Interaction of glucosamine with uracil and thymine: a computational study

Noncovalent interactions are ubiquitous and have been well recognized in chemistry, biology and material science. Yet, there are still recurring controversies over their natures, due to the wide range of noncovalent interaction terms. In this Essay, we employed the Valence Bond (VB) methods to address two types of interactions which recently have drawn intensive attention, i.e., the halogen bonding and the CH???HC dihydrogen bonding. The VB methods have the advantage of interpreting molecular structures and properties in the term of electron-localized Lewis (resonance) states (structures), which thereby shed specific light on the alteration of the bonding patterns. Due to the electron localization nature of Lewis states, it is possible to define individually and measure both polarization and charge transfer effects which have different physical origins. We demonstrated that both the ab initio VB method and the block-localized wavefunction (BLW) method can provide consistent pictures for halogen bonding systems, where strong Lewis bases NH₃, H₂O and NMe₃ partake as the halogen bond acceptors, and the halogen bond donors include dihalogen molecules and XNO₂ (X?=?Cl, Br, I). Based on the structural, spectral, and energetic changes, we confirm the remarkable roles of charge transfer in these halogen bonding complexes. Although the weak C-H???H-C interactions in alkane dimers and graphane sheets are thought to involve dispersion only, we show that this term embeds delicate yet important charge transfer, bond reorganization and polarization interactions.

     

Impacts of Bt maize inoculated with rhizobacteria on development and food utilization of Mythimna separata

The current trend of increasing proportion of cultivation of transgenic Bt crops is pushing towards dramatic destabilization of the agroecosystem, thus raising severe concerns about the sustainability of transgenic Bt crops as an effective management tool for the control of target insect pests in the future. Rhizobacteria is the key biological regulator to ameliorate soil‐nitrogen utilization efficiency of crop plants, especially transgenic Bt crops. A laboratory study quantified the impacts of transgenic Bt maize (Line IE09S034 with Cry1Ie vs. non‐Bt maize cv. Xianyu335) inoculated with Azospirillum brasilense (AB) and Azotobacter chroococcum (AC) on the growth, development and food utilization of a target lepidopteran insect, Mythimna separata. The results showed that the inoculation of rhizobacteria significantly prolonged the larval lifespan and pupal duration, increased RCR and AD, reduced pupal weight, pupation rate, fecundity, RGR, ECD and ECI, and shortened adult longevity of M. separata fed on transgenic Bt maize, while exact opposite trends were found in these measured indexes of growth, development and food utilization for M. separata fed on non‐Bt maize inoculated with AB and AC compared with the buffer control in both years. Thus, the results clearly depicted that the inoculation of rhizobacteria had opposite influences on the growth, development and food utilization of M. separata fed on transgenic Bt maize. Presumably, rhizobacteria inoculation can be used to stimulate plant–soil‐nitrogen uptake and promote plant growth for transgenic Bt maize and non‐Bt maize, simultaneously increasing Bt toxin production and enhancing resistance efficiency against target lepidopteran pests for transgenic Bt maize.     

Structure prediction of Bestrophin for the induced - fit docking of anthocyanins

Bestrophin, an integral membrane protein existing in basolateral region of the retina is a propitious target for drug discovery. Mutations in the Bestrophin protein cause Best Vitelliform Macular Dystrophy (BVMD) leading to retinal damages and loss of visual acuity. Owing to the lack of three dimensional structure and related structural homologs in the protein data bank, we modeled the bestrophin protein using Robetta ab initio method. Further, no treatment is available for the disease. In this situation, anthocyanins from natural sources are reported to combat retinal damages. Hence, we identified anthocyanins from Syzygium cumini fruit skin using Electrospray Ionization tandem mass spectrometry. These compounds were docked into the predicted bestrophin model to study the interactions within the active site. The results may provide a valuable insight into the structure of bestrophin and efficacy of anthocyanins in molecular docking studies.

