Despite many years of genetic and biochemical studies on the integrase (Int) recombination system, it is still not known whether the Int protein is competent for DNA cleavage as a monomer. We have addressed this question, as part of a larger study of Int functions critical for the formation of higher-order complexes, by isolating ‘‘multimer-specific’’ mutants. We identify a pair of oppositely c...

An increase in Src activity is commonly observed in epithelial cancers. Aberrant activation of the kinase activity is associated with malignant progression. However, the mechanisms that underlie the Src-induced malignant progression of cancer are not completely understood. We show here that v-Src, an oncogene that was first identified from a Rous sarcoma virus and a mutant variant of c-Src, lea...

The Escherichia coli DksA protein inserts into the RNA polymerase (RNAP) secondary channel, modifying the transcription initiation complex so that promoters with specific kinetic characteristics are regulated by changes in the concentrations of ppGpp and NTPs. We used footprinting assays to determine the specific kinetic intermediate, RP(I), on which DksA acts. Genetic approaches identified sub...

Based on molecular dynamics simulations and functional studies, a conformational mechanism is posited for forward translocation by RNA polymerase (RNAP). In a simulation of a ternary elongation complex, the clamp and downstream cleft were observed to close. Hinges within the bridge helix and trigger loop supported generation of translocation force against the RNA-DNA hybrid resulting in opening...

Recent technological advances have enabled many different types of data to be collected at a genome-wide and proteome-wide scale, including: DNA sequence from various genomes, gene expression data, protein-protein and protein-ligand interactions, and protein-DNA binding data. In addition, efforts in structural biology are yielding structural data on proteins, protein complexes, and proteinligan...

Grafts of autologous keratinocytes genetically altered to secrete a new gene product are a potential vehicle for gene therapy. T o consider the feasibility of such an approach, w e have examined the ability of keratinocytes to secrete and deliver apolipoprotein E (apoE) to the circulation of mice bearing grafts of h u m a n keratinocytes. The grafted keratinocytes secreted two forms of apoE, an...

The regulation of chromatin structure in eukaryotic cells involves abundant architectural factors such as high mobility group B (HMGB) proteins. It is not understood how these factors control the interplay between genome accessibility and compaction. In vivo, HMO1 binds the promoter and coding regions of most ribosomal RNA genes, facilitating transcription and possibly stabilizing chromatin in ...

CarD, an essential transcription regulator in Mycobacterium tuberculosis, directly interacts with the RNA polymerase (RNAP). We used a combination of in vivo and in vitro approaches to establish that CarD is a global regulator that stimulates the formation of RNAP-holoenzyme open promoter (RPo) complexes. We determined the X-ray crystal structure of Thermus thermophilus CarD, allowing us to gen...

Past earthquakes have demonstrated that old RC bridges may be seismically vulnerable. Bridge responses during the last decades illustrated the necessity of the seismic assessment of bridges especially those which were designed with old codes. In this research an existing concrete bridge representative of the most common bridges in the highway system in Iran are studied. Push over and nonlinear ...