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The polyanion, inorganic polyphosphate (polyP), is a procoagulant molecule which has become a promising therapeutic target in the development of antithrombotics. Neutralizing polyP’s prothrombotic activity using polycationic inhibitors is one of the viable strategies to design new polyP inhibitors. However, in this approach, a fine balance between the electrostatic interaction of polyP and the inhibitor is needed. Any unprotected polycations are known to interact with negatively charged blood components, potentially resulting in platelet activation, cellular toxicity, and bleeding. Thus, designing potent polycationic polyP inhibitors with good biocompatibility is a major challenge. Building on our previous research on universal heparin reversal agent (UHRA), we report polyP inhibitors with a modified steric shield design. The molecular weight, number of cationic binding groups, and the length of the polyethylene glycol (PEG) chains were varied to arrive at the desired inhibitor. We studied two different PEG lengths (mPEG-750 versus mPEG-350) on the polyglycerol scaffold and investigated their influence on biocompatibility and polyP neutralization activity. The polyP inhibitor with mPEG-750 brush layer, mPEG(750) UHRA-10, showed superior biocompatibility compared to its mPEG-350 analogs by a number of measured parameters without losing its neutralization activity. An increase in cationic binding groups (25 groups in mPEG(750) UHRA-8 and 32 in mPEG(750) UHRA-10 [HC]) did not alter the neutralization activity, which suggested that the mPEG-750 shield layer provides significant protection of cationic binding groups and thus helps to minimize unwanted nonspecific interactions. Furthermore, these modified polyP inhibitors are highly biocompatible compared to conventional polycations that have been previously used as polyP inhibitors (e.g., PAMAM dendrimers and polyethylenimine). Through this study, we demonstrated the importance of the design of steric shield toward highly biocompatible polyP inhibitors. This approach can be exploited in the design of highly biocompatible macromolecular inhibitors.

Inorganic polyphosphate (polyP) released by human platelets has recently been shown to activate blood clotting and identified as a potential target for the development of novel antithrombotics. Recent studies have shown that polymers with cationic binding groups (CBGs) inhibit polyP and attenuate thrombosis. However, a good molecular-level understanding of the binding mechanism is lacking for further drug development. While molecular dynamics (MD) simulation can provide molecule-level information, the time scale required to simulate these large biomacromolecules makes classical MD simulation impractical. To overcome this challenge, we employed metadynamics simulations with both all-atom and coarse-grained force fields. The force field parameters for polyethylene glycol (PEG) conjugated CBGs and polyP were developed to carry out coarse-grained MD simulations, which enabled simulations of these large biomacromolecules in a reasonable time scale. We found that the length of the PEG tail does not impact the interaction between the (PEG)(n)-CBG and polyP. As expected, increasing the number of the charged tertiary amine groups in the head group strengthens its binding to polyP. Our simulation shows that (PEG)(n)-CBG initially form aggregates, mostly with the PEG in the core and the hydrophilic CBG groups pointing toward water, then the aggregates approach the polyP and sandwich the polyP to form a complex. We found that the binding of (PEG)(n)-CBG remains intact against various lengths of polyP. Binding thermodynamics for two of the (PEG)(n)-CBG/polyP systems simulated were measured by isothermal titration calorimetry to confirm the key finding of the simulations that the length PEG tail does not influence ligand binding to polyP.

This study tested the claim that digital PCR (dPCR) can offer highly reproducible quantitative measurements in disparate laboratories. Twenty-one laboratories measured four blinded samples containing different quantities of a KRAS fragment encoding G12D, an important genetic marker for guiding therapy of certain cancers. This marker is challenging to quantify reproducibly using quantitative PCR (qPCR) or next generation sequencing (NGS) due to the presence of competing wild type sequences and the need for calibration. Using dPCR, 18 laboratories were able to quantify the G12D marker within 12% of each other in all samples. Three laboratories appeared to measure consistently outlying results; however, proper application of a follow-up analysis recommendation rectified their data. Our findings show that dPCR has demonstrable reproducibility across a large number of laboratories without calibration. This could enable the reproducible application of molecular stratification to guide therapy and, potentially, for molecular diagnostics.

A need exists for robust and cost-effective assays to detect a single or small set of actionable point mutations, or a complete set of clinically informative mutant alleles. Knowledge of these mutations can be used to alert the clinician to a rare mutation that might necessitate more aggressive clinical monitoring or a personalized course of treatment. An example is BRAF, a (proto)oncogene susceptible to either common or rare mutations in codon V600 and adjacent codons. We report a diagnostic technology that leverages the unique capabilities of droplet digital PCR to achieve not only accurate and sensitive detection of BRAF(V600E) but also all known somatic point mutations within the BRAF V600 codon. The simple and inexpensive two-well droplet digital PCR assay uses a chimeric locked nucleic acid/DNA probe against wild-type BRAF and a novel wild-type-negative screening paradigm. The assay shows complete diagnostic accuracy when applied to formalin-fixed, paraffin-embedded tumor specimens from metastatic colorectal cancer patients deficient for Mut L homologue-1.

Anticoagulants such as unfractionated heparin (UFH), low-molecular-weight heparins (LMWHs), fondaparinux, and direct oral anticoagulants (DOACs) targeting thrombin (IIa) or factor Xa (FXa) are widely used in prevention and treatment of thromboembolic disorders. However, anticoagulant-associated bleeding is a concern that demands monitoring and neutralization. Protamine, the UFH antidote, has limitations, while there is no antidote available for certain direct FXa inhibitors. Improved antidotes in development include UHRA (Universal Heparin Reversal Agent) for all heparin anticoagulants; andexanet alfa (andexanet), a recombinant antidote for both direct FXa inhibitors and LMWHs; and ciraparantag (PER977), a small-molecule antidote for UFH, LMWHs, and certain DOACs. The binding affinities of these antidotes for their presumed anticoagulant targets have not been compared. Here, isothermal titration calorimetry (ITC) was used to determine the affinity of each antidote for its putative targets. Clotting and chromogenic FXa assays were used to characterize neutralization activity, and electron microscopy was used to visualize the effect of each antidote on clot morphology in the absence or presence of anticoagulant. ITC confirmed binding of UHRA to all heparins, and binding of andexanet to edoxaban and rivaroxaban, and to the antithrombin–enoxaparin complex. PER977 was found to bind heparins weakly, but not the direct FXa inhibitors studied. For UHRA and andexanet, an affinity at or below the micromolar level was found to correlate with neutralization activity, while no reversal activity was observed for the PER977/anticoagulant systems. Standard metrics of clot structure were found to correlate weakly with PER977’s activity. This is the first study comparing 3 antidotes in development, with each exerting activity through a distinct mechanism.

