EQUIL: Simulation and data analysis of binding reactions with arbitrary chemical models

We have developed an algorithm for simulation and analysis of arbitrary chemical systems in equilibrium, with emphasis on ligand binding reactions. The program EQUIL can treat reactions involving multiple ligands, multiple binding sites, ternary complex models, allosteric effectors, competitive and noncompetitive binding, conformational changes, cooperativity, and generally any scheme that can be represented as a set of chemical equations. EQUIL is based on a general thermodynamic model of chemical equilibria; it does not involve nonlinear transformation of experimental data, but it does require the user to define the model of interaction between ligands and receptors by writing down the appropriate chemical reactions. EQUIL contains features of particular importance to ligand binding experiments: variable binding capacities, nonspecific binding, and the ability to simultaneously analyze data from different types of experiments. Furthermore, the simulation feature of EQUIL allows the user to investigate the feasibility of experiments that could possibly distinguish between different reaction models. We illustrate the use of this program on personal computers to analyze and simulate simple and complicated interactions between ligands and receptors.     

Chemical Memory Reactions Induced Bursting Dynamics in Gene Expression

Memory is a ubiquitous phenomenon in biological systems in which the present system state is not entirely determined by the current conditions but also depends on the time evolutionary path of the system. Specifically, many memorial phenomena are characterized by chemical memory reactions that may fire under particular system conditions. These conditional chemical reactions contradict to the extant stochastic approaches for modeling chemical kinetics and have increasingly posed significant challenges to mathematical modeling and computer simulation. To tackle the challenge, I proposed a novel theory consisting of the memory chemical master equations and memory stochastic simulation algorithm. A stochastic model for single-gene expression was proposed to illustrate the key function of memory reactions in inducing bursting dynamics of gene expression that has been observed in experiments recently. The importance of memory reactions has been further validated by the stochastic model of the p53-MDM2 core module. Simulations showed that memory reactions is a major mechanism for realizing both sustained oscillations of p53 protein numbers in single cells and damped oscillations over a population of cells. These successful applications of the memory modeling framework suggested that this innovative theory is an effective and powerful tool to study memory process and conditional chemical reactions in a wide range of complex biological systems.     

Advances in the chemistry of small molecule fluorescent probes

Small molecule fluorophores are essential tools for chemical biology. A benefit of synthetic dyes is the ability to employ chemical approaches to control the properties and direct the position of the fluorophore. Applying modern synthetic organic chemistry strategies enables efficient tailoring of the chemical structure to obtain probes for specific biological experiments. Chemistry can also be used to activate fluorophores; new fluorogenic enzyme substrates and photoactivatable compounds with improved properties have been prepared that facilitate advanced imaging experiments with low background fluorescence. Finally, chemical reactions in live cells can be used to direct the spatial distribution of the fluorophore, allowing labeling of defined cellular regions with synthetic dyes.     

Chemical geometrodynamics: Physical fields can cause asymmetric synthesis

This paper presents theoretical arguments that suggest that chiral combinations of physical fields which can induce motion of elementary particles or molecular systems can in principle cause asymmetric synthesis. The theory is founded on the application of parity and time reversal operators to chiral dynamical systems. The motion of these systems induced by a chiral set of physical fields is shown not to be invariant on parity and time reflection. The relationship between tetrahedral dissymmetry and belical dissymmetry is analyzed in terms of the moments of inertin of a tetrahedrally dissymmetric rotor rotating around each of the four bond axes. The magnitude of anticipated enantiomeric excess which would result from conducting a prochiral chemical reaction in a chiral set of physical fields is estimated to be very small, parts per million or less, for virtually all sets of readily accessible physical fields. The results of experiments in which prochiral chemical reactions were conducted in a sealed tube which was spinning perpendicular or paralled to the earth's surface, are reviewed as are experiments in which prochiral chemical reactions were conducted in intense oriented magnetic fields. Enantiomeric recognition may have been one of the principal mechanisms for amplifying small differences in the rates of a given prochiral chemical reaction.     

