Novel Druggable Hot Spots in Avian Influenza Neuraminidase H5N1 Revealed by Computational Solvent Mapping of a Reduced and Representative Receptor Ensemble

The influenza virus subtype H5N1 has raised concerns of a possible human pandemic threat because of its high virulence and mutation rate. Although several approved anti-influenza drugs effectively target the neuraminidase, some strains have already acquired resistance to the currently available anti-influenza drugs. In this study, we present the synergistic application of extended explicit solvent molecular dynamics (MD) and computational solvent mapping (CS-Map) to identify putative ‘hot spots’ within flexible binding regions of N1 neuraminidase. Using representative conformations of the N1 binding region extracted from a clustering analysis of four concatenated 40-ns MD simulations, CS-Map was utilized to assess the ability of small, solvent-sized molecules to bind within close proximity to the sialic acid binding region. Mapping analyses of the dominant MD conformations reveal the presence of additional hot spot regions in the 150- and 430-loop regions. Our hot spot analysis provides further support for the feasibility of developing high-affinity inhibitors capable of binding these regions, which appear to be unique to the N1 strain

Towards virtual forensic anthropology: Methodological and practical issues related to the use of clinical computed tomography (CT) data

Most European countries lack contemporary collections and are thus unable to develop or test forensic anthropological methods. Specifically, in the Netherlands, due to legislation and the high mean age of bodies donated to the body donation, compiling a skeletal collection that is representative of the current population in the Netherlands is not a possibility. A solution to the lack of representative skeletal population samples could be the use of clinical radiological data (such as computed tomography (CT) scans) as a proxy for skeletal collections. The data from these scans might be used to build a contemporary virtual skeletal database as the data acquired is of known demographics, representative of a contemporary, residing population, and is immediately available. Ultimately, the success of a virtual skeletal database derived from clinical CT scans, depends greatly on the precise modelling of the virtual bone models from the CT images, and the accuracy with which these models represent their actual dry bone counterparts. This presentation therefore focuses on the use of 3D virtual bone models derived from clinical CT scans, and the precision and accuracy of these models. Precision concerns the reliability of virtual bones models derived from clinical CT scan data, while accuracy assesses how well the virtual bones match the actual dry bones. Since forensic anthropology estimation methods are usually based on morphological (shape) or osteometric (size) features, the accuracy is explored for both these approaches

Towards virtual forensic anthropology:Methodological and practical issues related to the use of clinical computed tomography (CT) data

Most European countries lack contemporary collections and are thus unable to develop or test forensic anthropological methods. Specifically, in the Netherlands, due to legislation and the high mean age of bodies donated to the body donation, compiling a skeletal collection that is representative of the current population in the Netherlands is not a possibility. A solution to the lack of representative skeletal population samples could be the use of clinical radiological data (such as computed tomography (CT) scans) as a proxy for skeletal collections. The data from these scans might be used to build a contemporary virtual skeletal database as the data acquired is of known demographics, representative of a contemporary, residing population, and is immediately available. Ultimately, the success of a virtual skeletal database derived from clinical CT scans, depends greatly on the precise modelling of the virtual bone models from the CT images, and the accuracy with which these models represent their actual dry bone counterparts. This presentation therefore focuses on the use of 3D virtual bone models derived from clinical CT scans, and the precision and accuracy of these models. Precision concerns the reliability of virtual bones models derived from clinical CT scan data, while accuracy assesses how well the virtual bones match the actual dry bones. Since forensic anthropology estimation methods are usually based on morphological (shape) or osteometric (size) features, the accuracy is explored for both these approaches

Characterization of the varicella-zoster virus gene 61 protein

The protein predicted to be encoded by varicella-zoster virus (VZV) gene 61 exhibits limited amino acid sequence similarity to the herpes simplex virus type 1 nuclear phosphoprotein Vmw 110, which functions as a transcriptional activator. The gene 61 protein was expressed in its entirety, or as an amino- or carboxyterminal fragment in Escherichia coli and vaccinia virus recombinants, and monospecific rabbit antisera were raised against an E. coli fusion between fl-galactosidase and the majority of the gene 61 protein. Use of the antisera showed that the gene 61 protein is present in VZV-infected cell nuclei as a heterogeneous phosphoprotein of Mr 62K to 65K. Phosphorylation occurs in the amino- and, to a lesser extent, carboxy-terminal portions of the protein. The carboxy-terminal region directs transport of the protein to the nucleus, whereas the amino-terminal region, which contains a potential zinc-binding domain, is responsible for a punctate distribution. Preliminary mapping data indicated that gene 61 is transcribed as a 1.8 kb mRNA which initiates about 65 bp upstream from the translation initiation codon, at a position located appropriately with respect to potential regulatory elements

Delineation of a sequence required for nuclear localization of the protein encoded by varicella-zoster virus gene 61

All characterized alphaherpesviruses encode a protein whose N-terminal region contains a novel zinc-binding motif, the CaHC 4 domain. Homology between the different proteins is in general limited to key residues in this domain. In order to identify a separate landmark site in the C<sub>3</sub>HC<sub>4</sub> protein encoded by varicella-zoster virus gene 61, namely the region required for nuclear localization, we have analysed a range of mutants in transient expression and immunofluorescence experiments. A basic region (RGAKRR) at residues 387 to 392 was found to be required for nuclear localization, and residues 390 and 391 were critical

Characterization of the putative protein kinases specified by varicella-zoster virus genes 47 and 66

The proteins predicted to be encoded by varicella-zoster virus (VZV) genes 47 and 66 display sequence similarity to the serine/threonine family of protein kinases. Homologues ofgene 47 exist in c~-, fl- and ~-herpesviruses but homologues of gene 66 are specific to the ~- herpesviruses. Monospecific rabbit antisera were raised against two separate fusion proteins constructed from a portion of each protein fused to the carboxy terminus of fl-galactosidase. These antisera were used to characterize the 47 and 66 proteins in VZV-infected cells and in cells infected with vaccinia virus recombinants expressing each protein. The 47 protein is a 54K phosphoprotein which is distributed between the cytoplasmic and nuclear compartments of VZV-infected cells and is associated with the capsid/tegument fraction of purified VZV particles. Gene 66 encodes a 48K phosphoprotein when expressed by VZV or a vaccinia virus recombinant, and, in the latter case, the 66 protein was located exclusively in the cytoplasm. The 47 protein immunoprecipitated from VZV-infected cells could be phosphorylated in vitro, but the same protein produced by in vitro transcription and translation could not. This and other evidence indicates that additional proteins induced or encoded by VZV may be involved in the phosphorylation of the 47 protein

The impact of executive functions on verb production in patients with Parkinson's disease

A growing number of studies suggest that language problems in Parkinson's disease (PD) are a result of executive dysfunction. To test this hypothesis we compared Dutch verb production in sentence context in a group of 28 PD patients with a control group consisting of 28 healthy participants matched for age, gender and education. All subjects were assessed on both verb production in sentence context as well as on cognitive functions relevant for sentence processing. PD patients scored lower than healthy controls on the verb production ability-scale and showed a response pattern in which performance was worse (1) in base than in derived position; (2) in present than in past tense; (3) for intransitive than in transitive verbs. For the PD group the score on the verb production ability-scale correlated significantly with set-switching and working memory. These results provide support for previous research suggesting that executive dysfunctions underlie the performance of the PD patients on verb production. It is furthermore suggested that because of failing automaticity, PD patients rely more on the cortically represented executive functions. Unfortunately, due to the disturbed intimate relation between the basal ganglia and the frontal cortex, these executive functions are also dysfunctional. (C) 2009 Elsevier Srl. All rights reserved