Formed from a reciprocal translocation t(9:22)(q34;q11) of genetic material between the long arms of human chromosomes 9 and 22, the constitutively active breakpoint cluster region (BCR) Abelson 1 (ABL) tyrosine kinase BCR-ABL is known to be causative of chronic myelogenous leukemia (CML). In 98 % of CML patients harboring the t(9:22)(q34;q11) translocation, known as the Philadelphia chromosome, the chimeric BCR-ABL oncogene is created through cleavage of the BCR gene within its major breakpoint region (M-BCR) and breakage of the ABL gene within a 100-kbp region downstream of exon 2a. Clinical detection of the fused BCR-ABL oncogene currently relies on direct visualization by fluorescence in situ hybridization (FISH), a relatively tedious assay that typically offers a detection limit of ca. 2 %. Here, we describe a novel assay that uses droplet digital PCR (ddPCR) technology to reliably measure M-BCR status and the presence of BCR-ABL. When applied to cell-line models of CML, the assay accurately quantifies BCR-ABL frequency to a detection limit of 0.25 %. It therefore offers improved specificity relative to FISH, and may allow identification of variant translocation patterns, including derivative chromosome 9 deletions.

Bone density diseases such as osteoporosis affect a significant number of people worldwide. Lanthanide ions are functional mimics of calcium ions, able to substitute for Ca2+ in the bone mineral component, hydroxyapatite (HAP). Bone undergoes a continuous remodelling cycle and lanthanides can affect this cycle, exerting a positive influence on bone mineral. We have been engaged in efforts to find new lanthanide containing complexes as active agents for treatment of these diseases and have identified two lead compounds, 3-hydroxy-1,2-dimethylpyridin-4(1H)-one (Hdpp) and a phosphinate-EDTA derivative, bis[[bis(carboxymethyl)amino]-methyl]phosphinate (H5XT). In this paper, we report in vivo data for the first time for the two lead compounds. The pharmacokinetics of La(dpp)3 suggest the complex is rapidly cleared from plasma. We demonstrate that La3+ accumulates in the bone following IV dose of either La(dpp)3 or La(XT) and we have investigated the influence of each chelating ligand on the incorporation of La3+ into HAP using ITC and HAP-binding studies.

Copy number alterations (CNAs), a common genomic event during carcinogenesis, are known to affect a large fraction of the genome. Common recurrent gains or losses of specific chromosomal regions occur at frequencies that they may be considered distinctive features of tumoral cells. Here we introduce a novel multiplexed droplet digital PCR (ddPCR) assay capable of detecting recurrent CNAs that drive tumorigenesis of oral squamous cell carcinoma. Applied to DNA extracted from oral cell lines and clinical samples of various disease stages, we found good agreement between CNAs detected by our ddPCR assay with those previously reported using comparative genomic hybridization or single nucleotide polymorphism arrays. Furthermore, we demonstrate that the ability to target specific locations of the genome permits detection of clinically relevant oncogenic events such as small, submicroscopic homozygous deletions. Additional capabilities of the multiplexed ddPCR assay include the ability to infer ploidy level, quantify the change in copy number of target loci with high-level gains, and simultaneously assess the status and viral load for high-risk human papillomavirus types 16 and 18. This novel multiplexed ddPCR assay therefore may have clinical value in differentiating between benign oral lesions from those that are at risk of progressing to oral cancer.

Anticoagulant therapy-associated bleeding and pathological thrombosis pose serious risks to hospitalized patients. Both complications could be mitigated by developing new therapeutics that safely neutralize anticoagulant activity and inhibit activators of the intrinsic blood clotting pathway, such as polyphosphate (polyP) and extracellular nucleic acids. The latter strategy could reduce the use of anticoagulants, potentially decreasing bleeding events. However, previously described cationic inhibitors of polyP and extracellular nucleic acids exhibit both nonspecific binding and adverse effects on blood clotting that limit their use. Indeed, the polycation used to counteract heparin-associated bleeding in surgical settings, protamine, exhibits adverse effects. To address these clinical shortcomings, we developed a synthetic polycation, Universal Heparin Reversal Agent (UHRA), which is nontoxic and can neutralize the anticoagulant activity of heparins and the prothrombotic activity of polyP. Sharply contrasting protamine, we show that UHRA does not interact with fibrinogen, affect fibrin polymerization during clot formation, or abrogate plasma clotting. Using scanning electron microscopy, confocal microscopy, and clot lysis assays, we confirm that UHRA does not incorporate into clots, and that clots are stable with normal fibrin morphology. Conversely, protamine binds to the fibrin clot, which could explain how protamine instigates clot lysis and increases bleeding after surgery. Finally, studies in mice reveal that UHRA reverses heparin anticoagulant activity without the lung injury seen with protamine. The data presented here illustrate that UHRA could be safely used as an antidote during adverse therapeutic modulation of hemostasis.

U24 is a protein found in both roseoloviruses Human Herpes Virus type 6 and 7 (HHV-6 and HHV-7), with an N-terminus that is rich in prolines (PY motif in both HHV-6A and 7; PxxP motif in HHV-6A). Previous work has shown that the interaction between U24 and WW domains is important for endocytic recycling of T-cell receptors, but a cognate ligand was never identified. In this contribution, data was obtained from pull-downs, ITC, NMR and molecular dynamics simulations to show that a specific interaction exists between U24 and Nedd4 WW domains. ITC experiments were also carried out for U24 from HHV-6A phosphorylated at Thr6 (pU24-6A) and a peptide containing the PY motif from Nogo-A, a protein implicated in both the initial inflammatory and the neurodegenerative phases of multiple sclerosis (MS). The results suggest that phosphorylation of U24 from HHV-6A may be crucial for its potential role in MS.

