Biomedical subjects

Hyung J Kim

Publications and source records attributed to Hyung J Kim.

14 recordsLinked to original sources

PubMed2006

Rotational dynamics of a diatomic solute in the room-temperature ionic liquid 1-ethyl-3-methylimidazolium hexafluorophosphate.

Reorientational time correlation functions C(l)(t)( identical withP(l)[cos theta(t)]) for a diatomic solute in 1-ethyl-3-methylimidazolium hexafluorophosphate (EMI(+)PF(6) (-)) are analyzed via molecular dynamics computer simulations, where <...> denotes an equilibrium ensemble average, P(l) the lth order Legendre polynomial and theta(t) the angle between the solute orientation at time t and its initial direction. Overall results are indicative of heterogeneous dynamics in EMI(+)PF(6) (-). For a small nondipolar solute, C(l)(t) are well-described as stretched exponential functions in wide time ranges. One striking feature is that after rapid initial relaxation, C(2)(t) decays more slowly than C(1)(t). As a result, the correlation time associated with the former is considerably longer than that with the latter. This is ascribed to solvent structural fluctuations, which allow large-amplitude solute rotations. As the solute size grows, relaxation of C(l)(t) approaches exponential decay.

Journal Article↗

PubMed2006

Vibrational energy relaxation of a diatomic molecule in a room-temperature ionic liquid.

Vibrational energy relaxation (VER) dynamics of a diatomic solute in ionic liquid 1-ethyl-3-methylimidazolium hexafluorophosphate (EMI(+)PF(6) (-)) are studied via equilibrium and nonequilibrium molecular dynamics simulations. The time scale for VER is found to decrease markedly with the increasing solute dipole moment, consonant with many previous studies in polar solvents. A detailed analysis of nonequilibrium results shows that for a dipolar solute, dissipation of an excess solute vibrational energy occurs almost exclusively via the Lennard-Jones interactions between the solute and solvent, while an oscillatory energy exchange between the two is mainly controlled by their electrostatic interactions. Regardless of the anharmonicity of the solute vibrational potential, VER becomes accelerated as the initial vibrational energy increases. This is attributed primarily to the enhancement in variations of the solvent force on the solute bond, induced by large-amplitude solute vibrations. One interesting finding is that if a time variable scaled with the initial excitation energy is employed, dissipation dynamics of the excess vibrational energy of the dipolar solute tend to show a universal behavior irrespective of its initial vibrational state. Comparison with water and acetonitrile shows that overall characteristics of VER in EMI(+)PF(6) (-) are similar to those in acetonitrile, while relaxation in water is much faster than the two. It is also found that the Landau-Teller theory predictions for VER time scale obtained via equilibrium simulations of the solvent force autocorrelation function are in reasonable agreement with the nonequilibrium results.

Journal Article↗

PubMed2006

Free energy, entropy and volume of activation for electron transfer reactions in a polar solvent.

A continuum theory with account of cavity size fluctuations is employed to study free energy, volume and entropy of activation for nonadiabatic electron transfer (ET) reactions in polar solvents. By using a two-sphere cavity description, model calculations are performed for charge separation and recombination processes in acetonitrile under ambient conditions. It is found that the cavity size at the transition state varies with the free energy of reaction as well as with the thermodynamic conditions. In contrast to the Marcus theory predictions, the volume and entropy of activation show a monotonic behavior with the free energy of reaction and a strong correlation with each other. For example, for a given ET process, the volume and entropy of activation have the same sign. Their values for the charge separation and recombination processes are opposite in sign. These findings are in good qualitative agreement with measurements.

Journal Article↗

PubMed2006

Solvation in supercritical water.

Solvation in supercritical water under equilibrium and nonequilibrium conditions is studied via molecular dynamics simulations. The influence of solute charge distributions and solvent density on the solvation structures and dynamics is examined with a diatomic probe solute molecule. It is found that the solvation structure varies dramatically with the solute dipole moment, especially in low-density water, in accord with many previous studies on ion solvation. This electrostrictive effect has important consequences for solvation dynamics. In the case of a nonequilibrium solvent relaxation, if there are sufficiently many water molecules close to the solute at the outset of the relaxation, the solvent response measured as a dynamic Stokes shift is almost completely governed by inertial rotations of these water molecules. By contrast, in the opposite case of a low local solvent density near the solute, not only rotations but also translations of water molecules play an important role in solvent relaxation dynamics. The applicability of a linear response is found to be significantly restricted at low water densities.

