Effect of local molecular shape and anisotropic reactivity on the rate of diffusion-controlled reactions.

The role of distance-dependent anisotropic reactivity and molecular geometry in the vicinity of localized reaction centers in influencing the rate of bimolecular diffusion-controlled reactions is analyzed in detail, both analytically and numerically. The effect of local molecular shape is considered within the model of reflective hemispheres of small radius l(h) on the surfaces of otherwise spherical molecules of radius R (l(h) < R). The distance-dependent reactivity is modeled by reactive hemispheres of radius l(r) on top of the reflective hemispheres (l(r) < R). It is shown that the presence of the reflective hemispheres leads to a markedly large increase of the reaction rate. The maximum effect is ~R/l(h) > 1 times, as described by the ratio of local to average molecular curvature. It is observed for l(h) approximately R(l(r)/R)(1/2) > l(r). The effect of thickness of the reaction regions is described within the model of reactive cylinders of height l(r) and angular radius theta < 1. It is shown that the characteristic parameter in the expansion of the reaction rate as a function of l(r)/R is l(r)/(Rtheta(2)), and therefore, even for small relative thickness d = l(r)/theta, its effect on the rate is very strong, i.e., the conventional model of reactive patches, which assumes zero thickness of the reaction region, may considerably underestimate the reaction rate.     

Electrostatic potential of aminoacyl-tRNA synthetase navigates tRNA on its pathway to the binding site

In the first stage of a diffusion-controlled enzymatic reaction, aminoacyl-tRNA synthetases (aaRSs) interact with cognate tRNAs forming non-specific encounters. The aaRSs catalyzing the same overall aminoacylation reaction vary greatly in subunit organization, structural domain composition and amino acid sequence. The diffusional association of aaRS and tRNA was found to be governed by long-range electrostatic interactions when the homogeneous negative potential of tRNA fits to the patches of positive potential produced by aaRS; one patch for each tRNA substrate molecule. Considering aaRS as a molecule with anisotropic reactivity and on the basis of continuum electrostatics and Smoluchowski's theory, the reaction conditions for tRNA-aaRS diffusional encounters were formulated. The domains, categorized as enzymatically relevant, appeared to be non-essential for field sculpturing at long distances. On the other hand, a set of complementary domains exerts primary control on the aaRS isopotential surface formation. Subdividing the aaRS charged residues into native, conservative and non-conservative subsets, we evaluated the contribution of each group to long-range electrostatic potential. Surprisingly, the electrostatic potential landscapes generated by native and non-conservative subsets are fairly similar, thus suggesting the non-conservative subset is developed specifically for efficient tRNA attraction.     

Diffusion and reaction in the cell glycocalyx and the extracellular matrix

Many biologically important macromolecular reactions are assembled and catalyzed at the cell lipid-surface and thus, the extracellular matrix and the glycocalyx layer mediate transfer and exchange of reactants and products between the flowing blood and the catalytic lipid-surface. This paper presents a mathematical model of reaction–diffusion equations that simply describes the transfer process and explores its influence on surface reactivity for a prototypical pathway, the tissue factor (Tf) pathway of blood coagulation. The progressively increasing friction offered by the matrix and glycocalyx to reactants and to the product (coagulation factors X, VIIa and Xa) approaching the reactive surface is simulated and tested by solving the equations numerically with both, monotonically decreasing and constant diffusion profiles. Numerical results show that compared to isotropic transfer media, the anisotropic structure of the matrix and glycocalyx sharply decreases overall reaction rates and significantly increases the mean transit time of reactants; this implies that the anisotropy modifies the distribution of reactants. Results also show that the diffusional transfer, whether isotropic or anisotropic, influences reaction rates according to the order at which the reactants arrive at the boundary. Faster rates are observed when at least one of the reactants is homogeneously distributed before the other arrives at the boundary than when both reactants transfer simultaneously from the boundary.     

