Structural model of weak binding actomyosin in the prepowerstroke state.

We present the first in silico model of the weak binding actomyosin in the initial powerstroke state, representing the actin binding-induced major structural changes in myosin. First, we docked an actin trimer to prepowerstroke myosin then relaxed the complex by a 100-ns long unrestrained molecular dynamics. In the first few nanoseconds, actin binding induced an extra primed myosin state, i.e. the further priming of the myosin lever by 18° coupled to a further closure of switch 2 loop. We demonstrated that actin induces the extra primed state of myosin specifically through the actin N terminus-activation loop interaction. The applied in silico methodology was validated by forming rigor structures that perfectly fitted into an experimentally determined EM map of the rigor actomyosin. Our results unveiled the role of actin in the powerstroke by presenting that actin moves the myosin lever to the extra primed state that leads to the effective lever swing.

Drug effect prediction by polypharmacology-based interaction profiling.

Most drugs exert their effects via multitarget interactions, as hypothesized by polypharmacology. While these multitarget interactions are responsible for the clinical effect profiles of drugs, current methods have failed to uncover the complex relationships between them. Here, we introduce an approach which is able to relate complex drug-protein interaction profiles with effect profiles. Structural data and registered effect profiles of all small-molecule drugs were collected, and interactions to a series of nontarget protein binding sites of each drug were calculated. Statistical analyses confirmed a close relationship between the studied 177 major effect categories and interaction profiles of ca. 1200 FDA-approved small-molecule drugs. On the basis of this relationship, the effect profiles of drugs were revealed in their entirety, and hitherto uncovered effects could be predicted in a systematic manner. Our results show that the prediction power is independent of the composition of the protein set used for interaction profile generation.

Epichloë Fungal Endophytes Have More Host-Dependent Effects on the Soil Microenvironment than on the Initial Litter Quality.

Fungal endophytes have been extensively found in most terrestrial plants. This type of plant-microorganism symbiosis generates many benefits for plant growth by promoting nutrient availability, uptake, and resistance to environmental disease or stress. Recent studies have reported that fungal endophytes have a potential impact on plant litter decomposition, but the mechanisms behind its effect are not well understood. We proposed a hypothesis that the impacts of fungal endophytes on litter decomposition are not only due to a shift in the symbiont-induced litter quality but a shift in soil microenvironment. To test this hypothesis, we set-up a field trial by planting three locally dominant grass species (wild barley, drunken horse grass, and perennial ryegrass) with Epichloë endophyte-infected (E+) and -free (E-) status, respectively. The aboveground litter and bulk soil from each plant species were collected. The litter quality and the soil biotic and abiotic parameters were analyzed to identify their changes across E+ and E- status and plant species. While Epichloë endophyte status mainly caused a significant shift in soil microenvironment, plant species had a dominant effect on litter quality. Available nitrogen (N) and phosphorus (P) as well as soil organic carbon and microbial biomass in most soils with planting E+ plants increased by 17.19%, 14.28%, 23.82%, and 11.54%, respectively, in comparison to soils with planting E- plants. Our results confirm that fungal endophytes have more of an influence on the soil microenvironment than the aboveground litter quality, providing a partial explanation of the home-field advantage of litter decomposition.

The spinach YY genome reveals sex chromosome evolution, domestication, and introgression history of the species.

BACKGROUND: Spinach (Spinacia oleracea L.) is a dioecious species with an XY sex chromosome system, but its Y chromosome has not been fully characterized. Our knowledge about the history of its domestication and improvement remains limited. RESULTS: A high-quality YY genome of spinach is assembled into 952 Mb in six pseudo-chromosomes. By a combination of genetic mapping, Genome-Wide Association Studies, and genomic analysis, we characterize a 17.42-Mb sex determination region (SDR) on chromosome 1. The sex chromosomes of spinach evolved when an insertion containing sex determination genes occurred, followed by a large genomic inversion about 1.98 Mya. A subsequent burst of SDR-specific repeats (0.1-0.15 Mya) explains the large size of this SDR. We identify a Y-specific gene, NRT1/PTR 6.4 which resides in this insertion, as a strong candidate for the sex determination or differentiation factor. Resequencing of 112 spinach genomes reveals a severe domestication bottleneck approximately 10.87 Kya, which dates the domestication of spinach 7000 years earlier than the archeological record. We demonstrate that a strong selection signal associated with internode elongation and leaf area expansion is associated with domestication of edibility traits in spinach. We find that several strong genomic introgressions from the wild species Spinacia turkestanica and Spinacia tetrandra harbor desirable alleles of genes related to downy mildew resistance, frost resistance, leaf morphology, and flowering-time shift, which likely contribute to spinach improvement. CONCLUSIONS: Analysis of the YY genome uncovers evolutionary forces shaping nascent sex chromosome evolution in spinach. Our findings provide novel insights about the domestication and improvement of spinach.

