Silk reinforced with graphene or carbon nanotubes spun by spiders

Here, we report the production of silk incorporating graphene and carbon nanotubes directly by spider spinning, after spraying spiders with the corresponding aqueous dispersions. We observe a significant increment of the mechanical properties with respect to the pristine silk, in terms of fracture strength, Young's and toughness moduli. We measure a fracture strength up to 5.4 GPa, a Young's modulus up to 47.8 GPa and a toughness modulus up to 2.1 GPa, or 1567 J/g, which, to the best of our knowledge, is the highest reported to date, even when compared to the current toughest knotted fibres. This approach could be extended to other animals and plants and could lead to a new class of bionic materials for ultimate applications

Structural View of a Non Pfam Singleton and Crystal Packing Analysis

Comparative genomic analysis has revealed that in each genome a large number of open reading frames have no homologues in other species. Such singleton genes have attracted the attention of biochemists and structural biologists as a potential untapped source of new folds. Cthe_2751 is a 15.8 kDa singleton from an anaerobic, hyperthermophile Clostridium thermocellum. To gain insights into the architecture of the protein and obtain clues about its function, we decided to solve the structure of Cthe_2751.The protein crystallized in 4 different space groups that diffracted X-rays to 2.37 Å (P3(1)21), 2.17 Å (P2(1)2(1)2(1)), 3.01 Å (P4(1)22), and 2.03 Å (C222(1)) resolution, respectively. Crystal packing analysis revealed that the 3-D packing of Cthe_2751 dimers in P4(1)22 and C222(1) is similar with only a rotational difference of 2.69° around the C axes. A new method developed to quantify the differences in packing of dimers in crystals from different space groups corroborated the findings of crystal packing analysis. Cthe_2751 is an all α-helical protein with a central hydrophobic core providing thermal stability via π:cation and π: π interactions. A ProFunc analysis retrieved a very low match with a splicing endonuclease, suggesting a role for the protein in the processing of nucleic acids.Non-Pfam singleton Cthe_2751 folds into a known all α-helical fold. The structure has increased sequence coverage of non-Pfam proteins such that more protein sequences can be amenable to modelling. Our work on crystal packing analysis provides a new method to analyze dimers of the protein crystallized in different space groups. The utility of such an analysis can be expanded to oligomeric structures of other proteins, especially receptors and signaling molecules, many of which are known to function as oligomers

Computational analysis of a novel mutation in ETFDH gene highlights its long-range effects on the FAD-binding motif

<p>Abstract</p> <p>Background</p> <p>Multiple acyl-coenzyme A dehydrogenase deficiency (MADD) is an autosomal recessive disease caused by the defects in the mitochondrial electron transfer system and the metabolism of fatty acids. Recently, mutations in electron transfer flavoprotein dehydrogenase (<it>ETFDH</it>) gene, encoding electron transfer flavoprotein:ubiquinone oxidoreductase (ETF:QO) have been reported to be the major causes of riboflavin-responsive MADD. To date, no studies have been performed to explore the functional impact of these mutations or their mechanism of disrupting enzyme activity.</p> <p>Results</p> <p>High resolution melting (HRM) analysis and sequencing of the entire <it>ETFDH </it>gene revealed a novel mutation (p.Phe128Ser) and the hotspot mutation (p.Ala84Thr) from a patient with MADD. According to the predicted 3D structure of ETF:QO, the two mutations are located within the flavin adenine dinucleotide (FAD) binding domain; however, the two residues do not have direct interactions with the FAD ligand. Using molecular dynamics (MD) simulations and normal mode analysis (NMA), we found that the p.Ala84Thr and p.Phe128Ser mutations are most likely to alter the protein structure near the FAD binding site as well as disrupt the stability of the FAD binding required for the activation of ETF:QO. Intriguingly, NMA revealed that several reported disease-causing mutations in the ETF:QO protein show highly correlated motions with the FAD-binding site.</p> <p>Conclusions</p> <p>Based on the present findings, we conclude that the changes made to the amino acids in ETF:QO are likely to influence the FAD-binding stability.</p

Potential anticancer peptides design from the cysteine rich plant defensins: An in silico approach

Cancer is the second leading cause of mortality worldwide preceded by cardiovascular diseases. The therapeutic approaches for drug developmentinclude the use of small molecules, antibodies, peptidesor short nucleic acid sequences. The peptide-based drugs have been developed to treat many diseases like cardiovascular diseases, cancer, metabolic disorders, immunological diseases and viral infections. More than 80 peptide drugs are already in the market. These therapeutic peptides have several important benefits over antibodies and proteins due to their small size, ease for chemical synthesis and further the ability to penetrate cell membrane. Furthermore, peptide drugs have high specificity, activity, and affinity. The plant defensins BcDef1, TPP3, NaD1, 2N2R and 2LR3 have been studied for their role in wide range of diseases. This study focussed on the conformation of plant defensins rich in disulfide bonds. The structure for BcDef1 has been predicted from the conformational ensemble. Then, we designed anticancer peptides from these defensins with computational methods. The designed anticancer peptides have been studied for their immunogenicity as well as homology with human proteome. The role of designed peptides has been suggested for interferon-gamma induction, the later has been shown to possess a very important role in cancer

