Dissociation of different conformations of ubiquitin ions

The fragmentation pathways of different conformations of three charge states of ubiquitin ions are examined using ion mobility/collisional activation/time-of-flight techniques. Mass spectra for fragments for different conformers of a single charge state appear to be identical (within the experimental reproducibility). These results are consistent with a mechanism in which different conformers of each charge state rearrange to similar dissociation transition states prior to fragment formation.     

Solution and crystallographic studies of branched multivalent ligands that inhibit the receptor-binding of cholera toxin

The structure-based design of multivalent ligands offers an attractive strategy toward high affinity protein inhibitors. The spatial arrangement of the receptor-binding sites of cholera toxin, the causative agent of the severe diarrheal disease cholera and a member of the AB(5) bacterial toxin family, provides the opportunity of designing branched multivalent ligands with 5-fold symmetry. Our modular synthesis enabled the construction of a family of complex ligands with five flexible arms each ending with a bivalent ligand. The largest of these ligands has a molecular weight of 10.6 kDa. These ligands are capable of simultaneously binding to two toxin B pentamer molecules with high affinity, thus blocking the receptor-binding process of cholera toxin. A more than million-fold improvement over the monovalent ligand in inhibitory power was achieved with the best branched decavalent ligand. This is better than the improvement observed earlier for the corresponding nonbranched pentavalent ligand. Dynamic light scattering studies demonstrate the formation of concentration-dependent unique 1:1 and 1:2 ligand/toxin complexes in solution with no sign of nonspecific aggregation. This is in complete agreement with a crystal structure of the branched multivalent ligand/toxin B pentamer complex solved at 1.45 A resolution that shows the specific 1:2 ligand/toxin complex formation in the solid state. These results reiterate the power of the structure-based design of multivalent protein ligands as a general strategy for achieving high affinity and potent inhibition.     

Investigations of tellurium-modified self-assembled monolayers of benzenedithiol on gold surface as molecular gate

In this paper, we report the obtention of tellurium modified with self-assembled monolayers of benzenedithiol on a gold surface as a molecular gate. The switching and electronic transport characteristics of the modified gold surface were investigated by cyclic voltammetry (CV). The CV results indicate that the switching of benzenedithiol gates is controlled by the oxidation state of tellurium, which is regulated by the applied potentials.     

Stochastic simulation of catalytic surface reactions in the fast diffusion limit

The master equation of a lattice gas reaction tracks the probability of visiting all spatial configurations. The large number of unique spatial configurations on a lattice renders master equation simulations infeasible for even small lattices. In this work, a reduced master equation is derived for the probability distribution of the coverages in the infinite diffusion limit. This derivation justifies the widely used assumption that the adlayer is in equilibrium for the current coverages and temperature when all reactants are highly mobile. Given the reduced master equation, two novel and efficient simulation methods of lattice gas reactions in the infinite diffusion limit are derived. The first method involves solving the reduced master equation directly for small lattices, which is intractable in configuration space. The second method involves reducing the master equation further in the large lattice limit to a set of differential equations that tracks only the species coverages. Solution of the reduced master equation and differential equations requires information that can be obtained through short, diffusion-only kinetic Monte Carlo simulation runs at each coverage. These simulations need to be run only once because the data can be stored and used for simulations with any set of kinetic parameters, gas-phase concentrations, and initial conditions. An idealized CO oxidation reaction mechanism with strong lateral interactions is used as an example system for demonstrating the reduced master equation and deterministic simulation techniques.     

PNA-DNA duplexes, triplexes, and quadruplexes are stabilized with trans-cyclopentane units

Peptide nucleic acids (PNAs) are non-natural nucleic acid mimics that bind to complementary DNA and RNA with high affinity and selectivity. PNA can bind to nucleic acids in a number of different ways. Currently, the formation of PNA-oligonucleotide duplex, triplex, and quadruplex structures have been reported. PNAs have been used in numerous biomedicial applications, but there are few strategies to predictably improve the binding properties of PNAs by backbone modification. We have been studying the benefits of incorporating (S,S)-trans-cyclopentane diamine units (tcyp) into the PNA backbone. In this Communication, we report the improvement in stability associated with tcyp incorporation into PNA-DNA duplexes, triplexes, and quadruplexes. The broad utility of this modification across multiple types of PNA structures is unique and should prove useful in the development of applications that rely on PNA.     

