The Impact of Travel Time on Trimodal Therapy Compared to Cystectomy for Bladder Cancer

PURPOSE/OBJECTIVE(S)

Neoadjuvant chemotherapy followed by radical cystectomy (RC) and Transurethral Resection of Bladder Tumor (TURBT) followed by concurrent chemoradiation therapy (trimodal therapy, TMT) are both evidence-based approaches to the management of muscle-invasive bladder cancer, and no randomized evidence conclusively supports the use of one treatment over another. Literature suggests that increasing distance to radiation therapy (RT) facilities reduces the likelihood that patients will receive RT, though this has not been evaluated in bladder cancer. We hypothesize that greater travel time between a patient's home and their closest RT facility is associated with a lower likelihood of undergoing TMT.

MATERIALS/METHODS

Clinical data and the locations of patient residences and surgical facilities performing RC were obtained from the California Cancer Registry. RT facility locations were compiled from state regulatory databases and dosimetric accrediting bodies. Travel time was identified using the Google Distance Matrix API. California patients diagnosed with T2-4N0 bladder cancer in 2018-2019 who underwent TMT (> = 55Gy) or RC were included in this analysis. Chi-square tests, Kruskal-Wallis tests, and univariate and multivariate logistic regressions were performed to assess factors associated with an increased likelihood of receipt of TMT, and to compare travel times for patients receiving TMT vs RC.

RESULTS

A total of 536 patients met inclusion criteria, and 27.1% underwent TMT. Patients receiving TMT were more likely to be older, White, male, and live further from their nearest RT facility. After adjusting for age, sex, and race/ethnicity, patients undergoing TMT were more likely than RC patients to live more than 30 minutes away from the nearest RT facility (OR 1.53, p = 0.21, ref<15 minutes). On multivariate analysis, patients receiving TMT were less likely than surgical patients to live 30-60 minutes or >60 minutes from their treatment facility ((OR 0.5, p-value<0.01, and OR 0.23, p-value <.001), ref: <30 minutes). Only 26.2% of patients who received TMT were treated at their nearest RT facility, while 13.3% of patients undergoing RC were treated at their nearest surgical facility.

CONCLUSION

In a modern cohort of bladder cancer patients in California, about a quarter of T2-4N0 patients are undergoing bladder preservation. Patients undergoing TMT lived further from their nearest RT facility than patients undergoing surgery. Surgical patients were more likely to live >30 minutes from their treating facility than TMT patients. A minority of patients underwent treatment at the facility nearest to them, regardless of treatment modality chosen. Taken together, this suggests that proximity to the nearest RT facility may not be associated with a higher likelihood of undergoing TMT. Examination of actual treatment facilities (as opposed to the closest facility) shows that patients are traveling further for surgical care than TMT.

Bacterial chemoreceptor signaling complexes control kinase activity by stabilizing the catalytic domain of CheA

Motile bacteria have a chemotaxis system that enables them to sense their environment and direct their swimming toward favorable conditions. Chemotaxis involves a signaling process in which ligand binding to the extracellular domain of the chemoreceptor alters the activity of the histidine kinase, CheA, bound ~300 Å away to the distal cytoplasmic tip of the receptor, to initiate a phosphorylation cascade that controls flagellar rotation. The cytoplasmic domain of the receptor is thought to propagate this signal via changes in dynamics and/or stability, but it is unclear how these changes modulate the kinase activity of CheA. To address this question, we have used hydrogen deuterium exchange mass spectrometry to probe the structure and dynamics of CheA within functional signaling complexes of the Escherichia coli aspartate receptor cytoplasmic fragment, CheA, and CheW. Our results reveal that stabilization of the P4 catalytic domain of CheA correlates with kinase activation. Furthermore, differences in activation of the kinase that occur during sensory adaptation depend on receptor destabilization of the P3 dimerization domain of CheA. Finally, hydrogen exchange properties of the P1 domain that bears the phosphorylated histidine identify the dimer interface of P1/P1' in the CheA dimer and support an ordered sequential binding mechanism of catalysis, in which dimeric P1/P1' has productive interactions with P4 only upon nucleotide binding. Thus stabilization/destabilization of domains is a key element of the mechanism of modulating CheA kinase activity in chemotaxis, and may play a role in the control of other kinases.

Diethylpyrocarbonate-Based Covalent Labeling Mass Spectrometry of Protein Interactions in a Membrane Complex System

Membrane-associated proteins are important because they mediate interactions between a cell's external and internal environment and they are often targets of therapeutics. Characterizing their structures and binding interactions, however, is challenging because they typically must be solubilized using artificial membrane systems that can make measurements difficult. Mass spectrometry (MS) is emerging as a valuable tool for studying membrane-associated proteins, and covalent labeling MS has unique potential to provide higher order structure and binding information for these proteins in complicated membrane systems. Here, we demonstrate that diethylpyrocarbonate (DEPC) can be effectively used as a labeling reagent to characterize the binding interactions between a membrane-associated protein and its binding partners in an artificial membrane system. Using chemotaxis histidine kinase (CheA) as a model system, we demonstrate that DEPC-based covalent labeling MS can provide structural and binding information about the ternary complex of CheA with two other proteins that is consistent with structural models of this membrane-associated chemoreceptor system. Despite the moderate hydrophobicity of DEPC, we find that its reactivity with proteins is not substantially influenced by the presence of the artificial membranes. However, correct structural information for this multiprotein chemoreceptor system requires measurements of DEPC labeling at multiple reagent concentrations to enable an accurate comparison between CheA and its ternary complex in the chemoreceptor system. In addition to providing structural information that is consistent with the model of this complex system, the labeling data supplements structural information that is not sufficiently refined in the chemoreceptor model.

