Complexes of native ubiquitin and dodecyl sulfate illustrate the nature of hydrophobic and electrostatic interactions in the binding of proteins and surfactants

A previous study, using capillary electrophoresis (CE) [J. Am. Chem. Soc. 2008, 130, 17384-17393], reported that six discrete complexes of ubiquitin (UBI) and sodium dodecyl sulfate (SDS) form at different concentrations of SDS along the pathway to unfolding of UBI in solutions of SDS. One complex (which formed between 0.8 and 1.8 mM SDS) consisted of native UBI associated with approximately 11 molecules of SDS. The current study used CE and (15)N/(13)C-(1)H heteronuclear single quantum coherence (HSQC) NMR spectroscopy to identify residues in folded UBI that associate specifically with SDS at 0.8-1.8 mM SDS, and to correlate these associations with established biophysical and structural properties of this well-characterized protein. The ability of the surface charge and hydrophobicity of folded UBI to affect the association with SDS (at concentrations below the CMC) was studied, using CE, by converting lys-ε-NH(3)(+) to lys-ε-NHCOCH(3) groups. According to CE, the acetylation of lysine residues inhibited the binding of 11 SDS ([SDS] < 2 mM) and decreased the number of complexes of composition UBI-(NHAc)(8)·SDS(n) that formed on the pathway of unfolding of UBI-(NHAc)(8) in SDS. A comparison of (15)N-(1)H HSQC spectra at 0 mM and 1 mM SDS with calculated electrostatic surface potentials of folded UBI (e.g., solutions to the nonlinear Poisson-Boltzmann (PB) equation) suggested, however, that SDS binds preferentially to native UBI at hydrophobic residues that are formally neutral (i.e., Leu and Ile), but that have positive electrostatic surface potential (as predicted from solutions to nonlinear PB equations); SDS did not uniformly interact with residues that have formal positive charge (e.g., Lys or Arg). Cationic functional groups, therefore, promote the binding of SDS to folded UBI because these groups exert long-range effects on the positive electrostatic surface potential (which extend beyond their own van der Waals radii, as predicted from PB theory), and not because cationic groups are necessarily the site of ionic interactions with sulfate groups. Moreover, SDS associated with residues in native UBI without regard to their location in α-helix or β-sheet structure (although residues in hydrogen-bonded loops did not bind SDS). No correlation was observed between the association of an amino acid with SDS and the solvent accessibility of the residue or its rate of amide H/D exchange. This study establishes a few (of perhaps several) factors that control the simultaneous molecular recognition of multiple anionic amphiphiles by a folded cytosolic protein.     

Porous gadolinia-doped ceria with adjustable pore sizes using PI-b-PEO copolymer as the structure-directing agent

In this study, we report that by coupling the kinetics of both hydrolysis and condensation of the oxide precursors and the kinetics of self-assembly process of the block copolymer, we can synthesize both mesoporous and macroporous gadolinia-doped ceria (GDC) with one chemical composition but different processing conditions. Our process uses poly(isoprene-b-ethylene oxide) as the structure-directing agent and cerium and gadolinium acetylacetonates as the precursors for the sol?Cgel synthesis of GDC. By controlling the extent of the hydrolysis and condensation of the oxide precursor before mixing with the copolymer, we can adjust the hydrophilic domain size from nanometers to micrometers. As a result, highly crystalline porous GDC with dominant mesopores (15?nm?<?d?<?50?nm) or macropores (50?nm?<?d?<?5???m) are produced after removal of the copolymer via a two-step calcination treatment. The discovery of this study offers a facile and viable approach to produce meso- and macro-porous materials, in a ??one-pot?? synthesis with one chemical composition but different processing conditions to control pore sizes.     

Supramolecular host-guest interaction for labeling and detection of cellular biomarkers

Be my guest: A supramolecular host-guest interaction is utilized for highly efficient bioorthogonal labeling of cellular targets. Antibodies labeled with a cyclodextrin host molecule bind to adamantane-labeled magnetofluorescent nanoparticles (see picture) and provide an amplifiable strategy for biomarker detection that can be adapted to different diagnostic techniques such as molecular profiling or magnetic cell sorting.     

Arbitrary self-assembly of peptide extracellular microscopic matrices

Two faces for one matrix: A single bifaceted cyclopeptide block forms highly branched, porous, and intricate fibrillar networks, which span microscopic dimensions and mimic the extracellular matrix to support cell growth and proliferation. The peptide block has two domains connected with triglycine linkers (GGG); the domains consist of positively (blue) and negatively (red) charged heptads that provide interactions between different blocks.     

A Role for the 2' OH of Peptidyl-tRNA Substrate in Peptide Release on the Ribosome Revealed through RF-Mediated Rescue

The 2' OH of the peptidyl-tRNA substrate is thought to be important for catalysis of both peptide bond formation and peptide release in the ribosomal active site. The release reaction also specifically depends on a release factor protein (RF) to hydrolyze the ester linkage of the peptidyl-tRNA upon recognition of stop codons in the A site. Here, we demonstrate that certain amino acid substitutions (in particular those containing hydroxyl or thiol groups) in the conserved GGQ glutamine of release factor RF1 can rescue defects in the release reaction associated with peptidyl-tRNA substrates lacking a 2' OH. We explored this rescue effect through biochemical and computational approaches that support a model where the 2' OH of the P-site substrate is critical for orienting the nucleophile in a hydrogen-bonding network productive for catalysis.     

