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PubMed2003

Structure and dynamics of interfacial water in an Lalpha phase lipid bilayer from molecular dynamics simulations.

Based on molecular dynamics simulations, an analysis of structure and dynamics is performed on interfacial water at a liquid crystalline dipalmitoylphosphatidycholine/water system. Water properties relevant for understanding NMR relaxation are emphasized. The first and second rank orientational order parameters of the water O-H bonds were calculated, where the second rank order parameter is in agreement with experimental determined quadrupolar splittings. Also, two different interfacial water regions (bound water regions) are revealed with respect to different signs of the second rank order parameter. The water reorientation correlation function reveals a mixture of fast and slow decaying parts. The fast (ps) part of the correlation function is due to local anisotropic water reorientation whereas the much slower part is due to more complicated processes including lateral diffusion along the interface and chemical exchange between free and bound water molecules. The 100-ns-long molecular dynamics simulation at constant pressure (1 atm) and at a temperature of 50 degrees C of 64 lipid molecules and 64 x 23 water molecules lack a slow water reorientation correlation component in the ns time scale. The (2)H(2)O powder spectrum of the dipalmitoylphosphatidycholine/water system is narrow and consequently, the NMR relaxation time T(2) is too short compared to experimental results.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2003

Protein structure and dynamics in nonaqueous solvents: insights from molecular dynamics simulation studies.

Protein structure and dynamics in nonaqueous solvents are here investigated using molecular dynamics simulation studies, by considering two model proteins (ubiquitin and cutinase) in hexane, under varying hydration conditions. Ionization of the protein groups is treated assuming "pH memory," i.e., using the ionization states characteristic of aqueous solution. Neutralization of charged groups by counterions is done by considering a counterion for each charged group that cannot be made neutral by establishing a salt bridge with another charged group; this treatment is more physically reasonable for the nonaqueous situation, contrasting with the usual procedures. Our studies show that hydration has a profound effect on protein stability and flexibility in nonaqueous solvents. The structure becomes more nativelike with increasing values of hydration, up to a certain point, when further increases render it unstable and unfolding starts to occur. There is an optimal amount of water, approximately 10% (w/w), where the protein structure and flexibility are closer to the ones found in aqueous solution. This behavior can explain the experimentally known bell-shaped dependence of enzyme catalysis on hydration, and the molecular reasons for it are examined here. Water and counterions play a fundamental and dynamic role on protein stabilization, but they also seem to be important for protein unfolding at high percentages of bound water.

Carboxylic Ester Hydrolases↗
PubMed1999

Do axial dynamic fixators really produce axial dynamization?

The use of dynamic external fixators for the treatment of long bone fracture is widespread and well accepted. It is claimed that dynamization, i.e. small micromovements of compression/distraction at the fracture site, can be produced by allowing sliding of an inner rod within an outer housing. However, as the forces on the fixator are not direct but transferred from the bone via bone pins, there is a bending moment on the fixator. This produces "self-locking" and effectively prevents axial movements. We have studied the effect of this moment on the binding properties of the Orthofix system. The amount of movement at a simulated fracture site allowed before this locking occurs was measured and its implications discussed. It would appear that true axial dynamization does not take place using this system.

External Fixators↗
PubMed2002

Ion permeation and selectivity of OmpF porin: a theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory.

Three different theoretical approaches are used and compared to refine our understanding of ion permeation through the channel formed by OmpF porin from Escherichia coli. Those approaches are all-atom molecular dynamics (MD) in which ions, solvent, and lipids are represented explicitly, Brownian dynamics (BD) in which ions are represented explicitly, while solvent and lipids are represented as featureless dielectrics, and Poisson-Nernst-Planck (PNP) electrodiffusion theory in which both solvent and local ion concentrations are represented as a continuum. First, the ability of the different theoretical approaches in reproducing the equilibrium average ion density distribution in OmpF porin bathed by a 1M KCl symmetric salt solution is examined. Under those conditions the PNP theory is equivalent to the non-linear Poisson-Boltzmann (PB) theory. Analysis shows that all the three approaches are able to capture the important electrostatic interactions between ions and the charge distribution of the channel that govern ion permeation and selectivity in OmpF. The K(+) and Cl(-) density distributions obtained from the three approaches are very consistent with one another, which suggests that a treatment on the basis of a rigid protein and continuum dielectric solvent is valid in the case of OmpF. Interestingly, both BD and continuum electrostatics reproduce the distinct left-handed twisted ion pathways for K(+) and Cl(-) extending over the length of the pore which were observed previously in MD. Equilibrium BD simulations in the grand canonical ensemble indicate that the channel is very attractive for cations, particularly at low salt concentration. On an average there is 1.55 K(+) inside the pore in 10mM KCl. Remarkably, there is still 0.17 K(+) on average inside the pore even at a concentration as low as 1microM KCl. Secondly, non-equilibrium ion flow through OmpF is calculated using BD and PNP and compared with experimental data. The channel conductance in 0.2M and 1M KCl calculated using BD is in excellent accord with the experimental data. The calculations reproduce the experimentally well-known conductance-concentration relation and also reveal an asymmetry in the channel conductance (a larger conductance is observed under a positive transmembrane potential). Calculations of the channel conductance for three mutants (R168A, R132A, and K16A) in 1M KCl suggest that the asymmetry in the channel conductance arises mostly from the permanent charge distribution of the channel rather than the shape of the pore itself. Lastly, the calculated reversal potential in a tenfold salt gradient (0.1:1M KCl) is 27.4(+/-1.3)mV (BD) and 22.1(+/-0.6)mV (PNP), in excellent accord with the experimental value of 24.3mV. Although most of the results from PNP are qualitatively reasonable, the calculated channel conductance is about 50% higher than that calculated from BD probably because of a lack of some dynamical ion-ion correlations.