Protein rings are critical to the remarkable signaling properties of bacterial chemotaxis nanoarrays

Bacteria build an extensive sensory nanoarray to collect information that guides their swimming. In this issue of Science Signaling, Piñas et al. demonstrate that a key element of these arrays that enhances chemotaxis responses are hexameric rings of CheW, one of two types of rings that couple the responses of core signaling units to achieve remarkable signaling properties such as single-molecule detection.

A practical guide to teaching with Proteopedia

Proteopedia (proteopedia.org) is an open resource to explore the structure-function relationship of proteins and other biomolecules. This guide provides practical advice on how to incorporate Proteopedia into teaching the structure and function of proteins and other biomolecules. For 11 activities, we discuss desired outcomes, setting expectations, preparing students for the tasks, using resources within Proteopedia, and evaluating student work. We point out features of Proteopedia that make it especially suitable for teaching and give examples of how to avoid common pitfalls.

Hydrogen exchange of chemoreceptors in functional complexes suggests protein stabilization mediates long-range allosteric coupling

Bacterial chemotaxis receptors form extended hexagonal arrays that integrate and amplify signals to control swimming behavior. Transmembrane signaling begins with a 2-Å ligand-induced displacement of an α helix in the periplasmic and transmembrane domains, but it is unknown how the cytoplasmic domain propagates the signal an additional 200 Å to control the kinase CheA bound to the membrane-distal tip of the receptor. The receptor cytoplasmic domain has previously been shown to be highly dynamic as both a cytoplasmic fragment (CF) and within the intact chemoreceptor; modulation of its dynamics is thought to play a key role in signal propagation. This hydrogen deuterium exchange-MS (HDX-MS) study of functional complexes of CF, CheA, and CheW bound to vesicles in native-like arrays reveals that the CF is well-ordered only in its protein interaction region where it binds CheA and CheW. We observe rapid exchange throughout the rest of the CF, with both uncorrelated (EX2) and correlated (EX1) exchange patterns, suggesting the receptor cytoplasmic domain retains disorder even within functional complexes. HDX rates are increased by inputs that favor the kinase-off state. We propose that chemoreceptors achieve long-range allosteric control of the kinase through a coupled equilibrium: CheA binding in a kinase-on conformation stabilizes the cytoplasmic domain, and signaling inputs that destabilize this domain (ligand binding and demethylation) disfavor CheA binding such that it loses key contacts and reverts to a kinase-off state. This study reveals the mechanistic role of an intrinsically disordered region of a transmembrane receptor in long-range allostery.

Carbon-nitrogen REDOR to identify ms-timescale mobility in proteins

Protein dynamics play key mechanistic roles but are difficult to measure in large proteins and protein complexes. INEPT and CP solid-state NMR experiments have often been used to obtain spectra of protein regions that are mobile and rigid, respectively, on the nanosecond timescale. To complement this approach, we have implemented ¹³C{¹⁵N} REDOR to detect protein regions with backbone dynamics on the millisecond time scale that average the ≈1 kHz carbon-nitrogen dipolar coupling. REDOR-filtering of carbon correlation spectra removes signals from rigid backbone carbons and retains signals from backbone carbons with ms-timescale dynamics that would be missing in dipolar-driven NCA/NCO spectra. We use these experiments to investigate functionally important dynamics within the E coli Asp receptor cytoplasmic fragment (U-¹³C, ¹⁵N-CF) in native-like complexes with CheA and CheW. The CF backbone carbons exhibit only 60-75% of the expected REDOR dephasing, suggesting that 40-25% of the backbone experiences significant mobility that averages the ¹³C¹⁵N dipolar couplings to zero. Furthermore, the extent of this mobility changes with signaling state.

His-Tag-Mediated Dimerization of Chemoreceptors Leads to Assembly of Functional Nanoarrays

Transmembrane chemotaxis receptors are found in bacteria in extended hexagonal arrays stabilized by the membrane and by cytosolic binding partners, the kinase CheA and coupling protein CheW. Models of array architecture and assembly propose receptors cluster into trimers of dimers that associate with one CheA dimer and two CheW monomers to form the minimal "core unit" necessary for signal transduction. Reconstructing in vitro chemoreceptor ternary complexes that are homogeneous and functional and exhibit native architecture remains a challenge. Here we report that His-tag-mediated receptor dimerization with divalent metals is sufficient to drive assembly of nativelike functional arrays of a receptor cytoplasmic fragment. Our results indicate receptor dimerization initiates assembly and precedes formation of ternary complexes with partial kinase activity. Restoration of maximal kinase activity coincides with a shift to larger complexes, suggesting that kinase activity depends on interactions beyond the core unit. We hypothesize that achieving maximal activity requires building core units into hexagons and/or coalescing hexagons into the extended lattice. Overall, the minimally perturbing His-tag-mediated dimerization leads to assembly of chemoreceptor arrays with native architecture and thus serves as a powerful tool for studying the assembly and mechanism of this complex and other multiprotein complexes.

Signaling-Related Mobility Changes in Bacterial Chemotaxis Receptors Revealed by Solid-State NMR

Bacteria employ remarkable membrane-bound nanoarrays to sense their environment and direct their swimming. Arrays consist of chemotaxis receptor trimers of dimers that are bridged at their membrane-distal tips by rings of two cytoplasmic proteins, a kinase CheA and a coupling protein CheW. It is not clear how ligand binding to the periplasmic domain of the receptor deactivates the CheA kinase bound to the cytoplasmic tip ∼300 Å away, but the mechanism is thought to involve changes in dynamics within the cytoplasmic domain. To test these proposals, we applied solid-state NMR mobility-filtered experiments to functional complexes of the receptor cytoplasmic fragment (U–¹³C,¹⁵N-CF), CheA, and CheW. Assembly of these proteins into native-like, homogeneous arrays is mediated by either vesicle binding or molecular crowding agents, and paramagnetic relaxation enhancement is used to overcome sensitivity challenges in these large complexes. INEPT spectra reveal that a significant fraction of the receptor is dynamic on the nanosecond or shorter time scale, and these dynamics change with signaling state. The mobile regions are identified through a combination of biochemical and NMR approaches (protein truncations and unique chemical shifts). The INEPT spectra are consistent with an asymmetric mobility in the methylation region (N-helix mobility ≫ C-helix mobility) and reveal an increase in the mobility of the N-helix in the kinase-off state. This finding identifies functionally relevant dynamics in the receptor, and suggests that this N-helix segment plays a key role in propagating the signal.