Molecular modeling of the three-dimensional architecture of the RNA component of yeast RNase MRP.

RNase mitochondrial RNA processing (MRP) is a ribonucleoprotein endoribonuclease that is involved in RNA processing events in both the nucleus and the mitochondria. The MRP RNA is both structurally and evolutionarily related to RNase P, the ribonucleoprotein endoribonuclease that processes the 5'-end of tRNAs. Previous analysis of the RNase MRP RNA by phylogenetic analysis and chemical modification has revealed strikingly conserved secondary structural elements in all characterized RNase MRP RNAs. Utilizing successive constraint modeling and energy minimization I derived a three-dimensional model of the yeast RNase MRP RNA. The final model predicts several notable features. First, the enzyme appears to contain two separate structural domains, one that is highly conserved among all MRP and P RNAs and a second that is only conserved in MRP RNAs. Second, nearly all of the highly conserved nucleotides cluster in the first domain around a long-range interaction (LRI-I). This LRI-I is characterized by a ubiquitous uridine base, which points into a cleft between these two structural domains generating a potential active site for RNA cleavage. Third, helices III and IV (the yeast equivalent of the To-binding site) model as a long extended helix. This region is believed to be the binding site of shared proteins between RNase P and RNase MRP and would provide a necessary platform for binding these seven proteins. Indeed, several residues conserved between the yeast MRP and P RNAs cluster in the central region of these helixes. Lastly, characterized mutations in the MRP RNA localize in the model based on their severity. Those mutations with little or no effect on the activity of the enzyme localize to the periphery of the model, while the most severe mutations localize to the central portion of the molecule where they would be predicted to cause large structural defects. Press.     

Effects of asymmetric dispersal and environmental gradients on the stability of host–parasitoid systems

We consider host–parasitoid systems spatially distributed on a row of patches connected by dispersal. We analyze the effects of dispersal frequency, dispersal asymmetry, number of patches and environmental gradients on the stability of the host–parasitoid interactions. To take into account dispersal frequency, the hosts and parasitoids are allowed to move from one patch to a neighboring patch a certain number of times within a generation. When this number is high, aggregation methods can be used to simplify the proposed initial model into an aggregated model describing the dynamics of both the total host and parasitoid populations. We show that as the number of patches increases less asymmetric parasitoid dispersal rates are required for stability. We found that the 'CV²>1 rule' is a valid approximation for stability if host growth rate is low, otherwise the general condition of stability we establish should be preferred. Environmental variability along the row of patches is introduced as gradients on host growth rate and parasitoid searching efficiency. We show that stability is more likely when parasitoids move preferentially towards patches where they have high searching efficiency or when hosts go mainly to patches where they have a low growth rate.     

Removal of basic and reactive dyes using ethylenediamine modified rice hull

Wastewaters from textile industries may contain a variety of dyes that have to be removed before their discharge into waterways. Rice hull, an agricultural by-product, was modified using ethylenediamine to introduce active sites on its surface to enable it to function as a sorbent for both basic and reactive dyes. The sorption characteristics of Basic Blue 3 (BB3) and Reactive Orange 16 (RO16) by ethylenediamine modified rice hull (MRH) were studied under various experimental conditions. Sorption was pH and concentration dependent. Simultaneous removal of BB3 and RO16 occurred at pH greater than 4. The kinetics of dye sorption fitted a pseudo-second order rate expression. Increase in agitation rate had no effect on the sorption of BB3 but increased uptake of RO16 on MRH. Decreasing particle size increased the uptake of dyes in binary dye solutions. Equilibrium data could be fitted into both the Langmuir and Freundlich isotherms. Maximum sorption capacities calculated from the Langmuir model are 14.68 and 60.24 mg/g for BB3 and RO16, respectively in binary dye solutions. This corresponds to an enhancement of 4.5 and 2.4 fold, respectively, compared to single dye solutions. MRH therefore has the potential of being used as an efficient sorbent for the removal of both dyes in textile wastewaters.     