Journal Article↗

PubMed2006

Protection against H1, H5, H6 and H9 influenza A infection with liposomal matrix 2 epitope vaccines.

The recent emergence of multiple avian influenza A subtypes that cause human disease (i.e., H5N1, H9N2 and H7N7), coupled with the fear that one of these strains might precipitate a new pandemic, underscores the need to develop new technological approaches to immunization which elicit protective immune responses against multiple subtypes of influenza A. In response to this demand, several matrix 2 protein ectodomain segments (M2eA) corresponding to the H1N1, H5N1 and H9N2 influenza strains were formulated using a novel liposome-based vaccine technology and evaluated as potential immunogens for developing a "universal" influenza vaccine. Mice immunized with liposomal M2eA survived homologous challenges with H1N1 (100% survival) or H9N2 (80% survival) influenza strains. There were significant reductions in their lung viral load as well as in immunized mice challenged with the H5N1 subtype. The mice vaccinated with an M2eA segment corresponding to the H1N1 and H6N2 (a reassortant influenza A virus carrying the M2eA from PR8/34) strains elicited elevated IgG ELISA antibody titers to this M2eA epitope segment and antiserum from these immunized mice provided passive protection (100% survival) to naïve mice receiving a lethal dose of H6N2 influenza virus. These results provide the first evidence that recombinant M2eA epitopes to multiple subtypes elicited immune protection against a homologous challenge and provides further evidence in favor of the development of a "universal" influenza vaccine based on M2eA.

Amino Acid Sequence↗

PubMed2006

Solubility of water in a benzene-cyclohexane mixture.

The solubility of a water molecule in a binary mixture of nonpolar cyclohexane and quadrupolar benzene is studied with the ab initio method. A novel self-consistent reaction field theory that properly accounts for benzene quadrupole moments in the continuum solvent framework is used to describe the solvation effects of the solvent mixture. The free energy of transfer from pure cyclohexane to the mixture solvent is obtained with the neglect of nonelectrostatic contributions. A reasonable agreement with experiments indicates that the theoretical method presented here provides a promising approach to electronic structure calculations in quadrupolar solvents and their mixtures with nonpolar solvents.

Journal Article↗

PubMed2006

Temperature- and pressure-dependence of the outer-sphere reorganization free energy for electron transfer reactions: a continuum approach.

The outer-sphere reorganization free energy for electron-transfer reactions in polar solvents and its variations with temperature and pressure are studied in the dielectric continuum framework by extending the recent fluctuating cavity description [J. Chem. Phys. 2005, 123, 014504]. The diabatic free energies are obtained as a function of three variables, i.e., radii of two spherical cavities for the donor and acceptor moieties of an electron-transfer complex and a solvent coordinate that gauges an arbitrary configuration of solvent orientational polarization. Equilibrium cavities relevant to the reactant and product states are determined via the variational principle. This incorporates cavity size readjustment accompanying electron transfer and related electrostrictive effects. Another important consequence of the variational determination of equilibrium cavities is that their size depends on thermodynamic conditions. The application of the theoretical formulation presented here to electron self-exchange shows that in contrast to the prediction of the standard Marcus theory, the solvent reorganization free energy decreases with temperature. This is in excellent accord with a recent experiment on a mixed valence dinuclear iron complex in acetonitrile [J. Phys. Chem. A 1999, 103, 7888]. It is also found that electrostriction makes a significant contribution to outer-sphere reorganization. Model calculations for the dinuclear iron complex system show that about 25-30% of the total solvent reorganization free energy arises from cavity size changes, while solvent repolarization is responsible for the rest.

Journal Article↗

PubMed2005

On the temperature and pressure dependences of cavities in the dielectric continuum picture.

Cavity size at equilibrium and its variations with thermodynamic conditions are studied in the dielectric continuum framework of solvents. By employing Gibbs' theory of dividing surfaces, the fluctuating cavity description of Kim [H.J. Kim, J. Chem. Phys. 105, 6818 (1996)] is extended to include effects related to the local solvent density inhomogeneity near the cavity. The resulting theory is applied to study cavity size variations with temperature and pressure in dipolar and nondipolar solvents. Model calculations show that the cavity size tends to increase with temperature along an isobar and decrease with pressure along an isotherm.