Older Adulthood

Efforts to assess the effects of a variety of stressors to which older adults are exposed will be no more successful than measuring instruments are valid and appropriately sensitive to change. Research springing from the trait-state distinction has led to some important clarifications regarding properties of measuring instruments, ways of conceptualizing among-persons variation, and the multidimensionality of individuals' response patterns. To examine the suitability of several extant state measures for use with the elderly, 111 older (age 60+) adults were measured, then remeasured two weeks later, with a battery covering five state dimensions. Data are analyzed to test their hypothesized factor structure of the measures and, from a construct validity perspective, to evaluate the short-term stability (test-retest coefficients) of both scales and underlying factors. Results support the factorial validity of instruments developed for the measurement of anxiety and fatigue states when used in older adult populations.

Multidimensional Solid-State Nuclear Magnetic Resonance of a Functional Multiprotein Chemoreceptor Array

The bacterial chemoreceptor complex governs signal detection and the upstream elements of chemotactic behavior, but the detailed molecular mechanism is still unclear. We have assembled nativelike functional arrays of an aspartate receptor cytoplasmic fragment (CF) with its two cytoplasmic protein partners (CheA and CheW) for solid-state nuclear magnetic resonance (NMR) studies of structural changes involved in signaling. In this initial study of the uniformly (13)C- and (15)N-enriched CF in these >13.8 MDa size arrays, residue-type assignments are made for amino acids that together make up 90% of the protein. We demonstrate that homo- and heteronuclear two-dimensional spectra are consistent with structure-based chemical shift predictions: a number of major assignable correlations are consistent with the predominantly α-helical secondary structure, and minor correlations are consistent with the disordered C-terminal tail. Sub-parts per million line widths and spectral changes upon freezing of samples suggest these arrays are structurally homogeneous and sufficiently immobilized for efficient solid-state NMR.

Hydrogen exchange differences between chemoreceptor signaling complexes localize to functionally important subdomains

The goal of understanding mechanisms of transmembrane signaling, one of many key life processes mediated by membrane proteins, has motivated numerous studies of bacterial chemotaxis receptors. Ligand binding to the receptor causes a piston motion of an α helix in the periplasmic and transmembrane domains, but it is unclear how the signal is then propagated through the cytoplasmic domain to control the activity of the associated kinase CheA. Recent proposals suggest that signaling in the cytoplasmic domain involves opposing changes in dynamics in different subdomains. However, it has been difficult to measure dynamics within the functional system, consisting of extended arrays of receptor complexes with two other proteins, CheA and CheW. We have combined hydrogen exchange mass spectrometry with vesicle template assembly of functional complexes of the receptor cytoplasmic domain to reveal that there are significant signaling-associated changes in exchange, and these changes localize to key regions of the receptor involved in the excitation and adaptation responses. The methylation subdomain exhibits complex changes that include slower hydrogen exchange in complexes in a kinase-activating state, which may be partially consistent with proposals that this subdomain is stabilized in this state. The signaling subdomain exhibits significant protection from hydrogen exchange in complexes in a kinase-activating state, suggesting a tighter and/or larger interaction interface with CheA and CheW in this state. These first measurements of the stability of protein subdomains within functional signaling complexes demonstrate the promise of this approach for measuring functionally important protein dynamics within the various physiologically relevant states of multiprotein complexes.

Structure of bacterial cytoplasmic chemoreceptor arrays and implications for chemotactic signaling

Most motile bacteria sense and respond to their environment through a transmembrane chemoreceptor array whose structure and function have been well-studied, but many species also contain an additional cluster of chemoreceptors in their cytoplasm. Although the cytoplasmic cluster is essential for normal chemotaxis in some organisms, its structure and function remain unknown. Here we use electron cryotomography to image the cytoplasmic chemoreceptor cluster in Rhodobacter sphaeroides and Vibrio cholerae. We show that just like transmembrane arrays, cytoplasmic clusters contain trimers-of-receptor-dimers organized in 12-nm hexagonal arrays. In contrast to transmembrane arrays, however, cytoplasmic clusters comprise two CheA/CheW baseplates sandwiching two opposed receptor arrays. We further show that cytoplasmic fragments of normally transmembrane E. coli chemoreceptors form similar sandwiched structures in the presence of molecular crowding agents. Together these results suggest that the 12-nm hexagonal architecture is fundamentally important and that sandwiching and crowding can replace the stabilizing effect of the membrane.

DOI:http://dx.doi.org/10.7554/eLife.02151.001

Many bacteria swim through water by rotating tiny hair-like structures called flagella. In E. coli, if all the flagella on the surface of a bacterium rotate in a counterclockwise fashion, then it will swim in a particular direction, but if the flagella all rotate in an clockwise fashion, then the bacterium will stop swimming and start to tumble.

Bacteria use a combination of swimming and tumbling in order to move towards or away from certain chemicals. For example, a bacterium is able to move towards a source of nutrients because it is constantly evaluating its environment and will swim forward for longer periods of time when it recognizes the concentration of the nutrient is increasing. And if it senses that the nutrient concentration is decreasing, it will tumble in an effort to move in a different direction.

Many bacteria, such as E. coli, rely on proteins in their cell membrane called chemoreceptors to sense specific chemicals and then send signals that tell the flagella how to rotate. These transmembrane receptors and their role in chemotaxis—that is, movement towards or away from specific chemicals in the environment—have been widely studied. However, other bacteria also have chemoreceptors in the cytoplasm inside the bacterial cell, and much less is known about these.