Protein dynamics and enzyme catalysis: insights from simulations

The role of protein dynamics in enzyme catalysis is one of the most active and controversial areas in enzymology today. Some researchers claim that protein dynamics are at the heart of enzyme catalytic efficiency, while others state that dynamics make no significant contribution to catalysis. What is the biochemist - or student - to make of the ferocious arguments in this area? Protein dynamics are complex and fascinating, as molecular dynamics simulations and experiments have shown. The essential question is: do these complex motions have functional significance? In particular, how do they affect or relate to chemical reactions within enzymes, and how are chemical and conformational changes coupled together? Biomolecular simulations can analyse enzyme reactions and dynamics in atomic detail, beyond that achievable in experiments: accurate atomistic modelling has an essential part to play in clarifying these issues. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.     

Efficient extraction of mapping rules of atoms from enzymatic reaction data.

Many computational problems and methods have been proposed for analysis of biological pathways. Among them, this paper focuses on extraction of mapping rules of atoms from enzymatic reaction data, which is useful for drug design, simulation of tracer experiments, and consistency checking of pathway databases. Most of existing methods for this problem are based on maximal common subgraph algorithms. In this paper, we propose a novel approach based on graph partition and graph isomorphism. We show that this problem is NP-hard in general, but can be solved in polynomial time for wide classes of enzymatic reactions. We also present an O(n(1.5)) time algorithm for a special but fundamental class of reactions, where n is the maximum size of compounds appearing in a reaction. We develop practical polynomial-time algorithms in which the Morgan algorithm is used for computing the normal form of a graph, where it is known that the Morgan algorithm works correctly for most chemical structures. Computational experiments are performed for these practical algorithms using the chemical reaction data stored in the KEGG/LIGAND database. The results of computational experiments suggest that practical algorithms are useful in many cases.     

Effect of copper, manganese and cobalt ions on the chemical sensitivity of interoceptors]

Acute experiments were conducted on 82 cats; a study was made of the influence of copper, manganese and cobalt on the chemical sensitivity of interoceptors. Administration of copper chloride caused inversion of the reflex reactions of the blood pressure and respiration to acetylcholine, cobalt chloride weakened these reactions, and manganese chloride intensified them. It is supposed that changes in the interoceptive reflexes observed depended chiefly on the direct action of microelements on the functional condition of the interoceptors.     

Protein folding studied by real-time NMR spectroscopy

Real-time NMR spectroscopy developed to a generally applicable method to follow protein folding reactions. It combines the access to high resolution data with kinetic experiments allowing very detailed insights into the development of the protein structure during different steps of folding. The present review concentrates mainly on the progress of real-time NMR during the last 5 years. Starting from simple 1D experiments, mainly changes of the chemical shifts and line widths of the resonances have been used to analyze the different states populated during the folding reactions. Today, we have a broad spectrum of 1D, 2D, and even 3D NMR methods focusing on different characteristics of the folding polypeptide chains. More than 20 proteins have been investigated so far by these time-resolved experiments and the main results and conclusions are discussed in this report. Real-time NMR provides comprehensive contributions for joining experiment and theory within the 'new view' of protein folding.     

Confined-pyrolysis as an experimental method for hydrothermal organic synthesis

A closed pyrolysis system has been developed as a tool for studying the reactions of organic compounds under extreme hydrothermal conditions. Small high pressure stainless steel vessels in which the ratio of sediment or sample to water has been adjusted to eliminate the headspace at peak experimental conditions confines the organic components to the bulk solid matrix and eliminates the partitioning of the organic compounds away from the inorganic components during the experiment. Confined pyrolysis experiments were performed to simulate thermally driven catagenetic changes in sedimentary organic matter using a solids to water ratio of 3.4 to 1. The extent of alteration was measured by monitoring the steroid and triterpenoid biomarkers and polycyclic aromatic hydrocarbon distributions. These pyrolysis experiments duplicated the hydrothermal transformations observed in nature. Molecular probe experiments using alkadienes, alkenes and alkanes in H₂O and D₂O elucidated the isomerization and hydrogenation reactions of aliphatic compounds and the competing oxidative reactions occurring under hydrothermal conditions. This confined pyrolysis technique is being applied to test experiments on organic synthesis of relevance to chemical evolution for the origin of life.     