Effects of different vibration frequencies on muscle strength, bone turnover and walking endurance in chronic stroke.

This randomized controlled trial aimed to evaluate the effects of different whole body vibration (WBV) frequencies on concentric and eccentric leg muscle strength, bone turnover and walking endurance after stroke. The study involved eighty-four individuals with chronic stroke (mean age = 59.7 years, SD = 6.5) with mild to moderate motor impairment (Fugl-Meyer Assessment lower limb motor score: mean = 24.0, SD = 3.5) randomly assigned to either a 20 Hz or 30 Hz WBV intervention program. Both programs involved 3 training sessions per week for 8 weeks. Isokinetic knee concentric and eccentric extension strength, serum level of cross-linked N-telopeptides of type I collagen (NTx), and walking endurance (6-min walk test; 6MWT) were assessed at baseline and post-intervention. An intention-to-treat analysis revealed a significant time effect for all muscle strength outcomes and NTx, but not for 6MWT. The time-by-group interaction was only significant for the paretic eccentric knee extensor work, with a medium effect size (0.44; 95% CI: 0.01, 0.87). Both WBV protocols were effective in improving leg muscle strength and reducing bone resorption. Comparatively greater improvement in paretic eccentric leg strength was observed for the 30 Hz protocol.

PIDA-mediated intramolecular oxidative C-N bond formation for the direct synthesis of quinoxalines from enaminones.

A intramolecular oxidative C(sp2)-N bond formation mediated by hypervalent iodine(iii) to obtain quinoxalines from readily available N-(2-acetaminophenyl)enaminones was developed. A tandem process involving PIDA-mediated intramolecular condensation cyclization and a subsequent elimination was postulated, which was highly efficient and metal-free under mild conditions. Moreover, flexible structural modifications of quinoxalines bearing carbonyl groups are of interest for further transformations as building blocks in organic synthesis.

Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

Modern sugarcanes are polyploid interspecific hybrids, combining high sugar content from Saccharum officinarum with hardiness, disease resistance and ratooning of Saccharum spontaneum. Sequencing of a haploid S. spontaneum, AP85-441, facilitated the assembly of 32 pseudo-chromosomes comprising 8 homologous groups of 4 members each, bearing 35,525 genes with alleles defined. The reduction of basic chromosome number from 10 to 8 in S. spontaneum was caused by fissions of 2 ancestral chromosomes followed by translocations to 4 chromosomes. Surprisingly, 80% of nucleotide binding site-encoding genes associated with disease resistance are located in 4 rearranged chromosomes and 51% of those in rearranged regions. Resequencing of 64 S. spontaneum genomes identified balancing selection in rearranged regions, maintaining their diversity. Introgressed S. spontaneum chromosomes in modern sugarcanes are randomly distributed in AP85-441 genome, indicating random recombination among homologs in different S. spontaneum accessions. The allele-defined Saccharum genome offers new knowledge and resources to accelerate sugarcane improvement.

Publisher Correction: Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

In the version of this article originally published, the accession codes listed in the data availability section were incorrect and the section was incomplete. The text for this section should have read "The genome assembly and gene annotation have been deposited in the NCBI database under accession number QVOL00000000, BioProject number PRJNA483885 and BioSample number SAMN09753102. The data can also be downloaded from the following link: http://www.life.illinois.edu/ming/downloads/Spontaneum_genome/ ." The errors have been corrected in the HTML and PDF versions of the article.

Cobalt-Catalyzed Selective Synthesis of Isoquinolines Using Picolinamide as a Traceless Directing Group.