Now, Briegel et al. have examined the cytoplasmic chemoreceptors of two unrelated bacteria, R. sphaeroides and V. cholera, and found that the cytoplasmic chemoreceptors arrange themselves in hexagonal arrays, similar to the way that transmembrane chemoreceptors are arranged. However, the cytoplasmic chemoreceptors arrange themselves in a two-layer sandwich-like structure, whereas the transmembrane chemoreceptors are arranged in just one layer. The next step is to understand how chemical binding causes these arrays to send their signals to the motor. A complete understanding of this signaling system may ultimately allow scientists to re-engineer it to draw bacteria to targets of medical or environmental interest, such as cancer cells or contaminated soils.

DOI:http://dx.doi.org/10.7554/eLife.02151.002

New insights into bacterial chemoreceptor array structure and assembly from electron cryotomography

Bacterial chemoreceptors cluster in highly ordered, cooperative, extended arrays with a conserved architecture, but the principles that govern array assembly remain unclear. Here we show images of cellular arrays as well as selected chemoreceptor complexes reconstituted in vitro that reveal new principles of array structure and assembly. First, in every case, receptors clustered in a trimers-of-dimers configuration, suggesting this is a highly favored fundamental building block. Second, these trimers-of-receptor dimers exhibited great versatility in the kinds of contacts they formed with each other and with other components of the signaling pathway, although only one architectural type occurred in native arrays. Third, the membrane, while it likely accelerates the formation of arrays, was neither necessary nor sufficient for lattice formation. Molecular crowding substituted for the stabilizing effect of the membrane and allowed cytoplasmic receptor fragments to form sandwiched lattices that strongly resemble the cytoplasmic chemoreceptor arrays found in some bacterial species. Finally, the effective determinant of array structure seemed to be CheA and CheW, which formed a "superlattice" of alternating CheA-filled and CheA-empty rings that linked receptor trimers-of-dimer units into their native hexagonal lattice. While concomitant overexpression of receptors, CheA, and CheW yielded arrays with native spacing, the CheA occupancy was lower and less ordered, suggesting that temporal and spatial coordination of gene expression driven by a single transcription factor may be vital for full order, or that array overgrowth may trigger a disassembly process. The results described here provide new insights into the assembly intermediates and assembly mechanism of this massive macromolecular complex.

Population level analysis of evolved mutations underlying improvements in plant hemicellulose and cellulose fermentation by Clostridium phytofermentans

Background

The complexity of plant cell walls creates many challenges for microbial decomposition. Clostridium phytofermentans, an anaerobic bacterium isolated from forest soil, directly breaks down and utilizes many plant cell wall carbohydrates. The objective of this research is to understand constraints on rates of plant decomposition by Clostridium phytofermentans and identify molecular mechanisms that may overcome these limitations.

Results

Experimental evolution via repeated serial transfers during exponential growth was used to select for C. phytofermentans genotypes that grow more rapidly on cellobiose, cellulose and xylan. To identify the underlying mutations an average of 13,600,000 paired-end reads were generated per population resulting in ∼300 fold coverage of each site in the genome. Mutations with allele frequencies of 5% or greater could be identified with statistical confidence. Many mutations are in carbohydrate-related genes including the promoter regions of glycoside hydrolases and amino acid substitutions in ABC transport proteins involved in carbohydrate uptake, signal transduction sensors that detect specific carbohydrates, proteins that affect the export of extracellular enzymes, and regulators of unknown specificity. Structural modeling of the ABC transporter complex proteins suggests that mutations in these genes may alter the recognition of carbohydrates by substrate-binding proteins and communication between the intercellular face of the transmembrane and the ATPase binding proteins.

Conclusions

Experimental evolution was effective in identifying molecular constraints on the rate of hemicellulose and cellulose fermentation and selected for putative gain of function mutations that do not typically appear in traditional molecular genetic screens. The results reveal new strategies for evolving and engineering microorganisms for faster growth on plant carbohydrates.

Hydrogen exchange mass spectrometry of functional membrane-bound chemotaxis receptor complexes

The transmembrane signaling mechanism of bacterial chemotaxis receptors is thought to involve changes in receptor conformation and dynamics. The receptors function in ternary complexes with two other proteins, CheA and CheW, that form extended membrane-bound arrays. Previous studies have shown that attractant binding induces a small (∼2 Å) piston displacement of one helix of the periplasmic and transmembrane domains toward the cytoplasm, but it is not clear how this signal propagates through the cytoplasmic domain to control the kinase activity of the CheA bound at the membrane-distal tip, nearly 200 Å away. The cytoplasmic domain has been shown to be highly dynamic, which raises the question of how a small piston motion could propagate through a dynamic domain to control CheA kinase activity. To address this, we have developed a method for measuring dynamics of the receptor cytoplasmic fragment (CF) in functional complexes with CheA and CheW. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) measurements of global exchange of the CF demonstrate that the CF exhibits significantly slower exchange in functional complexes than in solution. Because the exchange rates in functional complexes are comparable to those of other proteins with similar structures, the CF appears to be a well-structured protein within these complexes, which is compatible with its role in propagating a signal that appears to be a tiny conformational change in the periplasmic and transmembrane domains of the receptor. We also demonstrate the feasibility of this protocol for local exchange measurements by incorporating a pepsin digest step to produce peptides with 87% sequence coverage and only 20% back exchange. This method extends HDX-MS to membrane-bound functional complexes without detergents that may perturb the stability or structure of the system.

