Kinetic Explanation Research Articles

Conditions for partial nitrification in biofilm reactors and a kinetic explanation

Nitrification is a two-step process in which ammonia is incompletely oxidized by ammonia-oxidizing bacteria or archaea (AOB) to nitrite, which is then further oxidized to nitrate by nitrite-oxidizing bacteria (NOB). Literature reports show that segregation of initially coexisting ammonia and nitrite oxidizing populations co-immobilized in gel cubes and cultured in a set-up with three reactors in series (without recirculation) is attained. In those studies NOB were present and nitrite was oxidized mainly in the last reactor. We developed a mathematical model for immobilized biomass that allows for one-dimensional gradients of metabolites and changes of porosity within the gel due to growth. The model reproduced the experimentally observed compartmentalization under the conditions used by Noto et al. (Noto et al., 1998. Water Res 32(3): 769- 773), using standard kinetic parameters of nitrifying bacteria including free ammonia inhibition of AOB and NOB. The model predicted compartmentalization when the ammonium load was sufficiently high and liquid phase mixing sufficiently limited (close to plug-flow). Modeling results demonstrated that inhibition of NOB by free ammonia did not substantially contribute to the compartmentalization in biofilm reactors. Additional simulations identified the higher oxygen affinity of AOB as the key parameter leading to compartmentalization (i.e., partial nitrification) in artificial and natural biofilms since they enable the formation of oxygen gradients. As a result, a tendency for compartmentalization was found even at equal competitiveness.

Architecture of Clathrin Fullerene Cages Reflects a Geometric Constraint—the Head-to-Tail Exclusion Rule—and a Preference for Asymmetry

Fullerene cages have n trivalent vertices, 12 pentagonal faces, and ( n – 20)/2 hexagonal faces. The smallest cage in which all of the pentagons are surrounded by hexagons and thus isolated from each other has 60 vertices and is shaped like a soccer ball. The protein clathrin self-assembles into fullerene cages of a variety of sizes and shapes, including smaller ones with adjacent pentagons as well as larger ones, but the variety is limited. To explain the range of clathrin architecture and how these fullerene cages self-assemble, we proposed a hypothesis, the “head-to-tail exclusion rule” (the “Rule”). Of the 5769 small clathrin cage isomers with n ≤ 60 vertices and adjacent pentagons, the Rule permits just 15, three identified in 1976 and 12 others. A “weak version” of the Rule permits another 99. Based on cryo-electron tomography, Cheng et al. reported six raw clathrin fullerene cages. One was among the three identified in 1976. Here, (1) we identify the remaining five. (2) Four are new and are among the 12 others permitted by the Rule. (3) One, also new, is among the 99 weak version cages. (4) Of particular note, none of the remaining 5565 excluded cages has been identified. These findings provide powerful experimental confirmation of the Rule and the principle on which it is based. (5) Surprisingly, the newly identified clathrin cages are among the least symmetric of those permitted. (6) By devising a method for counting assembly paths, (7) we show that asymmetric cages can be assembled by larger numbers of paths, thus providing a kinetic explanation for the prevalence of asymmetric cages. (8) Finally, we show that operation during cage growth of the Rule greatly increases the likelihood of producing a closed fullerene cage, specifically one of those permitted, but efficient assembly still appears to require internal remodeling.

Phosphocreatine recovery kinetics following low- and high-intensity exercise in human triceps surae and rat posterior hindlimb muscles

Previous studies have suggested the recovery of phosphocreatine (PCr) after exercise is at least second-order in some conditions. Possible explanations for higher-order PCr recovery kinetics include heterogeneity of oxidative capacity among skeletal muscle fibers and ATP production via glycolysis contributing to PCr resynthesis. Ten human subjects (28 +/- 3 yr; mean +/- SE) performed gated plantar flexion exercise bouts consisting of one contraction every 3 s for 90 s (low-intensity) and three contractions every 3 s for 30 s (high-intensity). In a parallel gated study, the sciatic nerve of 15 adult male Sprague-Dawley rats was electrically stimulated at 0.75 Hz for 5.7 min (low intensity) or 5 Hz for 2.1 min (high intensity) to produce isometric contractions of the posterior hindlimb muscles. [(31)P]-MRS was used to measure relative [PCr] changes, and nonnegative least-squares analysis was utilized to resolve the number and magnitude of exponential components of PCr recovery. Following low-intensity exercise, PCr recovered in a monoexponential pattern in humans, but a higher-order pattern was typically observed in rats. Following high-intensity exercise, higher-order PCr recovery kinetics were observed in both humans and rats with an initial fast component (tau < 15 s) resolved in the majority of humans (6/10) and rats (5/8). These findings suggest that heterogeneity of oxidative capacity among skeletal muscle fibers contributes to a higher-order pattern of PCr recovery in rat hindlimb muscles but not in human triceps surae muscles. In addition, the observation of a fast component following high-intensity exercise is consistent with the notion that glycolytic ATP production contributes to PCr resynthesis during the initial stage of recovery.

