Internal Standard Triggered-Parallel Reaction Monitoring Mass Spectrometry Enables Multiplexed Quantification of Candidate Biomarkers in Plasma

Despite advances in proteomic technologies, clinical translation of plasma biomarkers remains low, partly due to a major bottleneck between the discovery of candidate biomarkers and costly clinical validation studies. Due to a dearth of multiplexable assays, generally only a few candidate biomarkers are tested, and the validation success rate is accordingly low. Previously, mass spectrometry-based approaches have been used to fill this gap but feature poor quantitative performance and were generally limited to hundreds of proteins. Here, we demonstrate the capability of an internal standard triggered-parallel reaction monitoring (IS-PRM) assay to greatly expand the numbers of candidates that can be tested with improved quantitative performance. The assay couples immunodepletion and fractionation with IS-PRM and was developed and implemented in human plasma to quantify 5176 peptides representing 1314 breast cancer biomarker candidates. Characterization of the IS-PRM assay demonstrated the precision (median % CV of 7.7%), linearity (median R² > 0.999 over 4 orders of magnitude), and sensitivity (median LLOQ < 1 fmol, approximately) to enable rank-ordering of candidate biomarkers for validation studies. Using three plasma pools from breast cancer patients and three control pools, 893 proteins were quantified, of which 162 candidate biomarkers were verified in at least one of the cancer pools and 22 were verified in all three cancer pools. The assay greatly expands capabilities for quantification of large numbers of proteins and is well suited for prioritization of viable candidate biomarkers.

Targeted Mass Spectrometry Enables Multiplexed Quantification of Immunomodulatory Proteins in Clinical Biospecimens

Immunotherapies are revolutionizing cancer care, producing durable responses and potentially cures in a subset of patients. However, response rates are low for most tumors, grade 3/4 toxicities are not uncommon, and our current understanding of tumor immunobiology is incomplete. While hundreds of immunomodulatory proteins in the tumor microenvironment shape the anti-tumor response, few of them can be reliably quantified. To address this need, we developed a multiplex panel of targeted proteomic assays targeting 52 peptides representing 46 proteins using peptide immunoaffinity enrichment coupled to multiple reaction monitoring-mass spectrometry. We validated the assays in tissue and plasma matrices, where performance figures of merit showed over 3 orders of dynamic range and median inter-day CVs of 5.2% (tissue) and 21% (plasma). A feasibility study in clinical biospecimens showed detection of 48/52 peptides in frozen tissue and 38/52 peptides in plasma. The assays are publicly available as a resource for the research community.

HLA-F and MHC open conformers cooperate in antigen presentation during the inflammatory response

HLA-F is expressed as a protein independent of bound peptide or β2-microglobulin and surface expression is upregulated upon activation in dendritic cells, monocytes and most lymphocyte subsets. MHC class I (MHCI) is also expressed on proliferating lymphoid cells as open conformers (OCs), in addition to the ubiquitously expressed complexed form. Previous studies showed that HLA-F binds most MHCI proteins as open conformers without peptide but not as peptide bound complex. These studies were extended to show both HLA-F and MHCI OC are ligands for a subset of killer Ig-like receptors (KIRs), defining a new paradigm for MHCI function in the innate and acquired immune responses. The HLA-F/MHCI physical interaction was further implicated in the function of HLA-F and MHCI OCs in a general mode of exogenous MHCI antigen uptake and antigen presentation by activated immune cells that differs from the canonical MHCI endogenous antigen presentation. We are currently testing the hypothesis that antigen entry is governed by a synergy between specific structural characteristics of the exogenous antigen and the MHC-I allele types of target cells. New evidence is presented using HIV-1 p24 gag derived long polypeptides suggesting a requirement for HLA class I peptide epitope specificity in antigen uptake, upstream of antigen presentation, which subsequently can be presented by either or both of MHCI and MHCII. These experiments suggested that the physical proximity of HIV-1 class I and class II peptide epitopes within a p24 polypeptide can influence antigen presentation of epitopes through either MHCI or MHCII or both. A goal is to manipulate these features in designing effective immunogens for directed stimulation of antigen-specific host responses.