Membrane association of a protein increases the rate, extent, and specificity of chemical cross-linking

Many cellular processes involve interactions between membrane-associated proteins, and those interactions are enhanced by membrane association. We have used cross-linking reactions to compare the extent and specificity of protein interactions in solution versus on a membrane surface. Cysteine mutants of a soluble cytoplasmic fragment (CF) of the aspartate receptor, a transmembrane receptor involved in bacterial chemotaxis, are used in disulfide bond formation with the thiol-specific oxidant diamide and chemical cross-linking reactions with the trifunctional maleimide TMEA. CF binding to membranes is mediated by its N-terminal His tag binding to vesicles containing a nickel-chelating lipid, so cross-linking reactions conducted in the presence and absence of vesicles differ only in whether CF is bound to the vesicles or is free in solution. For multiple Cys throughout the CF, membrane association is shown to increase the rate and extent of these reactions. Cross-linking specificity, which is measured as the preference for cross-linking between Cys near each other in the native structure, is also enhanced by membrane association. These results provide an experimental demonstration that membrane binding enhances protein-protein interactions, an important consideration for understanding processes involving membrane-associated proteins. The experiments further demonstrate the importance of cross-linking conditions for these reactions that are often used to probe protein structure and dynamics and the potential of membrane association to restore native interactions of membrane-associated proteins for cross-linking studies.

Heat management strategies for solid-state NMR of functional proteins

Modern solid-state NMR methods can acquire high-resolution protein spectra for structure determination. However, these methods use rapid sample spinning and intense decoupling fields that can heat and denature the protein being studied. Here we present a strategy to avoid destroying valuable samples. We advocate first creating a sacrificial sample, which contains unlabeled protein (or no protein) in buffer conditions similar to the intended sample. This sample is then doped with the chemical shift thermometer Sm2Sn2O7. We introduce a pulse scheme called TCUP (for Temperature Calibration Under Pulseload) that can characterize the heating of this sacrificial sample rapidly, under a variety of experimental conditions, and with high temporal resolution. Sample heating is discussed with respect to different instrumental variables such as spinning speed, decoupling strength and duration, and cooling gas flow rate. The effects of different sample preparation variables are also discussed, including ionic strength, the inclusion of cryoprotectants, and the physical state of the sample (i.e. liquid, solid, or slurry). Lastly, we discuss probe detuning as a measure of sample thawing that does not require retuning the probe or using chemical shift thermometer compounds. Use of detuning tests and chemical shift thermometers with representative sample conditions makes it possible to maximize the efficiency of the NMR experiment while retaining a functional sample.

Ligand affinity and kinase activity are independent of bacterial chemotaxis receptor concentration: insight into signaling mechanisms

Binding of attractant to bacterial chemotaxis receptors initiates a transmembrane signal that inhibits the kinase CheA bound ~300 Å distant at the other end of the receptor. Chemoreceptors form large clusters in many bacterial species, and the extent of clustering has been reported to vary with signaling state. To test whether ligand binding regulates kinase activity by modulating a clustering equilibrium, we measured the effects of two-dimensional receptor concentration on kinase activity in proteoliposomes containing the purified Escherichia coli serine receptor reconstituted into vesicles over a range of lipid:protein molar ratios. The IC(50) of kinase inhibition was unchanged despite a 10-fold change in receptor concentration. Such a change in concentration would have produced a measurable shift in the IC(50) if receptor clustering were involved in kinase regulation, based on a simple model in which the receptor oligomerization and ligand binding equilibria are coupled. These results indicate that the primary signal, ligand control of kinase activity, does not involve a change in receptor oligomerization state. In combination with previous work on cytoplasmic fragments assembled on vesicle surfaces [Besschetnova, T. Y., et al. (2008) Proc. Natl. Acad. Sci. U.S.A.105, 12289-12294], this suggests that binding of ligand to chemotaxis receptors inhibits the kinase by inducing a conformational change that expands the membrane area occupied by the receptor cytoplasmic domain, without changing the number of associated receptors in the signaling complex.

Design and characterization of a calixarene inclusion compound for calibration of long-range carbon-fluorine distance measurements by solid-state NMR

An inexpensive, easily synthesized calixarene:fluorotoluene host:guest inclusion complex has been designed for optimization and calibration of solid-state NMR measurements of carbon-fluorine distances using Rotational Echo DOuble Resonance (REDOR). Complexation of the fluorotoluene with the calixarene host separates the molecules such that simple two-spin behavior is observed for one site with a 4.08 Å carbon-fluorine distance. Fluorotoluene dynamics within the calixarene matrix cause motional averaging of the dipolar couplings, which makes it possible to easily optimize REDOR experiments and test their accuracy for relatively long distance measurements (>6.6 Å). This provides a new tool for accurate REDOR measurements of long carbon-fluorine distances, which have important applications in the characterization of fluorine-containing drugs, proteins, and polymers.

Kinase-active signaling complexes of bacterial chemoreceptors do not contain proposed receptor-receptor contacts observed in crystal structures

The receptor dimers that mediate bacterial chemotaxis form high-order signaling complexes with CheW and the kinase CheA. From the packing arrangement in two crystal structures of different receptor cytoplasmic fragments, two different models have been proposed for receptor signaling arrays: the trimers-of-dimers and hedgerow models. Here we identified an interdimer distance that differs substantially in the two models, labeled the atoms defining this distance through isotopic enrichment, and measured it with (19)F-(13)C REDOR. This was done in two types of receptor samples: isolated bacterial membranes containing overexpressed, intact receptor and soluble receptor fragments reconstituted into kinase-active signaling complexes. In both cases, the distance found was not compatible with the receptor dimer-dimer contacts observed in the trimers-of-dimers or in the hedgerow models. Comparisons of simulated and observed REDOR dephasing were used to deduce a closest approach distance at this interface, which provides a constraint for the possible arrangements of receptor assemblies.

Nuclear medicine technologists and unauthorized self-injections

An Office of Investigation (OI) investigation by the U.S. Nuclear Regulatory Commission (NRC) determined that, on three separate occasions over the past 10 years, technologists in one licensed nuclear medicine program were injected with radiopharmaceuticals without Authorized User knowledge or approval. The most recent instance, the one that precipitated the investigation, was discovered by the licensee and self-reported to the NRC; the other two instances were discovered during the OI investigation and came as a complete surprise to the licensee. In a mediated Alternative Dispute Resolution (ADR) involving the licensee, a professional, independent mediator and representatives of the NRC, an agreement was worked out whereby the licensee would admit to the violations and work with the NRC to inform other licensees that this is not an acceptable practice and that there are additional precautions that licensees can and should take to assure that such violations do not happen on their watch.

