Precisely and Accurately Inferring Single-Molecule Rate Constants.

The kinetics of biomolecular systems can be quantified by calculating the stochastic rate constants that govern the biomolecular state vs time trajectories (i.e., state trajectories) of individual biomolecules. To do so, the experimental signal vs time trajectories (i.e., signal trajectories) obtained from observing individual biomolecules are often idealized to generate state trajectories by methods such as thresholding or hidden Markov modeling. Here, we discuss approaches for idealizing signal trajectories and calculating stochastic rate constants from the resulting state trajectories. Importantly, we provide an analysis of how the finite length of signal trajectories restricts the precision of these approaches and demonstrate how Bayesian inference-based versions of these approaches allow rigorous determination of this precision. Similarly, we provide an analysis of how the finite lengths and limited time resolutions of signal trajectories restrict the accuracy of these approaches, and describe methods that, by accounting for the effects of the finite length and limited time resolution of signal trajectories, substantially improve this accuracy. Collectively, therefore, the methods we consider here enable a rigorous assessment of the precision, and a significant enhancement of the accuracy, with which stochastic rate constants can be calculated from single-molecule signal trajectories.

The importance of the Lewis base in lithium mediated metallation and bond cleavage reaction of allyl amines and allyl phosphines.

Metallation of two analogous N- and P-allyl molecules Ph2NCH2CHCH2 and Ph2PCH2CHCH2 with nBuLi have shown contrasting reactivities based on the choice of Lewis donor. With metallation of the alpha carbon atom was achieved regardless of the Lewis donor used while in comparison metallation of showed an unexpected donor denticity dependence with P-C bond clevage induced with the tri-dentate PMDETA. Complementary DFT and solution studies rationalise this outcome.

Structural, vibrational, and rovibrational analysis of tetrafluoroethylene.

High resolution FTIR spectra of (13)C enriched tetrafluoroethylene (C(2)F(4)) were measured at 150 K at the Australian Synchrotron. Rovibrational transitions were assigned in the a-type symmetric and b-type antisymmetric CF(2) stretches of (12)C(13)CF(4) and (13)C(2)F(4) near 1170 cm(-1) and 1300 cm(-1), respectively. Ground vibrational state spectroscopic constants for both molecules were determined in addition to the upper state constants for ν(11) and ν(9) of (13)C(2)F(4) and ν(11), ν(2)+ν(6), and ν(5) of (12)C(13)CF(4). The ground state constants, along with those determined for the (12)C(2)F(4) isotopologue from previously published data, were used to determine a semi-experimental r(e) structure r(CC) = 132.36 ± 0.37 pm, r(CF) = 131.11 ± 0.23 pm, α(FCC) = 123.3 ± 0.3° in excellent agreement with ab initio structures. Lower resolution FTIR spectra were measured between 100 and 5000 cm(-1) at room temperature and band centres obtained for all modes of the three isotopologues; although only 5 out of 12 modes in (12)C(2)F(4) and (13)C(2)F(4) are infrared (IR) active, the others were inferred from combination and hot-band positions. A number of modes are observed to be infrared active only in the (12)C(13)CF(4) isotopologue due to its lower symmetry. Most notably, decoupling of the antisymmetric CF(2) motions in the two halves of (12)C(13)CF(4) results in 2 strongly IR active modes that involve motion at one carbon or the other.

UGT2B17 genetic polymorphisms dramatically affect the pharmacokinetics of MK-7246 in healthy subjects in a first-in-human study.

MK-7246, an antagonist of the chemoattractant receptor on T helper type 2 (Th2) cells, is being developed for the treatment of respiratory diseases. In a first-in-human study, we investigated whether genetic polymorphisms contributed to the marked intersubject variability in the pharmacokinetics of MK-7246 and its glucuronide metabolite M3. Results from in vitro enzyme kinetic studies suggested that UGT2B17 is probably the major enzyme responsible for MK-7246 metabolism in both the liver and the intestine. As compared with those with the UGT2B17*1/*1 wild-type genotype, UGT2B17*2/*2 carriers, who possess no UGT2B17 protein, had 25- and 82-fold greater mean dose-normalized values of area under the plasma concentration-time curve (AUC) and peak concentration of MK-7246, respectively, and a 24-fold lower M3-to-MK-7246 AUC ratio. The apparent half-life of MK-7246 was not as variable between these two genotypes. Therefore, the highly variable pharmacokinetics of MK-7246 is attributable primarily to the impact of UGT2B17 genetic polymorphisms and extensive first-pass metabolism of MK-7246.