Interplay between the static ordering and dynamical heterogeneities determining the dynamics of rotation and ordinary liquid phases in 1,6-anhydro-β-D-glucose

In this letter, we reported thorough the structural and molecular dynamics studies on 1,6-anhydro-β-D-glucose, the second compound reported so far that is capable to form rotator and supercooled liquid phases. In contrast to the data presented for ethanol, temperature dependences of structural dynamics in both phases are very comparable. On the other hand, X ray measurements revealed unusually long range ordering/correlations between molecules in the ODIC (d ≈ 95 Å) and supercooled phases (d ≈ 30-40 Å) of this carbohydrate. Our consideration clearly demonstrated that the interplay between length scales of static range ordering and dynamical heterogeneities as well as internal molecular arrangement seem to be the key to understanding the molecular dynamics of different materials characterized by varying degree of disorder in the vicinity of the glass transition temperature.

Modelling of glass-like carbon structure and its experimental verification by neutron and X-ray diffraction

Glass-like carbon is a well known carbon form that still poses many challenges for structural characterization owing to a very complex internal atomic organization. Recent research suggests that glassy carbon has a fullerene-related structure that evolves with the synthesis temperature. This article reports on direct evidence of curved planes in glassy carbons using neutron and X-ray diffraction measurements and their analysis in real space using the atomic pair distribution function formalism. Changes in the structure including the degree of curvature of the non-graphitizing glassy carbons as a function of the pyrolysis temperature in the range 800–2500°C (1073–2773 K) are studied using optimized models of the atomic structure. Averaged models of single coherent scattering domains as well as larger structural fragments consisting of thousands of atoms were relaxed using classical molecular dynamics. For such models the diffraction intensities and the pair distribution functions were computed. The compatibility of the computer-generated models was verified by comparison of the simulations with the experimental diffraction data in both reciprocal and real spaces. On the basis of features of the developed structural models for glass-like carbons, the origin of the properties such as high strength and hardness and low gas permeability can be better understood.

HLA-F and MHC-I Open Conformers Bind Natural Killer Cell Ig-Like Receptor KIR3DS1

Based on previous findings supporting HLA-F as a ligand for KIR3DL2 and KIR2DS4, we investigated the potential for MHC-I open conformers (OCs) as ligands for KIR3DS1 and KIR3DL1 through interactions measured by surface plasmon resonance. These measurements showed physical binding of KIR3DS1 but not KIR3DL1 with HLA-F and other MHC-I OC while also confirming the allotype specific binding of KIR3DL1 with MHC-I peptide complex. Concordant results were obtained with biochemical pull-down from cell lines and biochemical heterodimerization experiments with recombinant proteins. In addition, surface binding of HLA-F and KIR3DS1 to native and activated NK and T cells was coincident with specific expression of the putative ligand or receptor. A functional response of KIR3DS1 was indicated by increased granule exocytosis in activated cells incubated with HLA-F bound to surfaces. The data extend a model for interaction between MHC-I open conformers and activating KIR receptors expressed during an inflammatory response, potentially contributing to communication between the innate and adaptive immune response.

HLA-F and MHC open conformers in a novel HIV-1 immunization strategy

HLA-F is expressed as a protein independent of bound peptide or b2-microglobulin and surface expression is upregulated in dendritic cells, monocytes and most lymphocyte subsets upon activation. Classical MHC class I (MHCI) is also expressed on proliferating lymphoid cells as so-called ‘open conformers (OCs)’, in addition to the ubiquitously expressed form complexed with peptide and b2-microglobulin. Previous studies showed that HLA-F binds most MHCI proteins as open conformers without peptide but not as peptide bound complex. These studies were extended to show that both HLA-F and MHCI OC are ligands for a specific subset of killer Ig-like receptors (KIRs). The HLA-F/MHCI physical interaction was further implicated in the function of HLA-F and MHCI open conformers in a general mode of exogenous MHCI antigen uptake and antigen presentation by activated immune cells that differs from the canonical MHCI endogenous antigen presentation. We are currently testing the hypothesis that antigen entry is governed by a synergy between specific structural characteristics of the exogenous antigen and the MHC-I allele types of target cells. New evidence is presented using HIV-1 p24 gag derived long polypeptides suggesting a requirement for HLA class I peptide epitope specificity in antigen uptake, upstream of antigen presentation, which subsequently can be presented by either or both of MHCI and MHCII. These experiments suggested that the physical proximity of HIV-1 class I and class II peptide epitopes within a p24 polypeptide can govern antigen presentation of epitopes through either MHCI or MHCII or both. A goal is to manipulate these features in designing effective immunogens for directed stimulation of antigen-specific host responses.