Solid-State NMR Spin Diffusion for Measurement of Membrane-Bound Peptide Structure: Gramicidin A

A recently developed solid-state NMR method for measurement of depths in membrane systems is applied to gramicidin A, a membrane-bound peptide of known structure, to investigate the potential of this method. (15)N-detected, (1)H spin diffusion experiments demonstrate the resolution of the technique by measuring the 4-5 A depth differences between three (15)N-labeled backbone sites (Trp13, Val7, Gly2) in gramicidin A. We also show that (13)C-detected, (1)H spin diffusion experiments on unlabeled gramicidin A are sufficient to discriminate between the end-to-end dimer and double-helix structures of gramicidin A. Thus, spin diffusion solid-state NMR experiments can provide a simple approach, which does not require labeled samples, for testing structural models of membrane-bound peptides.

Quantum magneto-oscillations in a supramolecular Mn(II)-[3 x 3] grid

The magnetic grid molecule Mn(II)-[3 x 3] has been studied by high-field torque magnetometry at 3He temperatures. At fields above 5 T, the torque versus field curves exhibit an unprecedented oscillatory behavior. A model is proposed which describes these magneto-oscillations well.

Scanning tunnelling microscopy imaging of [3 x 3] Mn nonanuclear grids

The scanning tunnelling microscopy imaging of [3 x 3] Mn(II) nonanuclear grids on gold substrates is described. Self-assembled behaviour is observed at both high and low coverage, with submolecular resolution of individual molecules displayed at low deposition concentrations. The importance of proper image processing techniques is demonstrated in resolving the layer structure at high coverage.

Solid-state NMR studies of the structure and mechanisms of proteins

Magic-angle spinning solid-state NMR experiments are well suited to investigating the structures and mechanisms of important proteins that are inaccessible to X-ray crystallography and solution NMR spectroscopy, including membrane proteins and disease-related protein aggregates. Good progress has been made in the development of methods for the complete structure determination of small (<20 kDa) solid proteins using uniformly 13C, 15N-labeled samples. Studies of selectively labeled proteins focusing on labeled active sites have yielded insights into the mechanisms of enzymes and of membrane proteins involved in energy and signal transduction. Studies of selectively labeled synthetic peptides have yielded structural models for biomedically important systems, including amyloid fibrils and surface-associated peptides involved in biomineralization and cell adhesion. Novel NMR and biochemical methods are being developed to target solid-state NMR experiments within large proteins and whole cells. These approaches are being used to investigate mechanisms of transmembrane signaling by membrane receptors and to characterize binding interactions between antibiotics and bacterial cell walls. Thus, solid-state NMR is proving to be a valuable biophysical tool for probing structure and dynamics in a wide range of biomolecules.

Disability simulations and information: techniques for modifying the attitudes of elementary school music students

The purpose of this study was to determine the effect of different presentation formats (information and simulation) on the attitudes of elementary music students toward children with special needs. A questionnaire was initially administered to 11 elementary music classes (N = 198). Examination showed a 0.86 difference between highest and lowest rated disabilities on 6-point scale on the first administration. Females showed slightly more favorable attitudes than males for each of the 6 disability categories. Rank ordering indicated an identical ranking between genders with Learning Disabilities most accepted and Visual Impairments least accepted. Prior to the second administration, classes received different preparations: (a) information-based, (b) simulation-based, (c) contact-control. Results of the second administration showed no significant difference among treatment groups on gain scores with only a slight increase noted for the simulation-based treatment.

Site-directed rotational resonance solid-state NMR distance measurements probe structure and mechanism in the transmembrane domain of the serine bacterial chemoreceptor

The serine receptor of bacterial chemotaxis is an ideal system in which to investigate the molecular mechanism of transmembrane signaling. Solid-state nuclear magnetic resonance (NMR) techniques such as rotational resonance provide a means for measuring local structure and ligand-induced structural changes in intact membrane proteins bound to native membrane vesicles. A general site-directed biosynthetic (13)C labeling strategy is used to direct the distance measurements to a specific site; the distance is measured between a unique Cys residue and a non-unique, low-abundance residue (Tyr or Phe). A (13)C-(13)C internuclear distance measurement from (13)CO(i) to (13)C beta(i + 3) at the periplasmic edge of the second membrane-spanning helix (TM2) of 5.1 +/- 0.2 A is consistent with the predicted alpha-helical structure and thus demonstrates an accurate long-distance rotational resonance measurement in the 120 kDa membrane-bound receptor. These measurements require a correction for the rotational resonance exchange between the multiple labels of the non-unique amino acid and the natural-abundance (13)C, which is critical to distance measurements in complex systems. A second (13)C-(13)C distance measurement between the transmembrane helices provides a high-resolution measurement of tertiary structure in the transmembrane region. The measured 5.0-5.3 A distance in the presence and absence of ligand is consistent with structural models for the transmembrane region and a proposed signaling mechanism in which ligand binding induces a 1.6 A translation of TM2. This approach can be used for additional measurements of the structure of the transmembrane region and to determine whether the ligand-induced motion is indeed propagated through the transmembrane helices.

Field-dependent anisotropy change in a supramolecular Mn(II)- [3 x 3] grid

The magnetic anisotropy of a novel Mn(II)- [3x3] grid complex was investigated by means of high-field torque magnetometry. Torque vs field curves at low temperatures demonstrates a ground state with S>0 and exhibits a torque step due to a field-induced level crossing at B(*) approximately 7.5 T, accompanied by an abrupt change of magnetic anisotropy from easy-axis to hard-axis types. These observations are discussed in terms of a spin Hamiltonian formalism.

