NMR study of the phosphate-binding elements of Escherichia coli elongation factor Tu catalytic domain

Force-Induced Insulin Dimer Dissociation: A Molecular Dynamics Study

Understanding the forces and dynamics of insulin dissociation is critical for devising formulations for the treatment of insulin-dependent diabetes. In earlier work, we applied AFM-based force spectroscopy to covalently tethered and oriented insulin monomers to assess the effect of molecular orientation on insulin-insulin binding forces. We report here on steered molecular dynamics simulations of the insulin dissociation force spectroscopy experiment. Consistent with our experiments, our simulation results suggest that insulin dimer dissociation occurs near the limit of extensibility of the B-chain. We have also found that the forced dissociation of the insulin dimer is a rate-dependent process, involving significant conformational changes to the monomer(s). The insulin dimer dissociation pathway also depends on the relative strength of the inter-monomer interactions across the antiparallel beta-sheet interface and the intra-monomer interactions of residues A1 and A30 with the insulin B-chain. Our simulation results strongly support the design of bioactive insulin analogues that involves altering hydrogen bonding and hydrophobic interactions across the beta-sheet dimer interface.

Mechanisms of EF-Tu, a pioneer GTPase

This review considers several aspects of the function of EF-Tu, a protein that has greatly contributed to the advancement of our knowledge of both protein biosynthesis and GTP-binding proteins in general. A number of topics are described with emphasis on the function-structure relationships, in particular of EF-Tu's domains, the nucleotide-binding site, and the magnesium-binding network. Aspects related to the interaction with macromolecular ligands and antibiotics and to folding and GTPase activity are also presented and discussed. Comments and criticism are offered to draw attention to remaining discrepancies and problems.

Messenger RNA translation in prokaryotes: GTPase centers associated with translational factors

During the decoding of messenger RNA, each step of the translational cycle requires the intervention of protein factors and the hydrolysis of one or more GTP molecule(s). Of the prokaryotic translational factors, IF2, EF-Tu, SELB, EF-G and RF3 are GTP-binding proteins. In this review we summarize the latest findings on the structures and the roles of these GTPases in the translational process.

Effects of insertions and deletions in glnG (ntrC) of Escherichia coli on nitrogen regulator I-dependent DNA binding and transcriptional activation

Phosphorylated nitrogen regulator I (NRI, also called NTRC), encoded by glnG (ntrC), stimulates transcription in Escherichia coli and other enteric bacteria from sites analogous to eukaryotic enhancers. We isolated 30 mutants, obtained without phenotypic selection, that have either a small insertion or deletion within glnG. Mutants were classified by the ability of NRI to repress the glnAp1 and glnL promoters and to activate two versions of the nitrogen-regulated glnAp2 promoter; each activity was measured in cells grown with three concentrations of NRI. The results were interpreted within the framework of the three-domain hypothesis of NRI structure. NRI is thought to contain a phosphorylated regulatory domain that controls binding of ATP, a central domain that hydrolyzes ATP and interacts with RNA polymerase, and a DNA-binding region of unknown extent. Our results suggest that the 70 amino acids from residue 400 to the carboxyl terminus constitute a DNA-binding domain that includes residues for specific contacts and dimerization. Our results also suggest that (i) transcription from glnAp2 without specific NRI-binding sites requires binding to sites with some similarity to the specific sites, and (ii) if an NRI variant can stimulate transcription, then increasing the concentration of NRI diminishes glnA expression for all mutants but one.

Elongation factor Tu: a molecular switch in protein biosynthesis

Elongation factor Tu (EF-Tu), the most abundant protein in Escherichia coli, is a guanine nucleotide-binding protein that in the 'on' state acts as a carrier of amino acyl-tRNA to the ribosome. Our knowledge of this essential component of translation has brought substantial progress in the past decade thanks to the co-ordinated application of biochemical, physico-chemical and genetic methods. Crystallographic analysis at 2.6 A resolution and site-directed mutagenesis have revealed structural and functional similarities between the guanine nucleotide-binding domains of EF-Tu and human H-ras p21 protein. The regulation of the expression of the two EF-Tu-encoding genes in E. coli, particularly that of tufB, has been shown to involve diverse mechanisms. Several aspects of the functions of EF-Tu in the elongation cycle have been reinvestigated, leading to new insights. These studies have emphasized the manifold aspects of the mechanisms regulating the activity of EF-Tu in the bacterial cell.