Synthesis of Circular Oligodeoxynucleotide Conjugates VIA Transient Abasic Sites

Abstract

New chemical ligation or cyclisation reactions, using high reactivity of abasic sites with amines, are reported for the synthesis of oligonucleotide clamps and singlestranded circular oligonucleotides. Thermal denaturation experiments show that these molecules display very high binding affinities for complementary DNA oligomer by forming triple-helical complexes.     

Fluctuations in the polymerization of sickle hemoglobin. A simple analytic model

Using the stochastic theory of chemical reactions and the theory of first passage times, a simple analytic expression is derived for the distribution of delay times that has been observed in studies of the polymerization kinetics of sickle hemoglobin under conditions where the polymerization progress curves exhibit stochastic variation. The rate of homogeneous nucleation can be readily extracted from such experiments using this expression. This work constitutes a significant addition to the rather limited number of examples where contact can be successfully made between the stochastic theory of chemical kinetics and experiment.     

Influence of viscosity of enzymatic reactions studied with glucoamylase of Aspergillus niger.

Viscosity can be interpreted in terms of transport of momentum and, therefore, it should influence the kinetics of enzyme reactions. A theory, developed by Somogyi and Damjanovich ((1975) J. Theor. Biol. 51, 393--401), is based on this idea. Transport of momentum must always be accompanied by the transport of mass and this second influence of viscosity is a limiting factor for fast reactions in the liquid phase. A third aspect is, that the chemical potentials of the components of viscous solutions are altered. This paper reports experiments concerning the influence of the viscosigens (compounds that increase the viscosity of solvents), alginate, sucrose, and maltose on the kinetic behaviour of glucoamylase (1,4-alpha-D-glucan glucohydrolase, EC 3.2.1.3). The observed invariance of V and the decrease of Km are explained by the increase of chemical potentials and restriction of momentum transport.     

生物过程化学机制的单分子荧光探测

单分子荧光检测越来越广泛地被应用于生命科学领域。这项技术可以对生物过程的化学机制进行定量、仔细的探究,与传统系综实验形成很好的互补。本文简介近几年单分子荧光检测研究的若干典型实例,以此展示这项技术的特点、优势及其可能的应用。它们涉及从简单的生化反应到复杂的蛋白表达调控等重要的生物过程。     

Kinetic Modelling of in Vitro Lipid Peroxidation Experiments - 'Low Level' Validation of a Model of in Vivo Lipid Peroxidation

Kinetic modelling overcomes some of the drawbacks of purely intuitive thinking in integrating information accumulated on chemical reactions involved in oxidative stress. However, it is important to assess if current knowledge about the reactions that mediate lipid peroxidation already allows satisfactory modelling of this process in near-to-physiological conditions. In this paper, a set of increasingly complex in vitro experiments on antioxidants (a-tocopherol and ascorbate) and lipid peroxidation in heterogeneous systems is simulated. Quantitative to semiquantitative agreement is found between experimental and simulation results. In addition, this theoretical analysis provided useful insights, suggested new hypotheses and experiments and pointed out relevant aspects needing further research. The results encourage and serve as partial validation for the formulation of relatively detailed mathematical models of in vivo lipid peroxidation. Some important aspects of the formulation and analysis of such models are discussed.     

Vascular reactivity of the brain in the pigeon Columba livia

In experiments on awake relatively unrestrained pigeons, studies have been made on the reactions of the cerebrovascular bed to fixed functional loads of physical (orthostasis) and chemical (inhalation of hypoxic and hypercapnic gas mixtures) nature. Using hydrogen clearance method, the increase in the intensity of local cerebral blood flow in different structures of the telencephalon during inhalation of the mentioned gas mixtures was demonstrated. Bilateral vagotomy resulted in inversed reactions. Influence of functional loads was accompanied by changes in rheoencephalographic parameters. The data obtained suggest the existence of an evident reactivity of cerebral vessels in birds which is controlled by neurogenic mechanism of regulation of vascular tone.     

