Two GTPs are consumed on EF-Tu per peptide bond in poly(Phe) synthesis, in spite of switching stoichiometry of the EF-Tu·aminoacyl-tRNA complex with temperature

AbstractRecent observations indicate that the stoichiometry for the complex between EF-Tu · GTP and aminoacyl-tRNA (aa-tRNA) changes with temperature. At 37°C two EF-Tu · GTPs bind one aa-tRNA in an extended ternary complex, but at 0°C the complex has 1:1 stoichiometry. However, the present experiments show that there are two GTPs hydrolyzed on EF-Tu per peptide bond in poly(Phe) synthesis at 37°C as well as at 0°C. This indicates two different pathways for the enzymatic binding of aa-tRNA to the A-site on the ribosome

Nanomachine biocatalysts: Tools for cell-free artificial metabolic networks

Assembling cell-free, cascading multi-enzyme enzyme reactions into artificial metabolic networks for the conversion of low value renewable feedstocks into high value products represents a fourth wave of biocatalysis for renewable green chemistry and synthetic biology applications [1]. However, major limitations to both applications include the cost of producing multiple purified enzymes and of providing a continuous supply of diffusible cofactors or cosubstrates [2]. We have applied synthetic biology principles to produce fusion proteins between synthetic enzymes and their cofactor-recycling partner enzymes, with concomitant in situ recycling of a modified tethered cofactor, with an added conjugation protein element to allow immobilization of the nanomachines to a surface. This has enabled the construction of nanomachine flow reactors which can be combined in an interchangeable, “plug-and-play” manner to construct complex synthetic networks or Nanofactories. Synthesis of the anti-diabetic drug, D-fagomine, reductive amination to produce various chiral or conjugated amines (Fig. 1) and deracemization of alcohols have been used to exemplify the principles, and we have demonstrated tethered cofactor recycling of ATP, NAD(H)+ and NADP(H)+, as well as ligand-directed immobilization of a variety of enzymes to illustrate the use of these nanomachine biocatalysts as tools for the de novo construction of in vitro metabolic networks for synthetic biology. Our research is currently exploring the use of frugal innovation principles to integrate key capabilities in reactor design with on-line analytics for real-time reaction monitoring, and, subsequently, dynamic control over the platform’s fluidics via feedback loops. We aim to demonstrate the utility of such systems for cell-free metabolic engineering to enable fine chemical synthesis, with additional applications possible in bioremediation and environmental sensing. Please click Additional Files below to see the full abstract

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Orientation and characterization of immobilized antibodies for improved immunoassays (Review)

Orientation of surface immobilized capture proteins, such as antibodies, plays a critical role in the performance of immunoassays. The sensitivity of immunodiagnostic procedures is dependent on presentation of the antibody, with optimum performance requiring the antigen binding sites be directed toward the solution phase. This review describes the most recent methods for oriented antibody immobilization and the characterization techniques employed for investigation of the antibody state. The introduction describes the importance of oriented antibodies for maximizing biosensor capabilities. Methods for improving antibody binding are discussed, including surface modification and design (with sections on surface treatments, three-dimensional substrates, selfassembled monolayers, and molecular imprinting), covalent attachment (including targeting amine, carboxyl, thiol and carbohydrates, as well as "click" chemistries), and (bio)affinity techniques (with sections on material binding peptides, biotin-streptavidin interaction, DNA directed immobilization, Protein A and G, Fc binding peptides, aptamers, and metal affinity). Characterization techniques for investigating antibody orientation are discussed, including x-ray photoelectron spectroscopy, spectroscopic ellipsometry, dual polarization interferometry, neutron reflectometry, atomic force microscopy, and time-of-flight secondary-ion mass spectrometry. Future perspectives and recommendations are offered in conclusion

CYP101J2, CYP101J3, and CYP101J4, 1,8-cineolehydroxylating cytochrome P450 monooxygenases from Sphingobium yanoikuyae strain B2

We report the isolation and characterization of three new cytochrome P450 monooxygenases: CYP101J2, CYP101J3, and CYP101J4. These P450s were derived from Sphingobium yanoikuyae B2, a strain that was isolated from activated sludge based on its ability to fully mineralize 1,8-cineole. Genome sequencing of this strain in combination with purification of native 1,8-cineole-binding proteins enabled identification of 1,8-cineole-binding P450s. The P450 enzymes were cloned, heterologously expressed (N-terminally His(6) tagged) in Escherichia coli BL21(DE3), purified, and spectroscopically characterized. Recombinant whole-cell biotransformation in E. coli demonstrated that all three P450s hydroxylate 1,8-cineole using electron transport partners from E. coli to yield a product putatively identified as (1S)-2α-hydroxy-1,8-cineole or (1R)-6α-hydroxy-1,8-cineole. The new P450s belong to the CYP101 family and share 47% and 44% identity with other 1,8-cineole-hydroxylating members found in Novosphingobium aromaticivorans and Pseudomonas putida. Compared to P450(cin) (CYP176A1), a 1,8-cineole-hydroxylating P450 from Citrobacter braakii, these enzymes share less than 30% amino acid sequence identity and hydroxylate 1,8-cineole in a different orientation. Expansion of the enzyme toolbox for modification of 1,8-cineole creates a starting point for use of hydroxylated derivatives in a range of industrial applications. IMPORTANCE CYP101J2, CYP101J3, and CYP101J4 are cytochrome P450 monooxygenases from S. yanoikuyae B2 that hydroxylate the monoterpenoid 1,8-cineole. These enzymes not only play an important role in microbial degradation of this plant-based chemical but also provide an interesting route to synthesize oxygenated 1,8-cineole derivatives for applications as natural flavor and fragrance precursors or incorporation into polymers. The P450 cytochromes also provide an interesting basis from which to compare other enzymes with a similar function and expand the CYP101 family. This could eventually provide enough bacterial parental enzymes with similar amino acid sequences to enable in vitro evolution via DNA shuffling