Journal Article↗

PubMed2005

Purification and physical-chemical properties of methanobactin: a chalkophore from Methylosinus trichosporium OB3b.

Methanobactin is an extracellular, copper-binding chromopeptide from the methane-oxidizing bacterium, Methylosinus trichosporium OB3b, believed to be involved in copper detoxification, sequestration, and uptake. Although small (1217.2 Da), methanobactin possesses a complex three-dimensional macrocyclic structure with several unusual moieties. The molecule binds one copper and has the N-2-isopropylester-(4-thionyl-5-hydroxyimidazolate)-Gly(1)-Ser(2)-Cys(3)-Tyr(4)-pyrrolidine-(4-hydroxy-5-thionylimidazolate)-Ser(5)-Cys(6)-Met(7) sequence [Kim, H. J., et al. (2004) Science 305, 1612-1615]. We report methods for purifying methanobactin from M. trichosporium OB3b and present initial evidence of its physiological function. MALDI-TOF MS was used to systematically monitor samples for optimizing purification conditions, and for detecting and analyzing specific metal-methanobactin complexes. Purification was performed by first stabilizing the extracted compound with copper followed by separation using reversed-phase HPLC in neutral pH buffers. Purified methanobactin exhibited UV-visible maxima at 342 nm, a shoulder at 388 nm, and a broad peak at 282 nm. These features were lost upon CuCl(2) titration with appearance of new features at 335, 356, 290, and 255 nm. Furthermore, methanobactin contains two fluorescent moieties, which exhibit broad emissions at 440-460 nm (lambda(max)(ex) at 388 nm) and 390-430 nm (lambda(max)(ex) = 342 nm), respectively. Finally, methanobactin eliminates the growth lag in M. trichosporium OB3b and substantially increases growth rates when cultures are exposed to elevated copper levels.

Amino Acids↗

PubMed2005

A molecular dynamics computer simulation study of room-temperature ionic liquids. I. Equilibrium solvation structure and free energetics.

Solvation in 1-ethyl-3-methylmidazolium chloride and in 1-ethyl-3-methylimidazolium hexafluorophosphate near equilibrium is investigated via molecular dynamics computer simulations with diatomic and benzenelike molecules employed as probe solutes. It is found that electrostriction plays an important role in both solvation structure and free energetics. The angular and radial distributions of cations and anions become more structured and their densities near the solute become enhanced as the solute charge separation grows. Due to the enhancement in structural rigidity induced by electrostriction, the force constant associated with solvent configuration fluctuations relevant to charge shift and transfer processes is also found to increase. The effective polarity and reorganization free energies of these ionic liquids are analyzed and compared with those of highly polar acetonitrile. Their screening behavior of electric charges is also investigated.

Journal Article↗

PubMed2005

A molecular dynamics computer simulation study of room-temperature ionic liquids. II. Equilibrium and nonequilibrium solvation dynamics.

The molecular dynamics (MD) simulation study of solvation structure and free energetics in 1-ethyl-3-methylimidazolium chloride and 1-ethyl-3-methylimidazolium hexafluorophosphate using a probe solute in the preceding article [Y. Shim, M. Y. Choi and H. J. Kim, J. Chem. Phys. 122, 044510 (2005)] is extended to investigate dynamic properties of these liquids. Solvent fluctuation dynamics near equilibrium are studied via MD and associated time-dependent friction is analyzed via the generalized Langevin equation. Nonequilibrium solvent relaxation following an instantaneous change in the solute charge distribution and accompanying solvent structure reorganization are also investigated. Both equilibrium and nonequilibrium solvation dynamics are characterized by at least two vastly different time scales--a subpicosecond inertial regime followed by a slow diffusive regime. Solvent regions contributing to the subpicosecond nonequilibrium relaxation are found to vary significantly with initial solvation configurations, especially near the solute. If the solvent density near the solute is sufficiently high at the outset of the relaxation, subpicosecond dynamics are mainly governed by the motions of a few ions close to the solute. By contrast, in the case of a low local density, solvent ions located not only close to but also relatively far from the solute participate in the subpicosecond relaxation. Despite this difference, linear response holds reasonably well in both ionic liquids.

Journal Article↗

PubMed2004

Methanobactin, a copper-acquisition compound from methane-oxidizing bacteria.

