Modulation of frustration in folding by sequence permutation.

Folding of globular proteins can be envisioned as the contraction of a random coil unfolded state toward the native state on an energy surface rough with local minima trapping frustrated species. These substructures impede productive folding and can serve as nucleation sites for aggregation reactions. However, little is known about the relationship between frustration and its underlying sequence determinants. Chemotaxis response regulator Y (CheY), a 129-amino acid bacterial protein, has been shown previously to populate an off-pathway kinetic trap in the microsecond time range. The frustration has been ascribed to premature docking of the N- and C-terminal subdomains or, alternatively, to the formation of an unproductive local-in-sequence cluster of branched aliphatic side chains, isoleucine, leucine, and valine (ILV). The roles of the subdomains and ILV clusters in frustration were tested by altering the sequence connectivity using circular permutations. Surprisingly, the stability and buried surface area of the intermediate could be increased or decreased depending on the location of the termini. Comparison with the results of small-angle X-ray-scattering experiments and simulations points to the accelerated formation of a more compact, on-pathway species for the more stable intermediate. The effect of chain connectivity in modulating the structures and stabilities of the early kinetic traps in CheY is better understood in terms of the ILV cluster model. However, the subdomain model captures the requirement for an intact N-terminal domain to access the native conformation. Chain entropy and aliphatic-rich sequences play crucial roles in biasing the early events leading to frustration in the folding of CheY.

Development of a single-cell X-ray fluorescence flow cytometer.

An X-ray fluorescence flow cytometer that can determine the total metal content of single cells has been developed. Capillary action or pressure was used to load cells into hydrophilic or hydrophobic capillaries, respectively. Once loaded, the cells were transported at a fixed vertical velocity past a focused X-ray beam. X-ray fluorescence was then used to determine the mass of metal in each cell. By making single-cell measurements, the population heterogeneity for metals in the µM to mM concentration range on fL sample volumes can be directly measured, a measurement that is difficult using most analytical methods. This approach has been used to determine the metal composition of 936 individual bovine red blood cells (bRBC), 31 individual 3T3 mouse fibroblasts (NIH3T3) and 18 Saccharomyces cerevisiae (yeast) cells with an average measurement frequency of ∼4 cells min(-1). These data show evidence for surprisingly broad metal distributions. Details of the device design, data analysis and opportunities for further sensitivity improvement are described.

Sub-millisecond time-resolved SAXS using a continuous-flow mixer and X-ray microbeam.

Small-angle X-ray scattering (SAXS) is a well established technique to probe the nanoscale structure and interactions in soft matter. It allows one to study the structure of native particles in near physiological environments and to analyze structural changes in response to variations in external conditions. The combination of microfluidics and SAXS provides a powerful tool to investigate dynamic processes on a molecular level with sub-millisecond time resolution. Reaction kinetics in the sub-millisecond time range has been achieved using continuous-flow mixers manufactured using micromachining techniques. The time resolution of these devices has previously been limited, in part, by the X-ray beam sizes delivered by typical SAXS beamlines. These limitations can be overcome using optics to focus X-rays to the micrometer size range providing that beam divergence and photon flux suitable for performing SAXS experiments can be maintained. Such micro-SAXS in combination with microfluidic devices would be an attractive probe for time-resolved studies. Here, the development of a high-duty-cycle scanning microsecond-time-resolution SAXS capability, built around the Kirkpatrick-Baez mirror-based microbeam system at the Biophysics Collaborative Access Team (BioCAT) beamline 18ID at the Advanced Photon Source, Argonne National Laboratory, is reported. A detailed description of the microbeam small-angle-scattering instrument, the turbulent flow mixer, as well as the data acquisition and control and analysis software is provided. Results are presented where this apparatus was used to study the folding of cytochrome c. Future prospects for this technique are discussed.

Increased brain iron coincides with early plaque formation in a mouse model of Alzheimer's disease.

Elevated brain iron content, which has been observed in late-stage human Alzheimer's disease, is a potential target for early diagnosis. However, the time course for iron accumulation is currently unclear. Using the PSAPP mouse model of amyloid plaque formation, we conducted a time course study of metal ion content and distribution [iron (Fe), copper (Cu), and zinc (Zn)] in the cortex and hippocampus using X-ray fluorescence microscopy (XFM). We found that iron in the cortex was 34% higher than age-matched controls at an early stage, corresponding to the commencement of plaque formation. The elevated iron was not associated with the amyloid plaques. Interestingly, none of the metal ions were elevated in the amyloid plaques until the latest time point (56 weeks), where only the Zn content was significantly elevated by 38%. Since neuropathological changes in human Alzheimer's disease are presumed to occur years before the first cognitive symptoms appear, quantification of brain iron content could be a powerful marker for early diagnosis of Alzheimer's disease.

