Streamlined Multi-Attribute Assessment of an Array of Clinical-Stage Antibodies: Relationship Between Degradation and Stability

Clinical antibodies are an important class of drugs for the treatment of both chronic and acute diseases. Their manufacturability is subject to evaluation to ensure product quality and efficacy. One critical quality attribute is deamidation, a non-enzymatic process that is observed to occur during thermal stress, at low or high pH, or a combination thereof. Deamidation may induce antibody instability and lead to aggregation, which may pose immunogenicity concerns. The introduction of a negative charge via deamidation may impact the desired therapeutic function (i) within the complementarity-determining region, potentially causing loss of efficacy; or (ii) within the fragment crystallizable region, limiting the effector function involving antibody-dependent cellular cytotoxicity. Here we describe a transformative solution that allows for a comparative assessment of deamidation and its impact on stability and aggregation. The innovative streamlined method evaluates the intact protein in its formulation conditions. This breakthrough platform technology is comprised of a quantum cascade laser microscope, a slide cell array that allows for flexibility in the design of experiments, and dedicated software. The enhanced spectral resolution is achieved using two-dimensional correlation, co-distribution, and two-trace two-dimensional correlation spectroscopies that reveal the molecular impact of deamidation. Eight re-engineered immunoglobulin G4 scaffold clinical antibodies under control and forced degradation conditions were evaluated for deamidation and aggregation. We determined the site of deamidation, the overall extent of deamidation, and where applicable, whether the deamidation event led to self-association or aggregation of the clinical antibody and the molecular events that led to the instability. The results were confirmed using orthogonal techniques for four of the samples.

Measuring Molecular Diffusion in Dynamic Subcellular Nanostructures by Fast Raster Image Correlation Spectroscopy and 3D Orbital Tracking

Here we provide demonstration that fast fluorescence fluctuation spectroscopy is a fast and robust approach to extract information on the dynamics of molecules enclosed within subcellular nanostructures (e.g., organelles or vesicles) which are also moving in the complex cellular environment. In more detail, Raster Image Correlation Spectroscopy (RICS) performed at fast timescales (i.e., microseconds) reveals the fast motion of fluorescently labeled molecules within two exemplary dynamic subcellular nanostructures of biomedical interest, the lysosome and the insulin secretory granule (ISG). The measurement of molecular diffusion is then used to extract information on the average properties of subcellular nanostructures, such as macromolecular crowding or molecular aggregation. Concerning the lysosome, fast RICS on a fluorescent tracer allowed us to quantitatively assess the increase in organelle viscosity in the pathological condition of Krabbe disease. In the case of ISGs, fast RICS on two ISG-specific secreting peptides unveiled their differential aggregation propensity depending on intragranular concentration. Finally, a combination of fast RICS and feedback-based 3D orbital tracking was used to subtract the slow movement of subcellular nanostructures from the fast diffusion of molecules contained within them and independently validate the results. Results presented here not only demonstrate the acquired ability to address the dynamic behavior of molecules in moving, nanoscopic reference systems, but prove the relevance of this approach to advance our knowledge on cell function at the subcellular scale.

Cross-correlation analysis of X-ray photon correlation spectroscopy to extract rotational diffusion coefficients

X-ray photon correlation spectroscopy (XPCS) is a powerful technique that can probe a broad range of space and time scales and will become increasingly powerful due to coming advancements in coherence. Assessing translational and rotational diffusion is a key quantity in analyzing material structures and dynamics, with applications across molecular biology, drug discovery, and materials science. While methods for estimating translational diffusion coefficients from XPCS data are well-developed, there are no algorithms for measuring the rotational diffusion. Here, we present a mathematical formulation and algorithm based on angular-temporal cross-correlations for extracting this rotational information, providing tools for data analysis of XPCS. Although we focus on XPCS, the proposed method can be applied to other experimental techniques due to its generality.

Coefficients for translational and rotational diffusion characterize the Brownian motion of particles. Emerging X-ray photon correlation spectroscopy (XPCS) experiments probe a broad range of length scales and time scales and are well-suited for investigation of Brownian motion. While methods for estimating the translational diffusion coefficients from XPCS are well-developed, there are no algorithms for measuring the rotational diffusion coefficients based on XPCS, even though the required raw data are accessible from such experiments. In this paper, we propose angular-temporal cross-correlation analysis of XPCS data and show that this information can be used to design a numerical algorithm (Multi-Tiered Estimation for Correlation Spectroscopy [MTECS]) for predicting the rotational diffusion coefficient utilizing the cross-correlation: This approach is applicable to other wavelengths beyond this regime. We verify the accuracy of this algorithmic approach across a range of simulated data.

