Insights into human Lck SH3 domain binding specificity: different binding modes of artificial and native ligands

We analyzed the ligand binding specificity of the lymphocyte specific kinase (Lck) SH3 domain. We identified artificial Lck SH3 ligands using phage display. In addition, we analyzed Lck SH3 binding sites within known natural Lck SH3 binding proteins using an Lck specific binding assay on membrane-immobilized synthetic peptides. On one hand, from the phage-selected peptides, representing mostly special class I' ligands, a well-defined consensus sequence was obtained. Interestingly, a histidine outside the central polyproline motif contributes significantly to Lck SH3 binding affinity and specificity. On the other hand, we confirmed previously mapped Lck SH3 binding sites in ADAM15, HS1, SLP76, and NS5A, and identified putative Lck SH3 binding sites of Sam68, FasL, c-Cbl, and Cbl-b. Without exception, the comparatively diverse Lck SH3 binding sites of all analyzed natural Lck SH3 binding proteins emerged as class II proteins. Possible explanations for the observed variations between artificial and native ligands-which are not due to significant K(D) value differences as shown by calculating Lck SH3 affinities of artificial peptide PD1-Y(-3)R as well as for peptides comprising putative Lck SH3 binding sites of NS5A, Sos, and Sam68-are discussed. Our data suggest that phage display, a popular tool for determining SH3 binding specificity, must-at least in the case of Lck-not irrevocably mirror physiologically relevant protein-ligand interactions.     

Challenges in Developing Electrodes,Electrolytes, and Diagnostics Tools to Understand and Advance Sodium‐Ion Batteries

Considering the natural abundance and low cost of sodium resources, sodium‐ion batteries (SIBs) have received much attention for large‐scale electrochemical energy storage. However, smart structure design strategies and good mechanistic understanding are required to enable advanced SIBs with high energy density. In recent years, the exploration of advanced cathode, anode, and electrolyte materials, as well as advanced diagnostics have been extensively carried out. This review mainly focuses on the challenging problems for the attractive battery materials (i.e., cathode, anode, and electrolytes) and summarizes the latest strategies to improve their electrochemical performance as well as presenting recent progress in operando diagnostics to disclose the physics behind the electrochemical performance and to provide guidance and approaches to design and synthesize advanced battery materials. Outlook and perspectives on the future research to build better SIBs are also provided.     

Foreign gene expression in Hansenula polymorpha. A system for the synthesis of small functional peptides

 We describe the synthesis and purification of two functional peptides, namely human insulin-like growth factor II (IGF-II) and Xenopus laevis magainin II in Hansenula polymorpha after their synthesis as hybrid proteins fused to the C terminus of endogenous amine oxidase. The hybrid genes, placed under control of the H. polymorpha alcohol oxidase promoter (P_AOX), were integrated into the genomic alcohol oxidase locus, yielding stable production strains. High-level synthesis of the fusion proteins, exceeding 20% of total cellular protein, was obtained when the transformed strains were grown in methanol-limited chemostat cultures; when expressed by itself, i.e. in the absence of the amine oxidase gene, IGF-II could not be recovered from crude cell extracts, probably as a result of rapid proteolytic degradation. Accumulation in peroxisomes did not significantly affect the IGF-II protein stability when expressed in the absence of the carrier protein. Apparently, fusion to the large (±78 kDa) amine oxidase carrier particularly stabilizes the peptides and prevents them from proteolysis. After partial purification, the fusion partners were readily separated by factor Xa treatment. Received: 16 June 1995 / Accepted: 20 September 1995     

Isolation and Characterization of Clostridium butyricum DSM 5431 Mutants with Increased Resistance to 1,3-Propanediol and Altered Production of Acids

Clostridium butyricum mutants were isolated from the parent strain DSM 5431 after mutagenesis with N-methyl-N(prm1)-nitro-N-nitrosoguanidine and two selection procedures: osmotic pressure and the proton suicide method. Isolated mutants were more resistant to glycerol and to 1,3-propanediol (1,3-PD) than was the wild type, and they produced more biomass. In batch culture on 62 g of glycerol per liter, the wild type produced more acetic acid than butyrate, with an acetate/butyrate ratio of 5.0, whereas the mutants produced almost the same quantities of both acids or more butyrate than acetate with acetate/butyrate ratios from 0.6 to 1.1. The total acid formation was higher in the wild-type strain. Results of analysis of key metabolic enzymatic activities were in accordance with the pattern of fermentation product formation: either the butyrate kinase activity increased or the acetate kinase activity decreased in cell extracts of the mutants. A decreased level of the hydrogenase and NADH-ferredoxin activities concomitant with an increase in ferredoxin-NAD(sup+) reductase activities supports the conclusion that the maximum percentage of NADH available and used for the formation of 1,3-PD was higher for the mutants (97 to 100%) than for the wild type (70%). In fed-batch culture, at the end of the fermentation (72 h for the wild-type strain and 80 to 85 h for the mutants), 44% more glycerol was consumed and 50% more 1,3-PD was produced by the mutants than by the wild-type strain.     

