Tyrosyl rotamer interconversion rates and the fluorescence decays of N-acetyltyrosinamide and short tyrosyl peptides

It has long been recognized that the fluorescence lifetimes of amino acid residues such as tyrosine and tryptophan depend on the rotameric configuration of the aromatic side chain, but estimates of the rate of interchange of rotameric states have varied widely. We report measurements of the rotameric populations and interchange rates for tyrosine in N-acetyltyrosinamide (NATyrA), the tripeptide Tyr-Gly-Gly (YGG), and the pentapeptide Leu-enkephalin (YGGFL). The fluorescence lifetimes were analyzed to determine the rotameric interchange rates in the context of a model incorporating exchange among three rotameric states. Maximum entropy method analysis verified the presence of three fluorescence decay components for YGGFL and two for YGG and NATyrA. Rotameric exchange between the gauche(-) and trans states occurred on the nanosecond time scale, whereas exchange with the gauche(+) state occurred on a longer time scale. Good agreement was obtained with rotameric populations and exchange rates from molecular dynamics simulations. Quenching by iodide was used to vary the intrinsic fluorescence lifetimes, providing additional constraints on the determined interchange rates. The temperature dependence was measured to determine barriers to exchange of the two most populated rotamers of 3, 5, and 7 kcal/mol for NATyrA, YGG, and YGGFL, respectively.     

Alkylamine-ligated H93G myoglobin cavity mutant: a model system for endogenous lysine and terminal amine ligation in heme proteins such as nitrite reductase and cytochrome f

His93Gly sperm whale myoglobin (H93G Mb) has the proximal histidine ligand removed to create a cavity for exogenous ligand binding, providing a remarkably versatile template for the preparation of model heme complexes. The investigation of model heme adducts is an important way to probe the relationship between coordination structure and catalytic function in heme enzymes. In this study, we have successfully generated and spectroscopically characterized the H93G Mb cavity mutant ligated with less common alkylamine ligands (models for Lys or the amine group of N-terminal amino acids) in numerous heme iron states. All complexes have been characterized by electronic absorption and magnetic circular dichroism spectroscopy in comparison with data for parallel imidazole-ligated H93G heme iron moieties. This is the first systematic spectral study of models for alkylamine- or terminal amine-ligated heme centers in proteins. High-spin mono- and low-spin bis-amine-ligated ferrous and ferric H93G Mb adducts have been prepared together with mixed-ligand ferric heme complexes with alkylamine trans to nitrite or imidazole as heme coordination models for cytochrome c nitrite reductase or cytochrome f, respectively. Six-coordinate ferrous H93G Mb derivatives with CO, NO, and O(2) trans to the alkylamine have also been successfully formed, the latter for the first time. Finally, a novel high-valent ferryl species has been generated. The data in this study represent the first thorough investigation of the spectroscopic properties of alkylamine-ligated heme iron systems as models for naturally occurring heme proteins ligated by Lys or terminal amines.     

Effect of mechanical activation of reagents’ mixture on the high-temperature synthesis of Al<Subscript>2</Subscript>O<Subscript>3</Subscript>–TiB<Subscript>2</Subscript> composite powder

A powder mixture of Al/TiO₂/H₃BO₃ = 10/3/6 in molar ratio was used in this study to form the Al₂O₃–TiB₂ ceramic composite via thermite reactions (combustion synthesis). As no combustion synthesis occurred for an unmilled sample in a furnace, the mixture was milled in a planetary ball-mill for various milling times, and the as-milled samples were in situ synthesized in the furnace at a heating rate of 10 °C/min. The differential scanning calorimetry (DSC) measurements were performed with the same heating rate on the unmilled and the as-milled samples to evaluate the influences of the milling on the mechanisms and efficiencies of reactions. Although no combustion synthesis occurred for the unmilled sample in the furnace, two exothermic peaks were detected in its DSC curve after the melting of the Al. For the as-milled samples, significant changes revealed in the DSC curves, suggest that the milling process before the combustion synthesis changed the mechanisms and efficiencies of reactions. In addition, the intensity and the temperature of the exothermic peaks in the DSC curves changed by increasing the milling time. According to the XRD analyses, by enhancing the milling time, the purity of the final products would increase, confirming that the efficiency of the reactions increased. Finally, the microstructures of the as-milled and as-synthesized samples were examined by a SEM, and it was shown that the morphology of the reactant powders was altered by increasing the milling time.     

Bayesian process optimization using failure amplification method

This work is motivated by a problem of optimizing printed circuit board manufacturing using design of experiments. The data are binary, which poses challenges in model fitting and optimization. We use the idea of failure amplification method to increase the information supplied by the data and then use a Bayesian approach for model fitting. The Bayesian approach is implemented using Gaussian process models on a latent variable representation. It is demonstrated that the failure amplification method coupled with a Bayesian approach is highly suitable for optimizing a process with binary data. Copyright © 2010 John Wiley & Sons, Ltd.     