Augmented Two-Dimensional Correlation Spectroscopy for the Joint Analysis of Correlated Changes in Spectroscopic and Disparate Sources

Here, we present an augmented form of two-dimensional correlation spectroscopy, that integrates in a single format data from spectroscopic and multiple non-spectroscopic sources for analysis. The integration is affected by augmenting every spectrum in a hyperspectral data set with relevant non-spectroscopic data to permit two-dimensional correlation analysis^(2D-COS) of the ensemble of augmented spectra. A k-means clustering is then applied to the results of the perturbation domain decomposition to determine which Raman peaks cluster with any of the non-spectroscopic data. We introduce and explain the method with the aid of synthetic spectra and synthetic non-spectroscopic data. We then demonstrate this approach with data using Raman spectra from human embryonic stem cell aggregates undergoing directed differentiation toward pancreatic endocrine cells and parallel bioassays of hormone mRNA expression and C-peptide levels in spent medium. These pancreatic endocrine cells generally contain insulin or glucagon. Insulin has disulfide bonds that produce Raman scattering near 513 cm^-1, but no tryptophan. For insulin-positive cells, we found that the application of multisource correlation analysis revealed a high correlation between insulin mRNA and Raman scattering in the disulfide region. In contrast, glucagon has no disulfide bonds but does contain tryptophan. For glucagon-positive cells, we also observed a high correlation between glucagon mRNA and tryptophan Raman scattering (∼757 cm^-1). We conclude with a discussion of methods to enhance spectral resolution and its effects on the performance of multisource correlation analysis.

Static Solid Relaxation Ordered Spectroscopy: SS-ROSY

A two-dimensional pulse sequence is introduced for correlating nuclear magnetic resonance anisotropic chemical shifts to a relaxation time (e.g., T₁) in solids under static conditions. The sequence begins with a preparatory stage for measuring relaxation times, and is followed by a multiple pulse sequence for homonuclear dipolar decoupling. Data analysis involves the use of Fourier transform, followed by a one-dimensional inverse Laplace transform for each frequency index. Experimental results acquired on solid samples demonstrate the general approach, and additional variations involving heteronuclear decoupling and magic angle spinning are discussed.

Mechanism for correlation in a coherent electron beam

The correlation of electron counts from two detectors illuminated by a coherent electron beam is analyzed by associating the path of the electron beam through the lenses with the direct Coulomb interaction between two individual electrons. This is shown to lead to a full statistical description of the electron counts. The dominant contribution to the correlation is found to be due to the trajectory displacement caused by the repulsive Coulomb interaction between the first anode and the cathode tip, and the correlation of electron counts is found to depend on the amount of defocusing on the shift of the virtual source for two electrons within the correlation time. The Coulomb scatterings, which altered the direction of two neighbor electrons, occur during the acceleration, leading to a significant decrease in the electron density. The Coulomb potential with no screening will then cause large-angle scattering of nearest-neighbor electrons within the correlation time. These results are consistent with those obtained by a previous experiment.

A Single Hydrogen Molecule as an Intensity Chopper in an Electrically Driven Plasmonic Nanocavity

Photon statistics is a powerful tool for characterizing the emission dynamics of nanoscopic systems and their photophysics. Recent advances that combine correlation spectroscopy with scanning tunneling microscopy induced luminescence (STML) have allowed the measurement of the emission dynamics from individual molecules and defects, demonstrating their nature as single-photon emitters. The application of correlation spectroscopy to the analysis of the dynamics of a well-characterized adsorbate system in an ultrahigh vacuum remained to be demonstrated. Here, we combine single-photon time correlations with STML to measure the dynamics of individual H₂ molecules between a gold tip and an Au(111) surface. An adsorbed H₂ molecule performs recurrent excursions below the tip apex. We use the fact that the presence of the H₂ molecule in the junction modifies plasmon emission to study the adsorbate dynamics. Using the H₂ molecule as a chopper for STM-induced optical emission intensity, we demonstrate bunching in the plasmonic photon train in a single measurement over 6 orders of magnitude in the time domain (from microseconds to seconds) that takes only a few seconds. Our findings illustrate the power of using photon statistics to measure the diffusion dynamics of adsorbates with STML.