Abbreviations

PTP - Putative transmembrane proteins, VMD - Vitelliform macular dystrophy, BVMD - Best''s vitelliform macular dystrophy, RPE - Retinal pigment epithelium, ESI-MS/MS - Electrospray Ionization Tandem Mass Spectrometry, UNIPROT - Universal Protein Resource, PSIPRED - Protein secondary structure prediction, TMH - Transmembrane Helices, SCFS - Syzygium cumini fruit skin DP - Declustering Potential IFD - Induced Fit Docking.     

Structure and interactions of the helical and U-box domains of CHIP, the C terminus of HSP70 interacting protein

The heat-shock proteins Hsp70 and Hsp90 play a crucial role in regulating protein quality control both by refolding and by preventing the aggregation of misfolded proteins. It has recently been shown that Hsp70 and Hsp90 act not only in protein refolding but also cooperate with the C terminus of Hsp70 interacting protein (CHIP), a multidomain ubiquitin ligase, to mediate the degradation of unfolded proteins. We present the crystal structure of the helical linker domain and U-box domain of zebrafish CHIP (DrCHIP-HU). The structure of DrCHIP-HU shows a symmetric homodimer. The conformation of the helical linker domains and the relative positions of the helical and U-box domains differ substantially in DrCHIP-HU from those in a recently published structure of an asymmetric dimer of mammalian (mouse) CHIP. We used an in vitro ubiquitination assay to identify residues, located on two long loops and a central alpha helix of the CHIP U-box domain, that are important for interacting with the ubiquitin-conjugating enzyme UbcH5b. In addition, we used NMR spectroscopy to define a complementary interaction surface located on the N-terminal alpha helix and the L4 and L7 loops of UbcH5b. Our results provide insights into conformational variability in the domain arrangement of CHIP and into U-box-mediated recruitment of UbcH5b for the ubiquitination of Hsp70 and Hsp90 substrates.     

Pathway Palette: A rich internet application for peptide‐, protein‐ and network‐oriented analysis of MS data

Recent improvements in proteomic technologies have collectively yielded data sets that far exceed the capabilities of typical low‐throughput interpretation strategies. Unfortunately, tools designed to leverage the “peptide‐centric” content of MS‐based proteomics lag the current rate of data production. Here, we describe Pathway Palette ( http://blaispathways.dfci.harvard.edu ), a freely accessible internet application that enables researchers to easily transition from peptides to biological pathways, while simultaneously retaining the qualitative and quantitative aspects of the underlying MS data.     

Phosphoregulation of sorting signal-VHS domain interactions by a direct electrostatic mechanism

Phosphorylation of the cytosolic tails of transmembrane receptors can regulate their intracellular trafficking. The structural basis for such regulation, however, has not been explained in most cases. The cytosolic tail of the cation-independent mannose 6-phosphate receptor contains a serine residue within an acidic-cluster dileucine signal that is important for the function of the receptor in the biosynthetic sorting of lysosomal hydrolases. We show here that phosphorylation of this Ser enhances interactions of the signal with its recognition module, the VHS domain of the GGA proteins. Crystallographic analyses demonstrate that the phosphoserine residue interacts electrostatically with two basic residues on the VHS domain of GGA3, thus providing an additional point of attachment of the acidic-cluster dileucine signal to its recognition module.     

Age-Related Macular Degeneration and Incident Stroke: A Systematic Review and Meta-Analysis

Background

Age-related macular degeneration (AMD) is the leading cause of vision loss and blindness in people over 65 years old in the United States and has been associated with cardiovascular risk and decreased survival. There is conflicting data, however, regarding the contribution of AMD to the prediction of stroke.

Aim

To determine whether AMD is a risk indicator for incident stroke in a meta-analysis of available prospective and retrospective cohort studies published in the English literature.

Methods

We performed a systematic literature search of all studies published in English with Pub Med and other databases from 1966 to August 2014, reporting stroke incidence in patients with macular degeneration. Two investigators independently extracted the data. A random effects model was used to report Odds ratios (OR), with corresponding 95% confidence intervals (CI). Meta-regression using a mixed linear model was used to understand potential heterogeneity amongst studies.