Hydrogen exchange reveals a stable and expandable core within the aspartate receptor cytoplasmic domain

Intensive study of bacterial chemoreceptors has not yet revealed how receptor methylation and ligand binding alter the interactions between the receptor cytoplasmic domain and the CheA kinase to control kinase activity. Both monomeric and dimeric forms of an Asp receptor cytoplasmic fragment have been shown to be highly dynamic, with a small core of slowly exchanging amide hydrogens (Seeley, S. K., Weis, R. M., and Thompson, L. K. (1996) Biochemistry 35, 5199-5206). Hydrogen exchange studies of the wild-type cytoplasmic fragment and an S461L mutant thought to mimic the kinase-inactivating state are used to investigate the relationship between the stable core and dimer dissociation. Our results establish that (i) decreasing pH stabilizes the dimeric state, (ii) the stable core is present also in the transition state for dissociation, and (iii) this core is expanded significantly by small changes in electrostatic and hydrophobic interactions. These kinase-inactivating changes stabilize both the monomeric and the dimeric states of the protein, which has interesting implications for the mechanism of kinase activation. We conclude that the cytoplasmic domain is a flexible region poised for stabilization by small changes in electrostatic and hydrophobic interactions such as those caused by methylation of glutamate residues and by ligand-induced conformational changes during signaling.

Synthesis, structure, and magnetism of bimetallic manganese or nickel complexes of a bridging verdazyl radical

Two binuclear metal-radical complexes, formed by the reaction of M(hfac)(2) x 2H(2)O (M = Mn or Ni; hfac = hexafluoroacetylacetonate) with the 1,5-dimethyl-3-(4,6-dimethylpyrimidin-2-yl)-6-oxoverdazyl radical (3), were synthesized. The binuclear Mn complex 5 (i.e., 3[Mn(hfac)(2)](2)) crystallizes in the monoclinic space group C2/c: C(30)H(17)N(6)O(9)F(24)Mn(2), a = 29.947(3), b = 17.143(3), c = 16.276(3) A, beta = 123.748(3)*, Z = 4. The compound consists of two pseudo-octahedral Mn(II) ions, both bearing two hfac ancillary ligands, bridged by the bis(bidentate) radical 3. The temperature dependence of the magnetic susceptibility of 5 reveals moderate antiferromagnetic exchange between each of the Mn(II) ions and the verdazyl radical (J = -48 cm(-1)). The S = 9/2 ground spin state of the complex was corroborated by low-temperature magnetization versus field measurements. In contrast, the magnetic susceptibility versus temperature behavior of 6 (whose molecular structure is presumed to be analogous to that of 5) indicates that the two Ni(II) ions are strongly ferromagnetically coupled to the verdazyl radical (J = +220 cm(-1)). The magnetization versus field behavior of 5 is consistent with an S = 5/2 ground-state species.

Pentanuclear homoleptic M(5)L(6) (M = Mn(II), Co(II), Zn(II)) complexes formed by strict self-assembly

A series of trigonal bipyramidal pentanuclear complexes involving the alkoxo-diazine ligands poap and p3oap, containing the M(5)[mu-O](6) core is described, which form by a strict self-assembly process. [Co(5)(poap-H)(6)](ClO(4))(4).3H(2)O (1), [Mn(5)(poap-H)(6)](ClO(4))(4).3.5CH(3)OH.H(2)O (2), [Mn(5)(p3oap-H)(6)](ClO(4))(4).CH(3)CH(2)OH.3H(2)O (3), and [Zn(5)(poap-H)(6)](ClO(4))(4).2.5H(2)O (4) are homoleptic pentanuclear complexes, where there is an exact match between the coordination requirements of the five metal ions in the cluster, and the available coordination pockets in the polytopic ligand. [Zn(4)(poap)(poap-H)(3)(H(2)O)(4)] (NO(3))(5).1.5H(2)O (5) is a square [2 x 2] grid with a Zn(4)[mu-O](4) core, and appears to result from the presence of NO(3), which is thought to be a competing ligand in the self-assembly. X-ray structures are reported for 1, 4, and 5. 1 crystallized in the monoclinic system, space group P2(1)/n with a = 13.385(1) A, b = 25.797(2) A, c = 28.513(3) A, beta = 98.704(2) degrees, and Z = 4. 4 crystallized in the triclinic system, space group P1 with a = 13.0897(9) A, b = 18.889(1) A, c = 20.506(2) A, alpha = 87.116(1) degrees, beta = 74.280(2) degrees, gamma = 75.809(2) degrees, and Z = 2. 5 crystallized in the monoclinic system, space group P2(1)/n with a = 14.8222(7) A, b = 21.408(1) A, c = 21.6197(9) A, beta = 90.698(1) degrees, and Z = 4. Compounds 1-3 exhibit intramolecular antiferromagnetic coupling.

Strong supramolecular-based magnetic exchange in pi-stacked radicals. Structure and magnetism of a hydrogen-bonded verdazyl radical:hydroquinone molecular solid

The X-ray crystal structure and magnetic properties of a molecular crystal consisting of 1,5-dimethyl-3-(2-pyridyl)-6-oxoverdazyl radical and hydroquinone (pyvd:hq) are presented. The structure contains a two-dimensional network of hydrogen bonds involving the hydroquinones and the pyridine ring of the pyvd radical. The radicals adopt an unusual head-over-tail (antiparallel) pi-stacked array perpendicular to the hydrogen-bonded planes. The variable-temperature magnetic susceptibility data can be modeled using a one-dimensional antiferromagnetic chain model, with J = -58 cm(-1). The strength of the magnetic coupling is very unusual because there are no close intermolecular radical-radical contacts to provide conventional pathways for magnetic interactions. A pathway for coupling is proposed involving the mediation of magnetic exchange interactions between radical centers by the pyridine rings. Density functional calculations on the pyvd radical, as well as aggregates thereof based on the X-ray structure, have been employed in attempts to understand the possible mechanisms by which the strong magnetic interactions are achieved.