Kinetic Theory Explanation of a Circulating Fluidized Bed Ring Structure near Choking

The objective of this technical note is to give an alternate explanation of the ring structure behavior for the flow of fluidized catalytic cracking (FCC) particles in a riser recently obtained in L. S. Fan’s laboratory. Their recent explanation of this phenomenon is due to the low velocity at the center. While indeed this is one of the causes of the high concentration near the center, we show that an additional driving force for the higher concentration at the center is the low granular temperature caused by the dissipation of random kinetic energy at the center of the riser. An approximate analytical solution applied to the flow of FCC particles obtained in Fan’s laboratory again produces a dip in the granular temperature in the center and hence a rise in the particle concentration. This phenomenon occurs as a result of the constancy of solids pressure in the developed region of the riser. It is the so-called shear-induced diffusion effect well-known for neutrally buoyant particles in liquids.

Differences in the Transient Kinetics of the Binding of d-ADP and its Mirror Image l-ADP to Human 3-Phosphoglycerate Kinase Revealed by the Presence of 3-Phosphoglycerate

L-Nucleosides comprise a new class of antiviral and anticancer agents that are converted in vivo by a cascade of kinases to pharmacologically active nucleoside triphosphates. The last step of the cascade may be catalyzed by 3-phosphoglycerate kinase (PGK), an enzyme that has low specificity for nucleoside diphosphate (NDP): NDP + 1,3-bisphosphoglycerate <--> NTP + 3-phosphoglycerate. Here we compared the kinetics of the formation of the complexes of human PGK with d- and its mirror image l-ADP and the effect of 3-phosphoglycerate (PG) on these by exploiting the fluorescence signal of PGK that occurs upon its interaction with nucleotide substrate. Two types of experiment were carried out: equilibrium (estimation of dissociation constants) and stopped-flow (transient kinetics of the interactions). We show that under our experimental conditions (buffer containing 30% methanol, 4 degrees C) PGK binds d- and l-ADP with similar kinetics. However, whereas PG increased the dissociation rate constant for d-ADP by a factor of 8-which is a kinetic explanation for "substrate antagonism"-PG had little effect on this constant for l-ADP. We explain this difference by a molecular modeling study that showed that the beta-phosphates of d- and l-ADP have different orientations when bound to the active site of human PGK. The difference is unexpected because l-ADP is almost as catalytically competent as d-ADP [ Varga, A. et al. (2008) Biochem. Biophys. Res. Commun. 366, 994-1000].

Dynamics of Trigger Factor Interaction with Translating Ribosomes

In all organisms ribosome-associated chaperones assist early steps of protein folding. To elucidate the mechanism of their action, we determined the kinetics of individual steps of the ribosome binding/release cycle of bacterial trigger factor (TF), using fluorescently labeled chaperone and ribosome-nascent chain complexes. Both the association and dissociation rates of TF-ribosome complexes are modulated by nascent chains, whereby their length, sequence, and folding status are influencing parameters. However, the effect of the folding status is modest, indicating that TF can bind small globular domains and accommodate them within its substrate binding cavity. In general, the presence of a nascent chain causes an up to 9-fold increase in the rate of TF association, which provides a kinetic explanation for the observed ability of TF to efficiently compete with other cytosolic chaperones for binding to nascent chains. Furthermore, a subset of longer nascent polypeptides promotes the stabilization of TF-ribosome complexes, which increases the half-life of these complexes from 15 to 50 s. Nascent chains thus regulate their folding environment generated by ribosome-associated chaperones.