Diffusion-relaxation correlation spectroscopic imaging: A multidimensional approach for probing microstructure

PURPOSE

To propose and evaluate a novel multidimensional approach for imaging subvoxel tissue compartments called Diffusion-Relaxation Correlation Spectroscopic Imaging.

THEORY AND METHODS

Multiexponential modeling of MR diffusion or relaxation data is commonly used to infer the many different microscopic tissue compartments that contribute signal to macroscopic MR imaging voxels. However, multiexponential estimation is known to be difficult and ill-posed. Observing that this ill-posedness is theoretically reduced in higher dimensions, diffusion-relaxation correlation spectroscopic imaging uses a novel multidimensional imaging experiment that jointly encodes diffusion and relaxation information, and then uses a novel constrained reconstruction technique to generate a multidimensional diffusion-relaxation correlation spectrum for every voxel. The peaks of the multidimensional spectrum are expected to correspond to the distinct tissue microenvironments that are present within each macroscopic imaging voxel.

RESULTS

Using numerical simulations, experiment data from a custom-built phantom, and experiment data from a mouse model of traumatic spinal cord injury, diffusion-relaxation correlation spectroscopic imaging is demonstrated to provide substantially better multicompartment resolving power compared to conventional diffusion- and relaxation-based methods.

CONCLUSION

The diffusion-relaxation correlation spectroscopic imaging approach provides powerful new capabilities for resolving the different components of multicompartment tissue models, and can be leveraged to significantly expand the insights provided by MRI in studies of tissue microstructure. Magn Reson Med 78:2236-2249, 2017. © 2017 International Society for Magnetic Resonance in Medicine.

Second harmonic generation correlation spectroscopy for characterizing translationally diffusing protein nanocrystals

Second harmonic generation correlation spectroscopy (SHG-CS) is demonstrated as a new approach to protein nanocrystal characterization. A novel line-scanning approach was performed to enable autocorrelation analysis without sample damage from the intense incident beam. An analytical model for autocorrelation was developed, which includes a correction for the optical scattering forces arising when focusing intense, infrared beams. SHG-CS was applied to the analysis of BaTiO3 nanoparticles ranging from 200 to ∼500 nm and of photosystem I nanocrystals. A size distribution was recovered for each sample and compared with the size histogram measured by scanning electron microscopy (SEM). Good agreement was observed between the two independent measurements. The intrinsic selectivity of the second-order nonlinear optical process provides SHG-CS with the ability to distinguish well ordered nanocrystals from conglomerates and amorphous aggregates. Combining the recovered distribution of particle diameters with the histogram of measured SHG intensities provides the inherent hyperpolarizability per unit volume of the SHG-active nanoparticles. Simulations suggest that the SHG activity per unit volume is likely to exhibit relatively low sensitivity to the subtle distortions within the lattice that contribute to resolution loss in X-ray diffraction, but high sensitivity to the presence of multi-domain crystals.

Single-Molecule FRET Spectroscopy and the Polymer Physics of Unfolded and Intrinsically Disordered Proteins

The properties of unfolded proteins have long been of interest because of their importance to the protein folding process. Recently, the surprising prevalence of unstructured regions or entirely disordered proteins under physiological conditions has led to the realization that such intrinsically disordered proteins can be functional even in the absence of a folded structure. However, owing to their broad conformational distributions, many of the properties of unstructured proteins are difficult to describe with the established concepts of structural biology. We have thus seen a reemergence of polymer physics as a versatile framework for understanding their structure and dynamics. An important driving force for these developments has been single-molecule spectroscopy, as it allows structural heterogeneity, intramolecular distance distributions, and dynamics to be quantified over a wide range of timescales and solution conditions. Polymer concepts provide an important basis for relating the physical properties of unstructured proteins to folding and function.