Strong stabilization of amorphous calcium carbonate emulsion by ovalbumin: gaining insight into the mechanism of 'polymer-induced liquid precursor' processes.

The impact of the ovo proteins ovalbumin and lysozyme--present in the first stage of egg shell formation--on the homogeneous formation of the liquid amorphous calcium carbonate (LACC) precursor, was studied by a combination of complementing methods: in situ WAXS, SANS, XANES, TEM, and immunogold labeling. Lysozyme (pI = 9.3) destabilizes the LACC emulsion whereas the glycoprotein ovalbumin (pI = 4.7) extends the lifespan of the emulsified state remarkably. In the light of the presented data: (a) Ovalbumin is shown to behave commensurable to the 'polymer-induced liquid precursor' (PILP) process proposed by Gower et al. Ovalbumin can be assumed to take a key role during eggshell formation where it serves as an effective stabilization agent for transient precursors and prevents undirected mineralization of the eggshell. (b) It is further shown that the emulsified LACC carries a negative surface charge and is electrostatically stabilized. (c) We propose that the liquid amorphous calcium carbonate is affected by polymers by depletion stabilization and de-emulsification rather than 'induced' by acidic proteins and polymers during a so-called polymer-induced liquid-precursor process. The original PILP coating effect, first reported by Gower et al., appears to be a result of a de-emulsification process of a stabilized LACC phase. The behavior of the liquid amorphous carbonate phase and the polymer-induced liquid-precursor phase itself can be well described by colloid chemical terms: electrostatic and depletion stabilization and de-emulsification by depletion destabilization.

Phase-space analysis and experimental results for secondary focusing at X-ray beamlines.

Micro-focusing optical devices at synchrotron beamlines usually have a limited acceptance, but more flux can be intercepted if such optics are used to focus secondary sources created by the primary optics. Flux throughput can be maximized by placing the secondary focusing optics close to or exactly at the secondary source position. However, standard methods of beamline optics analysis, such as the lens equation or matching the mirror surface to an ellipse, work poorly when the source-to-optics distance is very short. In this paper the general characteristics of the focusing of beams with Gaussian profiles by a ;thin lens' are analysed under the paraxial approximation in phase space, concluding that the focusing of a beam with a short source-to-optics distance is distinct from imaging the source; slope errors are successfully included in all the formulas so that they can be used to calculate beamline focusing with good accuracy. A method is also introduced to use the thin-lens result to analyse the micro-focusing produced by an elliptically bent trapezoid-shaped Kirkpatrick-Baez mirror. The results of this analysis are in good agreement with ray-tracing simulations and are confirmed by the experimental results of the secondary focusing at the 18-ID Bio-CAT beamline (at the APS). The result of secondary focusing carried out at 18-ID using a single-bounce capillary can also be explained using this phase-space analysis. A discussion of the secondary focusing results is presented at the end of this paper.

Synchrotron X-ray imaging reveals a correlation of tumor copper speciation with Clioquinol's anticancer activity.

Tumor development and metastasis depend on angiogenesis that requires certain growth factors, proteases, and the trace element copper (Cu). Recent studies suggest that Cu could be used as a novel target for cancer therapies. Clioquinol (CQ), an antibiotic that is able to form stable complexes with Cu or zinc (Zn), has shown proteasome-inhibitory, androgen receptor-suppressing, apoptosis-inducing, and antitumor activities in human cancer cells and xenografts. The mechanisms underlying the interaction of CQ with cellular Cu, the alteration of the Cu/Zn ratio and the antitumor role of CQ in vivo have not been fully elucidated. We report here that Cu accumulates in tumor tissue and that the Cu/Zn balances in tumor, but not normal, tissue change significantly after the treatment with CQ. Cu speciation analysis showed that the Cu(I) species is predominant in both normal and tumor tissues and that Cu(II) content was significantly increased in tumor, but not normal tissue after CQ treatment. Our findings indicate that CQ can interact with cellular Cu in vivo, dysregulates the Cu/Zn balance and is able to convert Cu(I) to Cu(II) in tumor tissue. This conversion of Cu(I) to Cu(II) may be associated with CQ-induced proteasome inhibition and growth suppression in the human prostate tumor xenografts.

Biological applications of X-ray microprobes.