Three Phase Biofilter Model for the Removal of Styrene through the Microbial Route

A biofilter of 0.05m diameter and 0.58m height has been studied for the removal of styrene from a simulated air-styrene mixture through the microbial route using Pseudomonas putida. Coconut coir and other waste materials have been used as the immobilization matrix for the microorganisms. Gas flow rate (0.005-0.01kgm-2s-1), micronutrient liquid flow rate (5-10 kgm-2s-1), inlet styrene concentration (0.05-1.20 gm-3) and packing size (de = 0.08 - 0.18cm) have been used as parameters. The kinetic parameters of growth rate equation of bacterial strain have been determined using batch type experimental data. A Monod type reaction model has been observed to be appropriate for the explanation of growth kinetics of the microorganisms. The values of the kinetic parameters used are Ks = 0.8gm-3, µmax = 45h-1. A three-phase deterministic mathematical model has been developed incorporating the synergistic effect of simultaneous reaction and interphase (gas to liquid to biofilm) mass transfer of styrene using experimentally determined kinetic parameters and mass transfer coefficients calculated using standard correlations. Simulated results based on the model have been compared with the experimental ones satisfactorily.

Restricted Active Site Docking by Enzyme-bound Substrate Enforces the Ordered Cleavage of Prothrombin by Prothrombinase

The preferred pathway for prothrombin activation by prothrombinase involves initial cleavage at Arg(320) to produce meizothrombin, which is then cleaved at Arg(271) to liberate thrombin. Exosite binding drives substrate affinity and is independent of the bond being cleaved. The pathway for cleavage is determined by large differences in V(max) for cleavage at the two sites within intact prothrombin. By fluorescence binding studies in the absence of catalysis, we have assessed the ability of the individual cleavage sites to engage the active site of Xa within prothrombinase at equilibrium. Using a panel of recombinant cleavage site mutants, we show that in intact prothrombin, the Arg(320) site effectively engages the active site in a 1:1 interaction between substrate and enzyme. In contrast, the Arg(271) site binds to the active site poorly in an interaction that is approximately 600-fold weaker. Perceived substrate affinity is independent of active site engagement by either cleavage site. We further show that prior cleavage at the 320 site or the stabilization of the uncleaved zymogen in a proteinase-like state facilitates efficient docking of Arg(271) at the active site of prothrombinase. Therefore, we establish direct relationships between docking of either cleavage site at the active site of the catalyst, the V(max) for cleavage at that site, substrate conformation, and the resulting pathway for prothrombin cleavage. Exosite tethering of the substrate in either the zymogen or proteinase conformation dictates which cleavage site can engage the active site of the catalyst and enforces the sequential cleavage of prothrombin by prothrombinase.

Microscopic kinetic determinants of macroscopic currents: insights from coupling and uncoupling of GABAA receptor desensitization and deactivation

The time course of inhibitory postsynaptic currents (IPSCs) reflects GABA(A) receptor deactivation, the process of current relaxation following transient activation. Fast desensitization has been demonstrated to prolong deactivation, and these processes have been described as being 'coupled'. However, the relationship between desensitization and deactivation remains poorly understood. We investigated the 'uncoupling' of GABA(A) receptor macroscopic desensitization and deactivation using experimental conditions that affected these two processes differently. Changing agonist affinity preferentially altered deactivation, changing agonist concentration preferentially altered macroscopic desensitization, and a pore domain mutation prolonged deactivation despite blocking fast desensitization. To gain insight into the mechanistic basis for coupling and uncoupling, simulations were used to systematically evaluate the interplay between agonist affinity, gating efficacy, and desensitized state stability in shaping macroscopic desensitization and deactivation. We found that the influence of individual kinetic transitions on macroscopic currents depended not only on model connectivity, but also on the relationship among transitions within a given model. In addition, changing single rate constants differentially affected macroscopic desensitization and deactivation, thus providing parsimonious kinetic explanations for experimentally observed uncoupling. Finally, these findings permitted development of an algorithmic framework for kinetic interpretation of experimental manipulations that alter macroscopic current properties.

CytochromebdfromAzotobacter vinelandii: Evidence for High-Affinity Oxygen Binding

