Influence of fractal kinetics on molecular recognition

Molecular recognition is a central issue for nearly every biological mechanism. The analysis of molecular recognition to has been conducted within the framework of classical chemical kinetics, in which the kinetic orders of a reaction have positive integer values. However, recent theoretical and experimental advances have shown that the assumption inherent in this classical framework are invalid under a variety of conditions in shown that the assumptions inherent in this classical framework are invalid under a variety of condition in which the reaction environment may be considered nonideal. A good example is provided by reactions that are spatially constrainal and diffusion limited. Bio molecular reactions confined within two-dimensional membranes, one-dimensional channels or fractal surfaces in general exhibit kinetic orders that are noninteger. An appropriate framework for the study of these nonideal phenomena is provided by the Power-Law formalism, which includes as special cases the Mass-Action formalism of chemical kinetics and the Michaelis–Menten formalism of enzyme kinetics. The Power-Law formalism is an appropriate representation not only for fractal kinetics per se, but also for other nonideal kinetic phenomena, provided the range of variation in concentration is not too large. After defining some elementary concepts of molecular recognition, and showing how these are manifested in classical kinetic terms, this paper contrasts the implications of classical and fractal kinetics in a few simple cases. The principal distinction lies in the ability of fractal kinetics to nonlinearly transform, rather than proportionally transmit, the input S/N ratio. As a consequence, fractal kinetics create a threshold for the input signal below which no recognition occurs and above which amplified recognition takes place. Thus, fractal kinetics implies an intimate relationship between design of the physiological mechanisms regulating the environment of the process and design of the molecular process itself. These results also suggest that recognition in the presence of a favorable input ration would emphasize rapid reactions, while recognition in the presence of an unfavorable input ratio would emphasize slow reactions.     

A probabilistic framework for the exploration of enzymatic capabilities based on feasible kinetics and control analysis

BackgroundAnalysis of limiting steps within enzyme-catalyzed reactions is fundamental to understand their behavior and regulation. Methods capable of unravelling control properties and exploring kinetic capabilities of enzymatic reactions would be particularly useful for protein and metabolic engineering. While single-enzyme control analysis formalism has previously been applied to well-studied enzymatic mechanisms, broader application of this formalism is limited in practice by the limited amount of kinetic data and the difficulty of describing complex allosteric mechanisms.MethodsTo overcome these limitations, we present here a probabilistic framework enabling control analysis of previously unexplored mechanisms under uncertainty. By combining a thermodynamically consistent parameterization with an efficient Sequential Monte Carlo sampler embedded in a Bayesian setting, this framework yields insights into the capabilities of enzyme-catalyzed reactions with modest kinetic information, provided that the catalytic mechanism and a thermodynamic reference point are defined.ResultsThe framework was used to unravel the impact of thermodynamic affinity, substrate saturation levels and effector concentrations on the flux control and response coefficients of a diverse set of enzymatic reactions.ConclusionsOur results highlight the importance of the metabolic context in the control analysis of isolated enzymes as well as the use of statistically sound methods for their interpretation.General SignificanceThis framework significantly expands our current capabilities for unravelling the control properties of general reaction kinetics with limited amount of information. This framework will be useful for both theoreticians and experimentalists in the field.     

Electron transfer reactions between quinols and quinones in aqueous and aprotic media

The pathways of redox equilibration of quinols and quinones have been investigated. The rate-limiting reaction involves the couple QH^?/QH^· of the reducing quinol and the couple Q^?/Q of the oxidising quinone. Three general mechanistic points may be surmised: (i) protonation/deprotonation reactions are not rate-limiting; (ii) all transfers occur in one-equivalent steps; (iii) electron transfers, but not hydrogen atom transfers, are the dominant features. In aprotic media, no rapid route of equilibration is available since the ionic species which are necessary for thermodynamically feasible routes of electron transfer cannot exist to any great extent. The relation of these results to models of biological quinone systems is discussed.     