PURPOSE: To present an overview of the workshop on X-ray fluorescence microscopy (XFM). RESULTS: Talks presented at the workshop and the associated works are highlighted. CONCLUSIONS: Use of XFM in biomedical sciences is growing and may be advanced even further by adding (i) high resolution microprobes, and (ii) high throughput approaches to the XFM toolbox.

Clioquinol, a therapeutic agent for Alzheimer's disease, has proteasome-inhibitory, androgen receptor-suppressing, apoptosis-inducing, and antitumor activities in human prostate cancer cells and xenografts.

Tumor growth and metastasis depend on angiogenesis that requires the cofactor copper. Consistently, high levels of copper have been found in many types of human cancers, including prostate, breast, colon, and lung. Recent studies suggest that copper could be used as a novel selective target for cancer therapies. Clioquinol is capable of forming stable complexes with copper and currently used in clinics for treatment of Alzheimer's disease. Most recently, it has been reported that clioquinol possesses antitumor effects. However, the underlying molecular mechanism is unclear. We report here that after binding to copper, clioquinol can inhibit the proteasomal chymotrypsin-like activity, repress androgen receptor (AR) protein expression, and induce apoptotic cell death in human prostate cancer LNCaP and C4-2B cells. In addition, clioquinol alone exhibits similar effects in prostate cancer cell lines with elevated copper at concentrations similar to those found in patients. Addition of dihydrotestosterone did not affect clioquinol-mediated proteasome inhibition in both prostate cancer cell lines. However, dihydrotestosterone partially inhibited clioquinol-induced AR suppression and apoptosis only in androgen-dependent LNCaP cells. Animal studies show that clioquinol treatment significantly inhibits the growth of human prostate tumor C4-2B xenografts (by 66%), associated with in vivo proteasome inhibition, AR protein repression, angiogenesis suppression, and apoptosis induction. Our study provides strong evidence that clioquinol is able to target tumor proteasome in vivo in a copper-dependent manner, resulting in formation of an active AR inhibitor and apoptosis inducer that is responsible for its observed antiprostate tumor effect.

1s2p resonant inelastic X-ray scattering of iron oxides.

1s2p resonant inelastic X-ray scattering (RIXS) spectroscopy has been measured for a series of iron oxides, including octahedral and tetrahedral Fe(II) and Fe(III) systems. Their spectral shapes have been analyzed and explained using crystal-field multiplet simulations. The RIXS planes and the K-edge and L-edge X-ray absorption spectra related to these RIXS planes will be discussed with respect to their analytical opportunities. It is concluded that the full power and possibilities of 1s2p RIXS needs an overall resolution of 0.3 eV. This will yield a technique with more detailed information than K-edge and L-edge X-ray absorption combined, obtained in a single experiment. Another major advantage is that 1s2p RIXS involves only hard X-rays, and experiments under essentially any condition and on any system are feasible.

Microsecond barrier-limited chain collapse observed by time-resolved FRET and SAXS.

It is generally held that random-coil polypeptide chains undergo a barrier-less continuous collapse when the solvent conditions are changed to favor the fully folded native conformation. We test this hypothesis by probing intramolecular distance distributions during folding in one of the paradigms of folding reactions, that of cytochrome c. The Trp59-to-heme distance was probed by time-resolved Förster resonance energy transfer in the microsecond time range of refolding. Contrary to expectation, a state with a Trp59-heme distance close to that of the guanidinium hydrochloride (GdnHCl) denatured state is present after ~27 µs of folding. A concomitant decrease in the population of this state and an increase in the population of a compact high-FRET (Förster resonance energy transfer) state (efficiency>90%) show that the collapse is barrier limited. Small-angle X-ray scattering (SAXS) measurements over a similar time range show that the radius of gyration under native favoring conditions is comparable to that of the GdnHCl denatured unfolded state. An independent comprehensive global thermodynamic analysis reveals that marginally stable partially folded structures are also present in the nominally unfolded GdnHCl denatured state. These observations suggest that specifically collapsed intermediate structures with low stability in rapid equilibrium with the unfolded state may contribute to the apparent chain contraction observed in previous fluorescence studies using steady-state detection. In the absence of significant dynamic averaging of marginally stable partially folded states and with the use of probes sensitive to distance distributions, barrier-limited chain contraction is observed upon transfer of the GdnHCl denatured state ensemble to native-like conditions.

X-ray fluorescence imaging of the hippocampal formation after manganese exposure.