Adsorption and Unfolding of a Single Protein Triggers Nanoparticle Aggregation

The response of living systems to nanoparticles is thought to depend on the protein corona, which forms shortly after exposure to physiological fluids and which is linked to a wide array of pathophysiologies. A mechanistic understanding of the dynamic interaction between proteins and nanoparticles and thus the biological fate of nanoparticles and associated proteins is, however, often missing mainly due to the inadequacies in current ensemble experimental approaches. Through the application of a variety of single molecule and single particle spectroscopic techniques in combination with ensemble level characterization tools, we identified different interaction pathways between gold nanorods and bovine serum albumin depending on the protein concentration. Overall, we found that local changes in protein concentration influence everything from cancer cell uptake to nanoparticle stability and even protein secondary structure. We envision that our findings and methods will lead to strategies to control the associated pathophysiology of nanoparticle exposure in vivo.

4-Methylthio-butanyl derivatives from the seeds of Raphanus sativus and their biological evaluation on anti-inflammatory and antitumor activities

ETHNOPHARMACOLOGICAL RELEVANCE

Raphanus sativus seeds (Brassicaceae) known as Raphani Semen have long been used as anti-cancer and/or anti-inflammatory agents in Korean traditional medicine. This study was designed to isolate the bioactive constituents from the seed extracts of Raphanus sativus and evaluate their anti-inflammatory and antitumor activities.

MATERIAL AND METHODS

Bioassay-guided fractionation and chemical investigation of a methanolic extract of the seeds of Raphanus sativus led to the isolation and identification of seven 4-methylthio-butanyl derivatives. Structural elucidation of the isolated compounds was carried out using 1D and 2D nuclear magnetic resonance (NMR) spectroscopy techniques ((1)H, (13)C, COSY, HMQC and HMBC experiments) and mass spectrometry.

RESULTS

The isolated compounds were characterized as in the following: three new 4-methylthio-butanyl derivatives, sinapoyl desulfoglucoraphenin (1), (E)-5-(methylsulfinyl)pent-4-enoxylimidic acid methyl ester (2), and (S)-5-((methylsulfinyl)methyl)pyrrolidine-2-thione (3), together with four known compounds, 5-(methylsulfinyl)-4-pentenenitrile (4), 5-(methylsulfinyl)-pentanenitrile (5), sulforaphene (6), and sulforaphane (7). Full NMR data assignments of the three known compounds 4-6 were also reported for the first time. We evaluated the anti-neuroinflammatory effect of 1-7 in lipopolysaccharide-stimulated murine microglia BV2 cells. Compound 1 significantly inhibited nitrite oxide production with IC50 values of 45.36 μM. Moreover, it also reduced the protein expression of inducible nitric oxide synthase. All isolates were also evaluated for their antiproliferative activities against four human tumor cell lines (A549, SK-OV-3, SK-MEL-2, and HCT-15), and all of them showed antiproliferative activity against the HCT-15 cell, with IC50 values of 8.49-23.97 μM.

CONCLUSIONS

4-Methylthio-butanyl derivatives were one of the main compositions of Raphanus sativus seeds, and activities demonstrated by the isolated compounds support the ethnopharmacological use of Raphanus sativus seeds (Brassicaceae) as anti-cancer and/or anti-inflammatory agents.

An unexpectedly lichenase-stable hexasaccharide from cereal, horsetail and lichen mixed-linkage β-glucans (MLGs): implications for MLG subunit distribution