Simultaneous assessment of the pharmacokinetics of a pleuromutilin, lefamulin, in plasma, soft tissues and pulmonary epithelial lining fluid

BACKGROUND

Lefamulin is a pleuromutilin antibiotic under evaluation for the treatment of bacterial infections, including respiratory tract infections. Currently, there are no high-quality pharmacokinetic data on drug tissue concentrations of lefamulin available.

METHODS

A single dose of intravenous lefamulin (150 mg) was given to 12 healthy men. The registered EudraCT number for this study was 2010-021938-54. Lefamulin concentrations were simultaneously measured in plasma, skeletal muscle tissue, subcutaneous adipose tissue and epithelial lining fluid (ELF) over 24 h, and corresponding pharmacokinetic parameters were calculated. Microdialysis was used to measure unbound lefamulin concentrations in skeletal muscle tissue and subcutaneous adipose tissue, which were similar to unbound lefamulin concentrations in plasma. Bronchoalveolar lavage was performed 1, 2, 4 and 8 h post-dose to determine lefamulin concentrations in ELF.

RESULTS

Unbound lefamulin levels showed a 5.7-fold higher exposure in ELF compared with that in plasma, demonstrating good penetration to the target site.

CONCLUSIONS

Lefamulin may be an addition to the therapeutic armamentarium for the treatment of infections. Simultaneous measurements of unbound drug concentration can guide target attainment for future therapeutic trials.

The atomic scale structure of CXV carbon: wide-angle x-ray scattering and modeling studies

The disordered structure of commercially available CXV activated carbon produced from finely powdered wood-based carbon has been studied using the wide-angle x-ray scattering technique, molecular dynamics and density functional theory simulations. The x-ray scattering data has been converted to the real space representation in the form of the pair correlation function via the Fourier transform. Geometry optimizations using classical molecular dynamics based on the reactive empirical bond order potential and density functional theory at the B3LYP/6-31g* level have been performed to generate nanoscale models of CXV carbon consistent with the experimental data. The final model of the structure comprises four chain-like and buckled graphitic layers containing a small percentage of four-fold coordinated atoms (sp(3) defects) in each layer. The presence of non-hexagonal rings in the atomic arrangement has been also considered.

HLA-F and MHC class I open conformers are ligands for NK cell Ig-like receptors

Killer Ig-like receptors (KIRs) are innate immune receptors expressed by NK and T cells classically associated with the detection of missing self through loss of their respective MHC ligand. Some KIR specificities for allelic classical class I MHC (MHC-I) have been described, whereas other KIR receptor-ligand relationships, including those associated with nonclassical MHC-I, have yet to be clearly defined. We report in this article that KIR3DL2 and KIR2DS4 and the nonclassical Ag HLA-F, expressed as a free form devoid of peptide, physically and functionally interact. These interactions extend to include classical MHC-I open conformers as ligands, defining new relationships between KIR receptors and MHC-I. The data collectively suggest a broader, previously unrecognized interaction between MHC-I open conformers--including prototypical HLA-F--and KIR receptors, acting in an immunoregulatory capacity centered on the inflammatory response.

