Physiologically based pharmacokinetics of matrine in the rat after oral administration of pure chemical and ACAPHA.

ACAPHA, a botanical drug for the treatment of human esophageal cancer in China, is under investigation as a lung cancer chemoprevention agent at the BC Cancer Agency (Vancouver, BC, Canada). Little or no information is available on the pharmacokinetics of ACAPHA in animals. The objectives of this study were as follows: to examine the disposition kinetics of matrine, a bioactive marker of ACAPHA in the rat; to develop a physiologically based pharmacokinetic (PBPK) model for pure matrine; and to characterize the absorption and clearance of crude matrine in ACAPHA-treated rats using the PBPK model. Pure matrine (15 mg/kg) or crude matrine in the form of ACAPHA (0.38 or 3.8 g/kg) was administered to the rat by gavages. The rats were sacrificed at different time points postdosing. Blood and major organs were removed from the rat, extracted with toluene/butanol, and quantified for matrine using gas chromatography-mass spectrometry. An 11-compartment, flow-limited PBPK model of matrine was developed. The PBPK model was able to simulate closely the empirical data of rats treated with pure matrine. Because the absorption and clearance of crude matrine in ACAPHA-treated rats could not be parameterized a priori, they were estimated by fitting the experimental data to the PBPK model. Results of the study show that pure matrine is absorbed and eliminated by the rat at faster rates than crude matrine. Moreover, the ACAPHA matrix may change the pharmacokinetics of matrine in the rat significantly. The PBPK model is a valuable tool to gain insights into the disposition kinetics of a botanical drug.

A physiologically-based pharmacokinetic model of oseltamivir phosphate and its carboxylate metabolite for rats and humans.

Oseltamivir phosphate (OP, Tamiflu®) is a widely used prodrug for the treatment of influenza viral infections. Orally administered OP is rapidly hydrolyzed by the carboxylesterases in animals to oseltamivir carboxylate (OC), a potent influenza virus neuraminidase inhibitor. The goals of this study were to develop and validate a physiologically-based pharmacokinetic (PBPK) model of OP/OC in rats and humans, and to predict the internal tissue doses for OP and OC in humans after receiving OP orally. To this end, a PBPK model of OP/OC was first developed in the rat, which was then scaled up to humans by replacing the physiological and biochemical parameters with human-specific values. The proposed PBPK model consisted of an OP and an OC sub-models each containing nine first-order, flow-limited tissue/organ compartments. OP metabolism to OC was assumed to carry out mainly by hepatic carboxylesterases although extra-hepatic metabolism also occurred especially in the plasma. The PBPK model was developed and validated by experimental data from our laboratories and from the literature. The proposed PBPK model accurately predicted the pharmacokinetic behavior of OP and OC in humans and rats after receiving a single or multiple doses of OP orally or an OC dose i.v. The PBPK model was used to predict the internal tissue doses of OP and OC in a hypothetical human after receiving the recommended dose of 75 mg/kg OP b.i.d. for 6 days. Steady-state OC concentrations in the plasma and major organs such as the lung and the brain were higher than the minimum in vitro IC50 reported for H1N1 influenza virus neuraminidase, confirming OP is an effective, anti-viral agent. OP side-effects in the gastrointestinal tract and brain of humans were explainable by the tissue doses found in these organs. The PBPK model provides a quantitative tool to evaluate the relationship between an externally applied dose of OP and the internal tissue doses in humans. As such the model can be used to adjust the dose regimens for adult patients in disease states e.g., renal failure and liver damage.

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.

Database URL: https://www.wwpdb.org/.

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.

OneDep, a unified system for deposition, biocuration, and validation of experimentally determined structures of biological macromolecules to the PDB archive, has been developed as a global collaboration by the worldwide PDB (wwPDB) partners. This new system was designed to ensure that the wwPDB could meet the evolving archiving requirements of the scientific community over the coming decades. OneDep unifies deposition, biocuration, and validation pipelines across all wwPDB, EMDB, and BMRB deposition sites with improved focus on data quality and completeness in these archives, while supporting growth in the number of depositions and increases in their average size and complexity. In this paper, we describe the design, functional operation, and supporting infrastructure of the OneDep system, and provide initial performance assessments.

Structure-function studies of DNA polymerase lambda.