Mixed-linkage (1→3),(1→4)-β-d-glucan (MLG) is a biologically and technologically important hemicellulose, known to occur in three widely separated lineages: the Poales (including grasses and cereals), Equisetum (fern-allies), and some lichens e.g. Iceland moss (Cetraria islandica). Lichenase (E.C. 3.2.1.73) is widely assumed to hydrolyse all (1→4) bonds that immediately follow (1→3) bonds in MLG, generating predominantly the tetrasaccharide β-d-Glcp-(1→4)-β-d-Glcp-(1→4)-β-d-Glcp-(1→3)-d-Glc (G4G4G3G; MLG4), the corresponding trisaccharide (G4G3G; MLG3), and sometimes also laminaribiose (G3G; MLG2). The ratio of the oligosaccharides produced characterises each polysaccharide. We report here that digestion of MLG from barley (Hordeum vulgare), Equisetum arvense and C. islandica by Bacillus subtilis lichenase also yields the unexpectedly stable hexasaccharide, β-d-Glcp-(1→3)-β-d-Glcp-(1→4)-β-d-Glcp-(1→4)-β-d-Glcp-(1→4)-β-d-Glcp-(1→3)-d-Glc (G3G4G4G4G3G, i.e. MLG2-MLG4), identified by thin-layer chromatography, gel-permeation chromatography, HPLC (HPAEC), β-glucosidase digestion, (1)H/(13)C-NMR spectroscopy and mass spectrometry. On HPLC, G3G4G4G4G3G is the major constituent of a peak previously ascribed solely to the nonasaccharide G4G4G4G4G4G4G4G3G. Because it was widely presumed that lichenase would cleave G3G4G4G4G3G to MLG2+MLG4, our data both redefine the substrate specificity of Bacillus lichenase and show previous attempts to characterise MLGs by HPLC of lichenase-digests to be flawed. MLG2 subunits are particularly underestimated; often reported as negligible, they are here shown to be an appreciable constituent of MLGs from all three lineages. We also show that there is no appreciable yield of water-soluble lichenase products with DP>9; potential identities of products previously labelled DP>9 are suggested. Finally, this discovery also provides a opportunity to investigate the spatial distribution of subunits along the MLG chain. We show that MLG2 subunits in barley and Cetraria MLG are not randomly distributed, but predominantly found at the non-reducing end of MLG4 subunits.

Is aristolochic acid nephropathy a widespread problem in developing countries? A case study of Aristolochia indica L. in Bangladesh using an ethnobotanical-phytochemical approach

ETHNOPHARMACOLOGICAL RELEVANCE

Species of Aristolochia are associated with aristolochic acid nephropathy (AAN), a renal interstitial fibrosis and upper urinary tract cancer (UUC). Aristolochic acid nephropathy has been reported in ten countries but its true incidence is unknown and most likely underestimated. By combining an ethnobotanical and phytochemical approach we provide evidence for the risk of AAN occurring in Bangladesh. More specifically, we assess the intra-specific variation of aristolochic acid analogues in medicinally used Aristolochia indica samples from Bangladesh.

MATERIALS AND METHODS

Ethnobotanical information was collected from 16 kavirajes (traditional healers) in different study locations in Bangladesh. Plant samples were obtained from native habitats, botanical gardens, herbal markets and pharmaceutical companies. The samples were extracted using 70% methanol and were analysed using LC-DAD-MS and (1)H-NMR.

RESULTS

Roots as well as leaves are commonly used for symptoms such as snake bites and sexual problems. Among the informants knowledge about toxicity or side effects is very limited and Aristolochia indica is often administered in very high doses. Replacement of Aristolochia indica with other medicinal plants such as Rauvolfia serpentina (L.) Benth. ex Kurz was common. Aristolochia indica samples contained a variety of aristolochic acid analogues such as aristolochic acid I, aristolochic acid II, cepharadione A and related compounds.

CONCLUSIONS

AAN cases are likely to occur in Bangladesh and more awareness needs to be raised about the health risks associated with the use of Aristolochia indica and other species of Aristolochia as herbal medicines.

Adsorption of a Protein Monolayer via Hydrophobic Interactions Prevents Nanoparticle Aggregation under Harsh Environmental Conditions

We find that citrate-stabilized gold nanoparticles aggregate and precipitate in saline solutions below the NaCl concentration of many bodily fluids and blood plasma. Our experiments indicate that this is due to complexation of the citrate anions with Na⁺ cations in solution. A dramatically enhanced colloidal stability is achieved when bovine serum albumin is adsorbed to the gold nanoparticle surface, completely preventing nanoparticle aggregation under harsh environmental conditions where the NaCl concentration is well beyond the isotonic point. Furthermore, we explore the mechanism of the formation of this albumin 'corona' and find that monolayer protein adsorption is most likely ruled by hydrophobic interactions. As for many nanotechnology-based biomedical and environmental applications, particle aggregation and sedimentation are undesirable and could substantially increase the risk of toxicological side-effects, the formation of the BSA corona presented here provides a low-cost bio-compatible strategy for nanoparticle stabilization and transport in highly ionic environments.