Reduction of intrinsic kinetic and thermodynamic barriers for enzyme-catalysed proton transfers from carbon acid substrates

Many enzymes catalyse the heterolytic abstraction of the alpha-proton from a carbon acid substrate. Gerlt and Gassman have applied Marcus formalism to such proton transfer reactions to argue that transition states for concerted general acid-general base catalysed enolization at enzyme active sites occur late on the reaction coordinate (J. Am. Chem. Soc. 115 (1993) 11552). We postulate that as an enzyme evolves, it may decrease deltaG++ for a proton transfer step associated with substrate enolization by following the path of steepest descent on the two-dimensional surface corresponding to deltaG++, as defined by Marcus formalism. We show that for an enzyme that has decreased deltaG++ following the path of steepest descent, the values of the intrinsic kinetic (deltaG++(int,E)) and thermodynamic (deltaG(E)0) barriers for proton transfer reactions on the enzyme may be predicted from the known values of deltaG++(int,N) and deltaG(N)0 for the corresponding non-enzymic reaction and the free energy of activation on the enzyme (deltaG++(E)). In addition, the enzymic transition state will occur later on the reaction coordinate than the corresponding non-enzymic transition state (i.e. x++(E)>x++(N)) if the condition (6 - square root 2)/82deltaG++(int,N).     

Theoretical formalism for bead movement powered by single two-headed motors in a motility assay

Kinesins and dyneins are protein motors that can use the free energy of ATP hydrolysis to carry a cargo and move uni-directionally along a microtubule filament. The purpose of this paper is to derive the formalism connecting the ATP-driven translocation reactions of these motors on microtubule filaments and the movement of the bead carried by the motor in a motility assay in which the bead is clamped at an arbitrary constant force. The formalism is thus useful in elucidating the load-dependent kinetic mechanism of the free-energy transduction of the motor using the mechanical data obtained from the motility assay. The formalism is also useful in assessing the effect on the measured motility data of various physical and hydrodynamic parameters of the assay, such as the size of the bead, the viscosity of the medium, the stiffness of the elastic element connecting the motor and the bead, etc. In a previous paper [Biophys. J. 67 (2000) 313] (hereafter referred to as paper I), we have derived the formalism for the case that the motor in the assay has only one head. In this paper we extend the derivation to the case that the motor is two-headed. The formalism is derived based on a simple two-state hand-over-hand model for the movement of the motor on microtubule, but can be easily extended to more complicated kinetic models. Effects of various hydrodynamic parameters on the velocity of the bead are studied with numerical calculations of the model. The difference between the formalism presented in this paper and the widely used "chemical" formalism, in which the movement of the kinesin and the bead is described by pure chemical reactions, is discussed.     

Block copolymer microdomains: a novel medium for enzymatic reactions.

Block copolymers exhibit the phenomenon of microdomain formation in pure states as well as in solutions. The microdomains vest the block copolymer assemblies with the intriguing characteristics of microheterogeneous media. We demonstrate that this microheterogeneity in hydrophobic-hydrophilic block copolymer systems can be exploited for immobilizing enzymes and to carry out enzymatic reactions. Examples involving cholesterol oxidase and horseradish peroxidase are provided here. The observed changes in the enzymatic activity in block copolymer microdomains from that in the aqueous media are interpreted in terms of the hydrophobicity of the reaction microenvironment. The block copolymer microdomains are simple to generate, well defined, and easily reproducible. Therefore, they hold significant potential as media for enzymatic biosynthetic reactions when the substrates or the reaction products are water insoluble.     

Chemical modification of canavanine with p-nitrophenylglyoxal. Factors influencing the chemistry and reactivity of alpha-dicarbonyl-guanidino reactions

The role of structural features and deprotonation of guanidino derivatives on chemical reactions with p-nitrophenylglyoxal has been investigated. Canavanine, an arginine analog, reacts to form a yellow product, which absorbs maximally at 350 nm (epsilon = 6500) and at 278 nm (epsilon = 14 500). Elemental analysis, fast atom bombardment mass spectral analysis, n.m.r. and i.r. studies suggest that the product is a 5-(p-nitrophenyl)4-oxo-2 imidazoline derivative of canalaline. Kinetic studies show that the second order rate constant for the reaction increases with increasing pH in the range of pH 7-11.0. It is concluded that the pH dependence of the reaction can be explained by general base catalysis and not simply by a deprotonation of the guanidinoxy side chain. The reaction of arginine, polyarginine, and other derivatives differs markedly from that of canavanine. The results suggest that change in the tautomeric equilibria between the imino and amino forms of the guanidino group may partly account for differences in reaction of canavanine and arginine and the reactions of specific arginyl residues in proteins.     