Polysaccharide utilization loci (PUL) within the genomes of resident human gut Bacteroidetes are central to the metabolism of the otherwise indigestible complex carbohydrates known as “dietary fiber.” However, functional characterization of PUL lags significantly behind sequencing efforts, which limits physiological understanding of the human-bacterial symbiosis. In particular, the molecular basis of complex polysaccharide recognition, an essential prerequisite to hydrolysis by cell surface glycosidases and subsequent metabolism, is generally poorly understood. Here, we present the biochemical, structural, and reverse genetic characterization of two unique cell surface glycan-binding proteins (SGBPs) encoded by a xyloglucan utilization locus (XyGUL) from Bacteroides ovatus, which are integral to growth on this key dietary vegetable polysaccharide. Biochemical analysis reveals that these outer membrane-anchored proteins are in fact exquisitely specific for the highly branched xyloglucan (XyG) polysaccharide. The crystal structure of SGBP-A, a SusD homolog, with a bound XyG tetradecasaccharide reveals an extended carbohydrate-binding platform that primarily relies on recognition of the β-glucan backbone. The unique, tetra-modular structure of SGBP-B is comprised of tandem Ig-like folds, with XyG binding mediated at the distal C-terminal domain. Despite displaying similar affinities for XyG, reverse-genetic analysis reveals that SGBP-B is only required for the efficient capture of smaller oligosaccharides, whereas the presence of SGBP-A is more critical than its carbohydrate-binding ability for growth on XyG. Together, these data demonstrate that SGBP-A and SGBP-B play complementary, specialized roles in carbohydrate capture by B. ovatus and elaborate a model of how vegetable xyloglucans are accessed by the Bacteroidetes., IMPORTANCE The Bacteroidetes are dominant bacteria in the human gut that are responsible for the digestion of the complex polysaccharides that constitute “dietary fiber.” Although this symbiotic relationship has been appreciated for decades, little is currently known about how Bacteroidetes seek out and bind plant cell wall polysaccharides as a necessary first step in their metabolism. Here, we provide the first biochemical, crystallographic, and genetic insight into how two surface glycan-binding proteins from the complex Bacteroides ovatus xyloglucan utilization locus (XyGUL) enable recognition and uptake of this ubiquitous vegetable polysaccharide. Our combined analysis illuminates new fundamental aspects of complex polysaccharide recognition, cleavage, and import at the Bacteroidetes cell surface that may facilitate the development of prebiotics to target this phylum of gut bacteria.

The ability of droplet digital PCR (ddPCR) to accurately determine the concentrations of amplifiable targets makes it a promising platform for measuring copy number alterations (CNAs) in genomic biomarkers. However, its application to clinical samples, particularly formalin-fixed paraffin-embedded specimens, will require strategies to reliably determine CNAs in DNA of limited quantity and quality. When applied to cancerous tissue, those methods must also account for global genetic instability and the associated probability that the abundance(s) of one or more chosen reference loci do not represent the average ploidy of cells comprising the specimen. Here we present an experimental design strategy and associated data analysis tool that enables accurate determination of CNAs in a panel of biomarkers using multiplexed ddPCR. The method includes strategies to optimize primer and probes design to cleanly segregate droplets in the data output from reaction wells amplifying multiple independent templates, and to correct for bias from artifacts such as DNA fragmentation. We demonstrate how a panel of reference loci can be used to determine a stable CNA-neutral benchmark. These innovations, when taken together, provide a comprehensive strategy that can be used to reliably detect biomarker CNAs in DNA extracted from either frozen or FFPE tissue biopsies.

The zonal rate model (ZRM) has previously been applied for analyzing the performance of axial flow membrane chromatography capsules by independently determining the impacts of flow and binding related non-idealities on measured breakthrough curves. In the present study, the ZRM is extended to radial flow configurations, which are commonly used at larger scales. The axial flow XT5 capsule and the radial flow XT140 capsule from Pall are rigorously analyzed under binding and non-binding conditions with bovine serum albumin (BSA) as test molecule. The binding data of this molecule is much better reproduced by the spreading model, which hypothesizes different binding orientations, than by the well-known Langmuir model. Moreover, a revised cleaning protocol with NaCl instead of NaOH and minimizing the storage time has been identified as most critical for quantitatively reproducing the measured breakthrough curves. The internal geometry of both capsules is visualized by magnetic resonance imaging (MRI). The flow in the external hold-up volumes of the XT140 capsule was found to be more homogeneous as in the previously studied XT5 capsule. An attempt for model-based scale-up was apparently impeded by irregular pleat structures in the used XT140 capsule, which might lead to local variations in the linear velocity through the membrane stack. However, the presented approach is universal and can be applied to different capsules. The ZRM is shown to potentially help save valuable material and time, as the experiments required for model calibration are much cheaper than the predicted large-scale experiment at binding conditions. Biotechnol. Bioeng. 2013; 110: 1129–1141. © 2012 Wiley Periodicals, Inc.

If we can't get this right in public schools, we have little hope of getting this right in the public square of what is now the most religiously diverse nation on Earth.

Surface induced thrombus generation is a major clinical concern associated with vascular medical devices and implants. Here, we show that high graft density hydrophilic non-charged poly (N,N-dimethylacrylamide) (PDMA) brushes prevent the initiation of blood coagulation on synthetic surfaces. Using a multi-faceted analysis approach, we have identified that PDMA brushes greater than 0.27 chains/nm(2) graft density showed this highly desired property. Non-specific protein adsorption is greatly reduced on high density brushes compared to bare surface as evident from isothermal titration calorimetry, gel electrophoresis, and proteomic analyses. We have identified approximately 129 proteins of various types on bare and PDMA brush coated surfaces at a range of surface concentrations. Thromboelastography, platelet activation, and aggregation analyses show that only high graft density brushes are neutral to blood coagulation. Since the polymer brush synthesis can be adapted to most currently used biomedical materials, these results have significant impact in the design of highly hemocompatible surfaces.