Gadolinium-DTPA amphiphile nanoassemblies: Agents for magnetic resonance imaging and neutron capture therapy

Engineering biocompatible and physiologically stable nanoscaled therapeutics and imaging agents with the ability to target tumor tissue is a key challenge for the advancement of cancer therapeutics and diagnostic imaging. Here, we present chelating amphiphiles with the capacity to form nanoassembled colloidal particles containing high payloads of gadolinium (Gd) ions. We present the in situ synthesis and complexation of Gd with colloidal nanoassemblies (NAs) based on diethylenetriamine pentaacetic acid (DTPA) amphiphiles. This method allows for facile simultaneous incorporation of several metal ions for applications in multimodal imaging and therapeutics. The diverse internally nanostructured NAs made from sole precursor amphiphiles and their Gd-complexes were investigated by synchrotron small angle X-ray scattering (SAXS) and cryo-TEM. Depending on the molecular structure of the amphiphiles, the structures of NAs range from micelles to liposomes, to colloidal particles of inverse hexagonal (hexosomes) and inverse bicontinuous cubic phases (cubosomes), to multilayered nanospheres. The in vitro contrast activity of these NAs exhibited high relaxivity values as T1-weighted magnetic resonance imaging (MRI) contrast enhancement agents. Further, an α-Flag antibody fragment (Fab′) was bioconjugated to the surface of the Gd-complexed NAs. The binding ability of these targeted NAs to a FLAG-tagged protein was confirmed by SDS-PAGE. The in vitro cytotoxicity against two cell lines showed that except for the negatively charged micellar Gd-DTPA amphiphile, liposomal and higher order internally nanostructured NAs had low cell toxicity. The efficient cellular uptake of Gd-NAs by melanoma cancer cells was also investigated. This journal i

Paclitaxel-loaded self-assembled lipid nanoparticles as targeted drug delivery systems for the treatment of aggressive ovarian cancer

Chemotherapy using cytotoxic agents, such as paclitaxel (PTX), is one of the most effective treatments for advanced ovarian cancer. However, due to nonspecific targeting of the drug and the presence of toxic solvents required for dissolving PTX prior to injection, there are several serious side effects associated with this treatment. In this study, we explored self-assembled lipid-based nanoparticles as PTX carriers, which were able to improve its antitumour efficacy against ovarian cancer. The nanoparticles were also functionalized with epidermal growth factor receptor (EGFR) antibody fragments to explore the benefit of tumor active targeting. The formulated bicontinuous cubic- and sponge-phase nanoparticles, which were stabilized by Pluronic F127 and a lipid poly(ethylene glycol) stabilizer, showed a high capacity of PTX loading. These PTX-loaded nanoparticles also showed significantly higher cytotoxicity than a free drug formulation against HEY ovarian cancer cell lines in vitro. More importantly, the nanoparticle-based PTX treatments, with or without EGFR targeting, reduced the tumor burden by 50% compared to PTX or nondrug control in an ovarian cancer mouse xenograft model. In addition, the PTX-loaded nanoparticles were able to extend the survival of the treatment groups by up to 10 days compared to groups receiving free PTX or nondrug control. This proof-of-concept study has demonstrated the potential of these self-assembled lipid nanomaterials as effective drug delivery nanocarriers for poorly soluble chemotherapeutics, such as PTX

ToF-SIMS and Principal Component Analysis Investigation of Denatured, Surface-Adsorbed Antibodies

Antibody denaturation at solid–liquid interfaces plays an important role in the sensitivity of protein assays such as enzyme-linked immunosorbent assays (ELISAs). Surface immobilized antibodies must maintain their native state, with their antigen binding (Fab) region intact, to capture antigens from biological samples and permit disease detection. In this work, two identical sample sets were prepared with whole antibody IgG, F­(ab′)₂ and Fc fragments, immobilized to either a silicon wafer or a diethylene glycol dimethyl ether plasma polymer surface. Analysis was conducted on one sample set at day 0, and the second sample set after 14 days in vacuum, with time-of-flight secondary ion mass spectrometry (ToF-SIMS) for molecular species representative of denaturation. A 1003 mass fragment peak list was compiled from ToF-SIMS data and compared to a 35 amino acid mass fragment peak list using principal component analysis. Several ToF-SIMS secondary ions, pertaining to disulfide and thiol species, were identified in the 14 day (presumably denatured) samples. A substrate and primary ion independent marker for denaturation (aging) was then produced using a ratio of mass peak intensities according to denaturation ratio: [<i>I</i>_61.9534 + <i>I</i>_62.9846 + <i>I</i>_122.9547 + <i>I</i>_84.9609 + <i>I</i>_120.9461]/[<i>I</i>_30.9979 + <i>I</i>_42.9991 + <i>I</i>_73.0660 + <i>I</i>_147.0780]. The ratio successfully identifies denaturation on both the silicon and plasma polymer substrates and for spectra generated with Mn⁺, Bi⁺, and Bi₃⁺ primary ions. We believe this ratio could be employed to as a marker of denaturation of antibodies on a plethora of substrates