Optimization of van der Waals energy for protein side-chain placement and design

Computational determination of optimal side-chain conformations in protein structures has been a long-standing and challenging problem. Solving this problem is important for many applications including homology modeling, protein docking, and for placing small molecule ligands on protein-binding sites. Programs available as of this writing are very fast and reasonably accurate, as measured by deviations of side-chain dihedral angles; however, often due to multiple atomic clashes, they produce structures with high positive energies. This is problematic in applications where the energy values are important, for example when placing small molecules in docking applications; the relatively small binding energy of the small molecule is drowned by the large energy due to atomic clashes that hampers finding the lowest energy state of the docked ligand. To address this we have developed an algorithm for generating a set of side-chain conformations that is dense enough that at least one of its members would have a root mean-square deviation of no more than R Å from any possible side-chain conformation of the amino acid. We call such a set a side-chain cover set of order R for the amino acid. The size of the set is constrained by the energy of the interaction of the side chain to the backbone atoms. Then, side-chain cover sets are used to optimize the conformation of the side chains given the coordinates of the backbone of a protein. The method we use is based on a variety of dead-end elimination methods and the recently discovered dynamic programming algorithm for this problem. This was implemented in a computer program called Octopus where we use side-chain cover sets with very small values for R, such as 0.1 Å, which ensures that for each amino-acid side chain the set contains a conformation with a root mean-square deviation of, at most, R from the optimal conformation. The side-chain dihedral-angle accuracy of the program is comparable to other implementations; however, it has the important advantage that the structures produced by the program have negative energies that are very close to the energies of the crystal structure for all tested proteins.     

Molecular Signatures of Hemagglutinin Stem-Directed Heterosubtypic Human Neutralizing Antibodies against Influenza A Viruses

Recent studies have shown high usage of the IGHV1-69 germline immunoglobulin gene for influenza hemagglutinin stem-directed broadly-neutralizing antibodies (HV1-69-sBnAbs). Here we show that a major structural solution for these HV1-69-sBnAbs is achieved through a critical triad comprising two CDR-H2 loop anchor residues (a hydrophobic residue at position 53 (Ile or Met) and Phe54), and CDR-H3-Tyr at positions 98±1; together with distinctive V-segment CDR amino acid substitutions that occur in positions sparse in AID/polymerase-η recognition motifs. A semi-synthetic IGHV1-69 phage-display library screen designed to investigate AID/polη restrictions resulted in the isolation of HV1-69-sBnAbs that featured a distinctive Ile52Ser mutation in the CDR-H2 loop, a universal CDR-H3 Tyr at position 98 or 99, and required as little as two additional substitutions for heterosubtypic neutralizing activity. The functional importance of the Ile52Ser mutation was confirmed by mutagenesis and by BCR studies. Structural modeling suggests that substitution of a small amino acid at position 52 (or 52a) facilitates the insertion of CDR-H2 Phe54 and CDR-H3-Tyr into adjacent pockets on the stem. These results support the concept that activation and expansion of a defined subset of IGHV1-69-encoded B cells to produce potent HV1-69-sBnAbs does not necessarily require a heavily diversified V-segment acquired through recycling/reentry into the germinal center; rather, the incorporation of distinctive amino acid substitutions by Phase 2 long-patch error-prone repair of AID-induced mutations or by random non-AID SHM events may be sufficient. We propose that these routes of B cell maturation should be further investigated and exploited as a pathway for HV1-69-sBnAb elicitation by vaccination.     

Modelling of a targeted nanotherapeutic ‘stroma’ to deliver the cytokine LIF,or XAV939, a potent inhibitor of Wnt–β-catenin signalling,for use in human fetal dopaminergic grafts in Parkinson’s disease

The endogenous reparative capacity of the adult human brain is low, and chronic neurodegenerative disorders of the central nervous system represent one of the greatest areas of unmet clinical need in the developing world. Novel therapeutic strategies to treat them include: (i) growth factor delivery to boost endogenous repair and (ii) replacement cell therapy, including replacing dopaminergic neurons to treat Parkinson’s disease (PD). However, these approaches are restricted not only by rapid degradation of growth factors, but also by the limited availability of cells for transplant and the poor survival of implanted cells that lack the necessary stromal support. We therefore hypothesised that provision of a transient artificial stroma for paracrine delivery of pro-survival factors could overcome both of these issues. Using leukaemia inhibitory factor (LIF) – a proneural, reparative cytokine – formulated as target-specific poly(lactic-co-glycolic acid) (PLGA) nano-particles (LIF-nano-stroma), we discovered that attachment of LIF-nano-stroma to freshly isolated fetal dopaminergic cells improved their survival fourfold: furthermore, in vivo, the number of surviving human fetal dopaminergic cells tended to be higher at 3 months after grafting into the striatum of nude rats, compared with controls treated with empty nanoparticles. In addition, we also analysed the effect of a novel nano-stroma incorporating XAV939 (XAV), a potent inhibitor of the developmentally important Wnt–β-catenin signalling pathway, to investigate whether it could also promote the survival and differentiation of human fetal dopaminergic precursors; we found that the numbers of both tyrosine-hydroxylase-positive neurons (a marker of dopaminergic neurons) and total neurons were increased. This is the first demonstration that LIF-nano-stroma and XAV-nano-stroma each have pro-survival effects on human dopaminergic neurons, with potential value for target-specific modulation of neurogenic fate in cell-based therapies for PD.KEY WORDS: Parkinson’s disease, Nanotherapy, LIF, XAV939     