HLA-F and MHC-I open conformers cooperate in a MHC-I antigen cross-presentation pathway

Peptides that are presented by MHC class I (MHC-I) are processed from two potential sources, as follows: newly synthesized endogenous proteins for direct presentation on the surface of most nucleated cells and exogenous proteins for cross-presentation typically by professional APCs. In this study, we present data that implicate the nonclassical HLA-F and open conformers of MHC-I expressed on activated cells in a pathway for the presentation of exogenous proteins by MHC-I. This pathway is distinguished from the conventional endogenous pathway by its independence from TAP and tapasin and its sensitivity to inhibitors of lysosomal enzymes, and further distinguished by its dependence on MHC-I allotype-specific epitope recognition for Ag uptake. Thus, our data from in vitro experiments collectively support a previously unrecognized model of Ag cross-presentation mediated by HLA-F and MHC-I open conformers on activated lymphocytes and monocytes, which may significantly contribute to the regulation of immune system functions and the immune defense.

HLA-F and MHC-I open conformers cooperate in an MHC-I antigen cross presentation pathway. (P5015)

Peptides that are presented by MHC class I (MHC-I) are processed from two potential sources - newly synthesized endogenous proteins for direct presentation on the surface of most nucleated cells and exogenous proteins for cross-presentation typically by professional antigen presenting cells. Here we present data that implicates the non-classical HLA-F and open conformers of MHC-I expressed on activated cells in a pathway for the presentation of exogenous proteins by MHC-I. This pathway is distinguished from the conventional endogenous pathway by its independence from TAP and Tapasin and its sensitivity to inhibitors of lysosomal enzymes, and further distinguished by its dependence on MHC-I allotype-specific epitope recognition for antigen uptake. Thus, our data from in vitro experiments collectively support a previously unrecognized model of antigen cross-presentation mediated by HLA-F and MHC-I open conformers on activated lymphocytes and monocytes, which may significantly contribute to the regulation of immune system functions and the immune defense.

HLA-F and MHC-I open conformers are ligands for natural killer cell receptor KIR3DL2. (P5004)

Killer Immunoglobulin-like receptors (KIR) are innate immune receptors expressed by NK and T cells classically associated with the detection of missing-self through loss of their respective MHC ligand. Some KIR specificities for allelic classical class I MHC (MHC-I) have been described, while other KIR receptor-ligand relationships, including those associated with non-classical MHC-I, have yet to be clearly defined. We report here that KIR3DL2 and the non-classical antigen HLA-F, expressed as a free form devoid of peptide, physically and functionally interact. We further extend those results to include classical MHC-I open conformers as ligands, defining new allelic relationships with KIR3DL2 and MHC-I. The data collectively suggest a broader, previously unrecognized interaction between MHC-I open conformers - with HLA-F as a prototypical example - and KIR receptors, acting in an immunoregulatory capacity centered on the inflammatory response.

Graphene-like structure of activated anthracites

The structure of a series of activated carbons prepared from anthracite by chemical activation has been studied using wide-angle x-ray scattering, molecular dynamics and Raman spectroscopy. The BET surface areas of the investigated samples are in the range 1500-3430 m(2) g(-1) and the average pore sizes vary from 0.75 to 1.35 nm. The diffraction measurements were carried out to a maximum value of the scattering vector K(max) = 22 Å(-1). The obtained diffraction data have been converted to a real space representation in the form of the pair correlation function. The structure of the studied samples consists of one or two graphite-like layers, stacked without spatial correlations. The size of the ordered layer region is approximately 24 Å. The atomic arrangement within an individual layer has been described in terms of paracrystalline ordering, in which lattice distortions are propagated proportionally to the square root of inter-atomic distances. The paracrystalline structure has been simulated by introducing the Stone-Thrower-Wales, mono-vacancy and di-vacancy defects, randomly distributed in the network. These defects lead to the formation of a defected network with the presence of non-hexagonal rings in which distortion of the structure extends outside of a defect region. Computer generated structural models have been relaxed at room temperature using the reactive empirical bond order potential for intra-layer interactions and the Lennard-Jones potential for inter-layer interactions. For such generated models the structure factors and the pair correlation functions were computed. A good agreement between the simulation results and the experimental data in both reciprocal and real space provides evidence for the correctness of the proposed models. The Raman data support the validity of these models. Porosity of the activated anthracites is discussed in relation to their defective structure.

