Unusually stable β-sheet formation in an ionic self-complementary oligopeptide

A 16-residue amphiphilic oligopeptide (EAK16) with every other residue alanine and also containing glutamic acid and lysine (Ac-NH-AEAEAKAKAEAEAKAK-CONH₂) is able to form an unusually stable β-sheet structure. The β-sheet structure is stable at very low concentrations in water and at high temperatures. Various pH changes at 1.5, 3, 7, and 11 had little effect on the stability of the β-sheet structure. The β-sheet structure was not altered significantly even in the presence of 0.1% SDS, 7 molar guanidine hydrochloride, or 8 molar urea. One of the structural characteristics of the EAK16 is its ionic self-complementarity in that ionic bonds and hydrogen bonds between Glu and Lys can form readily between two oligopeptide β-sheet structures. This structural feature is probably one of the factors that promotes its extreme stability. This is the first example of such an extended ionic self-complementarity in a protein structure. EAK16 and its related peptides may have applications as useful biomaterials. It also offers a good model for studying the mechanism of β-sheet formation. Because the oligopeptide can self-assemble to form a membranous structure, it may have relevance to origin of life research. © 1994 John Wiley & Sons, Inc.     

Induction of T cell responses and recruitment of an inflammatory dendritic cell subset following tumor immunotherapy with Mycobacterium smegmatis

Mycobacteria and their cell wall components have been used with varying degrees of success to treat tumors, and Mycobacterium bovis BCG remains in use as a standard treatment for superficial bladder cancer. Mycobacterial immunotherapy is very effective in eliciting local immune responses against solid tumors when administered topically; however, its effectiveness in eliciting adaptive immune responses has been variable. Using a subcutaneous mouse thymoma model, we investigated whether immunotherapy with Mycobacterium smegmatis, a fast-growing mycobacterium of low pathogenicity, induces a systemic adaptive immune response. We found that M. smegmatis delivered adjacent to the tumor site elicited a systemic anti-tumor immune response that was primarily mediated by CD8⁺ T cells. Of note, we identified a CD11c⁺CD40^intCD11b^hiGr-1⁺ inflammatory DC population in the tumor-draining lymph nodes that was found only in mice treated with M. smegmatis. Our data suggest that, rather than rescuing the function of the DC already present in the tumor and/or tumor-draining lymph node, M. smegmatis treatment may promote anti-tumor immune responses by inducing the involvement of a new population of inflammatory cells with intact function.     

The determination of the proton-motive force during cyanide-insensitive respiration in plant mitochondria

The magnitude of the components of the proton-motive force (Δp) generated in the presence of antimycin A has been determined for potato, mung bean, skunk cabbage, and Arum spadix mitochondria, Δp was calculated from the distribution of rubidium, methylamine, and 5,5′-dimethyl-2,4-oxazolodine-dione. In the presence of antimycin A, the oxidation of succinate generates a Δp of 40–50 mV, and this value is independent of the degree of antimycin A insensitivity of the various mitochondria. Under such conditions, the addition of ADP failed to either stimulate the respiratory rate or reduce Δp. Although oxygen consumption via the alternative pathway was sensitive to hydroxamic acids, no change in the components of the proton motive force was detected. The addition of an uncoupler in the presence of antimycin A and succinate reduced Δp to zero while respiration remained unaltered. The oxidation of malate in the presence of antimycin A generates a Δp of 150 mV, which was reduced to 144 mV under State 3 conditions. The addition of salicylhydroxamic acid inhibited oxygen uptake and reduced Δp to 40 mV. It is concluded that the oxidation of succinate by the alternative respiratory pathway does not generate a proton-motive force and is not coupled to ATP synthesis. The oxidation of malate by the alternative pathway, however, can conserve energy as ATP presumably via coupling Site I of the main respiratory chain.     

Chlorproguanil?Dapsone?Artesunate versus Artemether?Lumefantrine: A Randomized,Double-Blind Phase III Trial in African Children and Adolescents with Uncomplicated Plasmodium falciparum Malaria

Background

Chlorproguanil−dapsone−artesunate (CDA) was developed as an affordable, simple, fixed-dose artemisinin-based combination therapy for use in Africa. This trial was a randomized parallel-group, double-blind, double-dummy study to compare CDA and artemether−lumefantrine (AL) efficacy in uncomplicated Plasmodium falciparum malaria and further define the CDA safety profile, particularly its hematological safety in glucose-6-phosphate dehydrogenase (G6PD) -deficient patients.