Localization of a hole on an adenine-thymine radical cation in B-form DNA in water.

A quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulation has been carried out using CP2K for a hole introduced into a B-form DNA molecule consisting of 10 adenine-thymine (A/T) pairs in water. At the beginning of the simulation, the hole wave function is extended over several adenines. Within 20-25 fs, the hole wave function contracts so that it is localized on a single A. At 300 K, it stays on this A for the length of the simulation, several hundred fs, with the wave function little changed. In a range of temperatures below 300 K, proton transfer from A to T is seen to take place within the A/T occupied by the hole; it is completed by ∼40 fs after the contraction. We show that the contraction is due to polarization of the water by the hole. This polarization also plays a role in the proton transfer. Implications for transport are considered.

Optical and vibrational properties of 1,2-benzenedicarboxylic anhydride.

The solvent-induced changes in the optical and spectroscopic properties of 1,2-benzenedicarboxylic anhydride are studied using time dependent Hartree-Fock and density functional theory calculations within the framework of two reaction field procedures. To investigate the influence of the cavity shape, the Onsager reaction field is compared with the polarized continuum model (PCM). It is observed that solvent polarity has noticeable effects on the vibrational properties as well as the linear and nonlinear optical characteristics of the molecule. Furthermore, the Onsager and PCM procedures may lead to contradicted harmonic vibrational frequencies; in the case of the studied molecule the Onsager model predicts the blue-shifted CH stretching band while PCM leads to red-shifted CH stretching mode.

An inhibitor of methionine aminopeptidase type-2, PPI-2458, ameliorates the pathophysiological disease processes of rheumatoid arthritis.

OBJECTIVE: To elucidate the role of methionine aminopeptidase type-2 (MetAP-2) in the clinical pathology of rheumatoid arthritis, arthritis was induced in rats by administration of peptidoglycan-polysaccharide (PG-PS). DESIGN: The inhibitor of MetAP-2, PPI-2458, was administered orally at 5 mg/kg every other day during 3 distinct phases of the disease. In vitro studies were performed to clarify in vivo findings. RESULTS: Ankle swelling was completely alleviated by MetAP-2 inhibition. Inhibition of MetAP-2 in blood and tissues correlated with protection against PG-PS-induced arthritis. Histopathology of the tarsal joints improved following PPI-2458 administration, including a significant improvement of bone structure. In in vitro studies, osteoclast formation and activity were inhibited by PPI-2458, a mechanism not previously attributed to MetAP-2 inhibition. CONCLUSIONS: The important role that MetAP-2 has in the pathophysiological disease processes of PG-PS arthritis provides a strong rationale for evaluating PPI-2458 as a disease modifying antirheumatic treatment for rheumatoid arthritis.

Alterations in attentional mechanisms in response to acute inflammatory pain and morphine administration.

Research indicates that pain negatively impacts attention; however, the extent of this impact and the mechanisms of the effect of pain on normal attentional processing remain unclear. This study 1) examined the impact of acute inflammatory pain on attentional processing, 2) examined the impact of morphine on attentional processing, and 3) determined if an analgesic dose of morphine would return attentional processing to normal levels. Male Sprague-Dawley rats were trained on the 5 choice serial reaction time task (5CSRTT), a test commonly used to assess the attentional mechanisms of rodents. Animals were injected with saline or 1, 3, or 6 mg/kg of morphine. Twenty minutes later, animals received a formalin (or saline) injection into one hind paw to induce an inflammatory condition and were then immediately tested in the 5CSRTT. The results show that the formalin injection significantly impaired performance, as measured by an increase in the number of trials in which the animal failed to attend to the task. Likewise, a high dose of morphine (6 mg/kg) produced similar decrements in task performance. Of primary importance is that 3 mg/kg of morphine produced analgesia with only mild sedation, and performance in the 5CSRTT was improved with this dose. This is the first study to use an animal model of acute pain to demonstrate the negative impact of pain on attention, and provides a novel approach to examine the neural correlates that underlie the disruptive impact of pain on attention.