Transient absorption measurements of excited states in DNA and LNA were performed using a femtosecond pump-probe arrangement with excitation at 266 nm and absorption monitored at 400 nm while varying the sample tem- perature between 5 °C and 70 °C. Samples consisted of adenine monophosphate monomer, polyadenine 12-mer in single- stranded form, and polyadenine 12-mer in hybridized form. Excited states decayed in a biphasic manner with short-lived ( 1) and long-lived ( 2) components, while the monomer had only a 'single' short-lived decay time. Temperature increases increased absorption intensities and reduced  1 until they approached those of the monomer at high temperatures (where stacking is minimal). These results suggest that the initial excitation in stacked regions is cooperative and involves several bases and that the number of bases involved is reduced with increasing temperature. In contrast, increasing temperatures had little effect on  2 while absorption intensities decreased, suggesting that very few, perhaps only two, stacked bases are involved and that their number is reduced at higher temperatures. We found no clear evidence of melting point transitions indicating that those excited states probed with our arrangement were not dependent on base pairing. Our results are con- sistent with and strengthen an emerging consensus model of excited state dynamics in DNA wherein a UV photon is ab- sorbed collectively by electronically coupled and thus well-stacked intrachain bases. This collective excitation results in a Frenkel exciton that is delocalized over these bases, and the Frenkel exciton then decays rapidly to a long-lived, lower en- ergy, dark intrachain exciplex.

Summary Assembly of the type-III secretion apparatus, which translocates proteins through both membranes of Gram-negative bacterial pathogens into host cells, requires the formation of an integral outer-membrane secretin ring. Typically, a small lipidated pilot protein is necessary for the stabilization and localization of this ring. Using NMR spectroscopy, we demonstrate that the C-terminal residues 553–570 of the Shigella flexneri secretin MxiD encompass the minimal binding domain for its cognate pilot MxiM. Although unstructured in isolation, upon complex formation with MxiM, these residues fold into an amphipathic turn-helix motif that caps the elongated hydrophobic cavity of the cracked β-barrel pilot. Along with a rearrangement of core aromatic residues, this prevents the binding of lipids within the cavity. The mutually exclusive association of lipids and MxiD with MxiM establishes a framework for understanding the role of a pilot in the outer-membrane insertion and multimerization of the secretin ring.

Naturally occurring hydroxyapatite, Ca5(PO4)3(OH) (HAP), is the main inorganic component of bone matrix, with synthetic analogues finding applications in bioceramics and catalysis. An interesting and valuable property of both natural and synthetic HAP is the ability to undergo cationic and anionic substitution. The lanthanides are well-suited for substitution for the Ca(2+) sites within HAP, because of their similarities in ionic radii, donor atom requirements, and coordination geometries. We have used isothermal titration calorimetry (ITC) to investigate the thermodynamics of ion exchange in HAP with a representative series of lanthanide ions, La(3+), Sm(3+), Gd(3+), Ho(3+), Yb(3+) and Lu(3+), reporting the association constant (Ka), ion-exchange thermodynamic parameters (ΔH, ΔS, ΔG), and binding stoichiometry (n). We also probe the nature of the La(3+):HAP interaction by solid-state nuclear magnetic resonance ((31)P NMR), X-ray diffraction (XRD), and inductively coupled plasma-optical emission spectroscopy (ICP-OES), in support of the ITC results.

The ability to translocate virulence proteins into host cells through a type III secretion apparatus (TTSS) is a hallmark of several Gram‐negative pathogens including Shigella, Salmonella, Yersinia, Pseudomonas , and enteropathogenic Escherichia coli . In common with other types of bacterial secretion apparatus, the assembly of the TTSS complex requires the preceding formation of its integral outer membrane secretin ring component. We have determined at 1.5 A the structure of MxiM28–142, the Shigella pilot protein that is essential for the assembly and membrane association of the Shigella secretin, MxiD. This represents the first atomic structure of a secretin pilot protein from the several bacterial secretion systems containing an orthologous secretin component. A deep hydrophobic cavity is observed in the novel ‘cracked barrel’ structure of MxiM, providing a specific binding domain for the acyl chains of bacterial lipids, a proposal that is supported by our various lipid/MxiM complex structures. Isothermal titration analysis shows that the C‐terminal domain of the secretin, MxiD525–570, hinders lipid binding to MxiM.

Vapour pressures of binary aqueous solutions of methanol, ethanol, 1-propanol, 2-propanol, 1-butanol, and 1-hexanol were measured at 25.00oC in small compositional increments over the entire compositional range. Without resorting to any fitting function, the partial pressures were calculated numerically by methods based on the Gibbs–Duhem relation. When the system had an azeotrope, near which the numerical methods caused large errors, a graphical readjustment was applied such that the concentration fluctuation, SXX(0) = RT(1 – xAL)/([Formula: see text]µ EAL/[Formula: see text]xAL), connected smoothly across the azeotrope. Values of SXX(0) from scattering experiments were also used as a guide for the readjustment procedure. Hence, we report here chemical potential data free from any model or any fitting function.Key Words: aqueous mono-ols, partial pressures by the Boissonnas method, concentration fluctuations.

A well-balanced human diet includes a significant intake of non-starch polysaccharides, collectively termed 'dietary fibre', from the cell walls of diverse fruits and vegetables. Owing to the paucity of alimentary enzymes encoded by the human genome, our ability to derive energy from dietary fibre depends on the saccharification and fermentation of complex carbohydrates by the massive microbial community residing in our distal gut. The xyloglucans (XyGs) are a ubiquitous family of highly branched plant cell wall polysaccharides whose mechanism(s) of degradation in the human gut and consequent importance in nutrition have been unclear. Here we demonstrate that a single, complex gene locus in Bacteroides ovatus confers XyG catabolism in this common colonic symbiont. Through targeted gene disruption, biochemical analysis of all predicted glycoside hydrolases and carbohydrate-binding proteins, and three-dimensional structural determination of the vanguard endo-xyloglucanase, we reveal the molecular mechanisms through which XyGs are hydrolysed to component monosaccharides for further metabolism. We also observe that orthologous XyG utilization loci (XyGULs) serve as genetic markers of XyG catabolism in Bacteroidetes, that XyGULs are restricted to a limited number of phylogenetically diverse strains, and that XyGULs are ubiquitous in surveyed human metagenomes. Our findings reveal that the metabolism of even highly abundant components of dietary fibre may be mediated by niche species, which has immediate fundamental and practical implications for gut symbiont population ecology in the context of human diet, nutrition and health.