Computer Simulation↗
PubMed1988

Mathematical modelling of dynamics and control in metabolic networks: VI. Dynamic bifurcations in single biochemical control loops.

A dynamic stability analysis of an extended form of the Goodwin equations is presented. The Goodwin equations are extended to include Michaelis-Menten kinetics for the removal of the end-product. Inclusion of saturation kinetic behavior substantially increases the likelihood of dynamic instability in this model control loop. Oscillations are found for reaction chains of low order, as low as second order, and low degrees of co-operativity, as low as v = 2, simultaneously, thus indicating that dynamic instability in this system exists for physiologically realistic parameter values. The branches of bifurcated solutions are computed numerically and unstable Hopf bifurcations are found. Further, solution branches from stable Hopf bifurcation points are found to "fold back", i.e. have periodic limit points, producing situations where multiple stable limit cycles exist.

Kinetics↗
PubMedDate not supplied

Simulation of long-term environmental dynamics of polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans using the dynamic multimedia environmental fate model and its implication to the time trend analysis of dioxins.

Long term environmental fate of polychlorinated dibenzo-p-dioxins (PCDD) and polychlorinated dibenzofurans (PCDF) were studied using the fugacity-based dynamic multimedia environmental fate model. New formulation about soil wind erosion into air was included into the model. Effect of process assumption, sensitivity analysis for parameters, and tentative validation against the measured sediment core analysis was performed. Mass fluxes between compartments were estimated by the dynamic modeling. From the model estimates, major mass fluxes coming from emission source were shown to go to the soil and water through wet/dry deposition, then go to degradation mainly in the soil and sediment. Major mass fluxes of TCDD and OCDD come from the impurities in CNP (Chlornitrofen) and PCP (Pentachlorophenol) directly into the soil. Consideration about multimedia environmental dynamics using the modeled mass fluxes was shown in the discussion.

Benzofurans↗
PubMed2003

Excited state charge-transfer dynamics study of poplar plastocyanin by ultrafast pump-probe spectroscopy and molecular dynamics simulation.

We have applied ultrafast pump-probe spectroscopy to investigate the excited state dynamics of the blue copper protein poplar plastocyanin, by exciting in the blue side of its 600-nm absorption band. The decay of the charge-transfer excited state occurs exponentially with a time constant of approximately 280 fs and is modulated by well visible oscillations. The Fourier transform of the oscillatory component, besides providing most of the vibrational modes found by conventional resonance Raman, presents additional bands in the low frequency region modes, which are reminiscent of collective motions of biological relevance. Notably, a high frequency mode at approximately 508 cm(-1), whose dynamics are consistent with that of the excited state and already observed for other blue copper proteins, is shown to be present also in poplar plastocyanin. This vibrational mode is reproduced by a molecular dynamics simulation involving the excited state of the copper site.

Computer Simulation↗
PubMed1998

Dynamic properties of individual water molecules in a hydrophobic pore lined with acyl chains: a molecular dynamics study.

