PubMed Health⌕ Search

Biomedical subjects

Richard Greaves

Publications and source records attributed to Richard Greaves.

2 recordsLinked to original sources

Autorepression of the human cytomegalovirus major immediate-early promoter/enhancer at late times of infection is mediated by the recruitment of chromatin remodeling enzymes by IE86.

The human cytomegalovirus major immediate-early protein IE86 is pivotal for coordinated regulation of viral gene expression throughout infection. A relatively promiscuous transactivator of viral early and late gene transcription, IE86 also acts during infection to negatively regulate its own promoter via direct binding to a 14-bp palindromic IE86-binding site, the cis repression sequence (crs), located between the major immediate-early promoter (MIEP) TATA box and the start of transcription. Although such autoregulation does not involve changes in the binding of basal transcription factors to the MIEP in vitro, it does appear to involve selective inhibition of RNA polymerase II recruitment. However, how this occurs is unclear. We show that autorepression by IE86 at late times of infection correlates with changes in chromatin structure around the MIEP during the course of infection and that this is likely to result from physical and functional interactions between IE86 and chromatin remodeling enzymes normally associated with transcriptional repression of cellular promoters. Firstly, we show that IE86-mediated autorepression is inhibited by histone deacetylase inhibitors. We also show that IE86 interacts, in vitro and in vivo, with the histone deacetylase HDAC1 and histone methyltransferases G9a and Suvar(3-9)H1 and that coexpression of these chromatin remodeling enzymes with IE86 increases autorepression of the MIEP. Finally, we show that mutation of the crs in the context of the virus abrogates the transcriptionally repressive chromatin phenotype normally found around the MIEP at late times of infection, suggesting that negative autoregulation by IE86 results, at least in part, from IE86-mediated changes in chromatin structure of the viral MIEP.

Blotting, Western↗

Active site identification through geometry-based and sequence profile-based calculations: burial of catalytic clefts.

Electrostatics calculations with proteins that are uniformly charged over volume can aid enzyme/non-enzyme discrimination. For known enzymes, such methods locate active sites to within 5% on the enzyme surface, in 77% of a test set. We now report that removing the dielectric boundary improves active site location to 80%, with optimal discrimination between enzymes and non-enzymes of around 80% specificity and 80% sensitivity. This calculation quantifies burial of solvent-accessible regions. Many of the true enzymes incorrectly assigned as non-enzymes have active sites at subunit boundaries. These are missed in monomer-based calculations. Catalytic and non-catalytic antibodies are studied in this context of active/binding site burial. Whilst catalytic antibodies, on average, have marginally higher active site burial than non-catalytic antibodies, these values are generally smaller than for non-antibody enzymes, possibly contributing to their relatively low turnover. Prediction of active site location improves further when sequence profile-based weights replace the uniform charge distribution, so that a combination of burial and amino acid conservation is assessed. Accuracy rises to 93% of active sites to within 5%, in the test set, for the optimal profile weights scheme. The equivalent value in a separate validation set is 89% to within 5%. Enzyme/non-enzyme and enzyme functional site predictions are made for structural genomics proteins, suggesting that a substantial majority of these are non-enzymes.

Antibodies↗