DNA polymerase lambda is a member of the X family of polymerases that is implicated in non-homologous end-joining of double-strand breaks in DNA and in base excision repair of DNA damage. To better understand the roles of DNA polymerase lambda in these repair pathways, here we review its structure and biochemical properties, with emphasis on its gap-filling polymerization activity, its dRP lyase activity and its unusual DNA synthetic (in)fidelity.

Density functional theory study on the structure and capillary phase transition of a polymer melt in a slitlike pore: effect of attraction.

A density functional theory is proposed to investigate the effects of polymer monomer-monomer and monomer-wall attractions on the density profile, chain configuration, and equilibrium capillary phase transition of a freely jointed multi-Yukawa fluid confined in a slitlike pore. The excess Helmholtz energy functional is constructed by using the modified fundamental measure theory, Wertheim's first-order thermodynamic perturbation theory, and Rosenfeld's perturbative method, in which the bulk radial distribution function and direct correlation function of hard-core multi-Yukawa monomers are obtained from the first-order mean spherical approximation. Comparisons of density profiles and bond orientation correlation functions of inhomogeneous chain fluids predicted from the present theory with the simulation data show that the present theory is very accurate, superior to the previous theory. The present theory predicts that the polymer monomer-monomer attraction lowers the strength of oscillations for density profiles and bond orientation correlation functions and makes the excess adsorption more negative. It is interesting to find that the equilibrium capillary phase transition of the polymeric fluid in the hard slitlike pore occurs at a higher chemical potential than in bulk condition, but as the attraction of the pore wall is increased sufficiently, the chemical potential for equilibrium capillary phase transition becomes lower than that for bulk vapor-liquid equilibrium.

Structure and adsorption of a hard-core multi-Yukawa fluid confined in a slitlike pore: grand canonical Monte Carlo simulation and density functional study.

Because of the increasing interest in studying the phenomenon exhibited by charge-stabilized colloidal suspensions in confining geometry, we present a density functional theory (DFT) for a hard-core multi-Yukawa fluid. The excess Helmholtz free-energy functional is constructed by using the modified fundamental measure theory and Rosenfeld's perturbative method, in which the bulk direct correlation function is obtained from the first-order mean spherical approximation. To validate the established theory, grand canonical ensemble Monte Carlo (GCMC) simulations are carried out to determine the density profiles and surface excesses of multi-Yukawa fluid in a slitlike pore. Comparisons of the theoretical results with the GCMC data suggest that the present DFT gives very accurate density profiles and surface excesses of multi-Yukawa fluid in the slitlike pore as well as the radial distribution functions of the bulk fluid. Both the DFT and the GCMC simulations predict the depletion of the multi-Yukawa fluid near a nonattractive wall, while the mean-field theory fails to describe this depletion in some cases. Because the simple form of the direct correlation function is used, the present DFT is computationally as efficient as the mean-field theory, but reproduces the simulation data much better than the mean-field theory.

A molecular-thermodynamic model for the interactions between globular proteins in aqueous solutions: applications to bovine serum albumin (BSA), lysozyme, alpha-chymotrypsin, and immuno-gamma-globulins (IgG) solutions.

To investigate globular protein-protein and protein-salt interactions in electrolyte solutions, a potential of mean force including hard-core repulsion, van der Waals attraction and electric double layer repulsion is proposed in this work. Both van der Waals attraction and double-layer repulsion are represented using hard spheres with two-Yukawa tails. The explicit analytical solution of osmotic pressure is derived from the first-order mean spherical approximation. From the comparison between the calculated and experimental values of osmotic pressures for aqueous bovine serum albumin (BSA), lysozyme, alpha-chymotrypsin, and immuno-gamma-globulins (IgG) solutions, we found that the proposed model is adequate for the description of the interactions between proteins at low ionic strength and small self-association of protein molecules. At high ionic strength, the charge inversions of protein molecules should be taken into account.

The focal adhesion targeting domain of focal adhesion kinase contains a hinge region that modulates tyrosine 926 phosphorylation.

