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Meningitis, pathogenicity near criticality: the epidemiology of meningococcal disease as a model for accidental pathogens.

We formulate and analyse a model for infectious diseases transmitted by asymptomatic carriers finding, that if harmless and pathogenic strains of the infected agent compete, frequent outbreaks of the pathogenic strains can occur. A counterintuitively high number of clustered outbreaks at low pathogenicity in our model compares well with observations in diseases with severe and often fatal results for the host, as for example in meningitis. These clustered outbreaks can be described by the typical scaling behaviour around criticality. The epidemic model is a susceptible-infected-recovered system (SIR) for the harmless infective agent, acting as a background to a mutant strain Y which occasionally creates severely affected hosts X. The full system of SIRYX is described in the master equation framework, confirming limiting assumptions about a reduced YX-system with the SIR-system in stationarity. In this limiting case we can analytically show convergence to power law scaling typical for critical states, as well as the divergence of the variance of outbreaks near criticality. These large fluctuations of outbreaks of accidental pathogens as mutants of otherwise harmless commensal organisms is the challenging new feature of our model for future epidemiology of diseases like meningococcal disease.

Carrier State↗

Group selection of early replicators and the origin of life.

A major problem of the origin of life has been that of information integration. As Eigen (1971) has shown, a mutant distribution of RNAs replicating without the aid of a replicase cannot integrate sufficient information for the functioning of a higher-level unit utilizing several types of encoded enzymes. He proposed the hypercycle model to bridge this gap in prebiology. It can be shown by a nonlinear game model, incorporating mutation of a hypercycle, that the selection properties of hypercycles make them inefficient information integrators as they cannot compete favourably with all kinds of less efficient information carriers or mutationally coupled hypercycles. The stochastic corrector model is presented as an alternative resolution of Eigen's paradox. It assumes that replicative templates are competing within replicative compartments, whose selective values depend on the internal template composition via a catalytic acid in replication and "metabolism". The dynamics of template replication are analyzed by numerical simulation of master equations. Due to the stochasticity in replication and compartment fission the best compartment types recur. An Eigen equation at the compartment level is set up and calculated. Even selfish template mutants cannot destroy the system though they make it less efficient. The genetic information of templates is evaluated at both levels, and the higher (compartment) level successfully constrains the lower (template) one. Compartmentation together with stochastic effects is sufficient to integrate information dispersed in competitive replicators. Compartment selection is considered to be group selection of replicators. Implications for the origin of life are discussed.

Biological Evolution↗

Influence of the hypercycle on the error threshold: a stochastic approach.

The role of fluctuations on the error threshold of the hypercycle has been studied by a stochastic approach on a very simplified model. For this model, the master equation was derived and its unique steady state calculated. This state implies the extinction of the system. But the actual time necessary to reach the steady state may be astronomically long whereas for times of experimental interest the system could be near some quasi-stationary states. In order to explore this possibility a Gillespie simulation of the stochastic process has been carried out. These quasi-stationary states correspond to the deterministic steady states of the system. The error threshold shifts towards higher values of the quality factor Q. Moreover, information about the fluctuations around the quasi-stationary states is obtained. The results are discussed in relation to the deterministic states.

Animals↗

A theory on the origin of cooperativity in DNA renaturation kinetics.

Theoretical proof for the existence of cooperativity (experimental evidences have already reported in our earlier work: Biochem. Biophys. Res. Commun., 293 (2002) 870) in the phenomenon of DNA renaturation has been obtained using a generalized birth-death master equation approach. Results have shown that no special searching mechanism (i.e. a facilitated mechanism) was necessary for complementary DNA strands to find their correct-contacts but searching by a 'random jump' method was enough to explain not only the observed cooperativity phenomenon but also the magnitude of correct-contact-forming rate constant. Impact of cooperativity phenomenon on length of primers and their specificity in polymerase chain reaction has also been discussed.

Base Pairing↗

Enzymes as molecular automata: a stochastic model of self-oscillatory glycolytic cycles in cellular metabolism.