Time-dependent closed form solutions for fully competitive enzyme reactions

An analytic formalism developed earlier to describe the time evolution of the basic enzyme reaction is extended to fully competitive systems. Time-dependent closed form solutions are derived for the three nominal cases of competition: even, slow and fast inhibitors, allowing for the first time the complete characterization of the reactions. In agreement with previous work, the time-independent Michaelis-Menten approach is shown to be inaccurate when a fast inhibitor is present. The validity of the quasi-steady-state approximation on which the present framework is based is also revised.     

A quantum chemical study of repair of O6-methylguanine to guanine by tyrosine: Evaluation of the winged helix-turn-helix model

The winged helix-turn-helix model for the repair of O6-MeG to guanine involving the reaction of O6-MeG with a tyrosine residue of the protein O6-alkylguanine-DNA alkyltransferase (AGT) was examined by studying the reaction mechanism and barrier energies. Molecular geometries of the species and complexes involved in the reaction, i.e. the reactant, intermediate and product complexes as well as transition states, were optimized employing density functional theory in gas phase. It was followed by single point energy calculations using density functional theory along with a higher basis set and second order Mφller-Plesset perturbation theory (MP2) along with two different basis sets in gas phase and aqueous media. For the solvation calculations in aqueous media, the integral equation formalism of the polarizable continuum model (IEF-PCM) was employed. Vibrational frequency analysis was performed for each optimized structure and genuineness of transition states was ensured by visualizing the vibrational modes. It is found that tyrosine can repair O6-MeG to guanine by a two-step reaction. The present results have been compared with those obtained considering the helix-turn-helix model where the repair reaction primarily involves cysteine and occurs in a single-step. It is concluded that the repair through tyrosine envisaged in the winged helix-turn-helix model would be less efficient than that through cysteine envisaged in the helix-turn-helix model.     

Computer-aided real-time estimation of reaction conversion for lipase-catalyzed esterification in solvent-free systems

Real-time conversion estimation through macroscopic balancing was investigated for enzymatic esterification reactions in a solvent-free system. In principle, the conversion of ester synthesis can be determined from the amount of water produced by the reaction because water is formed as a by-product in the same molar ratio as the product. In this study, we show that the water production rate, and thereby the reaction conversion, can be estimated on-line from measurements of the relative humidity of the inlet and outlet air and the material balances of water in the system. In order to test the performance of the real-time conversion estimation method, the lipase-catalyzed esterification reaction of n-capric acid and n-decyl alcohol in solvent-free media was conducted while controlling the water activity at various values. When the reaction conversions estimated on-line were compared with those analyzed off-line by gas chromatography, good agreement was obtained: the average mean absolute error was +/- 2.4% of the reaction conversion despite the simplicity of the method. The on-line estimation method presented here requires no expensive or complicated analytical instruments and no sampling of reaction medium. It can be used for monitoring nonaqueous enzymatic reactions where water is produced or consumed during reaction.     

Kinetic analysis of protein modification reactions at equilibrium.

A kinetic analysis is presented of reactions of protein modification, and/or of modification-induced enzyme inactivation, which can formally be described by a single exponential function, or by a summation of two exponential functions, of reaction time plus a constant term. The reaction schemes compatible with the kinetic formalism of these cases are given, and a simple kinetic criterion is described whereby the identification of one of these cases, strong negative protein modification co-operativity, may be carried out. The treatment outlined in this paper is applied to a case from the literature, the inactivation of glyceraldehyde-3-phosphate dehydrogenase by butane-2,3-dione [Asriyants, Benkevich & Nagradova (1983) Biokhimiya (Engl. Transl.) 48, 164-171].     

Anaphylaxis due to thiopental sodium anesthesia.