The Al+ -H(2) cation complex: rotationally resolved infrared spectrum, potential energy surface, and rovibrational calculations.

The infrared spectrum of the Al(+)-H(2) complex is recorded in the H-H stretch region (4075-4110 cm(-1)) by monitoring Al(+) photofragments. The H-H stretch band is centered at 4095.2 cm(-1), a shift of -66.0 cm(-1) from the Q(1)(0) transition of the free H(2) molecule. Altogether, 47 rovibrational transitions belonging to the parallel K(a)=0-0 and 1-1 subbands were identified and fitted using a Watson A-reduced Hamiltonian, yielding effective spectroscopic constants. The results suggest that Al(+)-H(2) has a T-shaped equilibrium configuration with the Al(+) ion attached to a slightly perturbed H(2) molecule, but that large-amplitude intermolecular vibrational motions significantly influence the rotational constants derived from an asymmetric rotor analysis. The vibrationally averaged intermolecular separation in the ground vibrational state is estimated as 3.03 A, decreasing by 0.03 A when the H(2) subunit is vibrationally excited. A three-dimensional potential energy surface for Al(+)-H(2) is calculated ab initio using the coupled cluster CCSD(T) method and employed for variational calculations of the rovibrational energy levels and wave functions. Effective dissociation energies for Al(+)-H(2)(para) and Al(+)-H(2)(ortho) are predicted, respectively, to be 469.4 and 506.4 cm(-1), in good agreement with previous measurements. The calculations reproduce the experimental H-H stretch frequency to within 3.75 cm(-1), and the calculated B and C rotational constants to within approximately 2%. Agreement between experiment and theory supports both the accuracy of the ab initio potential energy surface and the interpretation of the measured spectrum.

Infrared spectra of the Li+-(H2)n (n=1-3) cation complexes.

The Li+-(H2)n n=1-3 complexes are investigated through infrared spectra recorded in the H-H stretch region (3980-4120 cm-1) and through ab initio calculations at the MP2/aug-cc-pVQZ level. The rotationally resolved H-H stretch band of Li+-H2 is centered at 4053.4 cm-1 [a -108 cm-1 shift from the Q1(0) transition of H2]. The spectrum exhibits rotational substructure consistent with the complex possessing a T-shaped equilibrium geometry, with the Li+ ion attached to a slightly perturbed H2 molecule. Around 100 rovibrational transitions belonging to parallel Ka=0-0, 1-1, 2-2, and 3-3 subbands are observed. The Ka=0-0 and 1-1 transitions are fitted by a Watson A-reduced Hamiltonian yielding effective molecular parameters. The vibrationally averaged intermolecular separation in the ground vibrational state is estimated as 2.056 A increasing by 0.004 A when the H2 subunit is vibrationally excited. The spectroscopic data are compared to results from rovibrational calculations using recent three dimensional Li+-H2 potential energy surfaces [Martinazzo et al., J. Chem. Phys. 119, 11241 (2003); Kraemer and Spirko, Chem. Phys. 330, 190 (2006)]. The H-H stretch band of Li+-(H2)2, which is centered at 4055.5 cm-1 also exhibits resolved rovibrational structure. The spectroscopic data along with ab initio calculations support a H2-Li+-H2 geometry, in which the two H2 molecules are disposed on opposite sides of the central Li+ ion. The two equivalent Li+...H2 bonds have approximately the same length as the intermolecular bond in Li+-H2. The Li+-(H2)3 cluster is predicted to possess a trigonal structure in which a central Li+ ion is surrounded by three equivalent H2 molecules. Its infrared spectrum features a broad unresolved band centered at 4060 cm-1.

Rotationally resolved infrared spectrum of the Li+-D2 cation complex.