A stochastic model based on the molecular automata approach was developed to simulate the cyclic dynamics of glycolysis-gluconeogenesis in cell energy metabolism. The stochastic algorithm, based on Gillespie's method, simulates the master equation associated with any network of enzymatically controlled reactions. This model of the glycolytic-gluconeogenetic cycle was developed by assembling the stochastic kinetic reactions controlled by two enzymes: phosphofructokinase (PFKase) and fructose-1, 6-biphosphatase (FBPase). In order to obtain the hysteresis behaviour predicted by classical Sel'kov analysis, a minimum complexity is required in the allosteric regulations. This implies that the FBPase cannot have a single binding site for its transition to the inactive state (a minimum of two or three binding sites is necessary). Given the multimeric structure of this enzyme, this kinetic hypothesis is tenable. Other possible applications of the stochastic automata approach for different cases of channels, receptors and enzymatic control are suggested.

Animals↗

Dissociation energetics and mechanisms of leucine enkephalin (M + H)+ and (2M + X)+ ions (X = H, Li, Na, K, and Rb) measured by blackbody infrared radiative dissociation.

The dissociation kinetics of protonated leucine enkephalin and its proton and alkali metal bound dimers were investigated by blackbody infrared radiative dissociation in a Fourier-transform mass spectrometer. From the temperature dependence of the unimolecular dissociation rate constants, Arrhenius activation parameters in the zero-pressure limit are obtained. Protonated leucine enkephalin dissociates to form b(4) and (M-H(2)O)(+) ions with an average activation energy (E(a)) of 1.1 eV and an A factor of 10(10.5) s(-1). The value of the A factor indicates that these dissociation processes are rearrangements. The b(4) ions subsequently dissociate to form a(4) ions via a process with a relatively high activation energy (1.3 eV), but one that is entropically favored. For the cationized dimers, the thermal stability decreases with increasing cation size, consistent with a simple electrostatic interaction in these noncovalent ion-molecule complexes. The E(a) and A factors are indistinguishable within experimental error with values of approximately 1.5 eV and 10(17) s(-1), respectively. Although not conclusive, results from master equation modeling indicate that all these BIRD processes, except for b(4) --> a(4), are in the rapid energy exchange limit. In this limit, the internal energy of the precursor ion population is given by a Boltzmann distribution and information about the energetics and dynamics of the reaction are obtained directly from the measured Arrhenius parameters.

Journal Article↗

Dissociation energies of deoxyribose nucleotide dimer anions measured using blackbody infrared radiative dissociation.

The dissociation kinetics of deprotonated deoxyribose nucleotide dimers were measured using blackbody infrared radiative dissociation. Experiments were performed with noncovalently bound dimers of phosphate, adenosine (dAMP), cytosine (dCMP), guanosine (dGMP), thymidine (dTMP), and the mixed dimers dAMP.dTMP and dGMP.dCMP. The nucleotide dimers fragment through two parallel pathways, resulting in formation of the individual nucleotide or nucleotide + HPO3 ion. Master equation modeling of this kinetic data was used to determine threshold dissociation energies. The dissociation energy of (dGMP.dCMP-H)- is much higher than that for the other nucleotide dimers. This indicates that there is a strong interaction between the nucleobases in this dimer, consistent with the existence of Watson-Crick hydrogen bonding between the base pairs. Molecular mechanics simulations indicate that Watson-Crick hydrogen bonding occurs in the lowest energy structures of (dGMP.dCMP-H)-, but not in (dAMP.dTMP-H)-. The trend in gas phase dissociation energies is similar to the trend in binding energies measured in nonaqueous solutions within experimental error. Finally, the acidity ordering of the nucleotides is determined to be dTMP < dGMP < dCMP < dAMP, where dAMP has the highest acidity (largest delta Gacid).

Algorithms↗

Predicting peak shape in capillary zone electrophoresis: a generic approach to parametrizing peaks using the Haarhoff-Van der Linde (HVL) function.

