Effect of solution viscosity on intramolecular electron transfer in sulfite oxidase

Our previous studies have shown that the rate constant for intramolecular electron transfer (IET) between the heme and molybdenum centers of chicken liver sulfite oxidase varies from approximately 20 to 1400 s(-1) depending upon reaction conditions [Pacheco, A., Hazzard, J. T., Tollin, G., and Enemark, J. H. (1999) J. Biol. Inorg. Chem. 4, 390-401]. These two centers are linked by a flexible polypeptide loop, suggesting that conformational changes, which alter the Mo-Fe distance, may play an important role in the observed IET rates. In this study, we have investigated IET in sulfite oxidase using laser flash photolysis as a function of solution viscosity. The solution viscosity was varied over the range of 1.0-2.0 cP by addition of either polyethylene glycol 400 or sucrose. In the presence of either viscosogen, an appreciable decrease in the IET rate constant value is observed with an increase in the solvent viscosity. The IET rate constant exhibits a linear dependence on the negative 0.7th power of the viscosity. Steady-state kinetics and EPR experiments are consistent with the interpretation that viscosity, and not other properties of the added viscosogens, is responsible for the dependence of IET rates on the solvent composition. The results are consistent with the role of conformational changes on IET in sulfite oxidase, which helps to clarify the inconsistency between the large rate constant for IET between the Mo and Fe centers and the long distance (approximately 32 A) between these two metal centers observed in the crystal structure [Kisker, C., Schindelin, H., Pacheco, A., Wehbi, W., Garnett, R. M., Rajagopalan, K. V., Enemark, J. H., and Rees, D. C. (1997) Cell 91, 973-983].     

The hand, foot and mouth disease virus capsid: sequence analysis and prediction of antigenic sites from homology modelling

Enterovirus 71 (EV71) is the most common aetiological agent detected in cases of hand, foot and mouth disease (HFMD) resulting in incidences of neurological complications and fatality in recent years. A comparison of the capsid proteins implicated in the pathogenicity of the fatal and non-fatal strains of EV71, reveals a high degree of homology (93%-100% identity). To facilitate diagnostic immunoassays and vaccine development, a consensus structural model for the EV71 coat protein has been developed based primarily on the homologous structure of the bovine enterovirus. The overall architecture of the virion closely resembles those of related icosahedral picornaviruses. Detailed atomic modelling of the fatal 5865/SIN/00009 strain has been carried out, and the functional regions (known and predicted) from closely related viruses mapped onto the surface of the predicted structure. From the model, we have identified two putative immunogenic regions, one of which is unique to EV71. The hydrophobic pocket within VP1, found in bovine enterovirus, poliovirus and rhinovirus, is also conserved in EV71.     

APBioNet: the Asia-Pacific regional consortium for bioinformatics

Bioinformatics and computational biology, along with the related fields of genomics, proteomics, functional genomics and systems biology are new wave scientific disciplines that harness composite computational power across networks to advance biological knowledge at the most basic level and to direct traditional laboratory-based research efforts in the biomedical sciences. 'Fostering the growth of bioinformatics and allied disciplines in the Asia-Pacific region' is the motto of the first regional bioinformatics society, the Asia-Pacific Bioinformatics Network (APBioNet). APBioNet addresses the issues of hardware, software, databases and networks pertaining to bioinformatics, with the additional layer of pertinent education, training and research. Recent milestones achieved include hosting an international bioinformatics symposium in Asia and setting up large-scale regional grid-computing projects.     