Recently, a certain class of synthetic molecules has been shown to form ion channels, the pore of which is lined with hydrophobic acyl chains [M. Sokabe, in: F. Oosawa, H. Hayashi, T. Yoshioka (Eds.), Transmembrane Signaling and Sensation, JSSP/VNU Science Press BV, Tokyo, 1984, p. 119; F. Hayashi, M. Sokabe, M. Takagi, K. Hayashi, U. Kishimoto, Biochim. Biophys. Acta, 510 (1978) 305; M.J. Pregel, L. Jullien, J. Canceill, L. Lacombe, J.M. Lehn, J. Chem. Soc. Perkin Trans., 2 (1995) 417; Y. Tanaka, Y. Kobuke, M. Sokabe, Angew. Chem. Int. Ed. Engl., 34 (1995) 693; M. Sokabe, Z. Qi, K. Donowaki, H. Ishida, K. Okubo, Biophys. J., 70 (1996) A201; H. Ishida, K. Donowaki, Y. Inoue, Z. Qi, M. Sokabe, Chem. Lett. (1997) p. 953]. As an initial step towards understanding the physical mechanisms of ion permeation across such a hydrophobic pore, systematic molecular dynamics simulations were performed to investigate dynamic and energetic properties of water molecules inside the pore using a dimer of alanine-N'-acylated cyclic peptide as a channel model. Dynamic energy profiles for water molecules indicated that the energy barrier at the middle region of the pore is approximately 2-3 kcal/mol higher than that in the cap water region which was defined as a vicinity region of the channel entrance. Energetics analyses demonstrated that the mutual interactions among intrapore water molecules are the major factor to give favorable interaction (negative energy contribution) for themselves. The pore, despite being lined with acyl chains, has a favorable van der Waals interaction with intrapore water molecules. These results may help to explain why water-filled channels can be formed by the hydrophobic helices in natural channels.

Journal Article↗
PubMed1995

Dynamics of the dihydrofolate reductase-folate complex: catalytic sites and regions known to undergo conformational change exhibit diverse dynamical features.

Backbone and tryptophan side-chain dynamics of uniformly 15N-labeled Escherichia coli dihydrofolate reductase were determined for the binary folate complex. The 15N T1 and T2 relaxation times and [1H]-15N heteronuclear NOEs were measured for 118 protonated backbone nitrogen atoms. The generalized order parameter (S2), the effective correlation time for internal motions (tau e), and the contribution to spin-spin relaxation through 15N exchange broadening (Rex) were determined for each residue by model-free analysis. Back-calculation of the relaxation rates for each resonance showed that the calculated dynamical parameters accurately predict the experimental data. Diverse dynamical features were evident in the DHFR backbone. Six sites exhibited order parameters significantly below the weighted mean S2 value (for the complex) of 0.81 +/- 0.002: residues G67 and D69 of the adenosine binding domain, and "hinge" residues K38 and V88, exhibited low S2 (0.29 < or = S2 < or = 0.6) and high tau e values (700 ps < or = tau e < or = 2 ns), as did sites within the beta A-alpha B loop and the beta F-beta G loop. Thus, large amplitude backbone motions, on the picosecond and nanosecond time scales, occurred at regions implicated in transition-state stabilization and in ligand-dependent conformational change. Significant Rex values (> or = 1 s-1) were determined for 45% of assigned resonances, many of which arise from residues surrounding the folate binding site. The mean S2 values of the occupied folate binding site and the unoccupied NADPH binding site were similar, indicating the backbone of the latter is at least as conformationally restricted as that of the occupied folate site. We conclude that the observed time-dependent structural fluctuations of the binary complex are in fact associated with catalytic properties of the molecule.

Amino Acid Sequence↗
PubMed1990

Molecular dynamics study of the structure and dynamics of a protein molecule in a crystalline ionic environment, Streptomyces griseus protease A.

A large-scale molecular dynamics simulation of the behavior of a serine protease (Streptomyces griseus protease A) in a crystalline environment has been performed. All atoms (including hydrogens) of two protein molecules and the surrounding solvent of crystallization, consisting of both water and salt ions, were explicitly represented, and a relatively long range of interactions (up to 15 A) were included. The simulation is the longest so far reported for a protein in such an environment (60 ps). The use of the full crystalline environment allows a direct comparison of the structure and dynamic properties of the protein and surrounding solvent to be made with the experimental X-ray structure. Here we report the comparison of the protein structures and analyze the energetics of the system, including interaction with the aqueous environment. Subsequent papers will deal with other aspects of the simulation. The overall root mean square differences between the time-averaged molecular dynamics structure and that from crystallography, for all well-ordered, non-hydrogen atoms, are 1.67 and 1.25 A for the two molecules taken as the asymmetric unit. An extensive analysis of the conformation of substructural elements and individual residues and their deviation from experiment has revealed a strong influence of the ionic medium on their behavior. Implications of the results for free energy calculations and for future directions are also discussed.

Algorithms↗
PubMed2003

Dynamics and entropy of a calmodulin-peptide complex studied by NMR and molecular dynamics.