Cytochrome bd from Azotobacter vinelandii is a respiratory quinol oxidase that is highly efficient in reducing intracellular oxygen concentration, thus enabling nitrogen fixation under ambient aerobic conditions. Equilibrium measurements of O2 binding to ferrous heme d in the one-electron-reduced form of the A. vinelandii enzyme give Kd(O2) = 0.5 microM, close to the value for the Escherichia coli cytochrome bd (ca. 0.3 microM); thus, both enzymes have similar, high affinity for oxygen. The reaction of the A. vinelandii cytochrome bd in the one-electron-reduced and fully reduced states with O2 is extremely fast approaching the diffusion-controlled limit in water. In the fully reduced state, the rate of O2 binding depends linearly on the oxygen concentration consistently with a simple, single-step process. In contrast, in the one-electron-reduced state the rate of oxygen binding is hyperbolic, implying a more complex binding pattern. Two possible explanations for the saturation kinetics are considered: (A) There is a spectroscopically silent prebinding of oxygen to an unidentified low-affinity saturatable site followed by the oxygen transfer to heme d. (B) Oxygen binding to heme d requires an "activated" state of the enzyme in which an oxygen channel connecting heme d to the bulk is open. This channel is permanently open in the fully reduced enzyme (hence no saturation behavior) but flickers between the open and closed states in the one-electron-reduced enzyme.

Solid-state ionics in energy converters

Solid-state ionics, based on fast ionic transport in solids and characterized by anomalously large diffusion coefficients of ions at room temperature and unipolar conductivity (0.05–0.1 S cm−1), assumed in the last few years great importance in the context of creation and subsequent explanation of mechanisms and kinetics of electrode processes during the work of chemical power sources (CPS). It is demonstrated that products of cathodic reactions possess ionic conduction in a solid phase.

Mechanism of Block of the hERG K + Channel by the Scorpion Toxin CnErg1

The scorpion toxin CnErg1 binds to human ether-a-go-go related gene (hERG) K + channels with a 1:1 stoichiometry and high affinity. However, in contrast to other scorpion toxin-ion channel interactions, the inhibition of macroscopic hERG currents by high concentrations of CnErg1 is incomplete. In this study, we have probed the molecular basis for this incomplete inhibition. High concentrations of CnErg1 had only modest effects on hERG gating that could not account for the incomplete block. Furthermore, the residual current in the presence of 1 μM CnErg1 had normal single channel conductance. Analysis of the kinetics of CnErg1 interaction with hERG indicated that CnErg1 binding is not diffusion-limited. A bimolecular binding scheme that incorporates an initial encounter complex and permits normal ion conduction was able to completely reproduce both the kinetics and steady-state level of CnErg1-hERG binding. This scheme provides a simple kinetic explanation for incomplete block; that is, relatively fast backward compared to forward rate constants for the interconversion of the toxin-channel encounter complex and the blocked toxin-channel complex. We have also examined the temperature-dependence of CnErg1 binding to hERG. The dissociation constant, K d, for CnErg1 increases from 7.3 nM at 22°C to 64 nM at 37°C (i.e., the affinity decreases as temperature increases) and the proportion of binding events that lead to channel blockade decreases from 70% to 40% over the same temperature range. These temperature-dependent effects on CnErg1 binding correlate with a temperature-dependent decrease in the stability of the putative CnErg1 binding site, the amphipathic α-helix in the outer pore domain of hERG, assayed using circular dichroism spectropolarimetry. Collectively, our data provides a plausible kinetic explanation for incomplete blockade of hERG by CnErg1 that is consistent with the proposed highly dynamic conformation of the outer pore domain of hERG.

The logistic (Verhulst) model for sigmoid microbial growth curves revisited

The logistic (Verhulst) growth model and its various current modifications are all based on the notion that the isothermal momentary growth rate is proportional to the momentary population’s size and the fraction of resources that are still available in the habitat. The model as originally formulated is inappropriate for growth curves that exhibit a long lag time when plotted on semi logarithmic coordinates. This problem can be eliminated by replacing the number of organisms as the independent variable in the equation by the logarithmic growth ratio. Moreover, the actual growth rate’s dependence on the population’s momentary size and residual resources might have scaling factors that are different from unity as the original model requires. When these are incorporated into the equation, the resulting generalized model can account for almost all observed sigmoid growth patterns, isothermal and non-isothermal, except for those that show a true peak. This is demonstrated with published growth data of various bacteria in different media, including some that exhibit a particularly long ‘lag time’. Since most sigmoid isothermal growth curves can be described by empirical models that have only three adjustable parameters, the expanded model, like other modified versions of Verhulst’s equation, does not abide by the principle of parsimony. However, its scaling factors provide a tentative kinetic explanation of a large class of observed growth patterns without invoking hypothetical universal relationships between growth parameters, as some current models do.