Results

We identified 9 studies that reported stroke incidence in patients with and without early AMD (N = 1,420,978). No significant association was found between early AMD with incident stroke. Combined, these 9 studies demonstrated random effects (OR, 1.12; CI, 0.86–1.47; I² = 96%). Meta-regression on baseline covariates of age, sex, and year of publication did not significantly relate to heterogeneity.

Conclusions

We found no significant relationship between AMD and incident stroke. Further studies are needed to clarify other causes of decreased survival in patients with AMD.     

A Recessive Founder Mutation in Regulator of Telomere Elongation Helicase 1, RTEL1, Underlies Severe Immunodeficiency and Features of Hoyeraal Hreidarsson Syndrome

Dyskeratosis congenita (DC) is a heterogeneous inherited bone marrow failure and cancer predisposition syndrome in which germline mutations in telomere biology genes account for approximately one-half of known families. Hoyeraal Hreidarsson syndrome (HH) is a clinically severe variant of DC in which patients also have cerebellar hypoplasia and may present with severe immunodeficiency and enteropathy. We discovered a germline autosomal recessive mutation in RTEL1, a helicase with critical telomeric functions, in two unrelated families of Ashkenazi Jewish (AJ) ancestry. The affected individuals in these families are homozygous for the same mutation, R1264H, which affects three isoforms of RTEL1. Each parent was a heterozygous carrier of one mutant allele. Patient-derived cell lines revealed evidence of telomere dysfunction, including significantly decreased telomere length, telomere length heterogeneity, and the presence of extra-chromosomal circular telomeric DNA. In addition, RTEL1 mutant cells exhibited enhanced sensitivity to the interstrand cross-linking agent mitomycin C. The molecular data and the patterns of inheritance are consistent with a hypomorphic mutation in RTEL1 as the underlying basis of the clinical and cellular phenotypes. This study further implicates RTEL1 in the etiology of DC/HH and immunodeficiency, and identifies the first known homozygous autosomal recessive disease-associated mutation in RTEL1.     

Elevated CO2-mediated plant VOCs change aggravates invasive thrips occurrence by altering their host-selection behaviour

Globally rising atmosphere CO₂ has been predicted to affect the emission of plant volatile organic compounds (VOCs) and the interaction with insect herbivores. CO₂-mediated plant VOCs change might contribute to develop effective management strategies for insect pests by using VOCs related biological control methods. In this study, we analysed the effect of elevated CO₂ on the host-selection behaviour of western flower thrips (Frankliniella occidentalis) and studied how they were affected by the release of VOCs from kidney bean plants (Phaseolus vulgaris). A four-chamber olfactometer was used to quantify the host-selection of F. occidentalis for P. vulgaris. Elevated CO₂ increased F. occidentalis' selection for P. vulgaris wounded by mechanical damage (MD) and thrips infestation (TI) that might via regulating the gene expression of CSP1, CSP1-q, OBP1 and OBP1-q in F. occidentalis. Besides, we cultivated kidney beans at ambient CO₂ (400 ppm) and elevated CO₂ (800 ppm), and quantified the emission of plant VOCs by using GC-MS. Thirty VOCs belonging to ten chemical groups were identified from P. vulgaris, including aromatic hydrocarbons, ethers, alkanes, cycloalkanes, alcohols, alkenes, aromatic derivatives, phenols, ketones and esters. Furthermore, six VOCs from P. vulgaris were significantly affected by CO₂ level, wounding way and the interaction between them, including ethyl benzene, 1,3-dimethyl benzene, 1,3-dimethyl-4-ethyl benzene, (E,E,E,E)-squalene, 2,6-ditert-butyl-4-methyl phenol and dioctyl phthalate. Our study indicates that elevated CO₂ might increase the host-selection of F. occidentalis for wounded P. vulgaris due to the changed plant VOCs.