Effect of cyclization of N-terminal glutamine and carbamidomethyl-cysteine (residues) on the chromatographic behavior of peptides in reversed-phase chromatography

N-terminal loss of ammonia is a typical peptide modification chemical artifact observed in bottom-up proteomics experiments. It occurs both in vivo for N-terminal glutamine and in vitro following enzymatic cleavage for both N-terminal glutamine and cysteine alkylated with iodoacetamide. In addition to a mass change of −17.03 Da, modified peptides exhibit increased chromatographic retention in reversed-phase (RP) HPLC systems. The magnitude of this increase varies significantly depending on the peptide sequence and the chromatographic condition used. We have monitored these changes for extensive sets (more than 200 each) of tryptic Gln and Cys N-terminated species. Peptides were separated on 100 Å pore size C18 phases using identical acetonitrile gradient slopes with 3 different eluent compositions: 0.1% trifluoroacetic acid; 0.1% formic acid and 20 mM ammonium formate at pH 10 as ion-pairing modifiers. The observed effect of this modification on RP retention is the product of increased intrinsic hydrophobicity of the modified N-terminal residue, lowering or removing the effect of ion-pairing formation on the hydrophobicity of adjacent residues at acidic pHs; and possibly the increased formation of amphipathic helical structures when the positive charge is removed. Larger retention shifts were observed for Cys terminated peptides compared to Gln, and for smaller peptides. Also the size of the retention increase depends on the eluent conditions: pH 10 ? trifluoroacetic acid < formic acid. Different approaches for incorporation these findings in the peptide retention prediction models are discussed.     

Multiple time scale molecular dynamics for fluids with orientational degrees of freedom. II. Canonical and isokinetic ensembles

We have developed several multiple time stepping techniques to overcome the limitations on efficiency of molecular dynamics simulations of complex fluids. They include the modified canonical and isokinetic schemes, as well as the extended isokinetic Nosé-Hoover chain approach. The latter generalizes the method of Minary, Tuckerman, and Martyna for translational motion [Phys. Rev. Lett. 93, 150201 (2004)] to systems with both translational and orientational degrees of freedom. Although the microcanonical integrators are restricted to relatively small outer time steps of order of 16 fs, we show on the basis of molecular dynamics simulations of ambient water that in the canonical and isokinetic thermostats the size of these steps can be increased to 50 and 75 fs, respectively (at the same inner time step of 4 fs). Within the generalized isokinetic Nosé-Hoover chain algorithm we have derived, huge outer time steps of order of 500 fs can be used without losing numerical stability and affecting equilibrium properties.     

A three-way synergy of triple-modified Bi2WO6/Ag/N-TiO2 nanojunction film for enhanced photogenerated charges utilization

We demonstrate a general strategy to prepare Bi(2)WO(6)/Ag/N-TiO(2) film with double visible-light-active components bridged by Ag nanoparticles as an electron shuttle, which exhibits enhanced photocatalytic activity and photoelectrochemical performance under visible light.     

An autocatalytic chromogenic and fluorogenic photochemical reaction controlled by nucleic acids

The autocatalytic photochemical reaction, which is potentially controlled by any selected nucleic acid, is highly sequence specific and not inhibited by its products, was developed. This reaction generates colored and fluorescent products, which can be monitored by the naked eye.     

Structure and dynamics of the fast lithium ion conductor "Li7La3Zr2O12"