We have found that the Haarhoff-Van der Linde (HVL) peak function provides excellent fitting to the shapes of CZE peaks. Initially designed for overloaded peaks in gas chromatography, this function describes a Gaussian peak when there is no peak distortion, and a triangular peak when there is no diffusional peak broadening. As such, it is ideal for CZE peaks distorted by electromigration dispersion (EMD). Fitting peaks with this function gives four parameters: three of them can be related to the Gaussian peak that would have been obtained in case of no EMD; the last one is a measure of the peak distortion. Using moving boundary theory, this peak distortion parameter may readily be expressed in terms of analyte and background electrolyte mobilities and concentrations, electric field, and sample injection length. The variance of an HVL peak is shown to be described by a universal function, and a master equation is presented. The region where EMD adds less than 10% to the Gaussian variance is shown to be very narrowly spread around the mobility matching condition. Under typical CZE operating conditions with an analyte at 1% of the BGE concentration, significant peak distortion is always present. Because the total peak variance is not an addition of the Gaussian and triangular contributions, the HVL model and the methodology introduced here should always be used to correctly combine variances.

Journal Article↗

Picosecond time-resolved fluorescence studies on excitation energy transfer in a histidine 117 mutant of the D2 protein of photosystem II in Synechocystis 6803.

The role of the peripheral reaction center chlorophyll a molecule associated with His117 of the D2 polypeptide in photosystem II was investigated in Synechocystis sp. PCC 6803 using a combination of steady state, pump-probe, and picosecond time-resolved fluorescence spectroscopy. Data were obtained from intact cells and isolated thylakoid membranes of a control mutant and a D2-H117T mutant, both of which lacked photosystem I. Excitation energy transfer and trapping were investigated by analyzing the data with a kinetic model that used an exact numerical solution of the Pauli master equation, taking into account available photosystem II spectral and structural information. The results of our kinetic analysis revealed the observed difference in excited-state dynamics between the H117T mutant and the control to be consistent with a retardation of the rate of excitation energy transfer from the peripheral chlorophyll of D2 (Chl at His117) to the electron-transfer pigments and an increase of the rate constant for charge recombination in the H117T mutant. The kinetic model was able to account for the experimentally observed changes in absorption cross section and fluorescence decay kinetics between the control and mutant by invoking changes in only these two rate constants. The results rule out quenching of excitation by a chlorophyll cation radical as a mechanism responsible for the lower efficiency of excitation energy utilization in the H117T mutant. Our work also demonstrates the importance of the chlorophyll associated with His117 of the D2 protein for excitation energy transfer to the PSII electron-transfer pigments and for the effective stabilization of the primary radical pair.

Chlorophyll↗

On computer simulation methods used to study models of two-component lipid bilayers.

We show that the use of a computer simulation method introduced to calculate the equilibrium thermodynamic properties of a model of a two-component lipid bilayer membrane [Freire, E., & Snyder, B. (1980) Biochemistry 19, 88-94] is incorrect. This is done by comparing the method to that of Metropolis, which has been proven to generate equilibrium distribution of that model, and by showing that back-processes have been omitted in the implicit master equation of Freire and Snyder. We have illustrated this explicitly by first generating distributions according to the method of Freire and Snyder and then allowing the system to relax via the Kawasaki method, which uses the technique of Metropolis. We show that relaxation to a different distribution occurs. We also remark that the cluster distributions generated by the Freire-Snyder method are substantially different from those occurring in equilibrium distributions. Thus, conclusions about equilibrium thermodynamic properties such as specific heats and transition enthalpies or about transport properties or cluster properties at equilibrium cannot be drawn from the results obtained by using this method. Finally, we point out that the method of Freire and Snyder is appropriate to so-called aggregation models, which have been used to study irreversible growth; and we suggest biological systems that might be simulated by their method.

Computers↗

Mechanism of OH formation from ozonolysis of isoprene: a quantum-chemical study.