Ligand-exchange chiral extraction (LEXCEX) is an emerging technology for large-scale continuous resolution of enantiomers of amino acids and a wide range of chiral therapeutics and drug precursors. LEXCEX is based on the ability of a chiral ligand (Li), solubilized in the non-aqueous phase of a water/alcohol two-phase system through complexation with a transition metal ion (i.e., Cu), to preferentially extract one enantiomer (En) into the organic phase through formation of a ternary electroneutral complex. Here we show that the efficiency of the extraction depends, often strongly, on a number of process variables, including the selectivity of the ligand, the solubility of the enantiomers and complexes containing them in the organic phase, pH and transition-metal ion (Cu) concentration. Phase-equilibria in LEXCEX systems is governed by the complex chemical equilibria in both the aqueous and organic phases. To better understand this extraction process, we develop a model for ligand-exchange chiral extraction which couples a complete description of chemical equilibria in each phase with the overall phase equilibria of the system. The model requires the complete set of protonation constants and binary and ternary formation constants for each species present in either the aqueous or organic phase. When coupled with phase equilibrium constraints, the model quantitatively predicts extraction performance as a function of key operating parameters, thereby providing a simple computational approach to process optimization. Measured equilibrium formation constants for ternary complexes containing the N-decyl-l-hydropxy-proline ligand are found to depend strongly on solvent environment, with complex stabilities in general decreasing when the complex is transferred from water to n-octanol. The role of solvent in ternary complex stability is explored through a series of molecular mechanics simulations.

The influence of solvent composition on equilibria in chiral ligand-exchange systems is explored by measuring protonation constants and equilibrium formation constants for all free species and complexes, respectively, in systems at 25°C and an ionic strength of 0.1 M containing one of two classic chiral selector molecules ( l -proline or l -hydroxy proline), the copper(II) ion, and an amino acid enantiomer. This set of thermodynamic constants is combined with multiple-chemical-equilibria theory to determine solution composition as a function of pH and mole-fraction methanol (MeOH) in the solvent. Results indicate that the addition of MeOH increases the stabilities of both the hetero- and the homo-chiral ternary complexes. However, it also increases, often to a greater extent, the stability of each bis binary complex. As a result, the influence of MeOH addition on equilibria in chiral ligand-exchange systems is complex and cannot be predicted by mere inspection of the equilibrium constants for the hetero- and homo-chiral ternary complexes. These results therefore identify a potential limitation of using common global stoichiometric models to predict equilibria in chiral ligand-exchange systems. A more comprehensive model, based on the complete description of the multiple chemical equilibria, is proposed. Finally, the role of solvent in stabilizing ligand-exchange complexes is explored through a series of molecular mechanics simulations in the absence or presence of solvent molecules. Results suggest that solvent stabilizes both bis binary and ternary complexes, primarily through direct participation in the complex structure in the form of occupancy of one or both distal coordination sites.

We measured vapour pressures of aqueous acetonitrile (abbreviated as ACN) at 6, 20, and 37°C, from which excess chemical potentials of ACN (µ EACN) were calculated. We also determined excess partial molar enthalpies of ACN (H EACN) at 6, 20, 30, 37, and 45°C. From these data, excess partial molar entropies of ACN (S EACN) were calculated at 6, 20, and 37°C. Using density data by Benson's group, excess partial molar volumes of ACN (V EACN) were evaluated. The response function data by the same group were also used to evaluate amplitude and wavelength of mean-square fluctuations in terms of volume, entropy, and cross between volume and entropy. All the above quantities and their dependence on the mol fraction of solute, i.e., the effect of additional solute on the above quantities were used to study the effect of acetonitrile on the molecular organization of H2O. It was found that acetonitrile works as a stronger structure-making solute than methanol. Rather its effect on H2O is about the same as that of propan-1-ol.Key words: aqueous acetonitrile, interaction functions, fluctuations.

The family 2a carbohydrate-binding module (CBM2a) of xylanase 10A from Cellulomonas fimi binds to the crystalline regions of cellulose. It does not share binding sites with the N-terminal family 4 binding module (CBM4-1) from the cellulase 9B from C.fimi, a module that binds strictly to soluble sugars and amorphous cellulose. The binding of CBM2a to crystalline matrices is mediated by several residues on the binding face, including three prominent, solvent-exposed tryptophan residues. Binding to crystalline cellulose was analyzed by making a series of conservative (phenylalanine and tyrosine) and non-conservative substitutions (alanine) of each solvent-exposed tryptophan (W17, W54 and W72). Other residues on the binding face with hydrogen bonding potential were substituted with alanine. Each tryptophan plays a different role in binding; a tryptophan is essential at position 54, a tyrosine or tryptophan at position 17 and any aromatic residue at position 72. Other residues on the binding face, with the exception of N15, are not essential determinants of binding affinity. Given the specificity of CBM2a, the structure of crystalline cellulose and the dynamic nature of the binding of CBM2a, we propose a model for the interaction between the polypeptide and the crystalline surface.

The excess partial molar enthalpies of 1-propanol were determined in aqueous urea solutions. The total vapor pressures of 1-propanol−urea−H2O were also measured. The numerical analysis applied in a...

Vapor pressures for n-hexane−c-hexane were measured at extremely low concentrations of n-hexane. The vapor pressure data seemed to indicate within the experimental uncertainty that, in the range of the mole fraction of n-hexane xnH < 0.015, the solution obeys Henry's law. However, the excess partial molar enthalpy of n-hexane and c-hexane measured by a sensitive microcalorimeter showed that the Henry's law is not operative above xnH or xcH ≈ 2 × 10-4, the lowest accessible for the calorimetry technique available at present. The excess partial molar enthalpies of the following solutes were also determined in aqueous solutions in an extremely dilute region. Within the experimental technique at our disposal, we could not locate a finite range of Henry's law. Thus, whether the solute−solute interaction becomes actually absent or whether such absence depends on the nature of the solvent (H2O or organic) cannot be addressed at present. For aqueous solutions, however, the lower limits of the mole fraction of a s...