Chlorinations catalyzed by chloroperoxidase occur via diffusible intermediate(s) and the reaction components play multiple roles in the overall process

The chlorination mechanism of the fungal enzyme chloroperoxidase (CPO) has been debated for (1) active site chlorination and (2) diffusible species mediated chlorination. Based upon the conversion of approximately 35 different substrates belonging to different reactive groups, it was found that substrate dimensions and topography had no pronounced effect on rates of CPO chlorination reaction. Epoxidation of indene was dependent on its concentration where as chlorination was not. Also, effective conversion was seen in the chlorination mixture for substrates that could not be epoxidized or sulfoxidized. Some insoluble substrates and certain molecules that exceeded the active site dimensions were chlorinated at rates comparable to the rates required for CPO's more natural substrate, monochlorodimedone. By terminating the enzymatic reaction with an active site ligand (azide), the amount of diffusible species was correlated to CPO in the reaction mixture. The preferential utilization of a substrate, earlier attributed to the active site, is found to be due to the specificity afforded by the reaction environment. It was found that the reaction medium components of peroxide, chloride and hydronium ions affected the reaction rates through varying roles in the enzymatic and non-enzymatic process. Besides these experimental evidences, key mechanistic and kinetic arguments are presented to infer that the final chlorine transfer occurs outside the active site via a diffusible species.     

Intrachain reactions of supercoiled DNA simulated by Brownian dynamics

We considered an irreversible biochemical intrachain reaction of supercoiled DNA as a random event that occurs, with certain probability, at the instant of collision between two reactive groups bound to distant DNA sites. Using the Brownian dynamics technique, we modeled this process for a supercoiled DNA molecule of 2.5 kb length in dilute aqueous solution at an NaCl concentration of 0.1 M. We calculated the mean reaction time tau(Sigma) as a function of the intrinsic second-order rate constant k(I), the reaction radius R, and the contour separation S of the reactive groups. At the diffusion-controlled limit (k(I) --> infinity), the kinetics of reaction are determined by the mean time tau(F) of the first collision. The dependence of tau(F) on R is close to inversely proportional, implying that the main contribution to the productive collisions is made by bending of the superhelix axis. At sufficiently small k(I), the mean reaction time can be satisfactory approximated by tau(Sigma) = tau(F)(app) + 1/(k(I)c(L)), where c(L) is the local concentration of one reactive group around the other, and tau is an adjustable parameter, which we called the apparent time of the first collision. The value of tau depends on R very weakly and is approximately equal to the mean time of the first collision caused by mutual reptation of two DNA strands forming the superhelix. The quasi-one-dimensional reptation process provides the majority of productive collisions at small k(I) values.     

Tolerance of understory plants subject to herbivory by roe deer

Classical foraging theory states that animals feeding in a patchy environment can maximise their long term prey capture rates by quitting food patches when they have depleted prey to a certain threshold level. Theory suggests that social foragers may be better able to do this if all individuals in a group have access to the prey capture information of all other group members. This will allow all foragers to make a more accurate estimation of the patch quality over time and hence enable them to quit patches closer to the optimal prey threshold level. We develop a model to examine the foraging efficiency of three strategies that could be used by a cohesive foraging group to initiate quitting a patch, where foragers do not use such information, and compare these with a fourth strategy in which foragers use public information of all prey capture events made by the group. We carried out simulations in six different prey environments, in which we varied the mean number of prey per patch and the variance of prey number between patches. Groups sharing public information were able to consistently quit patches close to the optimal prey threshold level, and obtained constant prey capture rates, in groups of all sizes. In contrast all groups not sharing public information quit patches progressively earlier than the optimal prey threshold value, and experienced decreasing prey capture rates, as group size increased. This is more apparent as the variance in prey number between patches increases. Thus in a patchy environment, where uncertainty is high, although public information use does not increase the foraging efficiency of groups over that of a lone forager, it certainly offers benefits over groups which do not, and particularly where group size is large.     