Correction: Revised molecular phylogeny,global biogeography,and diversification of palms subfamily Coryphoideae (Arecaceae) based on low copy nuclear and plastid regions

Coryphoideae are palmate-leaved palms from the family Arecaceae consisting of 46 genera representing 421 species. Although several phylogenetic analyses based on different genomic regions have been carried out on Coryphoideae, a fully resolved molecular phylogenetic tree has not been reported yet. To achieve this, we applied two phylogenetic reconstruction methods: Maximum Likelihood and Bayesian Inference, using amplified sampling by retrieving chloroplast and nuclear DNA sequences from NCBI and adding newly produced sequences from Indian accession into the dataset. The same dataset (chloroplast + nuclear DNA sequences) was used to estimate divergence times and the evolutionary history of Coryphoideae with a Bayesian uncorrelated, lognormal relaxed-clock approach and a Statistical Divergence-Vicariance Analysis method, respectively. The phylogenetic analyses based on a combined chloroplast and nuclear DNA sequence dataset showed well-resolved relationships within the subfamily. Both phylogenetic trees divide Coryphoideae into two main groups: CSPT (Crysophileae, Sabaleae, Phoeniceae, and Trachycarpeae) and the Syncarpous group. These main groups are segregated into eight tribes (Trachycarpeae, Phoeniceae, Sabaleae, Crysophileae, Borasseae, Corypheae, Caryoteae, and Chuniophoeniceae) and four subtribes (Rhapidine, Livistoninae, Hyphaeninae, and Lataniinae) with strong support-values. Most previously unresolved and doubtful relationships within tribes Trachycarpeae and Crysophilieae are now resolved and well-supported. The reconstructed phylogenetic trees support all previous systematic revisions of the subfamily. All Indian sampled species of Arenga, Bentinckia, Hyphaene, and Trachycarpus show close relation with their respective congeneric species. Molecular dating results and integration of biogeography suggest that Coryphoideae originated in Laurasia at ~95.12 Ma and then diverged into the tropical and subtropical regions of the whole world. This study offers the correct combination of nuclear and plastid regions to test the current and future systematic revisions.

     

Synthesis and biological characterization of novel hybrid 7-[[2-(4-phenyl-piperazin-1-yl)-ethyl]-propyl-amino]-5,6,7,8-tetrahydro-naphthalen-2-ol and their heterocyclic bioisosteric analogues for dopamine D2 and D3 receptors

In a recent preliminary communication we described the development of a series of hybrid molecules for the dopamine D2 and D3 receptor subtypes. The design of these compounds was based on combining pharmacophoric elements of aminotetralin and piperazine molecular fragments derived from known dopamine receptor agonist and antagonist molecules. Molecules developed from this approach exhibited high affinity and selectivity for the D3 receptor as judged from preliminary [(3)H]spiperone binding data. In this report, we have expanded our previous finding by developing additional novel molecules and additionally evaluated functional activities of these novel molecules in the [(3)H]thymidine incorporation mitogenesis assay. The binding results indicated highest selectivity in the bioisosteric benzothiazole derivative N6-[2-(4-phenyl-piperazin-1-yl)-ethyl]-N6-propyl-4,5,6,7-tetrahydro-benzothiazole-2,6-diamine (14) for the D3 receptor whereas the racemic compound 7-([2-[4-(2,3-dichloro-phenyl)-piperazin-1-yl]-ethyl]-propyl-amino)-5,6,7,8-tetrahydro-naphthalen-2-ol (10c) showed the strongest potency. Mitogenesis studies to evaluate functional activity demonstrated potent agonist properties in these novel derivatives for both D2 and D3 receptors. In this regard, compound 7-[[4-(4-phenyl-piperazin-1-yl)-butyl]-prop-2-ynyl-amino]-5,6,7,8-tetrahydro-naphthalen-2-ol (7b) exhibited the most potent agonist activity at the D3 receptor, 10 times more potent than quinpirole and was also the most selective compound for the D3 receptor in this series. Racemic compound 10a was resolved; however, little separation of activity was found between the two enantiomers of 10a. The marginally more active enantiomer (-)-10a was examined in vivo using the 6-OH-DA induced unilaterally lesioned rat model to evaluate its activity in producing contralateral rotations. The results demonstrated that in comparison to the reference compound apomorphine, (-)-10a was quite potent in inducing contralateral rotations and exhibited longer duration of action.