Manganese (Mn) intoxication results in neurological conditions similar, but not identical, to idiopathic Parkinson's disease. While the mechanism(s) by which Mn exposure leads to neurotoxic effects remains unclear, studies by magnetic resonance imaging demonstrate a high Mn accumulation in the hippocampal formation (HPCf) of the brain. Metal quantification using this method is not possible. Using X-ray fluorescence imaging, we measured the distribution of Mn in the HPCf for a rodent model of chronic Mn exposure and quantitatively compared it with distributions of other biologically relevant metals. We found considerable increases in average Mn concentrations in all analyzed areas and we identified the dentate gyrus (DG) and the cornus ammonis 3 (CA3) layer as areas accumulating the highest Mn content (∼1.2 µg Mn per g tissue). The DG is significantly enriched with iron (Fe), while the CA3 layer has high zinc (Zn) content. Additionally, significant spatial correlations were found for Mn-Zn concentrations across the HPCf substructures and for Mn-Fe concentrations in the DG. Combined results support that at least two mechanisms may be responsible for Mn transport and/or storage in the brain, associated with either Fe or Zn. Subcellular resolution images of metal distribution in cells of the CA3 show diffuse Mn distributions consistent with Mn localization in both the cytoplasm and nucleus. Mn was not increased in localized intracellular Fe or copper accumulations. A consistent Mn-Zn correlation both at the tissue (40 µm × 40 µm) and cellular (0.3 µm × 0.3 µm) levels suggests that a Zn transport/storage mechanism in the HPCf is likely associated with Mn accumulation.

X-ray fluorescence imaging: a new tool for studying manganese neurotoxicity.

The neurotoxic effect of manganese (Mn) establishes itself in a condition known as manganism or Mn induced parkinsonism. While this condition was first diagnosed about 170 years ago, the mechanism of the neurotoxic action of Mn remains unknown. Moreover, the possibility that Mn exposure combined with other genetic and environmental factors can contribute to the development of Parkinson's disease has been discussed in the literature and several epidemiological studies have demonstrated a correlation between Mn exposure and an elevated risk of Parkinson's disease. Here, we introduce X-ray fluorescence imaging as a new quantitative tool for analysis of the Mn distribution in the brain with high spatial resolution. The animal model employed mimics deficits observed in affected human subjects. The obtained maps of Mn distribution in the brain demonstrate the highest Mn content in the globus pallidus, the thalamus, and the substantia nigra pars compacta. To test the hypothesis that Mn transport into/distribution within brain cells mimics that of other biologically relevant metal ions, such as iron, copper, or zinc, their distributions were compared. It was demonstrated that the Mn distribution does not follow the distributions of any of these metals in the brain. The majority of Mn in the brain was shown to occur in the mobile state, confirming the relevance of the chelation therapy currently used to treat Mn intoxication. In cells with accumulated Mn, it can cause neurotoxic action by affecting the mitochondrial respiratory chain. This can result in increased susceptibility of the neurons of the globus pallidus, thalamus, and substantia nigra pars compacta to various environmental or genetic insults. The obtained data is the first demonstration of Mn accumulation in the substantia nigra pars compacta, and thus, can represent a link between Mn exposure and its potential effects for development of Parkinson's disease.

Increased ß-amyloid deposition in Tg-SWDI transgenic mouse brain following in vivo lead exposure.

Previous studies in humans and animals have suggested a possible association between lead (Pb) exposure and the etiology of Alzheimer's disease (AD). Animals acutely exposed to Pb display an over-expressed amyloid precursor protein (APP) and the ensuing accumulation of beta-amyloid (Aß) in brain extracellular spaces. This study was designed to examine whether in vivo Pb exposure increased brain concentrations of Aß, resulting in amyloid plaque deposition in brain tissues. Human Tg-SWDI APP transgenic mice, which genetically over-express amyloid plaques at age of 2-3 months, received oral gavages of 50mg/kg Pb acetate once daily for 6 weeks; a control group of the same mouse strain received the same molar concentration of Na acetate. ELISA results revealed a significant increase of Aß in the CSF, brain cortex and hippocampus. Immunohistochemistry displayed a detectable increase of amyloid plaques in brains of Pb-exposed animals. Neurobehavioral test using Morris water maze showed an impaired spatial learning ability in Pb-treated mice, but not in C57BL/6 wild type mice with the same age. In vitro studies further uncovered that Pb facilitated Aß fibril formation. Moreover, the synchrotron X-ray fluorescent studies demonstrated a high level of Pb present in amyloid plaques in mice exposed to Pb in vivo. Taken together, these data indicate that Pb exposure with ensuing elevated Aß level in mouse brains appears to be associated with the amyloid plaques formation. Pb apparently facilitates Aß fibril formation and participates in deposition of amyloid plaques.