Impact of pH on activity of trimethoprim, fosfomycin, amikacin, colistin and ertapenem in human urine

OBJECTIVE

Although major impairment of activity at lower pH values has been reported for fluoroquinolones, acidification is a widely recommended practice for the prophylaxis and treatment of uncomplicated urinary tract infections (UTIs). Until now, there is little evidence for the influence of pH on the activity on other antimicrobial classes in urine.

METHODS

Bacterial growth curves of Staphylococcus aureus (ATCC 29213), Klebsiella oxytoca (ATCC 700324), Proteus mirabilis (ATCC 14153), Escherichia coli (ATCC 25922) and Enterococcus faecalis (ATCC 29212) were performed in Mueller-Hinton broth and in pooled human urine with a pH of between 5.0 and 8.0. Bacterial killing of trimethoprim, fosfomycin, amikacin, colistin and ertapenem against the five strains (where appropriate) was determined consecutively at concentrations equal to the MIC.

RESULTS

While no difference in the bacterial growth of E. coli, S. aureus, P. mirabilis and K. oxytoca was observed at different pH values, bacterial growth of E. faecalis was significantly reduced at low pH. Acidification to pH 5 impaired the antimicrobial activity of all investigated antibiotics, i.e. the net effect of bacterial growth and killing resulted in increased colony-forming units/ml at the end of the experiment.

CONCLUSION

The present in vitro findings indicate that acidification of urine during the treatment of UTIs should be carefully considered. While growth curves of one strain supports the concept of therapeutic or prophylactic acidification during UTIs, the most common pathogen, E. coli, was not affected by low pH. Independent of the investigated strain or antibiotic, pH values below 6 lead to a reduction of antimicrobial activity.

Fusicoccin affects cortical microtubule orientation in the isolated epidermis of sunflower hypocotyls

Epidermal peels isolated from sunflower hypocotyls provide a convenient model to study the relationship between cortical microtubule orientation and strain rate. Extension of peels can be modulated using chemical treatment and mechanical stress, i.e., by adding a chemical to the incubation medium and applying a load exceeding the yield threshold for irreversible (plastic) strain. In this study, peels were pre-incubated for ca. 12 h (long-term pre-incubation) or for 1 h (short-term pre-incubation). In the long-term pre-incubated peels, fusicoccin applied to the medium neither enhanced the rate of longitudinal plastic strain of loaded peels, nor affected microtubule orientation. However, fusicoccin increased the strain rate of short-term, pre-incubated peels and affected microtubule orientation in both extending (loaded) and non-extending (unloaded) peels. Without fusicoccin, microtubule orientation was generally longitudinal or steep, whereas in fusicoccin-treated unloaded peels it was transverse and oblique microtubules in peel portions corresponding to the apical part of the hypocotyl. Although the frequency of transverse orientation was increased through loading, there was no strong correlation between the rate of fusicoccin-induced strain and microtubule orientation. It is hypothesized that the insensitivity of long-term pre-incubated peels to fusicoccin with respect to strain rate is due to a lack of active plasma membrane H(+) -ATPases. Thus, the sensitivity of short-term, pre-incubated, unloaded (non-extending) peels to fusicoccin, with respect to microtubule orientation, indicates that orientation might be affected by electric currents resulting from fusicoccin stimulation of H(+) -ATPases.

Dielectric relaxation study on tramadol monohydrate and its hydrochloride salt

Dielectric relaxation measurements as well as differential scanning calorimetry and X-ray diffraction investigations were performed on tramadol monohydrate and its hydrochloride salt. Examined samples do not crystallize during cooling and in consequence they reach the glassy state. In the case of the hydrochloride tramadol we are able to monitor alpha-relaxation process despite large contribution of dc conductivity to the loss spectra. It is the first such study on the salt of the drug. Up to now the dielectric spectroscopy has been regarded as useless in measuring such kind of API (active pharmaceutical ingredient). In this paper we also made some suggestions about the nature of the secondary relaxations in the amorphous tramadol monohydrate and its salt. The knowledge about the molecular mechanisms, which govern the observed secondary relaxations seems to be the key in predicting the stability of the amorphous form of the examined API. Finally additional dissolving measurements on the amorphous and crystal tramadol hydrochloride were performed. As a result we understood that dissolution properties of the amorphous form of the considered drug are comparable to those of crystalline one. However, we have found out that amorphous tramadol hydrochloride has greater ability to form tablets than its crystalline equivalent. This finding shows that amorphous drugs can be alternative even for the freely solved pharmaceuticals such as tramadol hydrochloride, because the former one has better ability to form tablets. It implies that during tabletting of the amorphous drugs there is no need to use any excipients and chemicals improving compaction properties of the API.