Difucosylation of chitooligosaccharides by eukaryote and prokaryote α1,6-fucosyltransferases

BACKGROUND

The synthesis of eukaryotic N-glycans and the rhizobia Nod factor both involve α1,6-fucosylation. These fucosylations are catalyzed by eukaryotic α1,6-fucosyltransferase, FUT8, and rhizobial enzyme, NodZ. The two enzymes have similar enzymatic properties and structures but display different acceptor specificities: FUT8 and NodZ prefer N-glycan and chitooligosaccharide, respectively. This study was conducted to examine the fucosylation of chitooligosaccharides by FUT8 and NodZ and to characterize the resulting difucosylated chitooligosaccharides in terms of their resistance to hydrolysis by glycosidases.

METHODS

The issue of whether FUT8 or NodZ catalyzes the further fucosylation of chitooligosaccharides that had first been monofucosylated by the other. The oligosaccharide products from the successive reactions were analyzed by normal-phase high performance liquid chromatography, mass spectrometry and nuclear magnetic resonance. The effect of difucosylation on sensitivity to glycosidase digestion was also investigated.

RESULTS

Both FUT8 and NodZ are able to further fucosylate the monofucosylated chitooligosaccharides. Structural analyses of the resulting oligosaccharides showed that the reducing terminal GlcNAc residue and the third GlcNAc residue from the non-reducing end are fucosylated via α1,6-linkages. The difucosylation protected the oligosaccharides from extensive degradation to GlcNAc by hexosamidase and lysozyme, and also even from defucosylation by fucosidase.

CONCLUSIONS

The sequential actions of FUT8 and NodZ on common substrates effectively produce site-specific-difucosylated chitooligosaccharides. This modification confers protection to the oligosaccharides against various glycosidases.

GENERAL SIGNIFICANCE

The action of a combination of eukaryotic and bacterial α1,6-fucosyltransferases on chitooligosaccharides results in the formation of difucosylated products, which serves to stabilize chitooligosaccharides against the action of glycosidases.

Screening of synthetic PDE-5 inhibitors and their analogues as adulterants: analytical techniques and challenges

The popularity of phosphodiesterase type 5 (PDE-5) enzyme inhibitors for the treatment of erectile dysfunction has led to the increase in prevalence of illicit sexual performance enhancement products. PDE-5 inhibitors, namely sildenafil, tadalafil and vardenafil, and their unapproved designer analogues are being increasingly used as adulterants in the herbal products and health supplements marketed for sexual performance enhancement. To date, more than 50 unapproved analogues of prescription PDE-5 inhibitors were found as adulterants in the literature. To avoid detection of such adulteration by standard screening protocols, the perpetrators of such illegal products are investing time and resources to synthesize exotic analogues and devise novel means for adulteration. A comprehensive review of conventional and advance analytical techniques to detect and characterize the adulterants is presented. The rapid identification and structural elucidation of unknown analogues as adulterants is greatly enhanced by the wide myriad of analytical techniques employed, including high performance liquid chromatography (HPLC), gas chromatography-mass spectrometry (GC-MS), liquid chromatography mass-spectrometry (LC-MS), nuclear magnetic resonance (NMR) spectroscopy, vibrational spectroscopy, liquid chromatography-Fourier transform ion cyclotron resonance-mass spectrometry (LC-FT-ICR-MS), liquid chromatograph-hybrid triple quadrupole linear ion trap mass spectrometer with information dependent acquisition, ultra high performance liquid chromatography-time of flight-mass spectrometry (UHPLC-TOF-MS), ion mobility spectroscopy (IMS) and immunoassay methods. The many challenges in detecting and characterizing such adulterants, and the need for concerted effort to curb adulteration in order to safe guard public safety and interest are discussed.

Chemical structure of the carbohydrate backbone of the lipopolysaccharide from Piscirickettsia salmonis

Elucidation of the carbohydrate backbone structure of the lipopolysaccharide (LPS) from Piscirickettsia salmonis, the etiological agent of the salmonid rickettsial septicemia, is described. Structural information was established by a combination of monosaccharide and methylation analyses of LPS, and by NMR and mass spectrometries of oligosaccharides obtained through the use of various chemical degradations of the native polymer. The following structure of the backbone sugars was determined on the basis of the combined data from these experiments: [formula see text] The presence of two consecutive residues of diacetylated pseudaminic acid (Pse5,7Ac, 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-manno-non-2-ulosonic acid) in the LPS appears to be unique among polysaccharides containing this acidic sugar. Similarly, the presence of 4-aminoarabinose (Ara4N, 4-amino-4-deoxy-l-arabinopyranose) on O-4 of the α-GlcN1P of the lipid A moiety is a unique feature of this LPS.