L X-ray fluorescence cross sections experimentally determined for elements with 45 < Z < 50 at 9 keV.

Experimental determination of L fluorescence cross-sections for elements with 45

Carbonate-coordinated metal complexes precede the formation of liquid amorphous mineral emulsions of divalent metal carbonates.

During the mineralisation of metal carbonates MCO3 (M=Ca, Sr, Ba, Mn, Cd, Pb) liquid-like amorphous intermediates emerge. These intermediates that form via a liquid/liquid phase separation behave like a classical emulsion and are stabilized electrostatically. The occurrence of these intermediates is attributed to the formation of highly hydrated networks whose stability is mainly based on weak interactions and the variability of the metal-containing pre-critical clusters. Their existence and compositional freedom are evidenced by electrospray ionization mass spectrometry (ESI-MS). Liquid intermediates in non-classical crystallisation pathways seem to be more common than assumed.

Minireview: structural insights into early folding events using continuous-flow time-resolved small-angle X-ray scattering.

Small-angle X-ray scattering (SAXS) is a powerful method for obtaining quantitative structural information on the size and shape of proteins, and it is increasingly used in kinetic studies of folding and association reactions. In this minireview, we discuss recent developments in using SAXS to obtain structural information on the unfolded ensemble and early folding intermediates of proteins using continuous-flow mixing devices. Interfacing of these micromachined devices to SAXS beamlines has allowed access to the microsecond time regime. The experimental constraints in implementation of turbulence and laminar flow-based mixers with SAXS detection and a comparison of the two approaches are presented. Current improvements and future prospects of microsecond time-resolved SAXS and the synergy with ab initio structure prediction and molecular dynamics simulations are discussed.

X-ray diffraction from intact tau aggregates in human brain tissue.

We describe an instrument to record x-ray diffraction patterns from diseased regions of human brain tissue by combining an in-line visible light fluorescence microscope with an x-ray diffraction microprobe. We use thiazine red fluorescence to specifically label and detect the filamentous tau protein pathology associated with Pick's disease, as several labs have done previously. We demonstrate that thiazine red-enhanced regions within the tissue show periodic structure in x-ray diffraction that is not observed in healthy tissue. One observed periodicity (4.2 Å) is characteristic of cross-beta sheet structure, consistent with previous results from powder diffraction studies performed on purified, dried tau protein.

High-flux hard X-ray microbeam using a single-bounce capillary with doubly focused undulator beam.

A pre-focused X-ray beam at 12 keV and 9 keV has been used to illuminate a single-bounce capillary in order to generate a high-flux X-ray microbeam. The BioCAT undulator X-ray beamline 18ID at the Advanced Photon Source was used to generate the pre-focused beam containing 1.2 x 10(13) photons s(-1) using a sagittal-focusing double-crystal monochromator and a bimorph mirror. The capillary entrance was aligned with the focal point of the pre-focused beam in order to accept the full flux of the undulator beam. Two alignment configurations were tested: (i) where the center of the capillary was aligned with the pre-focused beam (;in-line') and (ii) where one side of the capillary was aligned with the beam (;off-line'). The latter arrangement delivered more flux (3.3 x 10(12) photons s(-1)) and smaller spot sizes (< or =10 microm FWHM in both directions) for a photon flux density of 4.2 x 10(10) photons s(-1) microm(-2). The combination of the beamline main optics with a large-working-distance (approximately 24 mm) capillary used in this experiment makes it suitable for many microprobe fluorescence applications that require a micrometer-size X-ray beam and high flux density. These features are advantageous for biological samples, where typical metal concentrations are in the range of a few ng cm(-2). Micro-XANES experiments are also feasible using this combined optical arrangement.

Spectrochemical analysis of dental calculus by synchrotron radiation X-ray fluorescence.

This work presents elemental composition studies of human dental calculus by X-ray fluorescence analysis using synchrotron radiation. The intrinsic characteristics of synchrotron light allow for a quantitative analysis of major, minor, and trace elements of very small samples in a single measurement. At present, several theories of calculus formation exist, but none of them can describe completely all the complicated mechanisms involved in the mineralization processes. For this reason, and taking into account that experimental data are long overdue, several calculi with certain degrees of formation were collected from adult patients for analysis. The ratio of calcium/phosphorus was used as an indicator of the major crystalline structure and the state of formation of the calculus. The results demonstrate a clear correlation between the concentrations of certain elements and the type of calculus (supra- or sub-gingival). In addition, the possible correlation between the elements was analyzed.