Evaluation of thin agar layer method for recovery of acid-injured foodborne pathogens

The thin agar layer (TAL) method of Kang and Fung was used to enumerate acid-injured foodborne pathogens. This method involves overlaying 14 ml of nonselective medium (tryptic soy agar [TSA]) onto a prepoured and solidified pathogen-specific, selective medium in a petri dish. After surface plating, injured cells resuscitated and grew on TSA during the first few hours of incubation; then, the selective agents from the selective medium diffused to the top layer, interacted with the recovered microorganisms, and started to produce typical reactions. Foodborne pathogens were exposed to 2% acetic acid for 1, 2, or 4 min, and the recovery rate with the TAL method was compared with the rate of TSA and pathogen-specific, selective media. No significant difference occurred between TSA and TAL (P > 0.05) for enumeration of acid-injured Escherichia coli O157:H7, Salmonella Typhimurium, Staphylococcus aureus, and Yersinia enterocolitica, and both recovered significantly higher numbers than the selective medium for each respective pathogen (P < 0.05). For recovery of acid-injured Listeria monocytogenes, no difference (P > 0.05) occurred among TSA, TAL, and selective media. However, fewer cells were recovered in the selective media. The TAL method is a one-step, convenient procedure for recovery of acid-injured cells.

"Inclusion" of information on mainstreaming in undergraduate music education curricula

The purpose of this study was to examine teacher training programs in music education to provide an overview of course offerings in Special Education available to Music Education majors. One Research Category 1, one state-funded regional, and one private institution were randomly chosen from each state when available. All schools offering a degree in music therapy were included for a total of 171 schools with usable data. Catalogues were examined to determine (a) existence of a course in special education for music education majors, (b) department through which course was offered (nonmusic content or music content specific), (c) required or elective status of course, (d) course title and credit hours, and (e) reference to mainstreaming in music methods course descriptions. The first three areas were compared by (a) category of school, (b) universities offering music therapy and those not, (c) MENC Region. Results revealed that 74% of schools had a course in special education available with 86% of these requiring at least one course with a total of 140 courses available. 110 were nonmusic content specific while 30 were music content specific. Eighty-nine percent of the nonmusic content courses were required, while only 43% of the content specific courses were required. Information was further broken down as indicated above.

Site-directed solid-state NMR measurement of a ligand-induced conformational change in the serine bacterial chemoreceptor

The challenging nature of studies of membrane proteins has made it difficult to determine the molecular mechanism of transmembrane signaling. For the bacterial chemoreceptor family, there are crystal structures of the internal and external domains, structural models of the transmembrane domain, and evidence for subtle ligand-induced conformational changes, but the signaling mechanism remains controversial. We have used a novel site-directed solid-state NMR distance measurement approach, using (13)C(19)F REDOR, to measure a ligand-induced change of 1.0 +/- 0.3 A in the distance between helices alpha 1 and alpha 4 of the ligand-binding domain in the intact, membrane-bound serine receptor. This distance change is shown not to be due to motion of the side chain and thus is due to motion of either the alpha 1 or the alpha 4 helix. Additional distance measurements can be used to determine the type of backbone motion and to follow it to the cytoplasm, to test and refine current proposals for the mechanism of transmembrane signaling. This is a promising general method for high-resolution measurements of local structure in intact, membrane-bound proteins.

Synthesis and structures of polymeric Mn, Co, Cu, and Zn complexes of 3-diphenylamino-4-hydroxycyclobut-3-ene-1,2-dione (diphenylaminosquarate) and of the salt [Ni(H2O)6][(C6H5)2NC4O3]2.2H2O

Reaction of M(NO3)2.xH2O (M = Mn, Co, Ni, Cu, Zn) with 3-diphenylamino-4-hydroxycyclobut-3-ene-1,2-dione (diphenylaminosquarate) produces the neutral polymeric species (M[mu-(C6H5)2NC4O3]2[H2O]2)n [M = Mn (1), Cu (2)]; (M[mu-(C6H5)2NC4O3][(C6H5)2NC4O3][H2O]3)n [M = Co (3), Zn (4)]; and in the case of Ni, the salt [Ni(H2O)6][(C6H5)2NC4O3]2.2H2O (5). Complexes 1 and 2 are isomorphous and crystallize in the monoclinic space group P2(1)/c with, for 1, a = 13.138(1) A, b = 10.900(2) A, c = 9.269(2) A, beta = 96.07(1) degrees, and Z = 2. Complexes 3 and 4 are also isomorphous and crystallize in the space group P2(1)/c with, for 3, a = 13.211(1) A, b = 11.038(1) A, c = 18.748(1) A, beta = 97.75(1) degrees, and Z = 4. The nickel salt, 5, crystallizes in the triclinic space group P1 with a = 6.181(1) A, b = 9.417(1) A, c = 15.486(1) A, alpha = 101.37(1) degrees, beta = 95.51(1) degrees, gamma = 107.57(1) degrees, and Z = 1. In 1 and 2, the metal coordination is octahedral, comprising four mu-1,3-bridging diphenylaminosquarate ligands and two trans aqua ligands. In 3 and 4, the metal coordination is again octahedral, comprising two mu-1,3-bridging and one pendant diphenylaminosquarate ligands, the octahedron being completed by three aqua ligands in a meridional configuration. In 5, the hexaaquanickel(II) ion is linked by O-H...O hydrogen bonds to a pair of diphenylaminosquarate anions. These anion-cation units are linked via included water molecules to form hydrogen-bonded chains. The diphenylaminosquarate ligands in the polymeric complexes 1-4 display multiple-bond localization, a feature which is absent in 5. Complex 1 exhibits weak antiferromagnetic coupling, whereas 2 shows no significant magnetic interactions.