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.

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.

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.

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.

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.

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.

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.

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.

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.

Determination of lysine pK values using [5-13C]lysine: application to the lyase domain of DNA Pol beta.

Determination of the protonation state of titratable protein residues is of critical importance for the interpretation of active site chemistry, as well as for understanding the role of electrostatic interactions in protein folding and stability. However, protein titration studies are limited by the fact that, at extreme pH values, increasing fractions of unfolded or partially unfolded structures may be present. This problem is particularly acute for lysine residues which have high pK values. In the present study, we point out that the use of the 13C resonance of lysine C-5 as a reporter for titration of the epsilon-amino group is preferable to the use of C-6 due to the 5-fold greater titration shift, so that reasonable results can be obtained using a two parameter fit of data obtained over a more limited pH range. A new synthetic procedure for [5-13C]lysine is described, and the pK value for Lys72 in the lyase domain of DNA polymerase beta has been determined using the [5-13C]lysine-labeled enzyme. The results agree well with recent studies of the Pol lambda lyase domain, demonstrating that the pK value for this residue is not optimized for Schiff base chemistry (Gao et al., Biochemistry 2006, 45, 1785-1794). We also have re-evaluated data for the pK of Lys73 in the TEM-1 beta-lactamase.

NMR determination of lysine pKa values in the Pol lambda lyase domain: mechanistic implications.

The base excision repair (BER) process requires removal of an abasic deoxyribose-5-phosphate group, a catalytic activity that has been demonstrated for the N-terminal 8 kDa domain of DNA polymerase beta (Pol beta), and for the homologous domain of DNA polymerase lambda (Pol lambda). Previous studies have demonstrated that this activity results from formation of a Schiff base adduct of the abasic deoxyribose C-1' with a lysine residue (K312 in the case of Pol lambda), followed by a beta-elimination reaction. To better understand the underlying chemistry, we have determined pKa values for the lysine residues in the Pol lambda lyase domain labeled with [epsilon-13C]lysine. At neutral pH, the H(epsilon) protons on 3 of the 10 lysine residues in this domain, K287, K291, and K312, exhibit chemical shift inequivalence that results from immobilization of the lysyl side chains. For K287 and K291, this results from the K287-E261 and K291-E298 salt bridge interactions, while for K312, immobilization apparently results from steric and hydrogen-bonding interactions that constrain the position of the lysine side chain. The pKa value of K312 is depressed to 9.58, a value indicating that at physiological pH K312 will exist predominantly in the protonated form. Titration of the domain with hairpin DNA containing a 5'-tetrahydrofuran terminus to model the abasic site produced shifts of the labeled lysine resonances that were in fast exchange but appeared to be complete at a stoichiometry of approximately 1:1.3, consistent with a dissociation constant of approximately 1 microM. The epsilon-proton shifts of K273 were the most sensitive to the addition of the DNA, apparently due to changes in the relative orientation between K273 and W274 in the DNA complex. The average pKa values increased by 0.55, consistent with the formation of some DNA-lysine salt bridges and with the general pH increase expected to result from a reduction in the net positive charge of the complex. A general increase in the Hill coefficients observed in the complex is consistent with the screening of the interacting lysine residues by the DNA. The pKa of K312 residue increased to 10.58 in the complex, probably due to salt bridge formation with the 5'-phosphate group of the DNA. The pKa values obtained for the lyase domain of Pol lambda in the present study are consistent with recent crystallographic studies of Pol beta complexed with 5-phosphorylated abasic sugar analogues in nicked DNA which reveal an open site with no obvious interactions that would significantly depress the pK value for the active site lysine residue. It is suggested that due to the heterogeneity of the damaged DNA substrates with which Pol lambda as well as other related polymerases may be required to bind, the unexpectedly poor optimization of the lyase catalytic site may reflect a compromise of flexibility with catalytic efficiency.

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.

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.