Ultrastructural organization of the surface of the cingulate cortex of the cerebrum in rats

In the cingulate cortex of rats the marginal glia is predominantly presented as fibrillar astrocytes, their bodies are situated immediately at the surface. Numerous axons, dendrites, synapses and myelinated fibers are often arranged near the very surface and are separated from it with only 1-2 thin processes of glial cells. Along the whole cortical surface one can see a limiting membrane--a layer of non-cellular substance, situating at the distance of 60-100 mcm from plasmalemmas of the marginal astrocytes. Using ruthenium red, it is possible to reveal the glycocalix layer on the surface of the limiting membrane, as well as cords of the electron opaque substance, that connect it with plasmolemma of the superficial astrocytes. Three types of the cingulate cortex surface are described in rats: superficial areas to which cells of the pia mater membrane adjoin; areas where cells of the pia mater membrane are situated at various distance from the cortical surface and areas of close adjoining of the right and left hemispheres of the cerebrum. Sometimes the cleft between the hemispheres is completely reduced, and narrow lamellar-like cells of the pia mater membrane are tightly inserted between the limiting membranes of both hemispheres or adjoin the blood vessel, situating between the hemispheres. At the surface numerous gap and desmosome-like junctions are observed. This is especially important at the border where the media are separated. At injection of neurotoxin 6-hydroxydopamine certain ultrastructural rearrangements are noted in cytoplasm of the marginal astrocytes, changes in the number and extension of intercellular junctions.(ABSTRACT TRUNCATED AT 250 WORDS)     

The apparently negatively cooperative phosphorylation of smooth muscle myosin at low ionic strength is related to its filamentous state

The correlation curve between phosphorylation and MgATPase activity suggests that the 20,000-dalton light chain of both heads of a smooth muscle myosin or heavy meromyosin (HMM) molecule must be phosphorylated before the MgATPase activity of either head can be activated by actin. The two heads of HMM appear to be phosphorylated randomly at equal rates, while those of myosin are phosphorylated in a negatively cooperative manner (Persechini, A., and Hartshorne, D.J. (1981) Science, 213, 1383-1385; Ikebe, M., Ogihara, S., and Tonomura, Y. (1982) J. Biochem. 91, 1809-1812). We have investigated the cause of this difference between HMM and myosin. We find that if myosin is first phosphorylated at high ionic strength (0.6 M KCl), where it is monomeric, and then assayed for MgATPase activity (in 0.05 M KCl), the data support a model where the two heads are phosphorylated randomly with equal rates (i.e. similarly to HMM). The correlation curves between MgATPase activity and dephosphorylation of fully phosphorylated myosin, both in a filamentous and monomeric state, are also best explained by a model where dephosphorylation of one head is sufficient to deactivate the entire molecule. With monomeric myosin, the dephosphorylation appears to occur randomly with equal rates, whereas with filamentous myosin the dephosphorylation appears to be negatively cooperative. The correlation between dephosphorylation of HMM and its MgATPase activity is more complex and is consistent with a positively cooperative dephosphorylation. Direct analyses of the time courses of phosphorylation of HMM and monomeric myosin show that a single exponential is sufficient to fit the data through greater than 90% of the reaction. However, when phosphorylation is carried out at low ionic strength (0.02 M KCl), where myosin is present as filaments, the time course consists of two exponential functions where the rate constant for the phosphorylation of one myosin head is 6-10 times greater than that for the other head which is located on the same molecule. This suggests that when myosin is polymerized into filaments the two previously indistinguishable heads either become nonequivalent or are subject to head-head interactions leading to a negatively cooperative phosphorylation reaction.     