The formation and unimolecular reactions of primary ozonides and carbonyl oxides arising from the O(3)-initiated reactions of isoprene have been investigated using density functional theory and ab initio molecular orbital calculations. The activation energies of O(3) cycloaddition to the two double bonds of isoprene are found to be comparable (3.3-3.4 kcal mol(-1)), implying that the initial two O(3) addition pathways are nearly equally accessible. The reaction energies of O(3) addition to isoprene are between -47 and -48 kcal mol(-1). Cleavage of primary ozonides to form carbonyl oxides occurs with a barrier of 11-16 kcal mol(-1) above the ground state of the primary ozonide, and the decomposition energies range from -5 to -13 kcal mol(-1). OH formation is shown to occur primarily via decomposition of the carbonyl oxides with the syn-positioned methyl (alkyl) group, which is more favorable than isomerization to form dioxirane (by 1.1-3.3 kcal mol(-1)). Using the transition-state theory and master equation formalism, we determine an OH yield of 0.25 from prompt and thermal decomposition of the carbonyl oxides.

Journal Article↗

Binding energies of water to sodiated valine and structural isomers in the gas phase: the effect of proton affinity on zwitterion stability.

The structures of valine (Val) and methylaminoisobutyric acid (Maiba) bound to a sodium ion, both with and without a water molecule, are investigated using both theory and experiment. Calculations indicate that, without water, sodiated Val forms a charge-solvated structure in which the sodium ion coordinates to the nitrogen and the carbonyl oxygen (NO-coordination), whereas Maiba forms a salt-bridge structure in which the sodium ion coordinates to both carboxylate oxygens (OO-coordination). The addition of a single water molecule does not significantly affect the relative energies or structures of the charge-solvated and salt-bridge forms of either cluster, although in Maiba the mode of sodium ion binding is changed slightly by the water molecule. The preference of Maiba to adopt a zwitterionic form in these complexes is consistent with its higher proton affinity. Experimentally, the rates of water evaporation from clusters of Val.Na(+)(H(2)O) and Maiba.Na(+)(H(2)O) are measured using blackbody infrared radiative dissociation (BIRD). The dissociation rates from the Val and Maiba complexes are compared to water evaporation rates from model complexes of known structure over a wide range of temperatures. Master equation modeling of the BIRD kinetic data yields a threshold dissociation energy for the loss of water from sodiated valine of 15.9 +/- 0.2 kcal/mol and an energy of 15.1 +/- 0.3 kcal/mol for the loss of water from sodiated Maiba. The threshold dissociation energy of water for Val.Na(+)(H(2)O) is the same as that for the charge-solvated model isomers, while the salt-bridge model complex has the same water threshold dissociation energy as Maiba.Na(+)(H(2)O). These results indicate that the threshold dissociation energy for loss of a water molecule from these salt-bridge complexes is approximately 1 kcal/mol less than that for loss of water from the charge-solvated complexes.

Butyrates↗

Energy migration in novel pH-triggered self-assembled beta-sheet ribbons.

Energy migration between tryptophan residues has been experimentally demonstrated in self-assembled peptide tapes. Each peptide contains 11 amino acids with a Trp at position 6. The peptide self-assembly is pH-sensitive and forms amphiphilic tapes, which further stack in ribbons (double tapes) and fibrils in water depending on the concentration. Fluorescence spectra, quenching, and anisotropy experiments showed that when the pH is lowered from 9 to 2, the peptide self-assembly buries the tryptophan in a hydrophobic and restricted environment in the interior of stable ribbons as expected on the basis of the peptide design. These fluorescence data support directly and for the first time the presence of such ribbons which are characterized by a highly packed and stable hydrophobic interior. In common with Trp in many proteins, fluorescence lifetimes are nonexponential, but the average lifetime is shorter at low pH, possibly due to quenching with neighboring Phe residues. Unexpectedly, time-resolved fluorescence anisotropy does not change significantly with self-assembly when in water. In highly viscous sucrose-water mixtures, the anisotropy decay at low pH was largely unchanged compared to that in water, whereas at high pH, the anisotropy decay increased significantly. We concluded that depolarization at low pH was not due to rotational diffusion but mainly due to energy migration between adjacent tryptophan residues. This was supported by a master equation kinetic model of Trp-Trp energy migration, which showed that the simulated and experimental results are in good agreement, although on average only three Trp residues were visited before emission.