Siderophores are extracellular iron-binding compounds that mediate iron transport into many cells. We present evidence of analogous molecules for copper transport from methane-oxidizing bacteria, represented here by a small fluorescent chromopeptide (C45N12O14H62Cu, 1216 daltons) produced by Methylosinus trichosporium OB3b. The crystal structure of this compound, methanobactin, was resolved to 1.15 angstroms. It is composed of a tetrapeptide, a tripeptide, and several unusual moieties, including two 4-thionyl-5-hydroxy-imidazole chromophores that coordinate the copper, a pyrrolidine that confers a bend in the overall chain, and an amino-terminal isopropylester group. The copper coordination environment includes a dual nitrogen- and sulfur-donating system derived from the thionyl imidazolate moieties. Structural elucidation of this molecule has broad implications in terms of organo-copper chemistry, biological methane oxidation, and global carbon cycling.

Amino Acids↗

PubMed2003

Effects of oxygen and nitrogen conditions on the transformation kinetics of 1,2-dichloroethenes by Methylosinus trichosporium OB3b and its sMMOC mutant.

Transformation kinetics of trans- and cis-dichloroethylenes (DCE) by Methylosinus trichosporium OB3b wild type (WT) and PP319, a mutant that expresses soluble methane monooxygenase at copper levels up to micro 12 microM Cu (sMMOC), were determined to assess the effects of O2 level and N2-fixation on degradation capabilities. Two issues were examined: (1) the influence of O2 level and nitrogen-limitation on DCE degradation kinetics and toxicity in both organisms, and (2) the relative utility of PP319 for contaminant degradation in bioreactors. When both organisms were grown under high O2 conditions (80% saturation in air), maximum transformation rates (Vmax) and apparent first-order rate constants (Vmax/KM) were lower compared with organisms grown under low O2 conditions (10% saturation in air) regardless of nitrogen level. Further, Vmax values were near zero in nitrogen-limited WT cultures when O2 was high (as expected), whereas PP319 retained moderate Vmax levels even at high O2 levels. In general, elevated O2 conditions reduced DCE degradation rates in OB3b, although the negative effects of O2 were less in PP319 than in the WT. Given that PP319 retained moderate DCE degradation rates under most O2 and copper conditions, the mutant appears to have some utility for biodegradation applications.

Biodegradation, Environmental↗

PubMed2003

Matrix metalloproteinase inhibitor regulates inflammatory cell migration by reducing ICAM-1 and VCAM-1 expression in a murine model of toluene diisocyanate-induced asthma.

BACKGROUND: Matrix metalloproteinase-9 (MMP-9) has been reported to play a crucial role in the transmigration of neutrophils, lymphocytes, and eosinophils. Neutrophils, eosinophils, and lymphocytes migrate from the blood to the lungs in response to inflammatory mediators produced in the airways and are subsequently released into the circulation. This traffic is mediated by adhesion molecules. However, little is known about the migration of inflammatory cells through the endothelial and epithelial basement membranes in toluene diisocyanate (TDI)-induced asthma. OBJECTIVES: An aim of this study was to evaluate the effect of MMP inhibitors on the expression of ICAM-1 and VCAM-1 in the migration of inflammatory cells in a murine model of TDI-induced asthma. METHODS: We used a murine model to investigate TDI-induced asthma to examine the possible involvement of ICAM-1 and VCAM-1 in the pathogenesis of that disease and the effect of MMP inhibitors on the expression of ICAM-1 and VCAM-1. RESULTS: In mice, the following typical pathophysiologic features develop in the lungs: increased numbers of inflammatory cells and increased expression of MMP-9, ICAM-1, and VCAM-1 mRNA and protein. Administration of MMP inhibitors reduced the increased numbers of inflammatory cells and the increased expression of ICAM-1 and VCAM-1 mRNA expression and protein. In addition, MMP inhibitors significantly abrogated the increased expression of IL-1beta, IL-4, and TNF-alpha mRNA in lung tissues and levels of IL-1beta, IL-4, and TNF-alpha in bronchoalveolar lavage fluids after TDI inhalation. CONCLUSIONS: These results suggest that MMP inhibitors regulate inflammatory cell migration by reducing ICAM-1 and VCAM-1 expression and possibly also by suppressing IL-1beta, IL-4, and TNF-alpha expression.

Animals↗