Rates of structural fluctuations of lysozyme in the range of thermal unfolding transition

The hydrogen–deuterium exchange reaction for the tryptophan residues in lysozyme have been followed in 4.5M LiBr at pH 7.2 in the temperature range of the unfolding transition by measuring the transmittance change at 293 nm. The exchange reaction proceeded in three phases at low temperature for native protein. The first and the second phases were ascribed to the H-D exchange reactions of three relatively exposed tryptophan residues on the molecular surface. The third phase corresponded to the H-D exchange reaction of the three tryptophan residues buried in the interior of the molecule. The H-D exchange reaction proceeded in two phases near the melting temperature and in a single phase at high temperature, where almost all molecules are unfolded. The H-D exchange of three tryptophan residues buried in folded molecules was caused by fluctuation between the folded and unfolded structure of the protein molecule. The rates of such a fluctuation were determined from the rates of the exchange reaction at various temperatures. These rates agreed very well with those determined from the temperature-jump method. This means that a protein molecule in solution fluctuates between the N- and D-states at every temperature within the transition region, where the N-form is the tightly folded native structure and the D-form the randomly coiled chain. From measurements of thermal unfolding of ester-108-lysozyme and the binding constant of (NAG)₃ to ester-108-lysozyme, it was found that almost all cross-linked molecules are in the folded state near 50°C and pH 7.2 in 4.5M LiBr, where intact molecules are unfolded. We also studied the H-D exchange reaction of ester-108-lysozyme. In the temperature region of 43–50°C, about 70% of the exchangeable tryptophan residues of ester-108-lysozyme were exchanged within 1 s immediately after the mixing of D₂O, in spite of the fact that almost all molecules are in the folded state. This was considered the premelting of the surface of a corss-linked molecule.     

Functional involvement of the LFA-1/ICAM-1 adhesion system in the autologous mixed lymphocyte reaction

The integrin surface molecule termed lymphocyte functional antigen-1 (LFA-1), and its physiological ligand intercellular adhesion molecule-1 (ICAM-1), have been proven to play a relevant role in several immune reactions where cell-to-cell contact is required: these reactions include allogeneic mixed lymphocyte reaction (MLR) and direct cytotoxicity. In the present study, we show that monoclonal antibodies (mAbs) directed to LFA-1 as well as to ICAM-1 molecules are able to inhibit T cell proliferation in autologous MLR (AMLR). Such an in vitro reaction is generally considered a functional model of Ia-mediated immunocompetent cell cooperation, and is impaired in several pathological conditions. It is noteworthy that the LFA-1 molecule is largely represented on the T cell surface, whereas ICAM-1 is poorly expressed on resting T cells: autologous stimulation slightly increases ICAM-1 expression. Pretreatment studies indicate that the inhibitory effect of anti-ICAM-1 mAb on T cell proliferation in AMLR is exerted on responder T cells.     

Glutathione-dependent binding of a photoaffinity analog of agosterol A to the C-terminal half of human multidrug resistance protein

MRP1 is a 190-kDa membrane glycoprotein that confers multidrug resistance (MDR) to tumor cells. MRP1 is characterized by an N-terminal transmembrane domain (TMD(0)), which is connected to a P-glycoprotein-like core region (DeltaMRP) by a cytoplasmic linker domain zero (L(0)). It has been demonstrated that GSH plays an important role in MRP1-mediated MDR. However, the mechanism by which GSH mediates MDR and the precise roles of TMD(0) and L(0) are not known. We synthesized [(125)I]11-azidophenyl agosterol A ([(125)I]azidoAG-A), a photoaffinity analog of the MDR-reversing agent, agosterol A (AG-A), to photolabel MRP1, and found that the analog photolabeled the C-proximal molecule of MRP1 (C(932-1531)) in a manner that was GSH-dependent. The photolabeling was inhibited by anticancer agents, reversing agents and leukotriene C(4). Based on photolabeling studies in the presence and absence of GSH using membrane vesicles expressing various truncated, co-expressed, and mutated MRP1s, we found that L(0) is the site on MRP1 that interacts with GSH. This study demonstrated that GSH is required for the binding of an unconjugated agent to MRP1 and suggested that GSH interacts with L(0) of MRP1. The photoanalog of AG-A will be useful for identifying the drug binding site within MRP1, and the role of GSH in transporting substrates by MRP1.     