The focal adhesion targeting (FAT) domain of focal adhesion kinase (FAK) is critical for recruitment of FAK to focal adhesions and contains tyrosine 926, which, when phosphorylated, binds the SH2 domain of Grb2. Structural studies have shown that the FAT domain is a four-helix bundle that exists as a monomer and a dimer due to domain swapping of helix 1. Here, we report the NMR solution structure of the avian FAT domain, which is similar in overall structure to the X-ray crystal structures of monomeric forms of the FAT domain, except that loop 1 is longer and less structured in solution. Residues in this region undergo temperature-dependent exchange broadening and sample aberrant phi and psi angles, which suggests that this region samples multiple conformations. We have also identified a mutant that dimerizes approximately 8 fold more than WT FAT domain and exhibits increased phosphorylation of tyrosine 926 both in vitro and in vivo.

Increased backbone mobility in beta-barrel enhances entropy gain driving binding of N-TIMP-1 to MMP-3.

The high-affinity inhibition of stromelysin 1 (MMP-3) by tissue inhibitor of metalloproteinases 1 (TIMP-1) helps control tissue remodeling and tumor development. The interaction of N-TIMP-1 with the catalytic domain of MMP-3 has been investigated by titration calorimetry and 15N NMR. Their unfavorable enthalpy of binding of +6.5 kcal mol(-1) is unusual among protein-protein associations, deviates from structure-based prediction, and is compensated by a net entropy increase providing at least 18 kcal mol(-1) of favorable free energy of binding at a 1M reference state. The small heat capacity of binding agrees well with the heat capacity predicted from 65% of the surface buried on binding being polar, and suggests that the hydrophobic effect can account for only part of the entropy of binding. Using NMR, binding-induced changes in the backbone of N-TIMP-1 were checked as one possible source of conformational entropy changes. MMP binding slightly increases rigidity in some contact sites in TIMP-1 but increases mobility remotely in the otherwise rigid beta-barrel core of N-TIMP-1, increasing 15N relaxation evidence of pico- to nanosecond and micro- to millisecond fluctuations of beta-strands A-F. Residual dipolar couplings suggest dynamic deviations from X-ray coordinates of the complex. These suggest that the beta-barrel has small backbone conformational fluctuations, while segments of strands betaB, betaE and betaF might experience fluctuations only in their backbone environment. This is a distinctive example of affinity between two well-structured proteins being enhanced by increased conformational entropy in the reservoir of a folding core.

Structure of inhomogeneous attractive and repulsive hard-core yukawa fluid: grand canonical Monte Carlo simulation and density functional theory study.

A density functional theory is proposed for an inhomogeneous hard-core Yukawa (HCY) fluid based on Rosenfeld's perturbative method. The excess Helmholtz energy functional is derived from a modified fundamental measure theory for the hard-core repulsion and a quadratic functional Taylor expansion for the long-ranged attractive or repulsive interactions. To test the established theory, grand canonical ensemble Monte Carlo simulations are carried out to simulate the density profiles of attractive and repulsive HCY fluid near a wall. Comparison with the results from the Monte Carlo simulations shows that the present density functional theory gives accurate density profiles for both attractive and repulsive HCY fluid near a wall. Both the present theory and simulations suggest that there is depletion for attractive HCY fluid at low temperature, but no depletion is found for repulsive HCY fluid. The calculated results indicate that the present density functional theory is better than those of the modified version of the Lovett-Mou-Buff-Wertheim and other density functional theories. The present theory is simple in form and computationally efficient. It predicts accurate radial distribution functions of both attractive and repulsive HCY fluid except for the repulsive case at high density, where the theory overestimates the radial distribution function in the vicinity of contact.

Protein-protein interaction analysis by nuclear magnetic resonance spectroscopy.

Nuclear magnetic resonance (NMR) is a powerful technique to study protein-protein interactions in solution. Various methods have been developed and applied successfully for locating binding sites on proteins. The application of NMR chemical-shift perturbation to map the protein-protein interfaces is described in this chapter, providing a practical guideline that can be followed to carry out the experiments.

Gas chromatography-mass spectrometry determination of matrine in human plasma.

A method was developed for the quantification of matrine in human plasma using a liquid-liquid extraction procedure followed by gas-chromatography-mass spectrometry (GC/MS) analysis. Deuterated matrine, an internal standard of the analysis, was spiked into the plasma samples before extraction. Linear detection responses were obtained for matrine concentrations ranging from 10 to 500 ng/ml. The intra-day and inter-day precision ranged from 0.4 to 4.0% and 1.0-3.5%, respectively. The intra-day accuracy was between -7.3 and 4.5%. The limit of quantification for matrine was 23 ng/ml. The extraction efficiency averaged about 38%. The validated GC/MS method will be used to quantify matrine in human plasma samples collected in a clinical trial study.