Anaphylaxis due to an anesthetic is one type of cardiovascular emergency that can occur during general anesthesia. Anaphylactic reactions to muscle relaxants have been documented. Barbiturates, used as sedatives, are well known to produce cutaneous reactions, but anaphylaxis after their ingestion seems to be rare. Generalized allergic reactions to thiopental sodium during anesthesia are mentioned in the product monograph for Penthothal sodium, and rare case reports of anaphylactic reactions to infused thiopental have appeared, generally in the anesthesiology literature. Documentation of the immunologic responses to thiopental sodium has been limited to the demonstration of an allergic reaction to thiopental by skin testing in some cases. This report describes a woman who, after having tolerated thiopental sodium and other general anesthetics, became sensitive to this agent and had a severe acute reaction at the time of induction of general anesthesia.     

Underlying immunopathology as a cause of adverse responses to two intravenous anaesthetic agents.

A patient who had shown some evidence of immunological sensitivity underwent several operations under general anaesthesia for otitis media without ill effect. On his second exposure to Althesin, however, he suffered a severe reaction. Facial angioneurotic oedema was accompanied by peripheral vasodilatation and sweating, and C3 conversion was observed in his plasma. Subsequent anaesthetics produced no reactions until four years later, when thiopentone and suxamethonium were given. This reaction was much milder, but C3 conversion again occurred. Although the clinical signs indicated an anaphylactoid reaction, the laboratory findings suggested that this patient had an underlying immunopathological condition involving complement activation, which could be triggered by any intravenous agent that activated complement. The judgment that a reaction to a particular drug is anaphylactic cannot be made on the basis of clinical signs alone. Simple laboratory analysis will show whether the reaction is due to an underlying immunopathological condition that may be triggered by any of several drugs.     

Structures of ionic liquids dictate the conversion and selectivity of enzymatic glycerolysis: theoretical characterization by COSMO-RS

Lipase-catalyzed glycerolysis of triolein has been examined using a group of tetraammonium-based ionic liquids (ILs) as media, specifically with functional groups in cation part. The results demonstrated that the reaction evolution and profile specificity of respective IL system could be quantitatively associated with the structural characteristics of the IL by means of quantum chemical and COSMO-RS calculation. Misfit interaction, Van der Waals interaction and chemical potential, etc. derived from COSMO-RS calculation are shown to be effective measures to delineate multiple interactions of ILs and then can be used to understand the effects of ILs on reactions. The hydrophobic substituents in the cation are found to contribute to the increase of triolein solubility and enhancement of initial reaction rate; while strong polar anion and polyethoxyl and free hydroxyl groups in the cation part dictate improved product selectivity through reducing activity coefficients of monoglycerides. Integration of these structures into the same molecule constitutes a promising group of ILs that could produce over 90% monoglyceride with almost 100% triglyceride conversion, as well as bulky productivity, of particular potential for industrial applications. Overall, this work has presented a first attempt to characterize the IL structure-dependency of reaction specificity by associating structural variations of ILs with thermodynamic property changes of resided compounds and subsequent effects on reaction specificity. This might be of general value to help to understand the multiple solvation interaction among IL reaction systems at molecular level and promote the application of IL-mediated reactions to practical interests.     

Accuracy of alternative representations for integrated biochemical systems

The Michaelis-Menten formalism often provides appropriate representations of individual enzyme-catalyzed reactions in vitro but is not well suited for the mathematical analysis of complex biochemical networks. Mathematically tractable alternatives are the linear formalism and the power-law formalism. Within the power-law formalism there are alternative ways to represent biochemical processes, depending upon the degree to which fluxes and concentrations are aggregated. Two of the most relevant variants for dealing with biochemical pathways are treated in this paper. In one variant, aggregation leads to a rate law for each enzyme-catalyzed reaction, which is then represented by a power-law function. In the other, aggregation produces a composite rate law for either net rate of increase or net rate of decrease of each system constituent; the composite rate laws are then represented by a power-law function. The first variant is the mathematical basis for a method of biochemical analysis called metabolic control, the latter for biochemical systems theory. We compare the accuracy of the linear and of the two power-law representations for networks of biochemical reactions governed by Michaelis-Menten and Hill kinetics. Michaelis-Menten kinetics are always represented more accurately by power-law than by linear functions. Hill kinetics are in most cases best modeled by power-law functions, but in some cases linear functions are best. Aggregation into composite rate laws for net increase or net decrease of each system constituent almost always improves the accuracy of the power-law representation. The improvement in accuracy is one of several factors that contribute to the wide range of validity of this power-law representation. Other contributing factors that are discussed include the nonlinear character of the power-law formalism, homeostatic regulatory mechanisms in living systems, and simplification of rate laws by regulatory mechanisms in vivo.     