The infrared spectrum of mass selected Li(+)-D(2) cations is recorded in the D-D stretch region (2860-2950 cm(-1)) in a tandem mass spectrometer by monitoring Li(+) photofragments. The D-D stretch vibration of Li(+)-D(2) is shifted by -79 cm(-1) from that of the free D(2) molecule indicating that the vibrational excitation of the D(2) subunit strengthens the effective Li(+)cdots, three dots, centeredD(2) intermolecular interaction. Around 100 rovibrational transitions, belonging to parallel K(a)=0-0, 1-1, and 2-2 subbands, are fitted to a Watson A-reduced Hamiltonian to yield effective molecular parameters. The infrared spectrum shows that the complex consists of a Li(+) ion attached to a slightly perturbed D(2) molecule with a T-shaped equilibrium configuration and a 2.035 A vibrationally averaged intermolecular separation. Comparisons are made between the spectroscopic data and data obtained from rovibrational calculations using a recent three dimensional Li(+)-D(2) potential energy surface [R. Martinazzo, G. Tantardini, E. Bodo, and F. Gianturco, J. Chem. Phys. 119, 11241 (2003)].

Infrared spectra of the Cl- -C2H4 and Br- -C2H4 anion dimers.

Infrared spectra of mass-selected Cl- -C2H4 and Br- -C2H4 complexes are recorded in the vicinity of the ethylene CH stretching vibrations (2700-3300 cm(-1) using vibrational predissociation spectroscopy. Spectra of both complexes exhibit 6 prominent peaks in the CH stretch region. Comparison with calculated frequencies reveal that the 4 higher frequency bands are associated with CH stretching modes of the C2H4 subunit, while the 2 weaker bands are assigned as overtone or combinations bands gaining intensity through interaction with the CH stretches. Ab initio calculations at the MP2/aug-cc-pVDZ level suggest that C2H4 preferentially forms a single linear H-bond with Cl- and Br- although a planar bifurcated configuration lies only slightly higher in energy (by 110 and 16 cm(-1), respectively). One-dimensional potential energy curves describing the in-plane intermolecular bending motion are developed which are used to determine the corresponding vibrational energies and wavefunctions. Experimental and theoretical results suggest that in their ground vibrational state the Cl- -C2H4 and Br- -C2H4 complexes are localized in the single H-bonded configuration, but that with the addition of modest amounts of internal energy, the in-plane bending wavefunction also has significant amplitude in the bifurcated structure.

Role of land-surface changes in arctic summer warming.

A major challenge in predicting Earth's future climate state is to understand feedbacks that alter greenhouse-gas forcing. Here we synthesize field data from arctic Alaska, showing that terrestrial changes in summer albedo contribute substantially to recent high-latitude warming trends. Pronounced terrestrial summer warming in arctic Alaska correlates with a lengthening of the snow-free season that has increased atmospheric heating locally by about 3 watts per square meter per decade (similar in magnitude to the regional heating expected over multiple decades from a doubling of atmospheric CO2). The continuation of current trends in shrub and tree expansion could further amplify this atmospheric heating by two to seven times.

Medical internet ethics: a field in evolution.

As in any new field, the merger of medicine, e-commerce and the Internet raises many questions pertaining to ethical conduct. Key issues include defining the essence of the patient-provider relationship, establishing guidelines and training for practicing online medicine and therapy, setting standards for ethical online research, determining guidelines for providing quality healthcare information and requiring ethical conduct for medical and health websites. Physicians who follow their professional code of ethics are obligated not to exploit the relationship they have with patients, nor allow anyone else working with them to do so. Physicians and therapists are obligated to serve those who place trust in them for treatment, whether in face-to-face or online Internet encounters with patients or clients. This ethical responsibility to patients and clients is often in direct conflict with the business model of generating profits. Healthcare professionals involved in Medical Internet Ethics need to define the scope of competent medical and healthcare on the Internet. The emerging ethical issues facing medicine on the Internet, the current state of medical ethics on the Internet and questions for future directions of study in this evolving field are reviewed in this paper.