Computer Simulation↗

Cycloalkene ozonolysis: collisionally mediated mechanistic branching.

Master equation calculations on a computational potential energy surface reveal that collisional stabilization at atmospheric pressure becomes important in the gas-phase ozonolysis of endocyclic alkenes for a carbon number between 8 and 15. Because the reaction products from endocyclic ozonolysis are tethered, this system is ideal for consideration of collisional energy transfer, as chemical activation is confined to a single reaction product. Collisional stabilization of the Criegee intermediate precedes collisional stabilization of the primary ozonide by roughly an order of magnitude in pressure. The stabilization of the Criegee intermediate leads to a dramatic transformation in the dominant oxidation pathway from a radical-forming process at low carbon number to a secondary ozonide-forming process at high carbon number. Secondary ozonide formation is important even for syn-isomer Criegee intermediates, contrary to previous speculation. We use substituted cyclohexenes as analogues for atmospherically important mono- and sesquiterpenes, which are major precursors for secondary organic aerosol formation in the atmosphere. Combining these calculations with literature experimental data, we conclude that the transformation from chemically activated to collisionally stabilized behavior most probably occurs between the mono- and sesquiterpenes, thus causing dramatically different atmospheric behavior.

Journal Article↗

Exciton migration in rigid-rod conjugated polymers: an improved Förster model.

The dynamics of interchain and intrachain excitation energy transfer taking place in a polyindenofluorene endcapped with perylene derivatives is explored by means of ultrafast spectroscopy combined with correlated quantum-chemical calculations. The experimental data indicate faster exciton migration in films with respect to solution as a result of the emergence of efficient channels involving hopping between chains in close contact. These findings are supported by theoretical simulations based on an improved Forster model. Within this model, the rates are expressed according to the Fermi golden rule on the basis of (i) electronic couplings that take account of the detailed shape of the excited-state wave functions (through the use of a multicentric monopole expansion) and (ii) spectral overlap factors computed from the simulated acceptor absorption and donor emission spectra with explicit coupling to vibrations (considered within a displaced harmonic oscillator model); inhomogeneity is taken into account by assuming a distribution of chromophores with different conjugation lengths. The calculations predict faster intermolecular energy transfer as a result of larger electronic matrix elements and suggest a two-step mechanism for intrachain energy transfer with exciton hopping along the polymer backbone as the limiting step. Injecting the calculated hopping rates into a set of master equations allows the modeling of the dynamics of exciton transport along the polyindenofluorene chains and yields ensemble-averaged energy-transfer rates in good agreement with experiment.

Journal Article↗

Structures and hydration enthalpies of cationized glutamine and structural analogues in the gas phase.

The structures of lithiated and sodiated glutamine, both with and without a water molecule, are investigated using experiment and theory. Loss of water from these complexes and from lithiated and sodiated complexes of asparagine methyl ester, asparagine ethyl ester, and glutamine methyl ester is probed with blackbody infrared radiative dissociation experiments performed over a wide temperature range. Threshold dissociation energies, E(o), for loss of a water molecule from these complexes are obtained from master equation modeling of these data. The values of E(o) are 63 +/- 1 and 53 +/- 1 kJ/mol for the lithiated and sodiated glutamine complexes, respectively. These values are similar to those for the nonzwitterionic model complexes and are in excellent agreement with calculated values. In contrast, water binding to the zwitterionic form is calculated to be significantly higher. These results indicate that glutamine in these lithiated and sodiated complexes with a water molecule are nonzwitterionic. Complexes with the asparagine side chain have slightly higher E(o) values than those with the glutamine side chain, a result consistent with more effective solvation of the metal ion due to the slightly longer side chain of glutamine. Calculations indicate that lithiated and sodiated glutamine are nonzwitterionic, with the metal ion interacting with the amine nitrogen and carbonyl oxygen from the amino acid backbone and the amide oxygen of the side chain. Addition of a water molecule does not affect the lowest-energy structure of lithiated glutamine, whereas, for sodiated glutamine, the lowest-energy zwitterionic and nonzwitterionic structures are essentially isoenergetic.