Methods and Findings

The trial was conducted at medical centers at 11 sites in five African countries between June 2006 and August 2007. 1372 patients (≥1 to <15 years old, median age 3 years) with acute uncomplicated P. falciparum malaria were randomized (2∶1) to receive CDA 2/2.5/4 mg/kg once daily for three days (N = 914) or six-doses of AL over three days (N = 458). Non-inferiority of CDA versus AL for efficacy was evaluated in the Day 28 per-protocol (PP) population using parasitological cure (polymerase chain reaction [PCR]-corrected). Cure rates were 94.1% (703/747) for CDA and 97.4% (369/379) for AL (treatment difference –3.3%, 95%CI –5.6, −0.9). CDA was non-inferior to AL, but there was simultaneous superiority of AL (upper 95%CI limit <0). Adequate clinical and parasitological response at Day 28 (uncorrected for reinfection) was 79% (604/765) with CDA and 83% (315/381) with AL. In patients with a G6PD-deficient genotype (94/603 [16%] hemizygous males, 22/598 [4%] homozygous females), CDA had the propensity to cause severe and clinically concerning hemoglobin decreases: the mean hemoglobin nadir was 75 g/L (95%CI 71, 79) at Day 7 versus 97 g/L (95%CI 91, 102) for AL. There were three deaths, unrelated to study medication (two with CDA, one with AL).

Conclusions

Although parasitologically effective at Day 28, the hemolytic potential of CDA in G6PD-deficient patients makes it unsuitable for use in a public health setting in Africa.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00344006","term_id":"NCT00344006"}}NCT00344006     

Raf Kinase Inhibitory Protein Protects Cells against Locostatin-Mediated Inhibition of Migration

Background

Raf Kinase Inhibitory Protein (RKIP, also PEBP1), a member of the Phosphatidylethanolamine Binding Protein family, negatively regulates growth factor signaling by the Raf/MAP kinase pathway. Since an organic compound, locostatin, was reported to bind RKIP and inhibit cell migration by a Raf-dependent mechanism, we addressed the role of RKIP in locostatin function.

Methods/Findings

We analyzed locostatin interaction with RKIP and examined the biological consequences of locostatin binding on RKIP function. NMR studies show that a locostatin precursor binds to the conserved phosphatidylethanolamine binding pocket of RKIP. However, drug binding to the pocket does not prevent RKIP association with its inhibitory target, Raf-1, nor affect RKIP phosphorylation by Protein Kinase C at a regulatory site. Similarly, exposure of wild type, RKIP-depleted HeLa cells or RKIP-deficient (RKIP^−/−) mouse embryonic fibroblasts (MEFs) to locostatin has no effect on MAP kinase activation. Locostatin treatment of wild type MEFs causes inhibition of cell migration following wounding. RKIP deficiency impairs migration further, indicating that RKIP protects cells against locostatin-mediated inhibition of migration. Locostatin treatment of depleted or RKIP^−/− MEFs reveals cytoskeletal disruption and microtubule abnormalities in the spindle.

Conclusions/Significance

These results suggest that locostatin''s effects on cytoskeletal structure and migration are caused through mechanisms independent of its binding to RKIP and Raf/MAP kinase signaling. The protective effect of RKIP against drug inhibition of migration suggests a new role for RKIP in potentially sequestering toxic compounds that may have deleterious effects on cells.     

Reactions of 4‐[Bis(2‐chloroethyl)amino]benzenebutanoic Acid (Chlorambucil) with DNA

4‐[Bis(2‐chloroethyl)amino]benzenebutanoic acid (=chlorambucil, 1 ; 2.5 mM ) was allowed to react with single‐ and double‐stranded calf thymus DNA at physiological pH (cacodylic acid, 50% base) at 37°. The DNA–chlorambucil adducts were identified by analyzing the DNA hydrolysates by NMR, UV, HPLC, LC/ESI‐MS/MS techniques as well as by spiking with authentic materials. ssDNA was more reactive than dsDNA, and the order of reactivity in ssDNA was Ade‐N1>Gua‐N7>Cyt‐N3>Ade‐N3. The most reactive site in dsDNA was Ade‐N3. The Gua‐N7 and Ade‐N3 adducts were hydrolytically labile. Ade‐N7 adduct could not be identified in the hydrolysates of ssDNA or dsDNA. The adduct Gua‐N7,N7, which consists of two units of Gua bound together with a unit derived from chlorambucil, is a cross‐linking adduct, and it was detected in the hydrolysates of ssDNA and dsDNA. Also several other adducts were detected which could be characterized by spiking with previously isolated authentic adducts or tentatively by MS. The role of chlorambucil–DNA adducts on the cytotoxicity and mutagenity of 1 is also discussed.     

Paravirtualization effect on single- and multi-threaded memory-intensive linear algebra software

Previous studies have revealed that paravirtualization imposes minimal performance overhead on High Performance Computing (HPC) workloads, while exposing numerous benefits for this field. In this study, we are investigating the impact of paravirtualization on the performance of automatically-tuned software systems. We compare peak performance, performance degradation in constrained memory situations, performance degradation in multi-threaded applications, and inter-VM shared memory performance. For comparison purposes, we examine the proficiency of ATLAS, a quintessential example of an autotuning software system, in tuning the BLAS library routines for paravirtualized systems. Our results show that the combination of ATLAS and Xen paravirtualization delivers native execution performance and nearly identical memory hierarchy performance profiles in both single and multi-threaded scenarios. Furthermore, we show that it is possible to achieve memory sharing among OS instances at native speeds. These results expose new benefits to memory-intensive applications arising from the ability to slim down the guest OS without influencing the system performance. In addition, our findings support a novel and very attractive deployment scenario for computational science and engineering codes on virtual clusters and computational clouds.