Influence of mercury traces on nitrogen post-discharge kinetics

This paper presents results obtained during spectroscopic observations of dc flowing post-discharges of a pure nitrogen plasma and a nitrogen plasma containing traces of mercury. The plasmas were studied by emission spectroscopy in the range of 300–850 nm where three nitrogen spectral systems were identified: NOβ bands were observed just above the noise level at the latest decay times over 35 ms. The discharge and post-discharge were studied in nitrogen with mercury traces at about 3.7 ppb. The total gas pressure was 700 Pa and the discharge current was kept at 150 mA. The relative populations of N2 (B 3Πg), N2 (C 3Πu) and N2+ (B 2Σ+u) states were calculated by the dependence on the post-discharge time in the range 3–40 ms. As the uncontrolled oxygen traces were recorded in the mercury flow, the experiment with a nitrogen–oxygen mixture at the same discharge conditions was added. The results showed strong quenching of the nitrogen pink afterglow by mercury traces. The kinetic explanation can be made through a strong depopulation of the level N2 (X 1Σ+g, v = 19) (creating the mercury 3P1 state) and of the levels N2 (X 1Σ+g, v = 28) or N2 (A 3Σ+u, v = 4) (creating the mercury 1S0 state). Both mercury states are origins of the UV light emission (254 and 185 nm, respectively) which could not be detected in our experimental setup.

Testing the transition state theory in stochastic dynamics of a genetic switch

Stochastic dynamics of chemical reactions in a mutually repressing two-gene circuit is numerically simulated. The circuit has a rich variety of different states when the kinetic change of DNA status is slow. The stochastic switching transition between those states are compared with the theoretical estimation of the switching rate derived from the idea similar to the transition state theory. Even though the circuit is kept far from equilibrium, the method gives a consistent explanation of the switching kinetics for a wide range of parameters. The transition state theory-like estimation, however, fails to describe transitions involving the state which has the extremely small numbers of protein molecules.

A new model of grain growth kinetics in UO 2 fuel pellets. Part 2: Normal grain growth kinetics controlled by pore migration

The grain growth model presented in Part 1 is further developed and applied to the analysis of the normal grain growth kinetics controlled by pore migration during fresh UO 2 thermal treatment (sintering). Additional consideration of fuel densification (i.e. porosity reduction) allows explanation of complicated grain growth kinetics characterised by non-integer growth exponents observed in recent tests.

Binding of Substrate in Two Conformations to Human Prothrombinase Drives Consecutive Cleavage at Two Sites in Prothrombin

Thrombin formation results from cleavage of prothrombin following Arg(271) and Arg(320). Both bonds are accessible for cleavage, yet the sequential action of prothrombinase on Arg(320) followed by Arg(271) is implied by the intermediate observed during prothrombin activation. We have studied the individual cleavage reactions catalyzed by prothrombinase by using a series of recombinant derivatives: wild type prothrombin (II(WT)) contained both cleavage sites; II(Q271) contained a single cleavable site at Arg(320); II(Q320) and II(A320) contained a single cleavable site at Arg(271); and II(QQ) was resistant to cleavage. Cleavage at Arg(320) in II(Q271) could account for the initial cleavage reaction leading to the consumption of either plasma prothrombin or II(WT), whereas cleavage at Arg(271) in either II(Q320) or II(A320) was found to be approximately 30-fold slower. Equivalent kinetic constants were obtained for three of the four possible half-reactions. Slow cleavage at Arg(271) in intact prothrombin resulted from an approximately 30-fold reduction in V(max). Thus, the observed pathway of bond cleavage by prothrombinase can be explained by the kinetic constants for the four possible individual cleavage reactions. II(Q320) was a competitive inhibitor of II(Q271) cleavage, and II(QQ) was a competitive inhibitor for each reaction with K(i) approximately K(m). The data are inconsistent with previous proposals and suggest a model in which substrates for each of the four possible half-reactions bind in a mutually exclusive manner and with equal affinity to prothrombinase in a cleavage site-independent way. Despite equivalent exosite binding interactions between all four possible substrates and the enzyme, we propose that ordered bond cleavage results from the constraints associated with the binding of substrates in one of two conformations to a single form of prothrombinase.

The Substrate -Membrane Interaction Constrains Bond Presentation and Cleavage in the Action of Prothrombinase on Prothrombin.