Constitutive activation of STAT3 is associated with the acquisition of an interleukin 6-independent phenotype by murine plasmacytomas and hybridomas.

Interleukin 6 (IL-6), the major growth factor for myeloma cells, signals through the activation of signal transducers and activators of transcription (STAT) proteins. An important step in the malignant progression of murine plasmacytomas is the transition from dependence on IL-6 to a state of IL-6 independence. To elucidate the mechanism whereby IL-6 independence occurs, intracellular signaling events elicited by IL-6 in both IL-6-dependent and -independent plasmacytomas and hybridomas were compared. It was found that STAT3, a key molecule involved in IL-6 signaling, was constitutively activated and phosphorylated in IL-6-independent cell lines compared to the IL-6-dependent cells. Further comparison of upstream signaling pathways revealed that JAK-1 was constitutively present in anti-phosphotyrosine immunoprecipitates of IL-6-independent cells; gp130 was constitutively phosphorylated in a subset of IL-6-independent plasmacytomas, whereas other IL-6-independent lines showed no detectable gp130 phosphorylation in the absence of exogenous IL-6. Secretion of a factor capable of supporting the growth of IL-6-dependent cells was observed in one of the IL-6-independent plasmacytomas, but not in others, making an autocrine mechanism an unlikely explanation for IL-6 independence. These findings provide evidence that the constitutive activation of STAT3, either in the absence of detectable receptor-proximal events or associated with the concomitant activation of gp130, can contribute to the process of IL-6 independence.

The synthesis, in vitro reactivity, and evidence for formation in humans of 5-phenyl-1,3-oxazinane-2,4-dione, a metabolite of felbamate.

Previously we have proposed and provided evidence for a metabolic scheme leading to 3-carbamoyl-2-phenylpropionaldehyde from the antiepileptic drug felbamate. This aldehyde was found to undergo reversible cyclization to form the more stable cyclic carbamate 4-hydroxy-5-phenyl-tetrahydro-1,3-oxazin-2-one or undergo elimination to form 2-phenylpropenal. The cyclic carbamate bears structural similarity to 4-hydroxycyclophosphamide and there is an intriguing parallelism between the pathway from the cyclic carbamate to 2-phenylpropenal and the known pathway from 4-hydroxycyclophosphamide to acrolein. The similarity of these transformations led us to consider 5-phenyl-1,3-oxazinane-2,4-dione, which could arise from an oxidation of the cyclic carbamate, as a potential metabolite of felbamate. As the formation of this dione species may have both potential pharmacologic and toxicologic implications for felbamate therapy, we wished to study its reactivity. We have developed a synthesis of 5-phenyl-1, 3-oxazinane-2,4-dione and evaluated its reactivity in vitro. This dione was found to undergo base-catalyzed decomposition to three products, one of which is the major human metabolite of felbamate, 3-carbamoyl-2-phenylpropionic acid. Furthermore, we have found evidence for the presence of the dione in human urine after felbamate treatment through the identification of its major in vitro decomposition product, 2-phenylacrylamide 11.

Evaluation of methods for transient transfection of a murine macrophage cell line, RAW 264.7.

Monocyte/macrophage cell lines are fastidious cells commonly used in transient transfection experiments. In the course of a study of gene regulation by lipopolysaccharide (LPS), we have compared several methods for DNA-mediated cell transfection to determine which would be optimally applicable to the macrophage line, RAW 264.7. Both the response level (LPS inducibility) and the degree of inter-assay variation were evaluated for each transfection technique. The following methods were compared: Lipofectin, LipofectAMINE, LipofectAMINE PLUS, SuperFect, Ca3(PO4)2 DNA co-precipitation, DEAE dextran-mediated transfection and electroporation. The transfected plasmid DNA included a luciferase reporter construct containing the junB minimal promoter under the control of an LPS-inducible 1300-bp regulatory fragment downstream of junB 5'-flanking sequence, as well as a beta-galactosidase reporter construct under the adenovirus promoter and enhancer used as an internal control. Electroporation, followed by a resting period of 16-24 h before stimulation with LPS, had the highest inducibility of all methods. DEAE dextran and Ca3(PO4)2 precipitation showed the least and the greatest inter-assay variation, respectively. For all other methods, inter-assay variability fell within this range. The results presented may serve as both a general reference and a guide for reporter gene studies in this or other macrophage cell lines.