All-atom, explicit water molecular dynamics simulations of calcium-loaded calmodulin complexed with a peptide corresponding to the smooth muscle myosin light chain kinase target were carried out at 295 and 346 K. Amide and side chain methyl angular generalized order parameters were calculated and analyzed in the context of the protein's structure and dynamics. The agreement between amide order parameters measured by NMR and those from the simulations was found to be good, especially at the higher temperature, indicating both better convergence for the latter and excellent transferrability of the CHARMM parameters to the higher temperature. Subtle dynamical features such as helix fraying were reproduced. A large range of order parameters for the nine calmodulin methionines was observed in the NMR, and reproduced quite well in the simulations. The major determinant of the methionine order parameter was found to be the proximity to side chains of aromatic residues. An upper bound estimate of the difference in backbone entropy between loop and helical regions was extracted from the order parameters using a model of motion in an effective potential. Although loop regions are more flexible than helical regions, it was found that the entropy loss per residue upon folding was only approximately 20% less for loops than for helices. Pairwise correlated motions, which could significantly lower entropy estimates obtained from order parameter analysis alone, were found to be largely absent.

Amides↗
PubMed2003

Structure and dynamics of metal ions in solution: QM/MM molecular dynamics simulations of Mn(2+) and V(2+).

Structural and dynamical properties of the transition metal ions V(2+) and Mn(2+) in aqueous solution, resulting from combined quantum mechanical (QM)/molecular mechanical (MM) molecular dynamics (MD) simulations have been compared. The necessity of polarization functions on the ligand's oxygen for a satisfactory description of such ions in aqueous solution is shown using V(2+) as test case. Radial distribution functions, coordination number distributions, and several angle distributions were pursued for a detailed structural comparison of the first hydration shells. Dynamical properties, such as the librational and vibrational motions of water molecules were evaluated by means of velocity autocorrelation functions. Approximative normal coordinate analyses were employed to calculate the rotational frequencies and vibrational motions around the three principal axes. The very low exchange rates for the first shell water exchanges only allow an investigation of the water exchange processes in the second shell, which take place within the picosecond range.

Cations, Divalent↗
PubMed2005

Conformational dynamics of the nicotinic acetylcholine receptor channel: a 35-ns molecular dynamics simulation study.

The nicotinic acetylcholine receptor (AChR) is the paradigm of ligand-gated ion channels, integral membrane proteins that mediate fast intercellular communication in response to neurotransmitters. A 35-ns molecular dynamics simulation has been performed to explore the conformational dynamics of the entire membrane-spanning region, including the ion channel pore of the AChR. In the simulation, the 20 transmembrane (TM) segments that comprise the whole TM domain of the receptor were inserted into a large dipalmitoylphosphatidylcholine (DPPC) bilayer. The dynamic behavior of individual TM segments and their corresponding AChR subunit helix bundles was examined in order to assess the contribution of each to the conformational transitions of the whole channel. Asymmetrical and asynchronous motions of the M1-M3 TM segments of each subunit were revealed. In addition, the outermost ring of five M4 TM helices was found to convey the effects exerted by the lipid molecules to the central channel domain. Remarkably, a closed-to-open conformational shift was found to occur in one of the channel ring positions in the time scale of the present simulations, the possible physiological significance of which is discussed.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2006

Dynamic thermodynamic and dynamic kinetic resolution of 2-lithiopyrrolidines.

Dynamic resolution has been studied as a method for the asymmetric synthesis of 2-substituted pyrrolidines. Highly enantioselective electrophilic substitutions of racemic 2-lithiopyrrolidines in the presence of a chiral ligand have been achieved. The organolithium compounds were prepared by tin-lithium exchange from the corresponding tributylstannanes and n-butyllithium or by deprotonation of N-(tert-butyloxycarbonyl)pyrrolidine with sec-butyllithium. A range of N-substituents and chiral ligands were investigated for the dynamic resolution. Electrophilic quench of the resolved diastereomeric 2-lithiopyrrolidine-chiral ligand complexes provided the enantiomerically enriched 2-substituted pyrrolidines. With N-alkyl derivatives, the resolution occurs conveniently at (or just below) room temperature and either enantiomer of the product can be formed by appropriate choice of the chiral ligand. The asymmetric induction occurs as a result of a thermodynamic preference for one of the diastereomeric complexes. The minor complex was found to have a faster rate of reaction with the electrophile. The use of N-allylic derivatives provides a means to prepare the N-unsubstituted pyrrolidine products. Best results were obtained with the N-2,3-dimethylbut-2-enyl derivative, and this N-substituent could be cleaved using 1-chloroethyl chloroformate. With N-Boc-2-lithiopyrrolidine, the enantioselectivity arises by a kinetic resolution and high levels of asymmetric induction in the presence of excess n-butyllithium can be obtained. Dynamic kinetic resolution of the N-Boc derivative is limited in the scope of electrophile that can be used.