Plasma protein binding may reduce antimicrobial activity by preventing intra-bacterial uptake of antibiotics, for example clindamycin

OBJECTIVES

although plasma protein binding (PPB) is accepted to be an essential factor in reducing antimicrobial activity, little is known about the underlying mechanisms. One possibility includes impaired penetration of an antimicrobial into bacterial cells in the presence of PPB. As a prerequisite for testing this hypothesis an optimized medium displaying high protein binding without impairing bacterial growth had to be identified for our model compound clindamycin.

METHODS

determination of PPB, bacterial growth and antimicrobial killing was performed in Mueller-Hinton broth (MHB) containing various amounts of human albumin or serum. [(3)H]clindamycin was used to investigate clindamycin penetration into Staphylococcus aureus.

RESULTS

of all investigated media only MHB(50%serum) and MHB(70%serum) achieved protein binding comparable to pure serum. In contrast, MHB(20%serum) and most media containing only albumin demonstrated considerably lower protein binding. Pure serum resulted in bacterial growth inhibition compared with MHB while MHB(16%albumin) and MHB(50%serum) did not result in significant differences in bacterial count after 24 h. However, in both MHB(16%albumin) and MHB(50%serum) the antimicrobial activity of clindamycin was reduced by >2 log(10) cfu/mL compared with pure MHB. The radioactive signal after administration of [(3)H]clindamycin to S. aureus was significantly decreased in pure serum as well as in MHB(16%albumin) and MHB(50%serum), while no significant difference was observed for MHB(4%albumin) and MHB(20%serum).

CONCLUSIONS

reduction of the intracellular radioactive signal in the presence of serum proteins correlated both with the degree of protein binding and reduction of antimicrobial activity supporting the hypothesis of impairment of activity by PPB by reducing intra-bacterial antimicrobial concentrations.

HLA-F complex without peptide binds to MHC class I protein in the open conformer form

HLA-F has low levels of polymorphism in humans and is highly conserved among primates, suggesting a conserved function in the immune response. In this study, we probed the structure of HLA-F on the surface of B lymphoblastoid cell lines and activated lymphocytes by direct measurement of peptide binding to native HLA-F. Our findings suggested that HLA-F is expressed independently of bound peptide, at least in regard to peptide complexity profiles similar to those of either HLA-E or classical MHC class I (MHC-I). As a further probe of native HLA-F structure, we used a number of complementary approaches to explore the interactions of HLA-F with other molecules, at the cell surface, intracellularly, and in direct physical biochemical measurements. This analysis demonstrated that HLA-F surface expression was coincident with MHC-I H chain (HC) expression and was downregulated upon perturbation of MHC-I HC structure. It was further possible to directly demonstrate that MHC-I would interact with HLA-F only when in the form of an open conformer free of peptide and not as a trimeric complex. This interaction was directly observed by coimmunoprecipitation and by surface plasmon resonance and indirectly on the surface of cells through coincident tetramer and MHC-I HC colocalization. These data suggest that HLA-F is expressed independently of peptide and that a physical interaction specific to MHC-I HC plays a role in the function of MHC-I HC expression in activated lymphocytes.