One Rule to Grow Them All: A General Theory of Neuronal Branching and Its Practical Application

Understanding the principles governing axonal and dendritic branching is essential for unravelling the functionality of single neurons and the way in which they connect. Nevertheless, no formalism has yet been described which can capture the general features of neuronal branching. Here we propose such a formalism, which is derived from the expression of dendritic arborizations as locally optimized graphs. Inspired by Ramón y Cajal''s laws of conservation of cytoplasm and conduction time in neural circuitry, we show that this graphical representation can be used to optimize these variables. This approach allows us to generate synthetic branching geometries which replicate morphological features of any tested neuron. The essential structure of a neuronal tree is thereby captured by the density profile of its spanning field and by a single parameter, a balancing factor weighing the costs for material and conduction time. This balancing factor determines a neuron''s electrotonic compartmentalization. Additions to this rule, when required in the construction process, can be directly attributed to developmental processes or a neuron''s computational role within its neural circuit. The simulations presented here are implemented in an open-source software package, the “TREES toolbox,” which provides a general set of tools for analyzing, manipulating, and generating dendritic structure, including a tool to create synthetic members of any particular cell group and an approach for a model-based supervised automatic morphological reconstruction from fluorescent image stacks. These approaches provide new insights into the constraints governing dendritic architectures. They also provide a novel framework for modelling and analyzing neuronal branching structures and for constructing realistic synthetic neural networks.     

The comparative characteristics of the biological and immunomodulating activities of enzyme preparations of microbial origin]

A number of enzyme preparations of microbial origin such as immunomodulators and immunostimulators have been studied in vitro according to reactions of rosette technique of cell (ROC) active and general, adhesion, activation of a complement and also the spontaneous activity and phagocytosis of neutrophils have been determined. The enzyme preparations of microbial origin have been shown to be capable of causing immunomodulation and of influencing the specific and nonspecific immune response. Unlike the enzymes of animal origin the enzymes of microbial origin are effective in smaller concentrations. The studied preparations modulate the immune response differently according to ROC, adhesion. Each of preparations has specific features of biological activity--bacterio-stationary in reaction to a certain group of microorganisms and some specific features of reaction with cell and levels of immune reactions.     

Changes in Risk of Immediate Adverse Reactions to Iodinated Contrast Media by Repeated Administrations in Patients with Hepatocellular Carcinoma

Background

To elucidate whether repeated exposures to iodinated contrast media increase the risk of adverse reaction.

Materials and Methods

We retrospectively reviewed 1,861 patients with hepatocellular carcinoma who visited authors’ institution, a tertiary referral center, between 2004 and 2008. We analyzed cumulative probability of adverse reactions and risk factors. We categorized all symptoms into hypersensitivity reactions, physiologic reactions, and other reactions, according to the American College of Radiology guidelines, and evaluated each category as an event. We estimated the association between hazard for adverse reactions and the number of cumulative exposures to contrast media. We also evaluated subsequent contrast media injections and adverse reactions.

Results

There were 23,684 contrast media injections in 1,729 patients. One hundred and thirty-two patients were excluded because they were given no contrast media during the study period. Adverse reactions occurred in 196 (0.83%) patients. The cumulative incidence at 10^th, 20^th, and 30^th examination was 7.9%, 15.2%, and 24.1%, respectively. Presence of renal impairment was found to be one of risk factors for adverse reactions. The estimated hazard of overall adverse reaction gradually decreased until around 10^th exposure and rose with subsequent exposures. The estimated hazard of hypersensitivity showed V-shaped change with cumulative number of exposures. The estimated hazard of physiologic reaction had a tendency toward decreasing and that of other reaction had a tendency toward increasing. Second adverse reaction was more severe than the initial in only one among 130 patients receiving subsequent injections.

Conclusion

Repeated exposures to iodinated contrast media increase the risk of adverse reaction.