Isolation of a peptide ligand for affinity purification of factor VIII using phage display

Polypeptides for use in affinity chromatography of factor VIII were identified using phage display technology. Phage libraries were designed to express polypeptide fusions containing five to seven residues flanked by two cysteines that form a disulfide bond. Individual bacteriophage were selected for the ability of these polypeptides to bind factor VIII, and then release the protein under mild elution conditions. Strong consensus sequences were observed that appear to be necessary for this reversible interaction. Chemically synthesized ligands identified by this screening were immobilized onto a chromatographic support and used for affinity purification of factor VIII from a complex feedstream. A chromatographic step was developed that provided a 10000-fold reduction in host cell proteins and DNA, while providing exceptional product recovery.     

Discovery of a new phosphotyrosine mimetic for PTP1B using breakaway tethering

Protein tyrosine phosphatases play important roles in many signaling cascades involved in human disease. The identification of druglike inhibitors for these targets is a major challenge, and the discovery of suitable phosphotyrosine (pY) mimetics remains one of the key difficulties. Here we describe an extension of tethering technology, "breakaway tethering", which is ideally suited for discovering such new chemical entities. The approach involves first irreversibly modifying a protein with an extender that contains both a masked thiol and a known pY mimetic. The extender is then cleaved to release the pY mimetic, unmasking the thiol. The resulting protein is screened against a library of disulfide-containing small molecule fragments; any molecules with inherent affinity for the pY binding site will preferentially form disulfides with the extender, allowing for their identification by mass spectrometry. The ability to start from a known substrate mimimizes perturbation of protein structure and increases the opportunity to probe the active site using tethering. We applied this approach to the anti-diabetic protein PTP1B to discover a pY mimetic which belongs to a new molecular class and which binds in a novel fashion.     

Ligand and base additive effects on the reversibility of nucleophilic addition in palladium-catalyzed allylic aminations monitored by nucleophile crossover

A nucleophile crossover experiment was used to monitor the reversibility of nucleophilic addition of benzylamine to π-allylpalladium complexes. Dppe, dppp, dppb, and PHOX showed more crossover than PPh₃ and dppm in both DMF and dichloromethane. Crossover was inhibited by the addition of DBU or Cs₂CO₃, but much less elimination to diene side products was observed with Cs₂CO₃. Analysis of percent crossover vs. percent reaction completion using the PHOX ligand revealed that with added DBU or Cs₂CO₃ crossover only began occurring after 100% completion had been reached.     

Isoform specific gene auto-regulation via miRNAs: a case study on miR-128b and ARPP-21

In this study, we investigate whether miRNAs located within “host” protein-coding genes may regulate the expression of their host genes. We find that 43 of 174 miRNAs encoded within RefSeq genes are predicted to target their host genes. Statistical analysis of this phenomenon suggests that gene auto-regulation via miRNAs may be under positive selective pressure. Our analysis also indicates that several of the 43 miRNAs have a much lower expectation of targeting their host genes by chance than others. Among these examples, we identify miR-128b:ARPP-21 (cyclic AMP-regulated phosphoprotein, 21 kD) as a case in which both the miRNA and the target site are also evolutionarily conserved. We provide experimental support for this miRNA:target interaction via reporter silencing assays, and present evidence that this isoform-specific gene auto-regulation has been preserved in vertebrate species in order to prevent detrimental consequences of ARPP-21 over-expression in brain.     

An ion mobility spectrometer sensor system for subsurface use

An ion mobility spectrometer (IMS) probe system for real-time, subsurface soil-gas sampling applications is presented. The system includes an IMS and supporting electronics encased in a 51 mm diameter stainless steel probe housing. The IMS was challenged in the laboratory with 2,6-di-tert-butylpyridine (DtBP) and tetrachloroethylene (PCE) in zero air yielding reduced ion mobility constants (K_o) values of 1.42 cm²/Vs (n = 3) and 1.79 ± 0.01 cm²/Vs (n = 3), respectively. A resolving power of 38 and 31 was obtained for DtBP and PCE, respectively. The system was deployed at a PCE-contaminated site to demonstrate its performance under field conditions. PCE was detected in the vapor samples as evidenced by peaks with a K_o value of 1.80 ± 0.01 cm²/Vs for two measurements that were taken 6 min apart. The presence of PCE at the contaminated site was confirmed by GC-MS analysis of a gas sample at an EPA-certified laboratory, suggesting that this IMS system can be used to detect PCE under field conditions.     

Circular Dichroism of Amino Acids: Following the Structural Formation of Phenylalanine

Circular dichroism (CD) is frequently used to assess the secondary structure of peptides and proteins, whereas less attention has been given to their building blocks, that is, single amino acids, as they do not possess a secondary structure. Here, we follow the CD signal of amino acids and reveal that several acids exhibit a unique CD pattern as a function of their concentration. Accordingly, we propose an eight‐level classification of the CD signal of the various amino acids. Special focus is given to the CD pattern of phenylalanine (Phe), for which we observe the formation of an ultra‐narrow CD peak (full width at high maximum of only 5 nm). This CD peak can be attributed to the formation of Phe‐based chiral structural features. Further support for the formation of an ordered structure is given by using NMR, and the additional self‐assembly process of Phe to tubular structures.     

Cubosomes: The Next Generation of Smart Lipid Nanoparticles?

Cubosomes are highly stable nanoparticles formed from the lipid cubic phase and stabilized by a polymer based outer corona. Bicontinuous lipid cubic phases consist of a single lipid bilayer that forms a continuous periodic membrane lattice structure with pores formed by two interwoven water channels. Cubosome composition can be tuned to engineer pore sizes or include bioactive lipids, the polymer outer corona can be used for targeting and they are highly stable under physiological conditions. Compared to liposomes, the structure provides a significantly higher membrane surface area for loading of membrane proteins and small drug molecules. Owing to recent advances, they can be engineered in vitro in both bulk and nanoparticle formats with applications including drug delivery, membrane bioreactors, artificial cells, and biosensors. This review outlines recent advances in cubosome technology enabling their application and provides guidelines for the rational design of new systems for biomedical applications.     

A generalization of Baer’s Lemma

There is a classical result known as Baer’s Lemma that states that an R-module E is injective if it is injective for R. This means that if a map from a submodule of R, that is, from a left ideal L of R to E can always be extended to R, then a map to E from a submodule A of any R-module B can be extended to B; in other words, E is injective. In this paper, we generalize this result to the category q _ω consisting of the representations of an infinite line quiver. This generalization of Baer’s Lemma is useful in proving that torsion free covers exist for q _ω.      

Improved synthesis of C4α- and C4β-methyl analogues of 2-aminobicyclo[3.1.0]hexane-2,6-dicarboxylate

An efficient and divergent synthesis of C4α- and C4β-methyl-substituted analogues of 2-aminobicyclo[3.1.0]hexane 2,6-dicarboxylate, which are important tools in the study of metabotropic glutamate receptor function, has been achieved. By taking advantage of an unanticipated facial selectivity of the bicyclo[3.1.0]hexane ring system, either the C4α- or C4β-methyl substituent was introduced in a highly stereoselective and high-yielding manner.