The excess chemical potentials, the excess partial molar entropies, and the partial molar volumes in tert-butyl alcohol (TBA)−dimethyl sulfoxide (DMSO)−H2O mixtures were determined. These data, together with previously published excess partial molar enthalpies (Fluid Phase Equilib. 1997, 136, 207) were used to evaluate intermolecular interactions. The TBA−TBA and TBA−DMSO, and DMSO−DMSO interactions were found to be crucially dependent on the composition. The net interaction in terms of chemical potential is very intricate. For example, net interactions of DMSO with a hydrophobic moiety (represented here by TBA) change from attractive to repulsive as the composition changes. This suggests that general discussions of the affinity of DMSO for nonpolar groups (or surfaces) are meaningful only by specifying the composition region. The interactions in terms of enthalpy and entropy are an order of magnitude larger and strongly compensating. Anomalous changes in the enthalpic/entropic interactions and hence qual...

This paper presents a thermodynamic framework for transforming models derived in the McMillan-Mayer framework into the Gibbs framework G(T, P, ni). Historically, the McMillan-Mayer theory has been used to develop the thermodynamics of dilute solutions of electrolytes, polymers and other solutes. The appropriate independent variables for the McMillan-Mayer dilute-solution theory are temperature, volume, chemical potential of the solvent, and number of moles of solutes. Hence, the proper thermodynamic potential is not the Helmholtz energy A(T, V, nj) but a modified Helmholtz energy A′(T, V, μ0, nj (j # 0)) where A′ = A - n0μ0. The most common theoretical developments for electrolyte solutions (e.g., Debye-Huckel theory, mean-spherical approximation) and many dilute polymer solution theories (e.g., osmotic virial expansion) yield excess values of A′, not A. As a result, the chemical potential of the solute, or its activity coefficient, should include a term −P Ex V j θ , whose presence has apparently not been explicitly recognized or discussed clearly (PEx is an excess pressure, and V j θ is the partial molar volume of solute j). The origin and influence of this additional term are explored.

Excess partial molar enthalpies were measured in ternary aqueous solutions, tert -butyl alcohol (TBA)-DMSO-H 2 O, and lysozyme (L)–alcohols (A)–H 2 O. The solute–solute interactions were evaluated as the derivatives of these data with respect to the mole fraction of a solute. In the water-rich region, where the so-called mixing scheme I is operating in binary aqueous solutions of TBA, DMSO or alcohols, two solutes in TBA–DMSO–H 2 O seem to modify the hydrogen bond network of H 2 O in an additive manner. Here, mixing scheme I refers to the way in which a solute (hydrophobic) modifies the molecular organization of H 2 O. Specifically, a solute enhances the hydrogen bond strength of H 2 O in its immediate vicinity. On the other hand, the probability of hydrogen bond in the bulk away from a solute is reduced, and it is still high enough, however, to keep the hydrogen bond network connected throughout the entire macroscopic system. As the composition of solute increases, the hydrogen bond probability in the bulk decreases to the point at which the macroscopic bond connectivity is no longer possible. At this point, a new mixing scheme, II, sets in. For L–A–H 2 O mixtures at infinite dilution of L, the L–A interaction changes drastically from repulsive to attractive at the boundary between I and II for binary aqueous alcohols. Moreover, a denatured lysozyme interacts with alcohols more strongly than the native form, and is more repulsive in mixing scheme I and more attractive in II. This behaviour is shown to be consistent with the alcohol-dependent enthalpy of denaturation of lysozyme found by Velicelebi and Sturtevant [Velicelebi and Sturtevant, Biochem. 18 (1979) 1180–86].

The surface diffusion rate of bacterial cellulases from Cellulomonas fimi on cellulose was quantified using fluorescence recovery after photobleaching analysis. Studies were performed on an exo-beta-1-4-glycanase (Cex), an endo-beta-1-4-glucanase (CenA), and their respective isolated cellulose-binding domains (CBDs). Although these cellulose-binding domains bind irreversibly to microcrystalline cellulose, greater than 70% of bound molecules are mobile on the cellulose surface. Surface diffusion rates are dependent on surface coverage and range from a low of 2 x 10(-11) to a maximum of 1.2 x 10(-10) cm2/s. The fraction of mobile molecules increases only slightly with increasing fractional surface coverage density. Results demonstrate that the packing of C. fimi cellulases and their isolated binding domains onto the cellulose surface is a dynamic process. This suggests that the exclusion of potential CBD binding sites on the cellulose due to steric effects of neighboring bound CBDs may not fully explain the apparent negative cooperativity exhibited in CBD adsorption isotherms. Comparison with the kinetics of cellulase hydrolysis of crystalline substrate suggests that surface diffusion rates do not limit cellulase activity.

The adsorption of both plasmid and chromosomal duplex DNA to silica is investigated with the aim of determining the dominant forces involved in the binding reaction. Changes in the initial slopes and plateau values of adsorption isotherms for DNA on microcrystalline silica particles are used to establish the sensitivity of the binding reaction to ionic strength, temperature and pH, and DNA size and conformation. Binding is driven by an increase in entropy, with little or no enthalpic contribution. Adsorption isotherm results indicate that three effects, namely: (i) shielded intermolecular electrostatic forces, (ii) dehydration of the DNA and silica surfaces, and (iii) intermolecular hydrogen bond formation in the DNA–silica contact layer, make the dominant contributions to the overall driving force for adsorption.

Droplet digital polymerase chain reaction (ddPCR) is a novel platform for exact quantification of DNA which holds great promise in clinical diagnostics. It is increasingly popular due to its digital nature, which provides more accurate quantification and higher sensitivity than traditional real-time PCR. However, clinical adoption has been slowed in part by the lack of software tools available for analyzing ddPCR data. Here, we present ddpcr – a new R package for ddPCR visualization and analysis. In addition, ddpcr includes a web application (powered by the Shiny R package) that allows users to analyze ddPCR data using an interactive graphical interface.

Seven years have passed since one of us (W.N.) published the last comprehensive review on the mechanism of globular protein adsorption to solid/water interfaces. Since that time, annual contributions to the field have steadily increased and substantial progress has been made in a number of important areas. This review takes a fresh look at the driving force for protein adsorption by combining recent advances with key results from the past. The analysis indicates that four effects, namely structural rearrangements in the protein molecule, dehydration of (parts of) the sorbent surface, redistribution of charged groups in the interfacial layer, and protein surface polarity usually make the primary contributions to the overall adsorption behavior.