Strain rate does not affect cortical microtubule orientation in the isolated epidermis of sunflower hypocotyls

A hypothesis exists that external and internal factors affect the orientation of cortical microtubules in as much as these lead to changes in cell elongation rate. Factors that stimulate elongation are proposed to lead to transverse microtubule orientation, whereas factors that inhibit elongation lead to longitudinal orientation. The elongation rate is equal to the rate of longitudinal irreversible strain in cell walls. Incubated epidermis peeled from sunflower hypocotyls does not extend unless it is stretched by loading and the pH of the incubation medium is appropriately low. Thus, peels provide a convenient model to investigate the relationship between longitudinal strain rate and cortical microtubule orientation. In the present study, it was found that peeling affects microtubule orientation. Peels were incubated for several hours in Murashige & Skoog medium (both unbuffered and buffered) to attain a steady state of microtubule orientation before loading. The effects of loading and pH on strain rate and orientation of microtubules under the outer epidermal walls were examined in three portions of peels positioned with respect to the cotyledonary node. Appropriate loading caused longitudinal strain of peels at pH 4.5 but not at pH 6.5. However, no clear effect of strain rate on microtubule orientation in the peels was observed. Independent of applied load and pH of the incubation medium, the microtubule orientation remained unchanged, i.e. orientation was mainly oblique. Our results show that strain rate does not affect cortical microtubule orientation in isolated epidermis of the sunflower hypocotyl model system, although orientation could be changed by white light.

Application of molecular dynamics simulations for structural studies of carbon nanotubes

Molecular dynamics studies based on the Brenner-Tersoff second-generation reactive empirical bond order potential and the Lennard-Jones carbon-carbon potential for intra- and inter-layer interactions have been performed for carbon nanotubes. These potentials reproduce reasonably the carbon-carbon distances and inter-layer spacing. The structure factors and the reduced radial distribution functions computed from the cartesian coordinates, resulting from energy minimisation and molecular dynamics simulations at 2 K and 300 K have been obtained for two models of two- and five-wall carbon nanotubes containing defects in the form of five and seven membered carbon rings. The results of computations have been compared with experimental data obtained from neutron and X-ray diffraction. The energy relaxation and the molecular dynamics simulations at 2 K and 300 K with appropriate values of the Debye-Waller factor lead practically to the same results which are in a good agreement with the experimental data indicating that molecular dynamics reproduce all structure features of the investigated carbon nanotubes together with thermal oscillations. Possible applications of this approach for other carbon nanotubes and related materials have been also discussed.

Membrane binding mechanisms of the PX domains of NADPH oxidase p40phox and p47phox

Phox (PX) domains are phosphoinositide (PI)-binding domains with broad PI specificity. Two cytosolic components of NADPH oxidase, p40(phox) and p47(phox), contain PX domains. The PX domain of p40(phox) specifically binds phosphatidylinositol 3-phosphate, whereas the PX domain of p47(phox) has two lipid binding sites, one specific for phosphatidylinositol 3,4-bisphosphate and the other with affinity for phosphatidic acid or phosphatidylserine. To delineate the mechanisms by which these PX domains interact with PI-containing membranes, we measured the membrane binding of these domains and respective mutants by surface plasmon resonance and monolayer techniques and also calculated the electrostatic potentials of the domains as a function of PI binding. Results indicate that membrane binding of both PX domains is initiated by nonspecific electrostatic interactions, which is followed by the membrane penetration of hydrophobic residues. The membrane penetration of the p40(phox) PX domain is induced by phosphatidylinositol 3-phosphate, whereas that of the p47(phox) PX domain is triggered by both phosphatidylinositol 3,4-bisphosphate and phosphatidic acid (or phosphatidylserine). Studies of enhanced green fluorescent protein-fused PX domains in HEK293 cells indicate that this specific membrane penetration is also important for subcellular localization of the two PX domains. Further studies on the full-length p40(phox) and p47(phox) proteins showed that an intramolecular interaction between the C-terminal Src homology 3 domain and the PX domain prevents the nonspecific monolayer penetration of p47(phox), whereas such an interaction is absent in p40(phox).

Absorption corrections and digital filtering of X-ray diffraction profiles recorded with a position-sensitive detector

Expressions for the absorption correction function are obtained in the form of integral equations for the case of a flat-plate sample and a position-sensitive detector. It is shown that the absorption correction used for both transmission and reflection geometries with a conventional diffractometer may be applied to a diffractometer equipped with a linear position-sensitive detector. The application of a Savitzky–Golay-type digital filter considerably facilitates the analysis of the data without losing pertinent information.