磁共振水成像对脊柱疾病诊断中的应用价值

目的:探讨磁共振水成像技术对脊柱疾病诊断的应用价值。方法:采用快速高级自旋回波(FASE)、重T2WI及脂肪抑制序列对300例病人检查行磁共振椎管水成像(MRmyelography,MRM)。结果:MRM显示正常25例,MRM异常275例,清楚显示原发病变与邻近脊髓腔、脊髓、神经根的相关关系。结论:MRM具有无创伤、无辐射、速度快,不需对比剂,患者易接受的特点。MRM与常规MRI图像结合可获得全面、客观的病变信息,MRM图像可取代X线脊髓造影和CT脊髓造影。     

Immortalized human hepatocytes as a tool for the study of hepatocytic (de-)differentiation

Primary human hepatocytes were immortalized by stable transfection with a recombinant plasmid containing the early region of simian virus (SV) 40. The cells were cultured in serum-free, hormonally defined medium during the immortalization procedure. Foci of dividing cells were seen after 3 months. Albumin- and fibrinogen-secreting cells were selected and cloned by limiting dilution to obtain homologous cell populations. The established IHH (immortalized human hepatocyte) cell lines were evaluated for their usefulness in studying the regulation of cell growth and of certain differentiated hepatocyte functions.IHH cells retain several differentiated features of normal hepatocytes. They display albumin secretion at a level comparable to cultured primary human hepatocytes (30 µg albumin/ml per day). A portion of the IHH cells are polarized, forming bile canaliculi-like vacuoles where exogeneous organic anions accumulate. The multidrug resistance (MDR) P-glycoprotein, known to be localized at the canalicular membrane, is also present in these vacuoles. The polarized features allowed the use of IHH cells for the study of localization of the newly characterized multidrug resistance protein MRP1. The homologues of MRP were found in hepatocytes, MRP1 and MRP2 (cMOAT), both functioning in ATP-dependent excretion of anionic conjugates. In differentiated hepatocytes, MRP1 expression is extremely low. In contrast, MRP1 is highly expressed in proliferating IHH cells, where it is localized in lateral membranes. A highly differentiated feature of short-term cultured primary hepatocytes which is not detectable in IHH cells is active uptake of the bile salt taurocholate. Furthermore, IHH cells secrete triglyceride (TG)-rich lipoproteins, apolipoprotein B (0.6 µg/ml per day), and apolipoprotein A-I (1 µg/ml per day). However, they secrete apoB-containing TG-rich lipoproteins mainly in the LDL density range, while short-term cultured primary hepatocytes mainly secrete TG-rich lipoproteins in the VLDL density range.In conclusion, functions that are rapidly lost in short-term hepatocyte cultures are, in general, not displayed by IHH cells. Immortalized human hepatocytes provide a valuable tool for studying the regulation of hepatocyte proliferation-related phenomena.     

A model for calculating the Bohr effect in hemoglobin equilibria.

The unusual aspects of the reaction of oxygen with hemoglobin are believed to be due to the free energy of the conformational change in the hemoglobin molecule upon oxygenation. The conformational free energy change due to oxygenation can be estimated in terms of the surface free energy of an emuslion droplet of the same size as the hemoglobin molecule. Calculations on the basis of this model lead to an equilibrium constant that varies with pH as in the acid and alkaline Bohr Effects, and that also varies with the ionic strength. The model used in this paper provides a simple way of estimating the variation of the equilibrium constant of a reaction involving a globular protein where the free energy of conformational changes can be evaluated in terms of surface properties.