The solid lithium-ion electrolyte "Li(7)La(3)Zr(2)O(12)" (LLZO) with a garnet-type structure has been prepared in the cubic and tetragonal modification following conventional ceramic syntheses routes. Without aluminium doping tetragonal LLZO was obtained, which shows a two orders of magnitude lower room temperature conductivity than the cubic modification. Small concentrations of Al in the order of 1 wt% were sufficient to stabilize the cubic phase, which is known as a fast lithium-ion conductor. The structure and ion dynamics of Al-doped cubic LLZO were studied by impedance spectroscopy, dc conductivity measurements, (6)Li and (7)Li NMR, XRD, neutron powder diffraction, and TEM precession electron diffraction. From the results we conclude that aluminium is incorporated in the garnet lattice on the tetrahedral 24d Li site, thus stabilizing the cubic LLZO modification. Simulations based on diffraction data show that even at the low temperature of 4 K the Li ions are blurred over various crystallographic sites. This strong Li ion disorder in cubic Al-stabilized LLZO contributes to the high conductivity observed. The Li jump rates and the activation energy probed by NMR are in very good agreement with the transport parameters obtained from electrical conductivity measurements. The activation energy E(a) characterizing long-range ion transport in the Al-stabilized cubic LLZO amounts to 0.34 eV. Total electric conductivities determined by ac impedance and a four point dc technique also agree very well and range from 1 × 10(-4) Scm(-1) to 4 × 10(-4) Scm(-1) depending on the Al content of the samples. The room temperature conductivity of Al-free tetragonal LLZO is about two orders of magnitude lower (2 × 10(-6) Scm(-1), E(a) = 0.49 eV activation energy). The electronic partial conductivity of cubic LLZO was measured using the Hebb-Wagner polarization technique. The electronic transference number t(e-) is of the order of 10(-7). Thus, cubic LLZO is an almost exclusive lithium ion conductor at ambient temperature.     

Recombination and chemical energy accommodation coefficients from chemical dynamics simulations: O/O2 mixtures reacting over a β-cristobalite (001) surface

A microkinetic model is developed to study the reactivity of an O/O(2) gas mixture over a β-cristobalite (001) surface. The thermal rate constants for the relevant elementary processes are either inferred from quasiclassical trajectory calculations or using some statistical approaches, resting on a recently developed interpolated multidimensional potential energy surface based on density functional theory. The kinetic model predicts a large molecular coverage at temperatures lower than 1000 K, in contrary to a large atomic coverage at higher temperatures. The computed atomic oxygen recombination coefficient, mainly involving atomic adsorption and Eley-Rideal recombination, is small and increases with temperature in the 700-1700 K range (0.01 < γ(O) < 0.02) in good agreement with experiments. In the same temperature range, the estimated chemical energy accommodation coefficient, the main contribution to which is the atomic adsorption process is almost constant and differs from unity (0.75 < β(O) < 0.80).     

A Criterion for Relative Compactness of a Sequence of Measure-Valued Random Processes

A criterion for relative compactness of a sequence of measure-valued processes is proved and exemplified.     

Water molecules in a protein cavity detected by a statistical-mechanical theory

Four water molecules confined in a small cavity of hen egg-white lysozyme were detected by means of the three-dimensional (3D) RISM theory, a statistical-mechanical theory of molecular solutions. This is the first theoretical realization of confined molecules in a protein without making nonsense tricks, such as placing the molecules in the space a priori. Possible impacts which the result may have on biochemistry and biophysics, including the molecular recognition, enzymatic reactions, etc., are discussed.     

Nanosensors having dipicolinic acid imprinted nanoshell for Bacillus cereus spores detection

Molecular imprinted polymers (MIPs) as a recognition element for sensors are increasingly of interest and MIP nanoclusters have started to appear in the literature. In this study, we have proposed a novel thiol ligand-capping method with polymerizable methacryloylamido-cysteine (MAC) attached to gold–silver nanoclusters, reminiscent of a self-assembled monolayer and have reconstructed surface shell by synthetic host polymers based on molecular imprinting method for recognition. In this method, methacryloylamidoantipyrine–terbium ((MAAP)₂–Tb(III)) has been used as a new metal-chelating monomer via metal coordination–chelation interactions and dipicolinic acid (DPA) which is main participant of Bacillus cereus spores used as a model. Nanoshell sensors with templates give a cavity that is selective for DPA. The DPA can simultaneously chelate to Tb(III) metal ion and fit into the shape-selective cavity. Thus, the interaction between Tb(III) ion and free coordination spheres has an effect on the binding ability of the gold–silver nanoclusters nanosensor. The binding affinity of the DPA imprinted nanoclusters has been investigated by using the Langmuir and Scatchard methods, and the respective affinity constants (K _affinity) determined were found to be 1.43 × 10⁴ and 9.1 × 10⁶ mol L^?1.