Supplemental Information 4: Actin depolymerization study

Melioidosis, an infection caused by the facultative intracellular pathogen Burkholderia pseudomallei, has been classified as an emerging disease with the number of patients steadily increasing at an alarming rate. B. pseudomalleipossess various virulence determinants that allow them to invade the host and evade the host immune response, such as the type III secretion systems (TTSS). The products of this specialized secretion system are particularly important for the B. pseudomallei infection. Lacking in one or more components of the TTSS demonstrated different degrees of defects in the intracellular lifecycle of B. pseudomallei. Further understanding the functional roles of proteins involved in B. pseudomallei TTSS will enable us to dissect the enigma of B. pseudomallei-host cell interaction. In this study, BipC (a translocator), which was previously reported to be involved in the pathogenesis of B. pseudomallei, was further characterized using the bioinformatics and molecular approaches. The bipCgene, coding for a putative invasive protein, was first PCR amplified from B. pseudomallei K96243 genomic DNA and cloned into an expression vector for overexpression in Escherichia coli. The soluble protein was subsequently purified and assayed for actin polymerization and depolymerization. BipC was verified to subvert the host actin dynamics as demonstrated by the capability to polymerize actin in vitro. Homology modeling was also attempted to predict the structure of BipC. Overall, our findings identified that the protein encoded by the bipC gene plays a role as an effector involved in the actin binding activity to facilitate internalization of B. pseudomalleiinto the host cells

Auxin production by the plant trypanosomatid Phytomonas\ud serpens and auxin homoeostasis in infected tomato fruits

Previously we have characterized the complete gene encoding a pyruvate decarboxylase (PDC)/indolepyruvate\ud decarboxylase (IPDC) of Phytomonas serpens, a trypanosomatid highly abundant in tomato fruits. Phylogenetic analyses\ud indicated that the clade that contains the trypanosomatid protein behaves as a sister group of IPDCs of γ-proteobacteria.\ud Since IPDCs are key enzymes in the biosynthesis of the plant hormone indole-3-acetic acid (IAA), the ability for IAA\ud production by P. serpens was investigated. Similar to many microorganisms, the production of IAA and related indolic\ud compounds, quantified by high performance liquid chromatography, increased inP. serpens media in response to amounts\ud of tryptophan. The auxin functionality was confirmed in the hypocotyl elongation assay. In tomato fruits inoculated with\ud P. serpensthe concentration of free IAA had no significant variation, whereas increased levels of IAA-amide and IAA-ester\ud conjugates were observed. The data suggest that the auxin produced by the flagellate is converted to IAA conjugates,\ud keeping unaltered the concentration of free IAA. Ethanol also accumulated inP. serpens-conditioned media, as the result of\ud a PDC activity. In the article we discuss the hypothesis of the bifunctionality of P. serpens PDC/IPDC and provide a\ud three-dimensional model of the enzyme.FAPESP) (grant number 2010/50957-1)(CNPq) (grant number 304793/2009-4)FAPESP (grant number 2008/50209-5

Analysis of the role of RNA silencing protein 1 (Rsp1) in the biogenesis of ~23-24 nt sRNAs in Tetrahymena thermophila

RNA interference (RNAi) pathways regulate a variety of biological processes, including normal cell growth and development, through the action of protein-RNA complexes containing small RNAs (sRNAs). Our research focused an RNAi pathway in the ciliated unicellular eukaryote Tetrahymena thermophila. This pathway produces ~23-24 nucleotide (nt) sRNAs through the action of RNA-dependent RNA polymerase (RdRP) complexes (complexes termed RdRCs) and their interaction with an RNA nuclease called Dicer 2 (Dcr2). The accumulation of sRNAs also requires a protein called RNA Silencing Protein 1 (Rsp1) which associates with a subset of RdRC proteins. In this study, we first sought to learn more about the potential function and evolutionary conservation of Rsp1 by examining its sequence. Our results indicate Rsp1 may have structural similarity to RNA polymerases, including RdRPs, but lacks the conserved catalytic residues for RNA synthesis. We also identified Rsp1-like predicted proteins in other Tetrahymena species, but no clear homologs in more distantly related organisms. Second, we tested three hypotheses for why Rsp1 is required for sRNA accumulation: 1) Rsp1 stabilizes the precursor RNA transcripts that are later processed into sRNA, 2) Rsp1 is necessary for the accumulation of RdRC proteins, and 3) Rsp1 is necessary for correct assembly of RdRCs. Our experimental results indicate that Rsp1 does not appear to regulate sRNA biogenesis by regulating the levels of sRNA precursors or RdRC proteins levels. Instead, purification of RdRCs revealed that in strains lacking Rsp1, RdRCs cannot be recovered. This suggests that RdRCs are disrupted somehow in the absence of Rsp1