Quantification in patient urine samples of felbamate and three metabolites: acid carbamate and two mercapturic acids.

PURPOSE: Previously we proposed and provided evidence for the metabolic pathway of felbamate (FBM), which leads to the reactive metabolite, 3-carbamoyl-2-phenylpropion-aldehyde. This aldehyde carbamate was suggested to be the reactive intermediate in the oxidation of 2-phenyl-1,3-propanediol monocarbamate to the major human metabolite 3-carbamoyl-2-phenylpropionic acid. In addition, the aldehyde carbamate was found to undergo spontaneous elimination to 2-phenylpropenal, commonly known as atropaldehyde. Moreover, atropaldehyde was proposed to play a role in the development of toxicity during FBM therapy. Evidence for atropaldehyde formation in vivo was reported with the identification of modified N-acetyl-cysteine conjugates of atropaldehyde in both human and rat urine after FBM administration. Identification of the atropaldehyde-derived mercapturic acids in urine after FBM administration is consistent with the hypothesis that atropaldehyde is formed in vivo and that it reacts with thiol nucleophiles. Based on the hypothesis that the potential for toxicity will correlate to the amount of atropaldehyde formed, we sought to develop an analytic method that would quantify the amount of relevant metabolites excreted in patient urine. METHODS: We summarize the results of an LC/MS method used to quantify FBM, 3-carbamoyl-2-phenylpropionic acid and two atropaldehyde-derived mercapturic acids in the patient population. RESULTS: Analysis was performed on 31 patients undergoing FBM therapy. The absolute quantities of FBM and three metabolites were measured. CONCLUSIONS: This method demonstrated sufficient precision for the identification of patients exhibiting "abnormal" levels of atropaldehyde conjugates and may hold potential for patient monitoring.

The synthesis and evaluation of temperature sensitive tubulin toxins.

The synthesis of several potent inhibitors of tubulin polymerization that exert their activities through interaction at the colchicine binding site is described. These agents were evaluated for their abilities to inhibit the polymerization of tubulin and the growth of neoplastic cell cultures. Additionally, the inhibition of tubulin polymerization activity of these agents was assessed over a temperature range of 30-45 degrees C to ascertain the effect of temperature on this activity. Several of the compounds possess significant inhibition of tubulin polymerization activity, and select compounds exhibit this activity in a temperature dependent manner.

Potentially reactive cyclic carbamate metabolite of the antiepileptic drug felbamate produced by human liver tissue in vitro.

Felbamate (FBM) is a novel antiepileptic drug that was approved in 1993 for treatment of several forms of epilepsy. After its introduction, toxic reactions (aplastic anemia and hepatotoxicity) associated with its use were reported. It is unknown whether FBM or one of its metabolites is responsible for these idiosyncratic adverse reactions. Although the metabolism of FBM has not been fully characterized, three primary metabolites of FBM have been identified, i.e. 2-hydroxy, p-hydroxy, and monocarbamate metabolites. In addition, the monocarbamate metabolite leads to a carboxylic acid, which is the major metabolite of FBM in humans. Formation of the hydroxylated products of FBM involves cytochrome P450 enzymes, but the enzymes involved in the formation and further metabolism of the monocarbamate have not yet been elucidated. Recently, mercapturate metabolites of FBM have been identified in human urine, and a metabolic scheme involving reactive aldehyde metabolite formation from the monocarbamate metabolite has been proposed. The present study confirmed the formation of the proposed metabolites using human liver tissue in vitro. The aldehyde intermediates were trapped as oxime derivatives, and the cyclic equilibrium product (proposed as a storage and transport form for the aldehydes) was monitored directly by HPLC or GC/MS. Formation of putative toxic aldehyde intermediates and the major carboxylic acid metabolite of FBM was differentially effected with the cofactors NADP+ and NAD+. It is possible that the cofactors may influence the relative metabolism via activation and inactivation pathways.