Density functional study on the structures and thermodynamic properties of small ions around polyanionic DNA.

A density functional theory (DFT) is presented for describing the distributions of small ions around an isolated infinitely long polyanionic DNA molecule in the framework of the restricted primitive model. The hard-sphere contribution to the excess Helmholtz energy functional is derived from the modified fundamental measure theory, and the electrostatic interaction is evaluated through a quadratic functional Taylor expansion. The predictions from the DFT are compared with integral equation theory (IET), the nonlinear Poisson-Boltzmann (PB) equation, and computer simulation data for the ionic density profiles, electrostatic potentials, and charge compensation functions at varieties of solution conditions. Good agreement between the DFT and computer simulations is achieved. The charge inversion phenomena of DNA are observed in a moderately concentrated solution of 2:1 and 2:2 electrolytes using the DFT, IET, and computer simulation, but can never be predicted from the PB equation. The predictions of charge inversion from the DFT prove to be more accurate than those from the IET when compared with computer simulation data. The preferential interaction coefficients from the DFT are also compared with those from the PB equation and Monte Carlo simulation, and it is shown that the DFT is superior to the PB equation.

Facile fabrication of three-dimensional graphene foam/poly(dimethylsiloxane) composites and their potential application as strain sensor.

A three-dimensional (3D) graphene foam (GF)/poly(dimethylsiloxane) (PDMS) composite was fabricated by infiltrating PDMS into 3D GF, which was synthesized by chemical vapor deposition (CVD) with nickel foam as template. The electrical properties of the GF/PDMS composite under bending stress were investigated, indicating the resistance of the GF/PDMS composite was increased with the bending curvature. To improve the bending sensitivity of the GF/PDMS composite, a thin layer of poly(ethylene terephthalate) (PET) was introduced as substrate to form double-layer GF/PDMS-PET composite, whose measurements showed that the resistance of the GF/PDMS-PET composite was still increased when bended to the side of PET, whereas its resistance would be decreased when bended to the side of GF. For both cases, the absolute value of the relative variation of electrical resistance was increased with the bending curvature. More importantly, the relative variation of electrical resistance for double-layer GF/PDMS-PET composite can be up to six times higher than single-layer GF/PDMS composite for the same bending curvature. These observations were further supported by the principle of mechanics of material. The 3D GF/PDMS-PET composite also has higher flexibility and environment stability and can be utilized as a strain sensor with high sensitivity, which can find important applications in real-time monitoring of buildings, such as a bridge, dam, and high-speed railway.

Small molecule annotation for the Protein Data Bank.

The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100,000 structures contain more than 20,000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present in a deposited structure may be attached to a polymer or may occur as a separate, non-covalently linked ligand. During curation of a newly deposited structure by wwPDB annotation staff, each molecule is cross-referenced to the PDB Chemical Component Dictionary (CCD). If the molecule is new to the PDB, a dictionary description is created for it. The information about all small molecule components found in the PDB is distributed via the ftp archive as an external reference file. Small molecule annotation in the PDB also includes information about ligand-binding sites and about covalent and other linkages between ligands and macromolecules. During the remediation of the peptide-like antibiotics and inhibitors present in the PDB archive in 2011, it became clear that additional annotation was required for consistent representation of these molecules, which are quite often composed of several sequential subcomponents including modified amino acids and other chemical groups. The connectivity information of the modified amino acids is necessary for correct representation of these biologically interesting molecules. The combined information is made available via a new resource called the Biologically Interesting molecules Reference Dictionary, which is complementary to the CCD and is now routinely used for annotation of peptide-like antibiotics and inhibitors.

Density functional study on the structural and thermodynamic properties of aqueous DNA-electrolyte solution in the framework of cell model.