Enhancement of ethanol production by simultaneous saccharification and fermentation (SSF) of rice straw using ethoxylated span 20

In this work, four nonionic surfactants based on sorbitan monolaurate (Span 20) were synthesized by introducing ethylene oxide gas (n?=?20, 40, 60, 80 ethylene oxide units) into Span 20 to give four new surfactants with different hydrophilic-lipophilic balance (HLB), namely, E(20), E(40), E(60), and E(80). The structures of the prepared nonionic surfactants were elucidated using Fourier-transform infrared (FT-IR) and (1)H-nuclear magnetic resonance (NMR) spectroscopy. The surface-tension measurements were recorded. The effects of the prepared nonionic surfactants on the simultaneous saccharification and fermentation (SSF) of microwave/alkali-pretreated rice straw to produce ethanol were investigated. From the obtained data, it was found that the addition of the nonionic surfactants at 2.5?g/L had a positive effect on SSF. The maximum ethanol yield (76 and 55%) was obtained after 72?hr for rice straw using Kluyveromyces marxianus and Saccharomyces cerevisiae, respectively. Also, it was found that the ethanol yield increases with increasing HLB of the prepared nonionic surfactants by increasing ethylene oxide units. The adsorption of nonionic surfactants on lignocelluloses is proposed to be due to hydrophobic and hydrogen bonding interactions between nonionic surfactants and the lignin part in the lignocelulose. It can be concluded that additions of surface-active compounds, such as nonionic surfactants, increase enzymatic conversion of rice straw for bioethanol purposes.     

An Optimized Immunohistochemistry Technique Improves NMO-IgG Detection: Study Comparison with Cell-Based Assays

Cell-based assays (CBA) have increased the sensitivity of the neuromyelitis optica (NMO)-IgG/aquaporin-4-antibody detection compared to classical tissue-based indirect assays. We describe the sensitivity of an optimized immunohistochemistry (IHC-o) to detect NMO-IgG/aquaporin-4-antibody in comparison with that of two CBA: an in-house (CBA-ih) and a commercial (CBA-c) assay (Euroimmun, Germany). Coded serum from 103 patients with definite NMO and 122 inflammatory controls were studied by IHC-o, CBA-ih, and CBA-c. IHC-o used the same protocol described to detect antibodies against cell surface antigens. CBA-ih used live cells transfected with the aquaporin-4-M23-isoform. The sensitivity of the IHC-o was 74.8% (95% confidence interval [CI] 65-83) and was similar to that of the CBA-ih 75.7% (95% CI 66-84) and the CBA-c 73.8% (95% CI 64-82). The specificity of the three assays was 100% (95% CI 97-100). Interassay concordance was high, 100 of 103 samples were coincident in all techniques. The optimized immunohistochemistry proves to be as sensitive and specific as the cell-based assays. This assay extends the available tools for NMO-IgG/aquaporin-4-antibody detection.     

Changes of organic constituents of crop residues and poultry wastes during fermentation for biogas production

Summary Rice straw, maize, and cotton stalks and poultry droppings, both as such and with either wheat straw litter or sawdust litter, were used as substrates for biogasification. Water slurry combinations, each containing a crop residue and a type of poultry wastes, were prepared to achieve a uniform C/N ratio 301 (w/w) and a total solids content 10% (w/v). Biogas generated and its methane component, as well as changes brought about in the major organic constituents of the feedstocks, were monitored in laboratory biogas digesters for 90 days at 35°C. The maximum cumulative volumes of biogas and methane, were respectively 30 and 14 l/l with rice straw plus wheat straw poultry droppings. The minimum volumes were 15 l biogas/l with cotton stalks + sawdust poultry droppings and 8 l methane/l with rice straw + sawdust poultry droppings. Rice straw combinations gave the highest rates of volatile solids disappearance, short-chain fatty acid formation, and NH₄ -N liberation. No consistent trend among the poultry wastes mixed with each crop residue was evident. Changes in water-soluble substances, protein, fats, hemicellulose, cellulose and lignin depended on the components of each feedstock mixture.

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Changement dans les composants organiques des résidus de récolte et des déchets avicoles lors de la fermentation pour la production de biogaz

Résumé La paille de riz, les fanes de maïs et les tiges de coton ainsi que le lisier avicole, comme tels ou en mélange avec la litière de paille de froment ou de sciure ont servi de substrats pour la biométhanisation. On a préparé des combinaisons de boues aqueuses, chacune contenant un résidu de récolte et un type de lisier avicole, de manière à respecter un rapport C/N uniforme de 301 (p/p) et un contenu total en solides de 10% (p/vol.). On a suivi le biogaz produit et son contenu en méthane, ainsi que les changements apparus dans les principaux constituents organiques des substrats, dans des digesteurs de laboratoire pendant 90 jours à 35°C. On a obtenu les volumes cumulés maximum respectivement de 30 l/l de biogaz et de 14/l de méthane pour la paille de riz plus le lisier avicole avec paille de froment. On a obtenu les volumes cumulés minimum de 15l/l de biogaz pour les tiges de coton avec le lisier avicole avec sciure de bois et de 8 l/l de méthane pour la paille de riz et le lisier de poule avec sciure de bois. Les combinaisons avec la paille de riz ont donné les vitesses les plus élevées de disparition des solides volatils, de formation d'acides gras à courte chaîne et de libération d'azote ammoniacal. Il n'y a pas de tendances évidentes pour les lisiers avicoles mélangés avec les divers résidus de récolte. Les changements en substances hydro-solubles, en protéines, graisses, hémicellulose, cellulose et lignine dépendent de la composition de chaque mélange de substrats.