Structure, dynamics and mapping of membrane-binding residues of micelle-bound antimicrobial peptides by natural abundance C NMR spectroscopy

Worldwide bacterial resistance to traditional antibiotics has drawn much research attention to naturally occurring antimicrobial peptides (AMPs) owing to their potential as alternative antimicrobials. Structural studies of AMPs are essential for an in-depth understanding of their activity, mechanism of action, and in guiding peptide design. Two-dimensional solution proton NMR spectroscopy has been the major tool. In this article, we describe the applications of natural abundance ¹³C NMR spectroscopy that provides complementary information to 2D ¹H NMR. The correlation of ¹³Cα secondary shifts with both 3D structure and heteronuclear ¹⁵N NOE values indicates that natural abundance carbon chemical shifts are useful probes for backbone structure and dynamics of membrane peptides. Using human LL-37-derived peptides (GF-17, KR-12, and RI-10), as well as amphibian antimicrobial and anticancer peptide aurein 1.2 and its analog LLAA, as models, we show that the cross peak intensity plots of 2D ¹H-¹³Cα HSQC spectra versus residue number present a wave-like pattern (HSQC wave) where key hydrophobic residues of micelle-bound peptides are located in the troughs with weaker intensities, probably due to fast exchange between the free and bound forms. In all the cases, the identification of aromatic phenylalanines as a key membrane-binding residue is consistent with previous intermolecular Phe-lipid NOE observations. Furthermore, mutation of one of the key hydrophobic residues of KR-12 to Ala significantly reduced the antibacterial activity of the peptide mutants. These results illustrate that natural abundance heteronuclear-correlated NMR spectroscopy can be utilized to probe backbone structure and dynamics, and perhaps to map key membrane-binding residues of peptides in complex with micelles. ¹H-¹³Cα HSQC wave, along with other NMR waves such as dipolar wave and chemical shift wave, offers novel insights into peptide-membrane interactions from different angles.     

The influence of aphid-produced honeydew on parasitoid fitness and nutritional state: A comparative study

Honeydew is a sugar-rich resource excreted by many hemipteran species and is a key food source for other insect species such as ants and parasitoid wasps. Here, we evaluated the nutritional value of 14 honeydews excreted by 13 aphid species for the generalist aphid parasitoid Lysiphlebus testaceipes to test a series of hypotheses concerning variation in the nutritional value of honeydew. There was a positive correlation between the body sugar content of honeydew-fed parasitoids and their longevity. This information is valuable for biological control researchers because it demonstrates that the nutritional state of honeydew-fed parasitoids in the wild can indicate their fitness, independently of the honeydew source they have fed on.Although the carbohydrate content and longevity of L. testaceipes differed greatly among the different honeydews, we did not find a significant effect of aphid or host plant phylogeny on these traits. This result suggests that honeydew is evolutionarily labile and may be particularly subject to ecological selection pressures. This becomes apparent when considering host aphid suitability: Schizaphis graminum, one of the most suitable and commonly used hosts of L. testaceipes, produced honeydew of the poorest quality for the parasitoid whereas Uroleucon sonchi, one of the few aphids tested that cannot be parasitized by L. testaceipes, excreted the honeydew with the highest nutritional value. These data are consistent with the hypothesis that hemipterans are subject to selection pressure to minimize honeydew quality for the parasitoids that attack them.     

International principles and standards for native seeds in ecological restoration

The growing demand for native seeds in ecological restoration and rehabilitation, whether for mining, forest, or ecosystem restoration, has resulted in a major global industry in the sourcing, supply, and sale of native seeds. However, there are no international guidance documents for ensuring that native seeds have the same standards of quality assurance that are regular practice in the crop and horticultural industries. Using the International Principles and Standards for the Practice of Ecological Restoration as a foundation document, we provide for the first time a synthesis of general practices in the native seed supply chain to derive the Principles and Standards for Native Seeds in Ecological Restoration (“Standards”). These practices and the underpinning science provide the basis for developing quality measures and guidance statements that are adaptable at the local, biome, or national scale. Importantly, these Standards define what is considered native seed in ecological restoration and highlight the differences between native seeds versus seeds of improved genetics. Seed testing approaches are provided within a logical framework that outline the many different dormancy states in native seed that can confound restoration outcomes. A “pro‐forma” template for a production label is included as a practical tool that can be customized for local needs and to standardize reporting to end‐users on the level of seed quality and germinability to be expected in a native seed batch. These Standards are not intended to be mandatory; however, the guidance statements provide the foundation upon which regulatory approaches can be developed by constituencies and jurisdictions.     