Journal Article↗
PubMed2005

Examination of dynamic facilitation in molecular dynamics simulations of glass-forming liquids.

Using data from molecular dynamics computer simulations of the one-component Dzugutov liquid and of BKS silica in metastable equilibrium supercooled states, we examine ideas introduced by Garrahan and Chandler (GC) in their dynamic facilitation (DF) model of the glass transition. Utilizing a recently introduced measure of DF, we find that DF is important for particle motion in both the supercooled Dzugutov liquid and in the BKS silica melt, that mobility propagates continuously, and that this effect becomes increasingly pronounced with decreasing T. We show that, in both systems, dynamic facilitation is strongest on the time scale of the late-beta relaxation, where clusters of highly mobile neighboring particles escaping from their cages are largest and, except for the silicon atoms in BKS silica, stringlike motion is most prominent. By comparing the two systems, we show that the temperature dependence of one measure of DF as the mode-coupling temperature is approached from high temperature is similar, once the temperature dependence of the structural relaxation time in each system is scaled out.

Journal Article↗
PubMed2005

Diffusion dynamics of the Li+ ion on a model surface of amorphous carbon: a direct molecular orbital dynamics study.

Diffusion processes of the Li+ ion on a model surface of amorphous carbon (Li+C96H24 system) have been investigated by means of the direct molecular orbital (MO) dynamics method at the semiempirical AM1 level. The total energy and energy gradient on the full-dimensional AM1 potential energy surface were calculated at each time step in the dynamics calculation. The optimized structure, where Li+ is located in the center of the cluster, was used as the initial structure at time zero. The dynamics calculation was carried out in the temperature range 100-1000 K. The calculations showed that the Li+ ion vibrates around the equilibrium point below 200 K, while the Li+ ion moves on the surface above 250 K. At intermediate temperatures (300 K < T < 400 K), the ion moves on the surface and falls in the edge regions of the cluster. At higher temperatures (600 K < T), the Li+ ion transfers freely on the surface and edge regions. The diffusion pathway of the Li+ ion was discussed on the basis of theoretical results.

Journal Article↗
PubMed2006

Dynamic fluctuations and spatial inhomogeneities in poly(N-isopropylacrylamide)/clay nanocomposite hydrogels studied by dynamic light scattering.

The contributions of the dynamic fluctuations and the frozen-in inhomogeneities to the total light scattering intensity observed in poly(N-isopropylacrylamide)/clay nanocomposite hydrogels were analyzed by applying the nonergodic method proposed by Pusey and van Megen. Approximately 90% of the total scattering intensity corresponds to the frozen-in component. The scattering intensity of the fluctuating component is smaller by far than that of a pure clay suspension, indicating that the thermal fluctuations of the clay particles are largely suppressed upon network formation. Accordingly, the fluctuating component consists of two contributions: one due to the polymer chains and the other, smaller one representing the residual mobility of the clay particles. The latter depends on how tightly the clay particles are fixed in the network. The dynamic features of the nanocomposite hydrogels are described by two relaxation modes. The fast one is purely diffusive and can be related to a dynamic correlation length of 6-8 nm, which is similar to that of a corresponding polymer solution. The relaxation time of the slow mode varies appreciably with sample position even though the data had been treated with the nonergodic method.

Journal Article↗
PubMed2006

Local density inhomogeneities and dynamics in supercritical water: A molecular dynamics simulation approach.

Molecular dynamics atomistic simulations in the canonical ensemble (NVT-MD) have been used to investigate the "Local Density Inhomogeneities and their Dynamics" in pure supercritical water. The simulations were carried out along a near-critical isotherm (Tr = T/Tc = 1.03) and for a wide range of densities below and above the critical one (0.2 rho(c) - 2.0 rho(c)). The results obtained reveal the existence of significant local density augmentation effects, which are found to be sufficiently larger in comparison to those reported for nonassociated fluids. The time evolution of the local density distribution around each molecule was studied in terms of the appropriate time correlation functions C(Delta)rhol(t). It is found that the shape of these functions changes significantly by increasing the density of the fluid. Finally, the local density reorganization times for the first and second coordination shell derived from these correlations exhibit a decreasing behavior by increasing the density of the system, signifying the density effect upon the dynamics of the local environment around each molecule.

Journal Article↗