RNA as a catalyst: Natural and designed ribozymes

RNA can catalyse chemical reactions through its ability to fold into complex three-dimensional structures and to specifically bind small molecules and divalent metal ions. The 2′-hydroxyl groups of the ribose moieties contribute to this exceptional reactivity of RNA, compared to DNA. RNA is not only able to catalyse phosphate ester transfer reactions in ribonucleic acids, but can also show aminoacyl esterase activity, and is probably able to promote peptide bond formation. Bearing its potential for functioning both as a genome and as a gene product, RNA is suitable for in vitro evolution experiments enabling the selection of molecules with new properties. The growing repertoire of RNA catalysed reactions will establish RNA as a primordial molecule in the evolution of life.     

Challenging fear: chemical alarm signals are not causing morphology changes in crucian carp (<Emphasis Type="Italic">Carassius carassius</Emphasis>)

Crucian carp develops a deep body in the presence of chemical cues from predators, which makes the fish less vulnerable to gape-limited predators. The active components originate in conspecifics eaten by predators, and are found in the filtrate of homogenised conspecific skin. Chemical alarm signals, causing fright reactions, have been the suspected inducers of such morphological changes. We improved the extraction procedure of alarm signals by collecting the supernatant after centrifugation of skin homogenates. This removes the minute particles that normally make a filtered sample get turbid. Supernatants were subsequently diluted and frozen into ice-cubes. Presence of alarm signals was confirmed by presenting thawed ice-cubes to crucian carp in behaviour tests at start of laboratory growth experiments. Frozen extracts were added further on three times a week. Altogether, we tested potential body-depth-promoting properties of alarm signals twice in the laboratory and once in the field. Each experiment lasted for a minimum of 50 days. Despite growth of crucian carp in all experiments, no morphology changes were obtained. Accordingly, we conclude that the classical alarm signals that are releasing instant fright reactions are not inducing morphological changes in this species. The chemical signals inducing a body-depth increase are suspected to be present in the particles removed during centrifugation (i.e., in the precipitate). Tissue particles may be metabolized by bacteria in the intestine of predators, resulting in water-soluble cues. Such latent chemical signals have been found in other aquatic organisms, but hitherto not reported in fishes.     

Stopped-flow solution scattering using synchrotron radiation: Apparatus,data collection and data analysis

We have constructed an experimental system, under remote control, for stopped-flow X-ray scattering using synchrotron radiation. It has been used, in conjunction with an annular detector and its associated electronics, to obtain good scattering curves, with time-slices as short as 200 ms, in a new study of the dissociation of the enzyme complex aspartate transcarbamylase. The data have been analysed by new statistical methods, and they agree well with the results from parallel chemical quench experiments. For studying dissociation reactions, stopped-flow X-ray scattering is a quite practical method, which need not use very much more material than conventional stopped-flow experiments.     

FURTHER OBSERVATIONS ON THE INFLUENCE OF SALTS WHEN INJECTED INTO THE ANIMAL BODY

A satisfactory correlation of our observations dealing with the influence of salts and those dealing with the influence of x-rays is not possible at present. Any far reaching conclusion is not permitted because the information we have at this time regarding the physical chemical conditions concerned in the process of injury, as well as that pertaining to the nature of radio-chemical reactions, is too meager. As far as the experiments with salts are concerned, it may be said that we are dealing with ion effects, and their importance in physiological processes is made clear by the investigations of Loeb (3) and those of Osterhout (4). The results that we have obtained in our experiments present an interesting analogy between the effect of x-rays and certain salts on the lymphoid elements of the animal body. We regard this analogy as significant in that it presents suggestions regarding the chemical nature of x-ray effects in the animal body.