A state-independent interaction between ligand and a conserved arginine residue in cyclic nucleotide-gated channels reveals a functional polarity of the cyclic nucleotide binding site

Activation of cyclic nucleotide-gated channels is thought to involve two distinct steps: a recognition event in which a ligand binds to the channel and a conformational change that both opens the channel and increases the affinity of the channel for an agonist. Sequence similarity with the cyclic nucleotide-binding sites of cAMP- and cGMP-dependent protein kinases and the bacterial catabolite activating protein (CAP) suggests that the channel ligand binding site consists of a beta-roll and three alpha-helices. Recent evidence has demonstrated that the third (or C) alpha-helix moves relative to the agonist upon channel activation, forming additional favorable contacts with the purine ring. Here we ask if channel activation also involves structural changes in the beta-roll by investigating the contribution of a conserved arginine residue that, in CAP and the kinases, forms an important ionic interaction with the cyclized phosphate of the bound ligand. Mutations that conserve, neutralize, or reverse the charge on this arginine decreased the apparent affinity for ligand over four orders of magnitude but had little effect on the ability of bound ligand to open the channel. These data indicate that the cyclized phosphate of the nucleotide approaches to within 2-4 A of the arginine, forming a favorable ionic bond that is largely unaltered upon activation. Thus, the binding site appears to be polarized into two distinct structural and functional domains: the beta-roll stabilizes the ligand in a state-independent manner, whereas the C-helix selectively stabilizes the ligand in the open state of the channel. It is likely that these distinct contributions of the nucleotide/C-helix and nucleotide/beta-roll interactions may also be a general feature of the mechanism of activation of other cyclic nucleotide-binding proteins.     

The role of negative superhelicity and length of homology in the formation of paranemic joints promoted by RecA protein

Escherichia coli RecA protein pairs homologous DNA molecules to form paranemic joints when there is an absence of a free end in the region of homologous contact. Paranemic joints are a key intermediate in homologous recombination and are important in understanding the mechanism for a search of homology. The efficiency of paranemic joint formation depended on the length of homology and the topological forms of the duplex DNA. The presence of negative superhelicity increased the pairing efficiency and reduced the minimal length of homology required for paranemic joint formation. Negative superhelicity stimulated joint formation by favoring the initial unwinding of duplex DNA that occurred during the homology search and was not essential in the maintenance of the paired structure. Regardless of length of homology, formation of paranemic joints using circular duplex DNA required the presence of more than six negative supercoils. Above six negative turns, an increasing degree of negative superhelicity resulted in a linear increase in the pairing efficiency. These results support a model of two distinct kinds of DNA unwinding occurring in paranemic joint formation: an initial unwinding caused by heterologous contacts during synapsis and a later one during pairing of the homologous molecules.     

A six-domain structural model for Escherichia coli translation initiation factor IF2. Characterisation of twelve surface epitopes

The Escherichia coli translation initiation factor IF2 is a 97 kDa protein which interacts with the initiator fMet-tRNAfMet, GTP and the ribosomal subunits during initiation of protein biosynthesis. For structural and functional investigations of the factor, we have raised and characterised monoclonal antibodies against E. coli IF2. Twelve epitopes have been localised at the surface of the protein molecule by three different methods: Interactions of the monoclonal antibodies with nested deletion mutants of IF2, comparison of the relative location of the epitopes in a competition immunoassay and cross-reactivity analyses of the monoclonal antibodies towards IF2 from Salmonella typhimurium, Klebsiella oxytoca, Enterobacter cloacae, Proteus vulgaris, and Bacillus stearothermophilus. These data are combined with predicted secondary structure and discussed in relation to a six-domain structural model for IF2. The model describes IF2 as a slightly elongated molecule with a structurally compact C-terminal domain, a well-conserved central GTP-binding domain, and a highly charged, solvent exposed N-terminal with protruding alpha-helical structures.     

Nutritional influences on bone mineral density: a cross-sectional study in premenopausal women

The association between current and past dietary intake and bone mineral density (BMD) was investigated in 994 healthy premenopausal women aged 45-49 y. BMD was measured with dual-energy X-ray absorptiometry (DXA). Dietary intake was assessed with a food-frequency questionnaire (FFQ). Energy-adjusted nutrient intakes were grouped into quartiles and mean BMD at the lumbar spine (LS), femoral neck (FN), femoral trochanter (FT), and femoral Wards (FW) were calculated. With higher intakes of zinc, magnesium, potassium, and fiber, LS BMD was significantly higher (P < 0.05-0.006), and a significant difference in LS BMD was also found between the lowest and highest quartiles for these nutrients and vitamin C intake (P < 0.05-0.01). These results remained significant after adjustment for important confounding factors. LS BMD and FT BMD were lower in women reporting a low intake of milk and fruit in early adulthood than in women with a medium or high intake (P < 0.01). High, long-term intake of these nutrients may be important to bone health, possibly because of their beneficial effect on acid-base balance.     

Induction of microsomal epoxide hydrolase activity in inbred mice by chronic phenytoin exposure

A lower microsomal epoxide hydrolase (mEH) activity has been associated with increased likelihood of fetal hydantoin syndrome. While phenytoin anticonvulsive regimens are long-term, there are no data regarding induction of mEH by chronic phenytoin exposure. Two inbred mouse strains which differ in their susceptibility (A/J > C57BL/6J) to phenytoin-induced oral clefting were treated with an oral gavage of phenytoin for 14 consecutive days. The mice were sacrificed on the 15th day, and hepatic microsomes were prepared. mEH activity was determined using benzo[a]pyrene-4,5-oxide. The dihydrodiol product was separated by HPLC and quantified. There was no significant difference (P = 0.15) in the phenytoin plasma level between the two strains on Day 15. There was no significant difference (P = 0.07) between control and sham control groups within each strain, so they were combined for further analysis. There was a significant strain difference (P = 0.0001) between the control and phenytoin-exposed group means, with the C57BL/6J strain having the greater activity before and after phenytoin exposure. The A/J phenytoin-exposed group activity was 51% higher (P = 0.01) than the A/J control, while the C57BL/6J phenytoin-exposed group activity was 78% higher (P = 0.001) than the C57BL/6J control. The greater mEH activity in the phenytoin-induced clefting resistant strain (C57BL/6J) before and after phenytoin exposure is consistent with a putative oxidative metabolism mechanism of phenytoin teratogenecity. Chronic phenytoin exposure induced mEH activity in both strains, although the strain with the greater enzyme activity prior to the exposure continued to have the greater activity following induction.     

Simple, inexpensive computerized rodent activity meters

We describe two approaches for using obsolescent computers, either an IBM PC XT or an Apple Macintosh Plus, to accurately quantify spontaneous rodent activity, as revealed by continuous monitoring of the spontaneous usage of running activity wheels. Because such computers can commonly be obtained at little or no expense, and other commonly available materials and inexpensive parts can be used, these meters can be built quite economically. Construction of these meters requires no specialized electronics expertise, and their software requirements are simple. The computer interfaces are potentially of general interest, as they could also be used for monitoring a variety of events in a research setting.