A new ultrafast and high-throughput mass spectrometric approach for the therapeutic drug monitoring of the multi-targeted anti-folate pemetrexed in plasma from lung cancer patients

An analytical assay has been developed and validated for ultrafast and high-throughput mass spectrometric determination of pemetrexed concentrations in plasma using matrix assisted laser desorption/ionization–triple quadrupole–tandem mass spectrometry. Patient plasma samples spiked with the internal standard methotrexate were measured by multiple reaction monitoring. The detection limit was 0.4 fmol/μL, lower limit of quantification was 0.9 fmol/μL, and upper limit of quantification was 60 fmol/μL, respectively. Overall observed pemetrexed concentrations in patient samples ranged between 8.7 (1.4) and 142.7 (20.3)?pmol/μL (SD). The newly developed mass spectrometric assay is applicable for (routine) therapeutic drug monitoring of pemetrexed concentrations in plasma from non-small cell lung cancer patients.     

Invariant Measures for Set-Valued Dynamical Systems

A continuous map on a compact metric space, regarded as a dynamical system by iteration, admits invariant measures. For a closed relation on such a space, or, equivalently, an upper semicontinuous set-valued map, there are several concepts which extend this idea of invariance for a measure. We prove that four such are equivalent. In particular, such relation invariant measures arise as projections from shift invariant measures on the space of sample paths. There is a similarly close relationship between the ideas of chain recurrence for the set-valued system and for the shift on the sample path space.

     

Synthesis of silylated methylenecyclopropanes

2-Trimethylsilylmethylenecyclopropane (=3) was synthesized by reaction of lithio methylenecyclopropane with TMSCl. The lithium salt of (=3) reacts with some electrophiles by α- or γ-attack depending on the nature of the electrophile. Whereas alkenylbromides $\text{8}$ and $\text{9}$ or alkinylbromide $\text{10}$ give exclusively α-attack, benzaldehyde reacts with γ-alkylation.     

Application of diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) for the identification of potential diagenesis and crystallinity changes in teeth

During burial, diagenetic alteration can invalidate the paleodietary signature, which the hydroxyapatite (Ca₅(PO₄)₃OH) matrix in incremental tissues, such as tooth enamel, provides. Thus, analytical methods that can evaluate diagenetic changes are crucial in anthropological and archaeological investigations. Modern deciduous tooth enamel (exfoliated) from Solis, Mexico and Kalama, Egypt, as well as Bronze Age (circa 2200 B.C.E.) adult enamel from (present-day) Tell Abraq, U.A.E. and adult enamel from the New York African Burial Ground (NYABG) in lower Manhattan, were analyzed using diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS). The samples were compared to synthetic hydroxyapatite powder and bone ash samples. The DRIFTS spectra of tooth enamel yielded similar infra red finger print pattern to previous pellet-based FTIR spectra in both absorbance and Kubelka–Munk units. The study demonstrates that DRIFTS is a convenient alternative to pellet-based transmission FTIR in testing diagenetic changes in hard tissue for archaeological investigations. Tooth enamel samples contained a higher carbonate–phosphate ratio than synthetic hydroxyapatite and bone ash standard samples. Correlations are reported between Crystallinity Index (CI_Ab) and carbonate–phosphate ratio, strontium–calcium ratio, and fluoride peak appearance. Crystallinity indexes (CI_Ab) were in the range of 2.6–3.8 (in absorbance units) and Kubelka–Munk Crystallinity indexes (CI_KM) were in the range of 3.1–4.9.