Importance of long-time simulations for rare event sampling in zinc finger proteins

Molecular dynamics (MD) simulation methods have seen significant improvement since their inception in the late 1950s. Constraints of simulation size and duration that once impeded the field have lessened with the advent of better algorithms, faster processors, and parallel computing. With newer techniques and hardware available, MD simulations of more biologically relevant timescales can now sample a broader range of conformational and dynamical changes including rare events. One concern in the literature has been under which circumstances it is sufficient to perform many shorter timescale simulations and under which circumstances fewer longer simulations are necessary. Herein, our simulations of the zinc finger NEMO (2JVX) using multiple simulations of length 15, 30, 1000, and 3000 ns are analyzed to provide clarity on this point.     

THE BINDING OF 5-HYDROXYTRYPTAMINE TO BUTANOL EXTRACTS OF RAT BRAIN STEM

Abstract— When butanol-water extracts of rat brain stem were incubated with [³H]5-HT, (5 × 10⁻⁷ m ), and the components resolved by chromatography on LH₂₀ Sephadex, a peak representing approximately 70% of the eluted radioactivity was found in chloroform-methanol 4:1. The peak was not found in identically prepared extracts from rat diaphragm, neither was a similar peak found when brain extracts were incubated with [¹⁴C]ACh (10⁻⁶ m ), suggesting a degree of selectivity. Binding was not saturated at concentrations of 5 × 10⁻⁵ m -5-HT. The binding was highly sensitive to the presence of water, requiring about 15% (v/v) for optimum binding. The implications of these findings are discussed in terms of a possible '5-HT receptor'.     

The nucleotide sequence of an unusual non-transcribed spacer and its ancestor in the rDNA in Chironomus thummi.

The nucleotide sequence of the non-transcribed spacer (NTS) in the ribosomal DNA (rDNA) of Chironomus thummi thummi and Chironomus thummi piger, including major parts of the external transcribed spacer, is described. The NTS of the two subspecies are very different in length, (thummi, 7 kb, piger, 2 kb); this is due to the insertion into the NTS of C.th. thummi of a large cluster of highly repetitive DNA sequences which are not present in the NTS of C. th. piger. The repetitive sequences, called Cla elements, are present in high copy number elsewhere in the genome of C. th. thummi and, in lower copy number, in the genome of C. th. piger in which they are mainly in the centromeric regions. Sequencing of the NTS of thummi and piger yielded information on the junctions between the Cla element cluster and the original NTS sequence, as well as on the sequence of the integration site before the transposition has occurred. The integration site is characterized by a dA cluster at the one end and a dT cluster at the other.     

Target highlights in CASP13: Experimental target structures through the eyes of their authors

The functional and biological significance of selected CASP13 targets are described by the authors of the structures. The structural biologists discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP13 experiment.     

Conservative repair of a chromosomal double-strand break by single-strand DNA through two steps of annealing

The repair of chromosomal double-strand breaks (DSBs) is essential to normal cell growth, and homologous recombination is a universal process for DSB repair. We explored DSB repair mechanisms in the yeast Saccharomyces cerevisiae using single-strand oligonucleotides with homology to both sides of a DSB. Oligonucleotide-directed repair occurred exclusively via Rad52- and Rad59-mediated single-strand annealing (SSA). Even the SSA domain of human Rad52 provided partial complementation for a null rad52 mutation. The repair did not involve Rad51-driven strand invasion, and moreover the suppression of strand invasion increased repair with oligonucleotides. A DSB was shown to activate targeting by oligonucleotides homologous to only one side of the break at large distances (at least 20 kb) from the break in a strand-biased manner, suggesting extensive 5' to 3' resection, followed by the restoration of resected DNA to the double-strand state. We conclude that long resected chromosomal DSB ends are repaired by a single-strand DNA oligonucleotide through two rounds of annealing. The repair by single-strand DNA can be conservative and may allow for accurate restoration of chromosomal DNAs with closely spaced DSBs.     

Multifunctional grains for the future: genetic engineering for enhanced and novel cereal quality

Cereals provide more than half the world population’s calorific intake, and have a variety of other important uses as food and beverage ingredients, livestock feeds, and as sources of renewable energy and industrial components. The technology to genetically modify many important cereals is now well-established, thereby presenting new opportunities to produce cereals with enhanced quality and novel properties. In 2007, GM (genetically modified) maize with insect and herbicide resistance was grown on over 30 million hectares worldwide, yet to date, there are no GM cereals with enhanced or novel grain (end-use) qualities being grown in commercial farmers’ fields. This review will discuss some of the latest GM technology developments reported to enhance the quality of cereals for food and other uses. Developments and opportunities involving gene manipulation for starch and protein quality, as well as non-starch polysaccharides, phenolic compounds and micronutrients will also be discussed. The current paucity of GM cereals with enhanced grain quality is not related to the absence of technological progress, rather it is the regulatory and consumer acceptance issues that have slowed the release of these crops.     

IGFBP-3 Can Either Inhibit or Enhance EGF-mediated Growth of Breast Epithelial Cells Dependent upon the Presence of Fibronectin

Progression of breast cancer is associated with remodeling of the extracellular matrix, often involving a switch from estrogen dependence to a dependence on EGF receptor (EGFR)/HER-2 and is accompanied by increased expression of the main binding protein for insulin-like growth factors (IGFBP-3). We have examined the effects of IGFBP-3 on EGF responses of breast epithelial cells in the context of changes in the extracellular matrix. On plastic and laminin with MCF-10A normal breast epithelial cells, EGF and IGFBP-3 each increased cell growth and together produced a synergistic response, whereas with T47D breast cancer cells IGFBP-3 alone had no effect, but the ability of EGF to increase cell proliferation was markedly inhibited in the presence of IGFBP-3. In contrast on fibronectin with MCF-10A cells, IGFBP-3 alone inhibited cell growth and blocked EGF-induced proliferation. With the cancer cells, IGFBP-3 alone had no effect but enhanced the EGF-induced increase in cell growth. The insulin-like growth factor-independent effects of IGFBP-3 alone on cell proliferation were completely abrogated in the presence of an EGFR, tyrosine kinase inhibitor, Iressa. Although IGFBP-3 did not affect EGFR phosphorylation [Tyr¹⁰⁶⁸], it was found to modulate receptor internalization and was associated with activation of Rho and subsequent changes in MAPK phosphorylation. The levels of fibronectin and IGFBP-3 within breast tumors may determine their dependence on EGFR and their response to therapies targeting this receptor.