The structural and electrostatic properties of two similar-sized globular proteins, hen egg-white lysozyme and bovine milk α-lactalbumin, adsorbed to microspheres of a negatively charged polystyrene latex, are determined from adsorption isotherms, plateau adsorption values, and isothermal titration microcalorimetry data. Particular attention is given to the application of proton-titration techniques for which a new robust protocol is presented which accurately predicts the contributions of the aqueous solution (i.e., the blank) to the overall titration behavior of the protein-containing sample. Plateau values for the adsorbed proteins show a complex dependence on pH with a maximum occurring at the isoelectric point of the protein/sorbent complex. Adsorbed-state titration curves differ markedly from the corresponding dissolved-state curves; the data suggest that α-lactalbumin undergoes substantial changes in secondary and tertiary structure upon adsorption. In the adsorbed state, α-lactalbumin does not exhibit the low-pH native-to-apo-state transition which promotes release of the Ca 2+ ion from the ion-binding pocket. Average p K a data for the two proteins suggest that a fraction of the charged carboxyl groups are in close proximity to the sorbent surface and the adsorbed protein is largely denatured. The data also indicate that protein adsorption is driven by a synergistic combination of sorbent dehydration, protein structural changes, and charge redistribution.

Electron paramagnetic resonance (EPR) spectroscopy and molecular dynamics (MD) simulations were used to investigate the dynamics of alpha-chymotrypsin in solvents ranging in dielectric constant from 72 to 1.9. EPR measurements showed that motions in the vicinity of two spin-labeled amino acids (Met-192 and Ser-195) decreased dramatically with decreasing solvent dielectric constant, a trend consistent with changes in the electrostatic force between charged residues of the protein. EPR results and MD simulations revealed a very similar functional dependence between rates of motion in the protein and the dielectric constant of the bulk solvent; however, predicted motions of protein atoms were markedly faster than measured motions of the spin labels. MD calculations for dielectric constants of 5 and 72 showed the greatest differences near the outer surface of the protein. In general, at the lower dielectric constant many atoms of the protein move more slowly, and many of the slowest residues are near the exterior. These results suggest that altered dynamics may contribute to the unusual properties--e.g., modified stereoselectivities--of enzymes in nearly dry organic solvents.

Charles C. Haynes is Executive Director of the First Liberty Institute at George Mason University and President of the National Council on Religion and Public Education. Exploding religious pluralism in the United States confronts our schools and our nation with unprecedented chal lenges and opportunities. Religious diver sity has expanded from the largely Protes tant pluralism of the eighteenth century to a pluralism that today includes growing numbers of believers from all of the world's religions, and a dramatic increase in the number of Americans with no religious preference at all (up from 2 percent of the population in the 1960s to nearly 12 per cent today).

The intrinsic antimicrobial resistance of the opportunistic human pathogen Pseudomonas aeruginosa is compounded in mutant strains that overexpress multidrug efflux pumps such as the prominent drug-proton antiporter, MexAB-OprM. The primary regulator of the mexAB-oprM operon is the MarR family repressor, MexR. An additional repressor, NalC, also regulates mexAB-oprM by controlling expression of ArmR, an antirepressor peptide that is hypothesized to prevent the binding of MexR to its cognate DNA operator via an allosteric protein–peptide interaction. To better understand how ArmR modulates MexR, we determined the MexR-binding region of ArmR as its C-terminal 25 residues and solved the crystal structure of MexR in a 2:1 complex with this ArmR fragment at 1.8 Å resolution. This structure reveals that the C-terminal residues of ArmR form a kinked α-helix, which occupies a pseudosymmetrical and largely hydrophobic binding cavity located at the centre of the MexR dimer. Although the ArmR-binding cavity partially overlaps with the small molecule effector-binding sites of other MarR family members, it possesses a larger and more complex binding surface to accommodate the greater size and specific physicochemical properties of a peptide effector. Comparison with the structure of apo-MexR reveals that ArmR stabilizes a dramatic conformational change that is incompatible with DNA-binding. Thus, this work defines the structural mechanism by which ArmR allosterically derepresses MexR-controlled gene expression in P. aeruginosa and reveals important insights into the regulation of multidrug resistance.

Hybridization thermodynamics measured by differential scanning calorimetry (DSC) and UV spectroscopy (UVM) are reported for 8- and 14-mer oligonucleotides containing two new LNA bases: 2,6 diaminopurine (D) and 2-thiothymidine (2sT). Oligonucleotides containing D or 2sT bases are shown to have enhanced stability and improved discrimination for several of the possible mismatched base pairs.

The ability of ultraviolet resonance Raman spectroscopy (UVRRS) to determine structural, environmental, and analytical information concerning low-concentration aqueous biomolecules makes it a powerful bioanalytical and biophysical technique. Unfortunately, its utility has been limited by experimental requirements that preclude in situ or in vivo studies in most cases. We have developed the first high-performance fiber-optic probes suitable for long-term use in pulsed UVRRS applications in the deep- UV (DUV, 205-250 nm). The probes incorporate recently developed improved ultraviolet (IUV) fibers that do not exhibit the rapid solarization and throughput decay that previously hampered the use of optical fibers for delivering pulsed, DUV light. A novel 90 degrees mirrored collection geometry is used to overcome the inner-filtering effects that plague flush-probe geometries. The IUV fibers are characterized with respect to their efficacy at transmitting pulsed, DUV laser light, and prototype probes are used to obtain pulsed UVRRS data of aromatic amino acids, proteins, and hormones at low concentrations with 205-240-nm pulsed excitation. Efficient probe geometries and fabrication methods are presented. The performance of the probes in examining resonance-enhanced Raman signals from absorbing chromophores is investigated, and the optimal excitation wavelength is shown to be significantly red-shifted from the maximum of the resonance Raman enhancement profile. Generally applicable procedures for determining optimal experimental conditions are also introduced.