Picolinamide has first been employed as a traceless directing group for the cobalt-catalyzed oxidative annulation of benzylamides with alkynes to synthesize isoquinolines through C-H/N-H bonds activation. Oxygen is used as a terminal oxidant. This protocol exhibits good functional group tolerance and excellent regioselectivity. Both terminal and internal alkynes can be efficiently applied to this catalytic system as substrates.

The rational designed antagonist derived from the complex structure of interleukin-6 and its receptor affectively blocking interleukin-6 might be a promising treatment in multiple myeloma.

Human interleukin-6 is involved in the maintenance and progression of several diseases such as multiple myeloma (MM), rheumatoid arthritis, or osteoporosis. Our previous work demonstrated that an interleukin-6 antagonist peptide (named PT) possessed potential bioactivity to antagonize the function of hIL-6 and could efficiently induce the growth arrest and apoptosis of XG-7 and M1 cells in a dose-dependent manner. In this study, the theoretical interaction of the peptide PT with its receptor was analyzed further more with molecular docking and molecular dynamics methods. The theoretical studies showed that PT possessed very high affinity to interleukin-6R and offered a practical means of imposing long-term blockade of interleukin-6 activity in vivo. According to the theoretical results, the biological evaluation of PT was researched on two different cells models with more sensitive approaches: (1) The antagonist activity of PT was studied on the interleukin-6 dependent MM cells (XG-7) cultured with interleukin-6. In the other interleukin-6 dependent MM cells (SKO-007), they survived themselves by auto/paracrine without the exogenous interleukin-6, and also could be antagonized by PT. The therapeutic value of PT only limited on the interleukin-6 dependent category in MM. (2) Myeloid leukemia M1 cells were induced for growth arrest and apoptosis in response to interleukin-6. The results supported our previous findings and showed that PT could be evaluated by protecting the cells from interleukin-6 induced apoptosis. In conclusion, PT could induce interleukin-6-dependent XG-7 and SKO-007 cells to apoptosis while inhibit interleukin-6-stimulated apoptosis in M1 cells.

Structure-based design and characterization of a Novel IL-6 antagonist peptide.

The development of rational methods to design antagonist peptides based on the 3-D structure of protein active region has, to now, been only marginally successful. This has been largely due to the difficulty of constraining the recognition elements of a mimetic structure to the relative conformational and spatial orientations present in the parent molecule. According to the 3-D complex structure of human interleukin-6 (hIL-6) and its receptor (hIL-6R), a novel antagonist peptide (named PT), which possessed potential bioactivity of hIL-6, was designed by the means of distance geometry, molecular modeling and molecular dynamics trajectory analysis. The bioactivity of the designed peptide (i.e. PT) was evaluated using XG-7 cells, a hIL-6-dependent B-cell line. PT possessed potential bioactivity to antagonize the function of hIL-6 and could efficiently induce the growth arrest and apoptosis of XG-7 cells in a dose-dependent manner.

One-Pot Regiospecific Synthesis of Quinoxalines via a CH2-Extrusion Reaction.

A convenient "one-pot" regiospecific synthesis of substituted quinoxalines from o-phenylenediamines and ynones under metal-free conditions has been developed. An intermolecular Michael addition reaction, a dehydration condensation, and a base-promoted C-α-CH2-extrusion were involved in this procedure, which features high regioselectivity, efficiency, and environmental friendliness. Various quinoxalines were provided in up to 95% yield for 33 examples.

A novel actin binding site of myosin required for effective muscle contraction.

F-actin serves as a track for myosin's motor functions and activates its ATPase activity by several orders of magnitude, enabling actomyosin to produce effective force against load. Although actin activation is a ubiquitous property of all myosin isoforms, the molecular mechanism and physiological role of this activation are unclear. Here we describe a conserved actin-binding region of myosin named the 'activation loop', which interacts with the N-terminal segment of actin. We demonstrate by biochemical, biophysical and in vivo approaches using transgenic Caenorhabditis elegans strains that the interaction between the activation loop and actin accelerates the movement of the relay, stimulating myosin's ATPase activity. This interaction results in efficient force generation, but it is not essential for the unloaded motility. We conclude that the binding of actin to myosin's activation loop specifically increases the ratio of mechanically productive to futile myosin heads, leading to efficient muscle contraction.

[Molecular mechanism of Wulongdan for improving the learning and memory abilities of rats with chronic cerebral ischemia].