A genetically encoded infrared probe

An orthogonal tRNA/aminoacyl-tRNA synthetase pair has been evolved that makes it possible to selectively and efficiently incorporate para-cyanophenylalanine (pCNPhe) into proteins in E. coli at sites specified by the amber nonsense codon, TAG. Substitution of pCNPhe for histidine-64 in myoglobin (Mb) affords a sensitive vibrational probe of ligand binding. This methodology provides a useful infrared reporter of protein structure, biomolecular interactions, and conformational changes.     

Identification and structural characterization of in vivo metabolites of ketorolac using liquid chromatography electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS)

In vivo metabolites of ketorolac (KTC) have been identified and characterized by using liquid chromatography positive ion electrospray ionization high resolution tandem mass spectrometry (LC/ESI-HR-MS/MS) in combination with online hydrogen/deuterium exchange (HDX) experiments. To identify in vivo metabolites, blood urine and feces samples were collected after oral administration of KTC to Sprague-Dawley rats. The samples were prepared using an optimized sample preparation approach involving protein precipitation and freeze liquid separation followed by solid-phase extraction and then subjected to LC/HR-MS/MS analysis. A total of 12 metabolites have been identified in urine samples including hydroxy and glucuronide metabolites, which are also observed in plasma samples. In feces, only O-sulfate metabolite and unchanged KTC are observed. The structures of metabolites were elucidated using LC-MS/MS and MS(n) experiments combined with accurate mass measurements. Online HDX experiments have been used to support the structural characterization of drug metabolites. The main phase I metabolites of KTC are hydroxylated and decarbonylated metabolites, which undergo subsequent phase II glucuronidation pathways.     

Identification and structural characterization of in vivo metabolites of ketorolac using liquid chromatography electrospray ionization tandem mass spectrometry (LC/ESI‐MS/MS)

In vivo metabolites of ketorolac (KTC) have been identified and characterized by using liquid chromatography positive ion electrospray ionization high resolution tandem mass spectrometry (LC/ESI‐HR‐MS/MS) in combination with online hydrogen/deuterium exchange (HDX) experiments. To identify in vivo metabolites, blood urine and feces samples were collected after oral administration of KTC to Sprague–Dawley rats. The samples were prepared using an optimized sample preparation approach involving protein precipitation and freeze liquid separation followed by solid‐phase extraction and then subjected to LC/HR‐MS/MS analysis. A total of 12 metabolites have been identified in urine samples including hydroxy and glucuronide metabolites, which are also observed in plasma samples. In feces, only O‐sulfate metabolite and unchanged KTC are observed. The structures of metabolites were elucidated using LC‐MS/MS and MSⁿ experiments combined with accurate mass measurements. Online HDX experiments have been used to support the structural characterization of drug metabolites. The main phase I metabolites of KTC are hydroxylated and decarbonylated metabolites, which undergo subsequent phase II glucuronidation pathways. Copyright © 2012 John Wiley & Sons, Ltd.     

Stimulus-responsiveness and drug release from porous silicon films ATRP-grafted with poly(N-isopropylacrylamide)

In this report, we employ surface-initiated atom transfer radical polymerization (SI-ATRP) to graft a thermoresponsive polymer, poly(N-isopropylacrylamide) (PNIPAM), of controlled thickness from porous silicon (pSi) films to produce a stimulus-responsive inorganic-organic composite material. The optical properties of this material are studied using interferometric reflectance spectroscopy (IRS) above and below the lower critical solution temperature (LCST) of the PNIPAM graft polymer with regard to variation of pore sizes and thickness of the pSi layer (using discrete samples and pSi gradients) and also the thickness of the PNIPAM coatings. Our investigations of the composite's thermal switching properties show that pore size, pSi layer thickness, and PNIPAM coating thickness critically influence the material's thermoresponsiveness. This composite material has considerable potential for a range of applications including temperature sensors and feedback controlled drug release. Indeed, we demonstrate that modulation of the temperature around the LCST significantly alters the rate of release of the fluorescent anticancer drug camptothecin from the pSi-PNIPAM composite films.     

Tailored polymers by free radical processes

This paper describes a versatile and effective method for the control of free radical polymerization and its use in the preparation of narrow polydispersity polymers of various architectures. Living character is conferred to conventional free radical polymerization by the addition of a thiocarbonylthio compound of general structure S=C(Z)SR, for example, S=C(Ph)SC(CH₃)₂Ph. The mechanism involves Reversible Addition-Fragmentation chain Transfer and, for convenience of referral, we have designated it the RAFT polymerization. The process is compatible with a very wide range of monomers including functional monomers such as acrylic acid, hydroxyethyl methacrylate, and dimethylaminoethyl methacrylate. Examples of narrow polydispersity (≤1.2) homopolymers, copolymers, gradient copolymers, end-functional polymers, star polymers, A-B diblock and A-B-A triblock copolymers are presented.