Synthesis of functionalized rab GTPases by a combination of solution- or solid-phase lipopeptide synthesis with expressed protein ligation

Prenylated proteins with non-native functionalities are generally very difficult to obtain by recombinant or enzymatic means. The semisynthesis of preparative amounts of prenylated Rab guanosine triphosphatases (GTPases) from recombinant proteins and synthetic prenylated peptides depends largely on the availability of functionalised prenylated peptides corresponding to the proteins' native structure or modifications thereof. Here, we describe and compare solution-phase and solid-phase strategies for the generation of peptides corresponding to the prenylated C terminus of Rab7 GTPase. The solid-phase with utilisation of a hydrazide linker emerges as the more favourable approach. It allows a fast and practical synthesis of pure peptides and gives a high degree of flexibility in their modification. To facilitate the analysis of semisynthetic proteins, the synthesised peptides were equipped with a fluorescent group. Using the described approach, we introduced fluorophores at several different positions of the Rab7 C terminus. The position of the incorporated fluorescent groups in the peptides did not influence the protein-ligation reaction, as the generated peptides could be ligated onto thioester-tagged Rab7. However, it was found that the positioning of the fluorescent group had an influence on the functionality of the Rab7 proteins; analysis of the interaction of the semisynthetic Rab7 proteins with REP (Rab escort protein) and GDI (guanosine diphosphate dissociation inhibitor) molecules revealed that modification of the peptide side chains or of the C-terminal isoprenoid did not significantly interfere with complex formation. However, functionalisation of the C terminus was found to have an adverse effect on complex formation and stability, possibly reflecting low structural flexibility of the Rab GDI/REP molecules in the vicinity of the lipid-binding site.     

Addressing the metabolic activation potential of new leads in drug discovery: a case study using ion trap mass spectrometry and tritium labeling techniques

Metabolic activation of drug candidates to electrophilic reactive metabolites that can covalently modify cellular macromolecules may result in acute and/or idiosyncratic immune system-mediated toxicities in humans. This presents a significant potential liability for the future development of these compounds as safe therapeutic agents. We present here an example of an approach where sites of metabolic activation within a new drug candidate series were rapidly identified using online liquid chromatography/multi-stage mass spectrometry on an ion trap mass spectrometer. This was accomplished by trapping the reactive intermediates formed upon incubation of compounds with rat and human liver microsomes as their corresponding glutathione conjugates and mass spectral characterization of these thiol adducts. Based on the structures of the GSH adducts identified, potential sites and mechanisms of bioactivation within the chemical structure were proposed. These metabolism studies were interfaced with iterative structural modifications of the chemical series in order to block these bioactivation sites within the molecule. This strategy led to a significant reduction in the propensity of the compounds to undergo metabolic activation as evidenced by reductions in the irreversible binding of radioactivity to liver microsomal material upon incubation of tritium-labeled compounds with this in vitro system. With the efficiency and throughput achievable with such an approach, it appears feasible to identify and address the metabolic activation potential of new drug leads during routine metabolite identification studies in an early drug discovery setting.     

On the High Viscosity of Aqueous Solution of Lysozyme Induced by Some Organic Solvents

A remarkably high viscosity has been induced in protein aqueous solutions by the addition of certain structurally related organic solvents. The effect has been observed for lysozyme aqueous solutions containing tetramethylurea (TMU), dimethylsulfoxide (DMSO), dimethylformamide, and hexamethylphosphortriamide. The effect has also been induced in ferrocytochrome c aqueous solutions by TMU. Critical concentrations for both the protein and organic solvent were verified for the onset of the viscosity increase. A common feature of the solvents which were able to induce the effect is a dipolar moiety (C=O, S → O and P → O) and a nonpolar region represented by the methyl groups. The resulting fluids show an extremely restricted flow and a typical non-Newtonian, pseudoplastic behavior. Use was made of¹H nuclear magnetic resonance (NMR) and Raman spectroscopy to characterize protein structural modifications and of¹³C NMR to investigate changes in relaxation times and chemical shifts in the solvent/water solutions. A systematic rheological characterization of the systems was undertaken for some of the solvents, and unusual patterns of viscous effects were identified for the solvent/water systems both with and without protein. The process was found to be at least partially reversible, as concluded from the recovered original solution rheological characteristics and the original protein¹H NMR spectrum, after eliminating the organic solvent by ultrafiltration. The whole process was characterized as consisting of two mutually independent stages. The first involves an extensive conformational transition of the polypeptide backbone, from a predominantly α-helical to increased random coiled and β-sheet structures, with the occurrence of nonorthodox protein secondary structures at regions above the solvent critical point. The second stage consists of short-lived interchain contacts leading to an entanglement of the macromolecular system as a whole. A microphase reversion in the organic solvent/water mixture, supported by¹³C NMR and rheological results, is proposed as the driving force causing the observed behavior.     