Prediction of collective diffusion coefficient of bovine serum albumin in aqueous electrolyte solution with hard-core two-Yukawa potential.

A new method to predict concentration dependence of collective diffusion coefficient of bovine serum albumin (BSA) in aqueous electrolyte solution is developed based on the generalized Stokes-Einstein equation which relates the diffusion coefficient to the osmotic pressure. The concentration dependence of osmotic pressure is evaluated using the solution of the mean spherical approximation for the two-Yukawa model fluid. The two empirical correlations of sedimentation coefficient are tested in this work. One is for a disordered suspension of hard spheres, and another is for an ordered suspension of hard spheres. The concentration dependence of the collective diffusion coefficient of BSA under different solution conditions, such as pH and ionic strength is predicted. From the comparison between the predicted and experimental values we found that the sedimentation coefficient for the disordered suspension of hard spheres is more suitable for the prediction of the collective diffusion coefficients of charged BSA in aqueous electrolyte solution. The theoretical predictions from the hard-core two-Yukawa model coupled with the sedimentation coefficient for a suspension of hard spheres are in good agreement with available experimental data, while the hard sphere model is unable to describe the behavior of diffusion due to its neglect of the double-layer repulsive charge-charge interaction between BSA molecules.

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.

Structures and adsorption of binary hard-core Yukawa mixtures in a slitlike pore: grand canonical Monte Carlo simulation and density-functional study.

The grand canonical ensemble Monte Carlo simulation and density-functional theory are applied to calculate the structures, local mole fractions, and adsorption isotherms of binary hard-core Yukawa mixtures in a slitlike pore as well as the radial distribution functions of bulk mixtures. The excess Helmholtz energy functional is a combination of the modified fundamental measure theory of Yu and Wu [J. Chem. Phys. 117, 10156 (2002)] for the hard-core contribution and a corrected mean-field theory for the attractive contribution. A comparison of the theoretical results with the results from the Monte Carlo simulations shows that the corrected theory improves the density profiles of binary hard-core Yukawa mixtures in the vicinity of contact over the original mean-field theory. Both the present corrected theory and the simulations suggest that depletion and desorption occur at low temperature, and the local segregation can be observed in most cases. For binary mixtures in the hard slitlike pore, the present corrected theory predicts more accurate surface excesses than the original one does, while in the case of the attractive pore, no improvement is found in the prediction of a surface excess of the smaller molecule.

Density-functional theory and Monte Carlo simulation study on the electric double layer around DNA in mixed-size counterion systems.

A density-functional approach and canonical Monte Carlo simulations are presented for describing the ionic microscopic structure around the DNA molecule immersed in mixed-size counterion solutions. In the density-functional approach, the hard-sphere contribution to the Helmholtz energy functional is obtained from the modified fundamental measure theory [Y.-X. Yu and J. Z. Wu, J. Chem. Phys. 117, 10156 (2002)], and the electrostatic contribution is evaluated through a quadratic functional Taylor expansion. The new theory is suitable to the systems containing ions of arbitrary sizes and valences. In the established canonical Monte Carlo simulation, an iterative self-consistent method is used to evaluate the long-range energy, and another iterative algorithm is adopted to obtain desired bulk ionic concentrations. The ion distributions from the density-functional theory (DFT) are in good agreement with those from the corresponding Monte Carlo (MC) simulations. It is found that the ratio of the bulk concentrations of two species of counterions (cations) makes significant contribution to the ion distributions in the vicinity of DNA. Comparisons with the electrostatic potential profiles from the MC simulations show that the accuracy of the DFT becomes low when a small divalent cation exists. Both the DFT and MC simulation results illustrate that the electrostatic potential at the surface of DNA increases as the anion diameter or the total cation concentration is increased and decreases as the diameter of one cation species is increased. The calculation of electrostatic potential using real ion diameters shows that the accuracy of DFT predictions for divalent ions is also acceptable.