The ST Pinch: A side chain-to-side chain hydrogen-bonded motif

The ST Pinch is a 12-membered hydrogen-bonded motif (Ser/Thr-Xaa-Ser/Thr) involving the side chain oxygen atoms of two Ser/Thr residues. We identified the ST Pinch in 104 proteins in a database containing high-resolution crystal structures. Conformational analysis of the ST Pinch in these proteins points to specific preferences for the Xaa residue and a high propensity of this residue to adopt positive φ angles. Our results suggest that this motif serves as a linker of secondary structural elements within proteins and is a new addition to the existing list of short hydrogen bond-stabilized motifs in proteins.     

Aflatoxin contamination in insect damaged seeds of horsegram under storage

Studies on one of the protein rich pulses, horsegram (Dolichos biflorus L.) were carried out to know how far these low risk pulses are free from aflatoxin contamination under severe insect infestation in storage. A total of 150 stored seed samples of horsegram were analyzed for the presence of aflatoxins by collecting 25 samples each of undamaged and insect damaged seeds of all the three varieties (PDM-1, PHG-1 and HG-96). More than 33% of insect damaged seed samples were contaminated with aflatoxin B₁ and B₂, whereas less than 8% of the undamaged seed samples contain only low levels of aflatoxin B₂. Higher levels of aflatoxin B₁ (up to 130 μg/kg) were reported in insect damaged seed samples of all the three varieties under study. The levels of aflatoxin B₂ were always lower than aflatoxin B₁ of the corresponding seed samples with insect damage. Aflatoxin B₁ was reported in both the undamaged and insect damaged seed samples of all the three varieties of horsegram. It is evident from the varietal response studies that PDM-1 and HG-96 varieties of horsegram are highly vulnerable to aflatoxin contamination whereas, PHG-1 variety is relatively less susceptible to it. In general, insect infestation leads to increase in fungal invasion (including aflatoxigenic fungi) and this further enhances the levels of aflatoxin contamination in horsegram seeds.     

Investigating hydrophobic ligand–receptor interactions in parathyroid hormone receptor using peptide probes

With an increasing number of new chemical entities entering clinical studies, and an increasing share of the market, peptides and peptidomimetics constitute one of the most promising classes of therapeutics. The success of synthetic peptides as therapeutics relies on the lead optimization step in which the lead candidates are modified to improve drug‐like properties of peptides related to potency, pharmacokinetics, solubility, and stability, among others. Peptidomimetics based on the N‐terminal stretch of the first 11 amino acids of the PTH have been investigated as potential lead compounds for the treatment of osteoporosis. On the basis of a peptide reported in the literature, referred to here as the Parent Peptide (H‐Aib‐Val‐Aib‐Glu‐Ile‐Gln‐Leu‐Nle‐His‐Gln‐Har‐NH₂), we conducted systematic SAR analyses to investigate the effects of altering peptide hydrophobicity on PTH receptor functional potency as measured by the cAMP (cyclic adenosine monophosphate) accumulation and β‐arrestin recruitment assays. Among hydrophobic residues, we found that the Val2 position shows the least flexibility in terms of the SAR studies, whereas the Leu7 position appeared to be most flexible. Through circular dichroism and nuclear magnetic resonance spectroscopy studies, we were able to establish that changes in hydrophobic residues significantly change the extent of peptide helicity and that the helical character correlates well with receptor agonist activity. Here, we report several novel PTH 1–11 peptidomimetics that show comparable or enhanced potency to stimulate G_s‐signaling over β‐arrestin recruitment as compared with such properties of PTH 1–34 and the Parent Peptide. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.     

Co-immobilization of dextransucrase and dextranase for the facilitated synthesis of isomalto-oligosaccharides: Preparation, characterization and modeling

Co-Immobilization of dextransucrase (DS) and dextranase (DN) into calcium alginate includes the co-entrapment of soluble DS and adsorbed DN. DS converts sucrose into dextran, which is the substrate for DN, so that isomalto-oligosaccharides (IMOs) are follow-up products of dextran hydrolysis. The boundary conditions for the successful preparation are investigated with respect to choice of DN adsorbate, surface modifications using blotting agents and optimal enzyme activity ratios. Further, repetitive batch experiments suggest the selection of medium activity ratios for continuous use (0.3 U(DN)U(-1) (DS), e.g.). Product formation at various cosubstrate:substrate concentrations as well as at different DN:DS ratios are discussed. Moreover, the complexity of the bi-enzymatic system can be reduced considering the molar ratios of cosubstrate:substrate (glucose:sucrose). Based on these factors, a mechanistic kinetic model is developed, which distinguishes the corresponding contributions of the two enzymes upon overall product formation. In general, at low glucose:sucrose ratios isomaltose synthesis is featured primarily by DN action. Yet with increasing amounts of glucose both the quantity and quality of DN substrate changes, so that its contribution to product formation decreases in an exponential manner; still the overall product yield continuously increases due to enhanced DS contribution.     