Cations↗

Binding energies of protonated betaine complexes: a probe of zwitterion structure in the gas phase.

The dissociation kinetics of proton-bound dimers of betaine with molecules of comparable gas-phase basicity were investigated using blackbody infrared radiative dissociation (BIRD). Threshold dissociation energies were obtained from these data using master equation modeling. For bases that have comparable or higher gas-phase basicity, the binding energy of the protonated base.betaine complex is approximately 1.4 eV. For molecules that are approximately 2 kcal/mol or more less basic, the dissociation energy of the complexes is approximately 1.2 eV. The higher binding energy of the former is attributed to an ion-zwitterion structure which has a much larger ion-dipole interaction. The lower binding energy for molecules that are approximately 2 kcal/mol or more less basic indicates that an ion-molecule structure is more favored. Semiempirical calculations at both the AM1 and PM3 levels indicate the most stable ion-molecule structure is one in which the base interacts with the charged quaternary ammonium end of betaine. These results indicate that the measurement of binding energies of neutral molecules to biological ions could provide a useful probe for the presence of zwitterions and salt bridges in the gas phase. From the BIRD data, the gas-phase basicity of betaine obtained from the kinetic method is found to be 239.2 +/- 1.0 kcal/mol. This value is in excellent agreement with the value of 239.3 kcal/mol (298 K) from ab initio calculations at the MP2/6-31+g** level. The measured value is slightly higher than those reported previously. This difference is attributed to entropy effects. The lower ion internal energy and longer time frame of BIRD experiments should provide values closer to those at standard temperature.

Journal Article↗

Hydration energies and structures of alkaline earth metal ions, M2+(H2O)n, n = 5-7, M = Mg, Ca, Sr, and Ba.

The evaporation of water from hydrated alkaline earth metal ions, produced by electrospray ionization, was studied in a Fourier transform mass spectrometer. Zero-pressure-limit dissociation rate constants for loss of a single water molecule from the hydrated divalent metal ions, M(2+)(H(2)O)(n) (M = Mg, Ca, and Sr for n = 5-7, and M = Ba for n = 4-7), are measured as a function of temperature using blackbody infrared radiative dissociation. From these values, zero-pressure-limit Arrhenius parameters are obtained. By modeling the dissociation kinetics using a master equation formalism, threshold dissociation energies (E(o)) are determined. These reactions should have a negligible reverse activation barrier; therefore, E(o) values should be approximately equal to the binding energy or hydration enthalpy at 0 K. For the hepta- and hexahydrated ions at low temperature, binding energies follow the trend expected on the basis of ionic radii: Mg > Ca > Sr > Ba. For the hexahydrated ions at high temperature, binding energies follow the order Ca > Mg > Sr > Ba. The same order is observed for the pentahydrated ions. Collisional dissociation experiments on the tetrahydrated species result in relative dissociation rates that directly correlate with the size of the metals. These results indicate the presence of two isomers for hexahydrated magnesium ions: a low-temperature isomer in which the six water molecules are located in the first solvation shell, and a high-temperature isomer with the most likely structure corresponding to four water molecules in the inner shell and two water molecules in the second shell. These results also indicate that the pentahydrated magnesium ions have a structure with four water molecules in the first solvation shell and one in the outer shell. The dissociation kinetics for the hexa- and pentahydrated clusters of Ca(2+), Sr(2+), and Ba(2+) are consistent with structures in which all the water molecules are located in the first solvation shell.

Journal Article↗