Structural motives controlling the binding affinity of 9,10-bis(methylpyridinium)anthracenes towards DNA

In the search of new DNA groove binding agents a series of substituted 9,10-methylpyridiniumanthracenes have been synthesized and their interactions with DNA have been studied by UV/vis absorption, CD and fluorescence spectroscopy. A minor groove binding mode is confirmed by DNA melting studies, strong CD effects, the dependence of the binding affinity on ionic strength, and the differentiation between AT and GC base pairs. No binding occurs to GC sequences. Binding constants to calf thymus DNA (ct-DNA) and poly(dA:dT) in the range between 1 × 10⁴ and 3 × 10⁵ M⁻¹ have been determined. The binding strength decreases with the size of substituents attached at the anthracene site. Variation of the substitution pattern of the charged groups shows that methyl groups in meta position cause slightly stronger binding than methyl groups in para position. In contrast, with these groups in ortho position, no binding interaction has been observed. The strongest binding is achieved with an expansion of the peripheral heterocycle from pyridine to quinoline. Molecular modeling reveals the pivotal role of the substitution pattern: Anthracenes with para and meta pyridines align along the minor grooves. On the other hand, the ortho derivative adopts no groove-alignment.     

Database of protein complexes with multivalent binding ability: Bival‐bind

Phenomena of multivalent binding of ligands with receptors are ubiquitous in biology and of growing interest in material sciences. Multivalency can enhance binding affinity dramatically. To understand the mechanism of multivalent binding in more detail model systems of bi‐ and multivalent receptors are needed, but are difficult to find. Furthermore it is useful to know about multivalent receptors, which can serve as targets to design multivalent drugs. The present contribution tries to close this gap. The Bival‐Bind database ( http://agknapp.chemie.fu‐berlin.de/bivalbind ) provides a relatively complete list – 2073 protein complexes with less than 90% sequence identity – out of the protein database, which can serve as bi‐ or multivalent receptors. Steric clashes of molecular spacers – necessary to connect the monomeric ligand units – with the receptor surface can diminish binding affinity dramatically and, thus, abolish the expected enhancement of binding affinity due to the multivalency. The potential multivalent receptors in the Bival‐Bind database are characterized with respect to the receptor surface topography. A height profile between the receptor binding pockets is provided, which is an important information to estimate the influence of unfavorable spacer receptor interaction. Proteins 2014; 82:744–751. © 2013 Wiley Periodicals, Inc.     

荧光增白剂对杆状病毒的增效机理研究概况

荧光增白剂对杆状病毒增效作用的机制或作用方式存在歧异,目前主要存在两种学术观点:一种认为荧光增白剂对杆状病毒的增强效应是通过作用于昆虫中肠细胞实现的;另一种观点则认为荧光增白剂对杆状病毒的增强作用是通过破坏昆虫围食膜结构的完整性实现的.就这两种学术观点及荧光增白剂增效作用研究概况作详细的介绍.     

Global nutritional profiling for mutant and chemical mode-of-action analysis in filamentous fungi

We describe a method for gene function discovery and chemical mode-of-action analysis via nutrient utilization using a high throughput Nutritional Profiling platform suitable for filamentous microorganisms. We have optimized the growth conditions for each fungal species to produce reproducible optical density growth measurements in microtiter plates. We validated the Nutritional Profiling platform using a nitrogen source utilization assay to analyze 21 Aspergillus nidulans strains with mutations in the master nitrogen regulatory gene, areA. Analysis of these data accurately reproduced expected results and provided new data to demonstrate that this platform is suitable for fine level phenotyping of filamentous fungi. Next, we analyzed the differential responses of two fungal species to a glutamine synthetase inhibitor, illustrating chemical mode-of-action analysis. Finally, a comparative phenotypic study was performed to characterize carbon catabolite repression in four fungal species using a carbon source utilization assay. The results demonstrate differentiation between two Aspergillus species and two diverse plant pathogens and provide a wealth of new data on fungal nutrient utilization. Thus, these assays can be used for gene function and chemical mode-of-action analysis at the whole organism level as well as interspecies comparisons in a variety of filamentous fungi. Additionally, because uniform distribution of growth within wells is maintained, comparisons between yeast and filamentous forms of a single organism can be performed.Electronic Supplementary Material Supplementary material is available in the online version of this article at The revised version of the PDF file was published online in January 2004. The figures are now in color.An erratum to this article can be found at     

Detecting emergent effects of multiple predator species

When foraging together, multiple predator species that share a single prey often cause prey mortality that cannot be predicted based on knowledge of predation by each species separately. Modeling and managing the effects of multiple predator species depend on accurately assessing these combined effects. Two methods are currently used to experimentally examine combined predation by multiple predator species: the additive and substitutive experimental designs. I simultaneously employed both experimental designs to examine predation by two crab species on shared mussel prey. I show that the two methods yield results that disagree both quantitatively and qualitatively, leading to very different conclusions about the way that predator species combine to affect prey mortality. This discrepancy occurred because the two methods examine complimentary, but not interchangeable questions. I advocate using an experimental design that incorporates both additive and substitutive designs to achieve a more complete understanding of the combined effects of multiple predator species.