Plasma Proteome Database as a resource for proteomics research

Plasma is one of the best studied compartments in the human body and serves as an ideal body fluid for the diagnosis of diseases. This report provides a detailed functional annotation of all the plasma proteins identified to date. In all, gene products encoded by 3778 distinct genes were annotated based on proteins previously published in the literature as plasma proteins and the identification of multiple peptides from proteins under HUPO's Plasma Proteome Project. Our analysis revealed that 51% of these genes encoded more than one protein isoform. All single nucleotide polymorphisms involving protein-coding regions were mapped onto the protein sequences. We found a number of examples of isoform-specific subcellular localization as well as tissue expression. This database is an attempt at comprehensive annotation of a complex subproteome and is available on the web at http://www.plasmaproteomedatabase.org.     

Alleviating CYP and hERG liabilities by structure optimization of dihydrofuran-fused tricyclic benzo[d]imidazole series – Potent,selective and orally efficacious microsomal prostaglandin E synthase-1 (mPGES-1) inhibitors: Part-2

In an effort to identify CYP and hERG clean mPGES-1 inhibitors from the dihydrofuran-fused tricyclic benzo[d]imidazole series lead 7, an extensive structure-activity relationship (SAR) studies were performed. Optimization of A, D and E-rings in 7 afforded many potent compounds with human whole blood potency in the range of 160–950?nM. Selected inhibitors 21d, 21j, 21m, 21n, 21p and 22b provided selectivity against COX-enzymes and mPGES-1 isoforms (mPGES-2 and cPGES) along with sufficient selectivity against prostanoid synthases. Most of the tested analogs demonstrated required metabolic stability in liver microsomes, low hERG and CYP liability. Oral pharmacokinetics and bioavailability of lead compounds 21j, 21m and 21p are discussed in multiple species like rat, guinea pig, dog, and cynomolgus monkey. Besides, these compounds revealed low to moderate activity against human pregnane X receptor (hPXR). The selected lead 21j further demonstrated in vivo efficacy in acute hyperalgesia (ED₅₀: 39.6?mg/kg) and MIA-induced osteoarthritic pain models (ED₅₀: 106?mg/kg).     

Anomalous Charge‐Extraction Behavior for Graphene‐Oxide (GO) and Reduced Graphene‐Oxide (rGO) Films as Efficient p‐Contact Layers for High‐Performance Perovskite Solar Cells

Reduced graphene oxides (rGO) are synthesized via reduction of GO with reducing agents as a hole‐extraction layer for high‐performance inverted planar heterojunction perovskite solar cells. The best efficiencies of power conversion (PCE) of these rGO cells exceed 16%, much greater than those made of GO and poly(3,4‐ethenedioxythiophene):poly(styrenesulfonate) films. A flexible rGO device shows PCE 13.8% and maintains 70% of its initial performance over 150 bending cycles. It is found that the hole‐extraction period is much smaller for the GO/methylammonium lead‐iodide perovskite (PSK) film than for the other rGO/PSK films, which contradicts their device performances. Photoluminescence and transient photoelectric decays are measured and control experiments are performed to prove that the reduction of the oxygen‐containing groups in GO significantly decreases the ability of hole extraction from PSK to rGO and also retards the charge recombination at the rGO/PSK interface. When the hole injection from PSK to GO occurs rapidly, hole propagation from GO to the indium‐doped tin oxide (ITO) substrate becomes a bottleneck to overcome, which leads to a rapid charge recombination that decreases the performance of the GO device relative to the rGO device.     

Rational Engineering and Characterization of an mAb that Neutralizes Zika Virus by Targeting a Mutationally Constrained Quaternary Epitope

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Capsicum annuum proteinase inhibitor ingestion negatively impacts the growth of sorghum pest Chilo partellus and promotes differential protease expression