Qualitative analysis of the fluorophosphonate-based chemical probes using the serine hydrolases from mouse liver and poly-3-hydroxybutyrate depolymerase (PhaZ) from Bacillus thuringiensis

The serine hydrolase family consists of more than 200 members and is one of the largest enzyme families in the human genome. Although up to 50?% of this family remains unannotated, there are increasing evidences that activities of certain serine hydrolases are associated with diseases like cancer neoplasia, invasiveness, etc. By now, several activity-based chemical probes have been developed and are applied to profile the global activity of serine hydrolases in diverse proteomes. In this study, two fluorophosphonate (FP)-based chemical probes were synthesized. Further examination of their abilities to label and pull down serine hydrolases was conducted. In addition, the poly-3-hydroxybutyrate depolymerase (PhaZ) from Bacillus thuringiensis was demonstrated as an appropriate standard serine hydrolase, which can be applied to measure the labeling ability and pull-down efficiency of FP-based probes. Furthermore, mass spectrometry (MS) was used to identify the serine residue that covalently bonded to the active probes. Finally, these FP-based probes were shown capable of establishing the serine hydrolase profiles in diverse mouse tissues; the serine hydrolases pulled down from mouse liver organ were further identified by MS. In summary, our study provides an adequate method to evaluate the reactivity of FP-based probes targeting serine hydrolases.

Neuronal growth promoting sesquiterpene-neolignans; syntheses and biological studies

The use of small molecules that can promote neuronal growth represents a promising approach to regenerative science. Along these lines we have developed separate short or modular syntheses of the natural products caryolanemagnolol and clovanemagnolol, small molecules previously shown to promote neuronal growth and induce choline acetyltransferase activity. The postulated biosynthetic pathways, potentially leading to the assembly of these molecules in nature, have guided the laboratory syntheses, allowing the preparation of both natural products in as few as two steps. With synthetic access to the compounds as single enantiomers we have examined clovanemagnolol's ability to promote the growth of embryonic hippocampal and cortical neurons. Clovanemagnolol has been shown to be a potent neurotrophic agent, promoting neuronal growth at concentrations of 10 nM.     

A microfluidic "baby machine" for cell synchronization

Common techniques used to synchronize eukaryotic cells in the cell cycle often impose metabolic stress on the cells or physically select for size rather than age. To address these deficiencies, a minimally perturbing method known as the "baby machine" was developed previously. In the technique, suspension cells are attached to a membrane, and as the cells divide, the newborn cells are eluted to produce a synchronous population of cells in the G1 phase of the cell cycle. However, the existing "baby machine" is only suitable for cells which can be chemically attached to a surface. Here, we present a microfluidic "baby machine" in which cells are held onto a surface by pressure differences rather than chemical attachment. As a result, our method can in principle be used to synchronize a variety of cell types, including cells which may have weak or unknown surface attachment chemistries. We validate our microfluidic "baby machine" by using it to produce a synchronous population of newborn L1210 mouse lymphocytic leukemia cells in G1 phase.     

Preparation and Characterization of Substituted 3‐Benzothiazol‐2‐Ylcoumarins

A series of substituted 3‐benzothiazolylcoumarins was prepared from condensation of 2‐hydroxy‐benzaldehyde and 2‐cyanomethylbenzothiazole to investigate the effect of the nature and position of substituents on their absorption and fluorescent behavior. Compounds with a substituent containing a heteroatom which attached at the C6 position showed a split broad absorption band. Solutions of these compounds in various solvents exhibited brilliant blue fluorescence. The emission intensity for compounds with an alkoxy group at the C6 or C7 position in DMF was approximately 7‐ and 15‐fold higher than for the corresponding precursor and quinine sulfate solution, respectively. These compounds also exhibit high thermal stability in solid state.     

Risk arbitrage in the Nikkei put warrant market of 1989–1990

This paper discusses the Nikkei put warrant market in Toronto and New York during 1989–1990. Three classes of long term American puts were traded which when evaluated in yen are ordinary, product and exchange asset puts, respectively. Type I do not involve exchange rates for yen investors. Type II, called quantos, fix in advance the exchange rate to be used on expiry in the home currency. Type III evaluate the strike and spot prices of the Nikkei Stock Average in the home currency rather than in yen. For typically observed parameters, type I are theoretically more valuable than type II which in turn are more valuable than type III. In late 1989 and early 1990 there were significant departures from fair values in various markets. This was a market with a set of complex financial instruments that even sophisticated investors needed time to learn about to price properly. Investors in Canada were willing to buy puts at far more than fair value based on historical volatility. In addition, US investors overpriced type II puts fixed in dollars rather than the type I's in yen. This led to cross border and US traded (on the same exchange) low risk hedges. The market's convergence to efficiency (that is, all puts priced within transaction cost bands) took about one month after the introduction of the US puts in early 1990 leading to significant profits for the hedgers.