Ultrafast folding and molecular dynamics of a linear hydrophobic β-hairpin

The first computational study of the folding and dynamics of a hydrophobic β-hairpin containing a central heterochiral diproline segment is reported. Linear hydrophobic sequences containing centrally positioned diproline motifs, heterochiral (DL/LD) and homochiral (LL/DD)), are investigated for their ability to form β-hairpins. Heterochiral diproline motifs (LD/DL) reveal the formation of stable β-hairpins with the backbone adopting β-turn conformation and the formation of backbone hydrogen bonds with antiparallel cross-strand registry, whereas the homochiral diproline (LL/DD) containing sequences tend to adopt PP_II helix conformation. The competition between the β-turn formation and the backbone H-bond ladder of the antiparallel β-strands in heterochiral diproline containing sequences is employed to validate the hypothesis that β-turn formation precedes inter-strand registry in the folding of a β-hairpin (“zipper” mechanism). The observation of noncanonical hydrogen bonds leads to a folded β-hairpin-like conformation and points to the existence of relatively stable transition state intermediates, between the unfolded (extended) and folded (β-hairpin) states. The MD simulations are in excellent agreement with the experimental studies on the model system and constitute the very first computational investigation of the folding and dynamics of a completely hydrophobic synthetic β-hairpin containing heterogeneous residues of mixed chirality.     

Aflatoxin contamination of pearl millet during field and storage conditions with reference to stage of grain maturation and insect damage

Aflatoxin contamination in five varieties of pearl millet (ICMH-451, ICMP-50I, ICTP-8203, WCC-75 and ICMV-155) was studied from field and storage conditions in three districts of Andhra Pradesh State, India and the inter-relationships between various parameters such as stage of grain maturation in the field and insect pest infestation in storage in relation to aflatoxin production were evaluated. Aflatoxin contamination was more frequent in the seed samples collected from the fields during rainy season than winter season. All major aflatoxins were isolated from one or the other varieties of pearl millet, whereas aflatoxin G₂ was not commonly observed in the seed samples collected during winter. Among all the varieties tested, ICMH-451 was vulnerable to aflatoxin contamination whereas ICMV-155 was the least susceptible variety. The higher amount of aflatoxins was observed in the matured seed samples followed by pre-matured and milky stage. Among all the toxins reported in the field, aflatoxin B₁ was found in higher concentration (185 (μg/kg) followed by B₂ (105 μg/kg). The four major types of aflatoxins with higher levels (35, 40, 140, 190 μg/kg of G₁, G₂, B₂, B₁ were reported in the rainy season seed samples after six months of storage, whereas aflatoxin G₁ was not observed in any variety of stored seed sample from winter. Statistical analysis revealed that the aflatoxin incidence in relation to different parameters studied was significantly different for each factor. The relationship between aflatoxin contamination and insect damaged-grain clearly indicated that the seed samples with 16-40% of insect damage contained higher amounts of aflatoxins (758 μg/kg). Presented at the 29^th Mykotoxin-Workshop, Fellbach, Germany, May 14–16, 2007     

Crab Pentapeptide and Its Anti-inflammatory Activity on Macrophage Cells

International Journal of Peptide Research and Therapeutics - Marine fishes have long been known due to their nutritional and pharmaceutical importance. In this study, marine crab (C. natator) body...     

Cabozantinib-induced edema in zebrafish represents an adverse effect characterized by defects in lymphatic vasculature and renal function

Tyrosine kinase inhibitors (TKIs) are a major class of targeted cancer therapy drugs. Overcoming the limitations of approved TKIs and the development of new TKIs continues to be an important need. The adoption of higher throughput and accessible animal models to evaluate TKI adverse effects will help in this regard. We exposed zebrafish larvae to a set of 22 Food and Drug Administration-approved TKIs and assessed mortality, early developmental abnormalities, and gross morphological abnormalities posthatching. We found edema posthatching as a consistent and prominent consequence of VEGFR inhibitors, and of cabozantinib in particular. The edema occurred at concentrations that did not cause lethality or any other abnormality, and was independent of the developmental stage. Further experiments identified loss of blood and lymphatic vasculature, and suppression of renal function in larvae exposed to 10 µM cabozantinib. Molecular analysis showed downregulation of the vasculature marker genes vegfr, prox1a, sox18, and the renal function markers nephrin and podocin as the potential molecular basis for the above defects, implicating them in the mechanism of cabozantinib-induced edema. Our findings reveal edema as a previously unreported phenotypic effect of cabozantinib and identify the likely mechanistic basis. These findings also highlight the need for studies investigating edema due to vascular and renal dysfunction as a potential clinical adverse effect of cabozantinib, and possibly other VEGFR inhibitors.