Two-electron interference in a coherent beam

The interference between quantum amplitude for two electrons, emitted from two source points, to be detected at two detection points, is a direct result of quantum exchange statistics. Such interference is observed in the coincidence probability, compared with that of statistically independent electrons, by computing the time correlation function from the arrival times of the electrons. When the two detectors are separated by a distance less than the coherence length, the coincidence probability is suppressed for electrons (antibunching) due to the Pauli principle, even though they do not interact with each other. However, electrons are charged particles. The Coulomb potential, which governs the scattering of one charged particle by another, is so long ranged. It is obvious that we must consider the Pauli principle and the Coulomb interactions simultaneously. This paper deals with basic experimental and theoretical investigations of the antibunching behavior of electrons in a free beam by considering the Pauli principle and the direct Coulomb interaction between two individual electrons. The experimentally found dependences are described in a model which considers the Coulomb scattering and theoretical values of correlation signals evaluated by analytical calculations agree with those determined by experiment. A study of the time correlation function from the arrival times of the electrons will lead to an understanding of the physical processes that take place in electron guns.

In situ measurement of bovine serum albumin interaction with gold nanospheres

We present in situ observations of adsorption of bovine serum albumin (BSA) on citrate-stabilized gold nanospheres. We implemented scattering correlation spectroscopy as a tool to quantify changes in the nanoparticle brownian motion resulting from BSA adsorption onto the nanoparticle surface. Protein binding was observed as an increase in the nanoparticle hydrodynamic radius. Our results indicate the formation of a protein monolayer at similar albumin concentrations as those found in human blood. Additionally, by monitoring the frequency and intensity of individual scattering events caused by single gold nanoparticles passing the observation volume, we found that BSA did not induce colloidal aggregation, a relevant result from the toxicological viewpoint. Moreover, to elucidate the thermodynamics of the gold nanoparticle-BSA association, we measured an adsorption isotherm which was best described by an anticooperative binding model. The number of binding sites based on this model was consistent with a BSA monolayer in its native state. In contrast, experiments using poly(ethylene glycol)-capped gold nanoparticles revealed no evidence for adsorption of BSA.

Use of the Frank sequence in pulsed EPR

The Frank polyphase sequence has been applied to pulsed EPR of triarylmethyl radicals at 25 6 MHz (9.1 mT magnetic field), using 256 phase pulses. In EPR, as in NMR, use of a Frank sequence of phase steps permits pulsed FID signal acquisition with very low power microwave/RF pulses (ca. 1.5 mW in the application reported here) relative to standard pulsed EPR. A 0.2 mM aqueous solution of a triarylmethyl radical was studied using a 16 mm diameter cross-loop resonator to isolate the EPR signal detection system from the incident pulses.

GFT projection NMR spectroscopy for proteins in the solid state

Recording of four-dimensional (4D) spectra for proteins in the solid state has opened new avenues to obtain virtually complete resonance assignments and three-dimensional (3D) structures of proteins. As in solution state NMR, the sampling of three indirect dimensions leads per se to long minimal measurement time. Furthermore, artifact suppression in solid state NMR relies primarily on radio-frequency pulse phase cycling. For an n-step phase cycle, the minimal measurement times of both 3D and 4D spectra are increased n times. To tackle the associated 'sampling problem' and to avoid sampling limited data acquisition, solid state G-Matrix Fourier Transform (SS GFT) projection NMR is introduced to rapidly acquire 3D and 4D spectral information. Specifically, (4,3)D (HA)CANCOCX and (3,2)D (HACA)NCOCX were implemented and recorded for the 6 kDa protein GB1 within about 10% of the time required for acquiring the conventional congeners with the same maximal evolution times and spectral widths in the indirect dimensions. Spectral analysis was complemented by comparative analysis of expected spectral congestion in conventional and GFT NMR experiments, demonstrating that high spectral resolution of the GFT NMR experiments enables one to efficiently obtain nearly complete resonance assignments even for large proteins.