The mammalian molecule melanotransferrin (mTf), also called p97, is a member of the transferrin family of molecules. It exists in both secreted and glycosylphosphatidylinositol-anchored forms and is thought to play a role in angiogenesis and in transporting iron across the blood brain barrier. The binding affinity of iron to this molecule has not been formally established. Here, the binding of ferric ion (chelated with a 2-fold molar ratio of nitrilotriacetate) to mTf has been studied using isothermal titration calorimetry and differential scanning calorimetry. One iron-binding site was determined for mTf with similar binding characteristics to other transferrins. In the absence of bicarbonate, binding occurs quickly with an apparent association constant of 2.6 x 10(7) M(-1) at 25 degrees C. The presence of bicarbonate introduces kinetic effects that prevent direct determination of the apparent binding constant by isothermal titration calorimetry. Differential scanning calorimetry thermograms of mTf unfolding in the presence and absence of iron were therefore used to determine the apparent binding constant in the bicarbonate-containing system; at pH 7.5 and 25 degrees C, iron binding occurs in a 1:1 ratio with a K(app) of 4.4 x 10(17) M(-1). This affinity is intermediate between the high and low affinity lobes of transferrin and suggests that mTf is likely to play a significant role in iron transport where the high affinity lobe of transferrin is occupied or where transferrin is in proportionally low concentrations.

The ability of Serial Analysis of Gene Expression (SAGE) to provide a quantitative picture of global gene expression relies not only on the depth and accuracy of sequencing into the SAGE library, but also on the efficiency of each step required to generate the SAGE library from the starting mRNA material. The first critical step is the ligation of adaptors containing a Type IIS recognition sequence to the anchored 3' end cDNA population that permits the release of short sequence tags (SSTs) from defined sites within the 3' end of each transcript. Using an in vitro transcript as a template, we observed that only a small fraction of anchored 3' end cDNA are successfully ligated with added SAGE adaptors under typical reaction conditions currently used in the SAGE protocol. Although the introduction of approximately 500-fold molar excess of adaptor or the inclusion of 15% (w/v) PEG-8000 increased the yield of the adaptor-modified product, complete conversion to the desired adaptor:cDNA hetero-ligation product is not achieved. An alternative method of ligation, termed as directed ligation, is described which exploits a favourable mass-action condition created by the presence of NlaIII during ligation in combination with a novel SAGE adaptor containing a methylated base within the ligation site. Using this strategy, we were able to achieve near complete conversion of the anchored 3' end cDNA into the desired adaptor-modified product. This new protocol therefore greatly increases the probability that a SST will be generated from every transcript, greatly enhancing the fidelity of SAGE. Directed ligation also provides a powerful means to achieve near-complete ligation of any appropriately designed adaptor to its respective target.

Dynamic Monte Carlo (DMC) simulations of the adsorption of simple protein-like chains are used to more clearly define the molecular basis for the dependence of adsorption thermodynamics on the stability of the unique lowest-energy “native state” conformation of the chain. Arai and Norde were among the first to show that proteins of low native-state stability strongly denature upon adsorption to weakly attractive sorbent surfaces, while relatively modest changes in conformation are observed in stable proteins under identical adsorption conditions. When the protein has a low native-state stability, favorable adsorption entropies are typically observed in such systems, leading to the general belief that the chain gains conformational entropy during adsorption through a net reduction in intramolecular interactions specific to the native-state structure. Analysis of energy landscapes generated from our DMC simulation results show that a net loss in specific intramolecular interactions can lead to a positive Δ ads S under certain adsorption conditions. However, the influence of chain conformation on Δ ads S is found to correlate more directly with the manner in which the unique states of the system are distributed among the energy levels available to the adsorbed chain. Δ ads S is found to tend toward a maximum for adsorption processes described by thermally averaged energy landscapes in which the energy levels carrying the highest Boltzmann weights have a high degree of conformational degeneracy. This condition is met when the average interaction energy between the chain and the sorbent equals that between two hydrophobic segments of the chain.

Two-dimensional dynamic Monte Carlo simulations are applied to the protein-like HP chain model to investigate the influence of lateral confinement of the adsorbed chain on adsorption thermodynamics and the ensemble of accessible chain conformations. The structure of the model makes it possible to enumerate all possible chain conformations and thereby define with precision the relation between adsorption thermodynamics and changes in accessible chain conformations resulting from the adsorption process. Lateral confinement of the adsorbed chain is shown to dramatically reduce the number of accessible energy states and unique chain conformations such that, under certain conditions, adsorption is predicted to actually stabilize the chain against denaturation. Lateral confinement preferentially eliminates expanded conformations of the adsorbed chain, shifting the equilibrium from the unfolded state toward the native state. As a result, the conformational entropy of the adsorbed chain is predicted to be lower than that of the chain free in solution. The protein-like HP chain responds to an increase in the hydrophobicity of the sorbent surface by strongly favoring those conformations that minimize the overall internal energy of the system. As a result, adsorption severely destabilizes the native-state conformation. The ability of our simulation results to provide insights into underlying mechanisms for nonspecific protein adsorption is illustrated through qualitative comparison with activity data for hen egg-white lysozyme adsorbed on silica at different surface concentrations.

Dynamic Monte Carlo simulations of short linear HP-type copolymers exhibiting proteinlike characteristics are used to investigate both chain dynamics and changes in chain conformational entropy and their contributions to the energetics of adsorption onto a solid-liquid interface. The dMC results show that the conformations and energies of adsorbed chains are highly degenerate. The ensemble-averaged energy of the adsorbed state is dependent on temperature, chain sequence, native-state stability, and sorbent surface geometry and hydrophobicity. Mesoscopic thermodynamic analyses reveal that, although increased chain conformational entropy contributes to the driving force for adsorption in certain cases, many conditions exist where the change in conformational entropy is either negligible or unfavorable due to constraints imposed by the need to form a large and specific number of favorable intra- and intermolecular contacts and by the impenetrable nature of the sorbent surface. Step-number-averaged energy trajectories, based on sampling of a large number of energy trajectories and thus conformational states at each step number, suggest that the search for a global energy minimum is gradual, so that adsorption is first reversible but becomes apparently irreversible with longer exposure to the sorbent. These results appear to be connected to the conformational adaptability of the chain both on the surface and in solution, and an adsorption model taking chain conformational dynamics into account is proposed.