OBJECTIVE: To evaluate the effect of Wulongdan on the learning and memory abilities of rats with chronic cerebral ischemia and explore the mechanisms. METHODS: Male SD Rat models of chronic cerebral ischemia were established by permanent ligation of the bilateral carotid arteries. Three weeks after the operation, the rats were randomly divided into sham-operated group, chronic cerebral ischemia group (model group), high-dose drug group, low-dose drug group and Yinxingye group and received the corresponding treatments on a daily basis for 5 consecutive weeks. Morris water maze was used to assess the learning and memory abilities of the rats, and Western blotting was carried out for detecting the expressions of NR1 and NR2B in the hippocampus and cerebral cortex. RESULTS: Compared with the model group, the rats in high-dose drug, low-dose drug and Yinxingye groups showed significantly shorter time of finding platform in Morris water maze test (P<0.05 or 0.01). The rats in the model group showed significantly lowered expressions of NR1 and NR2B of the cortex and hippocampus than those in the sham-operated group (P<0.01). In comparison with the model group, the high-dose Wulongdan group and Yinxingye group both showed significantly increase expressions of NR1 and NR2B (P<0.01), but their expression levels still remained significantly lower than those in the sham-operated group (P<0.01). CONCLUSION: Wulongdan can enhance the learning and memory abilities of rats with chronic cerebral ischemia, the mechanisms of which may involve increased expressions of NR1 and NR2B in the hippocampus and cortex.

Experimental investigation of the seesaw mechanism of the relay region that moves the myosin lever arm.

A seesaw-like movement of the relay region upon the recovery step of myosin was recently simulated in silico. In this model the relay helix tilts around its pivoting point formed by a phenylalanine cluster (Phe(481), Phe(482), and Phe(652)), which moves the lever arm of myosin. To study the effect of the elimination of the proposed pivoting point, these phenylalanines were mutated to alanines in two Dictyostelium myosin II motor domain constructs (M(F481A, F482A) and M(F652A)). The relay movement was followed by the fluorescence change of Trp(501) located in the relay region. The steady-state and transient kinetic fluorescence experiments showed that the lack of the phenylalanine fulcrum perturbs the formation of the "up" lever arm state, and only moderate effects were found in the nucleotide binding, the formation of the "down" lever arm position, and the ATP hydrolysis steps. We conclude that the lack of the fulcrum decouples the distal part of the relay from the nucleotide binding site upon the recovery step. Our molecular dynamics simulations also showed that the conformation of the motor is not perturbed by the mutation in the down lever arm state, however, the lack of the pivoting point rearranges the dynamic pattern of the kink region of the relay helix.

Expression, purification and characterization of soluble human interleukin-6 receptor alpha-chain and its mutant protein in Escherichia coli.

To investigate the function of the N-terminal immunoglobulin (Ig)-like domain of the human interleukin-6 receptor alpha-chain (hIL-6R), we constructed a soluble human interleukin-6 receptor (shIL-6R) (named EC05, amino acids 20-354) and soluble variants of the shIL-6R lacking the Ig-like domain (named EC70, amino acids 105-354). The two extracellular portions of hIL-6R were expressed as soluble fusion proteins with thioredoxin in Escherichia coli and purified by using Ni-NTA agarose. Western blot showed that purified proteins were immunoreactive with the antibody against hIL-6R. They also possessed specific binding activity with human interleukin-6 (hIL-6) in ELISA analysis.

A novel hIL-6 antagonist peptide from computer-aided design contributes to suppression of apoptosis in M1 cells.

Based on the complex crystal structure of human interleukin-6 (hIL-6) and its receptor (hIL-6R), a novel hIL-6 antagonist peptide (named PT) was designed using computer-guided design method. Dealing with molecular docking and molecular dynamics methods, the interaction between PT and hIL-6R was analyzed. The theoretical studies showed that PT possessed very high affinity to hIL-6R and offered a practical means of imposing long-term blockade of hIL-6 activity in vivo. This effect was examined due to growth arrest and apoptosis induced by hIL-6 in myeloblastic cell line M1 cells in a dose-dependent manner. The findings demonstrate that PT could also act as an excellent antagonist candidate for the induction of growth arrest and apoptosis. Furthermore, murine M1 myeloid cell line, which was induced by the physiological inducer hIL-6 to undergo apoptosis and growth arrest, could be used as a subtle model system to test hIL-6 antagonist.