diversity implies that MocR specifically responds to different classes of effector molecules. Therefore, it is of interest to compare the AAT domains of MocR from six bacteria phyla. Multi dimensional scaling and cluster analyses suggested that at least three subgroups exist within the population that reflects functional specialization rather than taxonomic origin. The AAT-domains of the three clusters display variable degree of similarity to different fold type-I PLP enzyme families. The results support the hypothesis that independent fusion events generated at least three different MocR subgroups
Approcci metodologici al cambiamento nello sviluppo del governo clinico a livello locale: la metodologia RAID
No full textApprocci metodologici nello sviluppo del governo clinico a livello locale: il ciclo PDSA
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