A density functional theory (DFT) in the framework of cell model is proposed to calculate the structural and thermodynamic properties of aqueous DNA-electrolyte solution with finite DNA concentrations. The hard-sphere contribution to the excess Helmholtz energy functional is derived from the modified fundamental measure theory, and the electrostatic interaction is evaluated through a quadratic functional Taylor expansion around a uniform fluid. The electroneutrality in the cell leads to a variational equation with a constraint. Since the reference fluid is selected to be a bulk phase, the Lagrange multiplier proves to be the potential drop across the cell boundary (Donnan potential). The ion profiles and electrostatic potential profiles in the cell are calculated from the present DFT-cell model. Our DFT-cell model gives better prediction of ion profiles than the Poisson-Boltzmann (PB)- or modified PB-cell models when compared to the molecular simulation data. The effects of polyelectrolyte concentration, ion size, and added-salt concentration on the electrostatic potential difference between the DNA surface and the cell boundary are investigated. The expression of osmotic coefficient is derived from the general formula of grand potential. The osmotic coefficients predicted by the DFT are lower than the PB results and are closer to the simulation results and experimental data.

Multiple paxillin binding sites regulate FAK function.

BACKGROUND: FAK localization to focal adhesions is essential for its activation and function. Localization of FAK is mediated through the C-terminal focal adhesion targeting (FAT) domain. Recent structural analyses have revealed two paxillin-binding sites in the FAT domain of FAK. To define the role of paxillin binding to each site on FAK, point mutations have been engineered to specifically disrupt paxillin binding to each docking site on the FAT domain of FAK individually or in combination. RESULTS: These mutants have been characterized and reveal an important role for paxillin binding in FAK subcellular localization and signaling. One paxillin-binding site (comprised of alpha-helices 1 and 4 of the FAT domain) plays a more prominent role in localization than the other. Mutation of either paxillin-binding site has similar effects on FAK activation and downstream signaling. However, the sites aren't strictly redundant as each mutant exhibits phosphorylation/signaling defects distinct from wild type FAK and a mutant completely defective for paxillin binding. CONCLUSION: The studies demonstrate that the two paxillin-binding sites of FAK are not redundant and that both sites are required for FAK function.

Inactivation of N-TIMP-1 by N-terminal acetylation when expressed in bacteria.

The high-affinity binding of tissue inhibitors of metalloproteinases (TIMPs) to matrix metalloproteinases (MMPs) is essential for regulation of the turnover of the extracellular matrix during development, wound healing, and progression of inflammatory diseases, such as cancer, atherosclerosis, and arthritis. Bacterially expressed N-terminal inhibitory domains of TIMPs (N-TIMPs) have been used extensively for biochemical and biophysical study of interactions with MMPs. Titration of N-TIMP-1 expressed in E. coli indicates, however, that only about 42% of the protein is active as an MMP inhibitor. The separation of inactive from fully active N-TIMP-1 has been achieved both by MMP affinity and by high-resolution cation exchange chromatography at an appropriate pH, based on a slight difference of charge. Purification by cation exchange chromatography with a Mono S column enriches the active portion of N-TIMP-1 to >95%, with K(i) of 1.5 nM for MMP-12. Mass spectra reveal that the inactive form differs from active N-TIMP-1 in being N-terminally acetylated, underscoring the importance of the free alpha-NH(2) of Cys1 for MMP inhibition. N(alpha)-acetylation of the CTCVPP sequence broadens the N-terminal sequence motifs reported to be susceptible to alpha-amino acetylation by E. coli N-acetyl transferases.

Preferential interaction between DNA and small ions in mixed-size counterion systems: Monte Carlo simulation and density functional study.

Competitive binding between counterions around DNA molecule is characterized using the preferential interaction coefficient of individual ion in single and mixed electrolyte solutions. The canonical Monte Carlo (MC) simulation, nonlinear Poisson-Boltzmann (PB) equation, and density functional theory (DFT) proposed in our previous work [Wang, Yu, Gao, and Luo, J. Chem. Phys. 123, 234904 (2005)] are utilized to calculate the preferential interaction coefficients. The MC simulations and theoretical results show that for single electrolyte around DNA, the preferential interaction coefficient of electrolyte decreases as the cation size is increased, indicating that the larger cation has less accumulation ability in the vicinity of DNA. For the mixed electrolyte solution, it is found that cation diameter has a significant effect on the competitive ability while anion diameter has a negligible effect. It proves that the preferential interaction coefficients of all ions decrease as the total ionic concentration is increased. The DFT generally has better performance than the PB equation does when compared to the MC simulation data. The DFT behaves quite well for the real ionic solutions such as the KCl-NaCl-H2O, NaCl-CaCl2-H2O, and CaCl2-MgCl2-H2O systems.