Identification and Crystallization of a Protease-Resistant Core of Calnexin That Retains Biological Activity

Calnexin is a molecular chaperone that facilitates folding of glycoproteins in the endoplasmic reticulum (ER). The cloned lumenal domain of canine calnexin, cnxΔTMC, retains its biological activity without the transmembrane and cytosolic region. For the purpose of structure determination we generated a crystallizable core by mild proteolysis and identified its termini by N-terminal sequencing and molecular mass determination. A truncated gene was cloned accordingly. Its product, cnxΔN25C15, was purified to apparent homogeneity and crystallized. This truncated variant remains biologically active as shown by its binding to monoglucosylated oligosaccharides and functional interaction with ERp57. A heavy atom derivative was identified.     

Advancements in the design and scalable production of viral gene transfer vectors

The last 10 years have seen a rapid expansion in the use of viral gene transfer vectors, with approved therapies and late stage clinical trials underway for the treatment of genetic disorders, and multiple forms of cancer, as well as prevention of infectious diseases through vaccination. With this increased interest and widespread adoption of viral vectors by clinicians and biopharmaceutical industries, there is an imperative to engineer safer and more efficacious vectors, and develop robust, scalable and cost‐effective production platforms for industrialization. This review will focus on major innovations in viral vector design and production systems for three of the most widely used viral vectors: Adenovirus, Adeno‐Associated Virus, and Lentivirus.     

Regulation of acetate kinase and butyrate kinase by acids in Clostridium acetobutylicum

Abstract The effects of acetic acid and butyric acid on acetate kinase, butyrate kinase and acetoacetate decarboxylase levels are studied. It is shown that acetate kinase biosynthesis is regulated by acetic acid whereas butyric acid has no effect. Acetate kinase specific activity is found to be maximal at the beginning of the fermentation, and decreases as acetic acid concentration increases in the medium. Butyrate kinase is not regulated by the end-product acids; its specific activity is constant during the fermentation. In the presence of acetic acid, acetoacetate decarboxylase biosynthesis represents a 4-fold increase in activity over a culture without acetate and a 1.7-fold increase over that obtained in presence of butyrate. The technique of fermentation used allows us to show that bacterial growth and solventogenesis may occur simultaneously.     

Chemometric Tools to Highlight the Variability of the Chemical Composition and Yield of Lebanese Origanum syriacum L. Essential Oil

This study deals with the variation in the yield and composition of Lebanese Origanum syriacum L. essential oil (EO) according to harvesting time, drying methods used, and geographical location. Plant material was harvested twice a month all over 2013 and 2014 from Qartaba and Achkout located at high altitude and from Byblos at low altitude. EOs of the aerial parts were obtained by hydrodistillation. The highest yields were obtained at full flowering stage and slightly reduced after flowering. The GC/MS analysis revealed the presence of 50 components representing 90.49 – 99.82%, 88.79 – 100%, and 95.28 – 100% of the total oil extracted from plants harvested from Qartaba, Achkout, and Byblos, respectively. The major components in the oils were: carvacrol (2.1 – 79.8%), thymol (0.3 – 83.7%), p‐cymene (2.8 – 43.8%), thymoquinone (0.4 – 27.7%), γ‐terpinene (0.4 – 10.0%), octan‐3‐ol (0.3 – 4.9%), caryophyllene oxide (0.2 – 4.7%), oct‐1‐en‐3‐ol (0.3 – 3.7%), β‐caryophyllene (0.7 – 3.2%), cis‐sabinene hydrate (0.1 – 2.8%), terpinen‐4‐ol (0.1 – 2.8%), and α‐terpinene (0.2 – 2.2%). Independent components analysis (ICA) revealed that two groups were discriminated, reflecting compositional differences in the EOs profiles of the Lebanese oregano samples: O. syriacum grown in Qartaba and Achkout belongs to carvacrol chemotype, while O. syriacum grown in Byblos belongs to thymol chemotype. The flowering phase was the most productive period in terms of yield, bringing marked changes in the EO composition by increasing the amounts of carvacrol or thymol, and decreasing those of thymoquinone and p‐cymene.     

A scaffoldless technique for self-generation of three-dimensional keratinospheroids on liquid crystal surfaces

We describe a new scaffold-free three-dimensional (3D) cell culture model using cholesteryl ester based lyotropic liquid crystal (LC) substrates. Keratinocytes were deposited randomly on the LC surface where they self-assembled into 3D microtissues or keratinospheroids. The cell density required to form spheroids was optimized. We investigated cell viability using dead/live cell assays. The adhesion characteristics of cells within the microtissues were determined using histological sectioning and immunofluorescence staining. Fourier transform infrared spectroscopy (FTIR) was used to characterize the biochemistry of the keratinospheroids. We found that both cells and microtissues could migrate on the LC surface. The viability study indicated approximately 80% viability of cells in the microtissues up to 20 days of culture. Strong intercellular adhesion was observed in the stratification of the multi-layered microspheroids using field emission-scanning electron microscopy (FE-SEM) and histochemical staining. The cytoskeleton and vinculins of the cells in the microtissues were expressed diffusely, but the microtissues were enriched with lipids and nucleic acids, which indicates close resemblance to the conditions in vivo. The basic 3D culture model based on LC may be used for cell and microtissue migration studies in response to cytochemical treatment.