Thrombin formation is catalyzed by human prothrombinase almost exclusively through sequential cleavage at Arg320 followed by cleavage at Arg271 in prothrombin. Activation site mutants in which the individual sites have been rendered uncleavable indicate that Arg271 in intact prothrombin is hydrolyzed ~26-fold more slowly than Arg320. This finding provides an adequate kinetic explanation for the observed pathway of prothrombin activation by prothrombinase via the formation of meizothrombin. However, deviations from this behavior are implied by findings in the absence of membranes or with prothrombin species that are defective in membrane binding. We have investigated the contribution of the substrate-membrane interaction to the individual cleavage reactions by comparing the action of prothrombinase on a series of recombinant prothrombin derivatives expressed in the presence or absence of reduced vitamin K to yield either fully-carboxylated (Gla) or un-carboxylated (desGla) protein. The variants included wild type prothrombin (IIWT) containing both cleavage sites, IIQ271 with a single cleavable site at Arg320 and IIQ320 with a single cleavable site at Arg271. Quantitative analysis of 4-carboxyglutamic acid content established the intended extent of carboxylation for all Gla and desGla isoforms. Analysis of prothrombin activation by prothrombinase indicated a ~10 fold reduction in the rate of active product formation with desGla-IIWT compared to Gla-IIWT. Surprisingly, analysis by SDS-PAGE and quantitative densitometry revealed only a modest decrease (~ 2.5-fold) in the rate of consumption of desGla-IIWT. However, marked differences were evident in the intermediates produced. Bond cleavage of desGla-IIWT proceeded with a major contribution from cleavage at Arg271 followed by Arg320, in an order opposite to that observed with Gla-IIWT. Thus, the reduced rate of active product formation with desGla-IIWT reflects, in large part, the formation of a zymogen intermediate as a result of an altered order in which bonds are cleaved by prothrombinase. Comparison of the rates of cleavage of individual bonds in Gla and desGla versions of IIQ271 and IIQ320 revealed the kinetic basis for this change. Elimination of membrane binding led to a ~5 fold reduction in the rate of cleavage at Arg320 but surprisingly yielded a ~10-fold enhancement in cleavage at Arg271. Lack of Gla is not uniformly deleterious to all reactions of prothrombin activation. Compensating rate effects on the individual reactions imply a change in the restricted presentation of cleavage sites to the active site of Xa within prothrombinase upon the loss of the substrate-membrane interaction. Thus, substrate-membrane interactions appear to work in concert with exosite binding to modulate bond cleavage order by maximizing accessibility of the Arg320 bond to the active site while restricting that of Arg271. Loss of the membrane anchoring component leads to increased accessibility of the Arg271 site and a concomitant decrease in the rate of cleavage at Arg320. These observations have major implications for prothrombinase function on cell surfaces with limited binding sites for prothrombin, as well as the impact of warfarin therapy on prothrombinase function in vivo.

Electron Spin Resonance Studies of Kinetic Effects of Substituent and Crown Ether on Intramolecular Sodium Cation Exchange in 2,5-Di-Tert-Amyl- and 2,5-Di-Tert-Butyl-1,4-Benzoquinone Radical Anions

Abstract Upon an addition of crown ethers to a solution of 2,5-di-tert-amyl-1,4-benzoquinone (2,5-DAQ) and 2,5-di-tert-butyl-1,4-benzoquinone (2,5-DBQ) radical anions, the significant broadening of the two-center lines was observed in their electron spin resonance (ESR) spectra. The formation constants for the complexation of sodium cation with three kinds of crown ethers in 2,5-DAQ and 2,5-DBQ radical ion pairs were estimated, and the intramolecular two-site jumping rates of sodium cation complexed with crown ethers were determined. Differential effects of steric and crown ether were found in the intramolecular sodium cation migration. The stabilization of inclusion complex of sodium cation with crown ethers gives rise to the acceleration effects on the rates of intramolecular migration of cation/crown-ether complex. Based on the results, a kinetic explanation for the intramolecular sodium cation migration in the presence of crown ethers was given.

Sequence-dependent Kinetic Model for Transcription Elongation by RNA Polymerase

We present a kinetic model for the sequence-dependent motion of RNA polymerase (RNAP) during transcription elongation. For each NTP incorporation, RNAP has a net forward translocation of one base-pair along the DNA template. However, this process may involve the exploration of back-tracked and forward-tracked translocation modes. In our model, the kinetic rates for the reaction pathway, calculated based on the stabilities of the transcription elongation complex (TEC), necessarily lead to sequence-dependent NTP incorporation rates. Simulated RNAP elongation kinetics is in good agreement with data from transcription gels and single-molecule studies. The model provides a kinetic explanation for well-known back-tracked pauses at transcript positions with unstable TECs. It also predicts a new type of pause caused by an energetically unfavorable transition from pre to post-translocation modes.