BackgroundChilo partellus is an important insect pest infesting sorghum and maize. The larvae internalize in the stem, rendering difficulties in pest management. We investigated the effects of Capsicum annuum proteinase inhibitors (CanPIs) on C. partellus larvae by in-vitro and in-vivo experiments.MethodsRecombinant CanPI-7 (with four-Inhibitory Repeat Domains, IRDs), -22 (two-IRDs) and insect proteinase activities were estimated by proteinase assays, dot blot assays and in gel activity assays. Feeding bioassays of lab reared C. partellus with CanPI-7 and -22 were performed. C. partellus proteinase gene expression was done by RT-PCR. In-silico structure prediction of proteinases and CanPI IRDs was carried out, their validation and molecular docking was done for estimating the interaction strength.ResultsLarval proteinases of C. partellus showed higher activity at alkaline pH and expressed few proteinase isoforms. Both CanPIs showed strong inhibition of C. partellus larval proteinases. Feeding bioassays of C. partellus with CanPIs revealed a dose dependent retardation of larval growth, reduction of pupal mass and fecundity, while larval and pupal periods increased significantly. Ingestion of CanPIs resulted in differential up-regulation of C. partellus proteinase isoforms, which were sensitive to CanPI-7 but were insensitive to CanPI-22. In-silico interaction studies indicated the strong interaction of IRD-9 (of CanPI-22) with Chilo proteinases tested.ConclusionsOf the two PIs tested, CanPI-7 prevents induction of inhibitor insensitive proteinases in C. partellus so it can be explored for developing C. partellus tolerance in sorghum.General significanceIngestion of CanPIs, effectively retards C. partellus growth; while differentially regulating the proteinases.     

Pathological role of a point mutation (T315I) in BCR‐ABL1 protein—A computational insight

BCR‐ABL protein is one of the most potent target to treat chronic myeloid leukemia (CML). Apart from other mutations, T315I is especially challenging as it confers resistance to all first‐ and second‐generation tyrosine kinase inhibitors. So, a thorough study of altered behavior upon mutation is crucially needed. To understand the resistance mechanism of mutant BCR‐ABL protein, we organized a long‐term molecular dynamics simulation (500 ns) and performed the detailed comparative conformational analysis. We found that due to mutation at 315th position (threonine to isoleucine), original structures deviated from normal, and attained a flexible conformation. Our observations pave a clear path toward designing new inhibitors against resistant BCR‐ABL1 protein and suggest a strategy where additional flexibility governed by mutation could be given an appropriate consideration.     

Arrangement and size distribution of repeat and single copy DNA sequences in four species ofCucurbitaceae

DNA sequence organization patterns have been studied in fourCucurbitaceae plant species, namely,Luffa cylindrica (sponge gourd),L. acutangula (ridge gourd),Benincasa hispida (ash gourd) andCoccinia indica (ivy gourd). Extensive interspersion of repeat and single copy sequences has been observed in sponge gourd and ridge gourd. In ash gourd and ivy gourd, however, there is a limited interspersion of these sequences and a large portion of the single copy DNA remains uninterspersed. The interspersed repetitive sequences are composed of a major class (75–80%) of short repeats (300 base pairs long) and a minor class (15–20%) of long repeats (2 000–4 000 base pairs) in all the four species. The average length of single copy sequences dispersed among repeats is 1 800–2 900 base pairs. In spite of these gross similarities in the genome organization in the four species, the fraction of repeats and single copy sequences involved in short and long period interspersion patterns, and fraction of single copy sequences remaining uninterrupted by repeats are vastly different. The probable implications of these differences with respect to speciation events and rates of genome evolution are discussed.Molecular Analysis ofCucurbitaceae Genomes, III. — NCL Communication No.: 3595.     

Construction and Screening of Indica Rice Genomic Library for Sequences Homologous to Sorghum Storage Protein Kafirin

Rice DNA of about 50 kb was isolated, partially digested with EcoRI and fractionated on 10–40% sucrose density gradient to obtain DNA fragments in the size range of 10–20 kb. Bacteriophage vector Charon 4A was also digested with EcoRI and two arms were purified by sucrose density gradient centrifugation. The purified Charon 4A arms and size fractionated rice DNA were ligated and used for in vitro packaging. The development of in vitro packaging extract made it possible to construct a genomic library which represented 7–8 rice genomes, considering the haploid DNA content of rice as 1 pg. This library was screened using a heterologous kafirin cDNA probe from Sorghum bicolor and three clones homologous to kafirin, were identified.