Assignment strategies for large proteins by magic-angle spinning NMR: the 21-kDa disulfide-bond-forming enzyme DsbA

We present strategies for chemical shift assignments of large proteins by magic-angle spinning solid-state NMR, using the 21-kDa disulfide-bond-forming enzyme DsbA as prototype. Previous studies have demonstrated that complete de novo assignments are possible for proteins up to approximately 17 kDa, and partial assignments have been performed for several larger proteins. Here we show that combinations of isotopic labeling strategies, high field correlation spectroscopy, and three-dimensional (3D) and four-dimensional (4D) backbone correlation experiments yield highly confident assignments for more than 90% of backbone resonances in DsbA. Samples were prepared as nanocrystalline precipitates by a dialysis procedure, resulting in heterogeneous linewidths below 0.2 ppm. Thus, high magnetic fields, selective decoupling pulse sequences, and sparse isotopic labeling all improved spectral resolution. Assignments by amino acid type were facilitated by particular combinations of pulse sequences and isotopic labeling; for example, transferred echo double resonance experiments enhanced sensitivity for Pro and Gly residues; [2-(13)C]glycerol labeling clarified Val, Ile, and Leu assignments; in-phase anti-phase correlation spectra enabled interpretation of otherwise crowded Glx/Asx side-chain regions; and 3D NCACX experiments on [2-(13)C]glycerol samples provided unique sets of aromatic (Phe, Tyr, and Trp) correlations. Together with high-sensitivity CANCOCA 4D experiments and CANCOCX 3D experiments, unambiguous backbone walks could be performed throughout the majority of the sequence. At 189 residues, DsbA represents the largest monomeric unit for which essentially complete solid-state NMR assignments have so far been achieved. These results will facilitate studies of nanocrystalline DsbA structure and dynamics and will enable analysis of its 41-kDa covalent complex with the membrane protein DsbB, for which we demonstrate a high-resolution two-dimensional (13)C-(13)C spectrum.

Gapped pulses for frequency-swept MRI

A recently introduced method called SWIFT (SWeep Imaging with Fourier Transform) is a fundamentally different approach to MRI which is particularly well suited to imaging objects with extremely fast spin-spin relaxation rates. The method exploits a frequency-swept excitation pulse and virtually simultaneous signal acquisition in a time-shared mode. Correlation of the spin system response with the excitation pulse function is used to extract the signals of interest. With SWIFT, image quality is highly dependent on producing uniform and broadband spin excitation. These requirements are satisfied by using frequency-modulated pulses belonging to the hyperbolic secant family (HSn pulses). This article describes the experimental steps needed to properly implement HSn pulses in SWIFT. In addition, properties of HSn pulses in the rapid passage, linear region are investigated, followed by an analysis of the pulses after inserting the "gaps" needed for time-shared excitation and acquisition. Finally, compact expressions are presented to estimate the amplitude and flip angle of the HSn pulses, as well as the relative energy deposited by the SWIFT sequence.

Stochastic excitation and Hadamard correlation spectroscopy with bandwidth extension in RF FT-EPR

The application of correlation spectroscopy employing stochastic excitation and the Hadamard transform to time-domain Fourier transform electron paramagnetic resonance (FT-EPR) spectroscopy in the radiofrequency (RF) band is described. An existing, time-domain FT-EPR spectrometer system with a Larmor frequency (L(f)) of 300 MHz was used to develop this technique by incorporating a pseudo-random pulse sequence generator to output the maximum length binary sequence (MLBS, 10- and 11-bit). Software developed to control the EPR system setup, acquire the signals, and post process the data, is outlined. The software incorporates the Hadamard transform algorithm to perform the required cross-correlation of the acquired signal and the MLBS after stochastic excitation. To accommodate the EPR signals, bandwidth extension was accomplished by sampling at a rate many times faster than the RF pulse repetition rate, and subsequent digital signal processing of the data. The results of these experiments showed that there was a decrease in the total acquisition time, and an improved free induction decay (FID) signal-to-noise (S/N) ratio compared to the conventional coherent averaging approach. These techniques have the potential to reduce the RF pulse power to the levels used in continuous wave (CW) EPR while retaining the advantage of time-domain EPR methods. These methods have the potential to facilitate the progression to in vivo FT-EPR imaging of larger volumes.