Effects of medium and chemical modification on thermal characteristics of Β-lactoglobulin

The thermal properties of -lactoglobulin (-LG) were studied by differential scanning calorimetry (DSC) under different medium conditions.pH, neutral salts, protein perturbants, and polyols all affected the DSC characteristics of -LG. Acylation with fatty acids also changed the thermal properties, particularly peak width at half-height. The results suggest that the structural stability of -LG is controlled by non-covalent forces, particularly electrostatic and hydrophobic interactions. Disulfide bonds did not contribute to the thermal response of -LG. Fatty N-acyl-amino acids caused marked increases in thermal stability and decreases in denaturation enthalpy, and additional peaks were observed in the presence of some palmitoyl derivatives.Contribution No. 2310, Centre for Food and Animal Research.We thank D. Raymond for her excellent technical assistance.     

Influence of velocity and surface temperature of alumina particles on the properties of plasma sprayed coatings

In this paper are described the main characteristics of the plasma spraying process of alumina deposits, i.e., the temperature and flow field of the plasma jets obtained with the classical spraying torches, the injection of the particles into the plasma jet, the particle surface temperature and velocities in the plasma (measured for calibrated alumina particles), and the coating generation. The measurements on the alumina particles are compared with the predictions of a mathematical model. The experimental and computed particle velocities are in rather good agreement. However, this is not the case for the particle surface temperature. Possible reasons for the discrepancy are proposed (influence of the carrier gas, thermophoretic forces, and poor penetration of the particles into the plasma core even for an injection velocity twice that of the optimal calculated one, as shown by recent measurements). Finally the correlations between the particle velocities and surface temperature, and the properties of the alumina coating (porosity, crystal structure, mechanical properties) are studied.     

Rapid quantification of HIV protease inhibitors in human plasma by high-performance liquid chromatography coupled with electrospray ionization tandem mass spectrometry

HIV protease inhibitors are important antiretroviral drugs which have substantially reduced the morbidity and mortality associated with HIV-1 infection. Recent data have shown relationships between plasma concentrations of the protease inhibitors and clinical response, which makes therapeutic drug monitoring valuable. We have developed and validated an assay, using liquid chromatography coupled with electrospray tandem mass spectrometry (LC/MS/MS), for the routine quantification of the six licensed protease inhibitors (amprenavir, indinavir, lopinavir, nelfinavir, ritonavir and saquinavir) and the pharmacologically active nelfinavir metabolite M8 in plasma. The sample pretreatment consisted of protein precipitation with a mixture of methanol and acetronitrile using only 100 microl of plasma. Chromatographic separation was performed on an Inertsil ODS3 column (50 x 2.0 mm i.d., particle size 5 microm), with a quick stepwise gradient using an acetate buffer (pH 5) and methanol, at a flow rate of 0.5 ml min(-1). The analytical run time was 5.5 min. The use of a 96-well plate autosampler allowed batch sizes up to 150 patient samples. The triple-quadrupole mass spectrometer was operated in the positive ion mode and multiple reaction monitoring was used for drug quantification. The method was validated over the concentration ranges 0.01-10 microg ml(-1) for indinavir and saquinavir, 0.1-10 microg ml(-1) for amprenavir, 0.05-10 microg ml(-1) for nelfinavir and ritonavir, 0.1-20 microg ml(-1) for lopinavir and 0.01-5 microg ml(-1) for M8. Saquinavir-d(5) and indinavir-d(6) were used as internal standards. The coefficients of variation were always <10% for both intra-day and inter-day precisions for each compound. Mean accuracies were also between the designated limits (+/-15%). The validated concentration ranges proved to be adequate in daily practice. This robust and fast LC/MS/MS assay is now successfully applied for routine therapeutic drug monitoring and pharmacokinetic studies in our hospital.     

Influence of the Excited States of Atomic Nitrogen N(<Superscript>2</Superscript>D), N(<Superscript>2</Superscript>P) and N(R) on the Transport Properties of Nitrogen. Part II: Nitrogen Plasma Properties

In this paper, the calculated values of the viscosity and thermal conductivity of nitrogen plasma are presented taking into account five (e, N, N⁺, N₂ and N₂⁺) or eight (e, N(⁴S), N(²P), N(²D), N(R), N⁺, N₂ and N₂⁺) species. The calculations are based on the supposition that the temperature dependent probability of occupation of the states is given by the Boltzmann factor. The domain for which the calculations are performed, is for p = 1 and 10 atm in the temperature range from 5,000 K to 15,000 K. Classical collision integrals are used in calculating the transport coefficients and we have introduced new averaged collision integrals where the weight associated at each interacting species pair is the probable collision frequency. The influence of the collision integral values and energy transfer between two different species is studied. These results are compared which those of published theoretical studies.     

Sorption of aliphatic ketones from aqueous solutions by starch cryotextures

Capillary gas chromatography was applied to study the sorption of aliphatic ketones (C₆—C₁₁), including metamers, from aqueous solutions by corn starch cryotextures. The amount of ketones sorbed by cryotextures depends linearly on their concentrations in the initial sol. Equations describing the concentration dependence of sorption were proposed. The shape of sorption isotherms reflects the strength of sorption. The binding constants and the number of binding sites were determined for weakly sorbed ketones. The length of alkyl substituent and the position of the functional group are the crucial factors governing the sorption of ketones under conditions of excess binding sites. It was found that the degree of sorption increases with an increase in the carbon chain length from 6 to 9 carbon atoms. The presence of cooperation of binding sites for ketone sorption by cryotextures was demonstrated. The major part of ketones is sorbed irreversibly. This fact points to the formation of supramolecular complexes. Ketones with lower molecular masses are better sorbed by cryotextures than by native starch grains.     

Relative stability of major types of beta-turns as a function of amino acid composition: a study based on Ab initio energetic and natural abundance data

Folding properties of small globular proteins are determined by their amino acid sequence (primary structure). This holds both for local (secondary structure) and for global conformational features of linear polypeptides and proteins composed from natural amino acid derivatives. It thus provides the rational basis of structure prediction algorithms. The shortest secondary structure element, the beta-turn, most typically adopts either a type I or a type II form, depending on the amino acid composition. Herein we investigate the sequence-dependent folding stability of both major types of beta-turns using simple dipeptide models (-Xxx-Yyy-). Gas-phase ab initio properties of 16 carefully selected and suitably protected dipeptide models (for example Val-Ser, Ala-Gly, Ser-Ser) were studied. For each backbone fold most probable side-chain conformers were considered. Fully optimized 321G RHF molecular structures were employed in medium level [B3LYP/6-311++G(d,p)//RHF/3-21G] energy calculations to estimate relative populations of the different backbone conformers. Our results show that the preference for beta-turn forms as calculated by quantum mechanics and observed in Xray determined proteins correlates significantly.     

Characteristics of vinyl iodide microwave plasma etching of GaAs/AlGaAs and InP/InGaAs heterostructures

Vinyl iodide (C₂H₃I) microwave discharges with additions of H₂ and Ar are found to provide faster etch rates than conventional CH₄/H₂/Ar discharges for InP, InGaAs, GaAs, and AlGaAs. This is a result of the relatively high volatilities of indium, gallium, and aluminum iodide species. The etched features are smooth and anisotropic over a wide range of do self-biases (–150 to –350 V), process pressures (1–20mTorr), and microwave powers (150–500 W). The polymer that forms on the mask during the plasma exposure can be readily removed in O₂ discharges. Electron spectroscopy for chemical analysis (ESCA) showed that the etched surfaces are slightly deficient in the group V elements under most conditions, but changes to the optical properties of the semiconductors are minimal. No defects are visible by transmission electron microscopy (TEM) in GaAs or InP samples etched at dc biases –250 V.