Academic literature on the topic 'Complex Reaction Mechanism - Molecular Processes'
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Journal articles on the topic "Complex Reaction Mechanism - Molecular Processes"
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Hirst, Judy. "Towards the molecular mechanism of respiratory complex I." Biochemical Journal 425, no. 2 (December 23, 2009): 327–39. http://dx.doi.org/10.1042/bj20091382.
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Complex I (NADH:quinone oxidoreductase) is crucial to respiration in many aerobic organisms. In mitochondria, it oxidizes NADH (to regenerate NAD+ for the tricarboxylic acid cycle and fatty-acid oxidation), reduces ubiquinone (the electrons are ultimately used to reduce oxygen to water) and transports protons across the mitochondrial inner membrane (to produce and sustain the protonmotive force that supports ATP synthesis and transport processes). Complex I is also a major contributor to reactive oxygen species production in the cell. Understanding the mechanisms of energy transduction and reactive oxygen species production by complex I is not only a significant intellectual challenge, but also a prerequisite for understanding the roles of complex I in disease, and for the development of effective therapies. One approach to defining a complicated reaction mechanism is to break it down into manageable parts that can be tackled individually, before being recombined and integrated to produce the complete picture. Thus energy transduction by complex I comprises NADH oxidation by a flavin mononucleotide, intramolecular electron transfer from the flavin to bound quinone along a chain of iron–sulfur clusters, quinone reduction and proton translocation. More simply, molecular oxygen is reduced by the flavin, to form the reactive oxygen species superoxide and hydrogen peroxide. The present review summarizes and evaluates experimental data that pertain to the reaction mechanisms of complex I, and describes and discusses contemporary mechanistic hypotheses, proposals and models.
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Kulakova, A. M., M. G. Khrenova, and A. V. Nemukhin. "Molecular mechanism of chromogenic substrate hydrolysis in the active site of human carboxylesterase-1." Biomeditsinskaya Khimiya 67, no. 3 (2021): 300–305. http://dx.doi.org/10.18097/pbmc20216703300.
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Human carboxylesterases are involved in the protective processes of detoxification during the hydrolytic metabolism of xenobiotics. Knowledge of the molecular mechanisms of substrates hydrolysis in the enzymes active site is necessary for the rational drug design. In this work, the molecular mechanism of the hydrolysis reaction of para-nitrophenyl acetate in the active site of human carboxylesterase was determined using modern methods of molecular modeling. According to the combined method of quantum mechanics/molecular mechanics calculations, the chemical reaction occurs within four elementary steps, including two steps of the acylation stage, and two steps of the deacylation stage. All elementary steps have low energy barriers, with the gradual lowering of the intermediate energies that stimulates reaction in the forward direction. The molecular docking was used to estimate the binding constants of the enzyme-substrate complex and the dissociation constant of enzyme-product complexes. The effective kinetic parameters of the enzymatic hydrolysis in the active site of carboxylesterase are determined by numerical solution of the differential kinetic equations.
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Zedler, Linda, Sven Krieck, Stephan Kupfer, and Benjamin Dietzek. "Resonance Raman Spectro-Electrochemistry to Illuminate Photo-Induced Molecular Reaction Pathways." Molecules 24, no. 2 (January 10, 2019): 245. http://dx.doi.org/10.3390/molecules24020245.
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Electron transfer reactions play a key role for artificial solar energy conversion, however, the underlying reaction mechanisms and the interplay with the molecular structure are still poorly understood due to the complexity of the reaction pathways and ultrafast timescales. In order to investigate such light-induced reaction pathways, a new spectroscopic tool has been applied, which combines UV-vis and resonance Raman spectroscopy at multiple excitation wavelengths with electrochemistry in a thin-layer electrochemical cell to study [RuII(tbtpy)2]2+ (tbtpy = tri-tert-butyl-2,2′:6′,2′′-terpyridine) as a model compound for the photo-activated electron donor in structurally related molecular and supramolecular assemblies. The new spectroscopic method substantiates previous suggestions regarding the reduction mechanism of this complex by localizing photo-electrons and identifying structural changes of metastable intermediates along the reaction cascade. This has been realized by monitoring selective enhancement of Raman-active vibrations associated with structural changes upon electronic absorption when tuning the excitation wavelength into new UV-vis absorption bands of intermediate structures. Additional interpretation of shifts in Raman band positions upon reduction with the help of quantum chemical calculations provides a consistent picture of the sequential reduction of the individual terpyridine ligands, i.e., the first reduction results in the monocation [(tbtpy)Ru(tbtpy•)]+, while the second reduction generates [(tbtpy•)Ru(tbtpy•)]0 of triplet multiplicity. Therefore, the combination of this versatile spectro-electrochemical tool allows us to deepen the fundamental understanding of light-induced charge transfer processes in more relevant and complex systems.
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Zhang, Lanjun, Yujia Han, Dexin Xu, Qin Jiang, Haihui Xin, Chenhui Fu, and Wenjing He. "Study on the Reaction Path of -CH3 and -CHO Functional Groups during Coal Spontaneous Combustion: Quantum Chemistry and Experimental Research." Energies 15, no. 13 (July 4, 2022): 4891. http://dx.doi.org/10.3390/en15134891.
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Coal spontaneous combustion (CSC) is a disaster that seriously threatens safe production in coal mines. Revealing the mechanism of CSC can provide a theoretical basis for its prevention and control. Compared with experimental research is limited by the complexity of coal molecular structure, the quantum chemical calculation method can simplify the complex molecular structure and realize the exploration of the mechanism of CSC from the micro level. In this study, toluene and phenylacetaldehyde were used as model compounds, and the quantum chemical calculation method was adopted. The reaction processes of the methyl and aldehyde groups with oxygen were investigated with the aid of the Gaussian 09 software, using the B3LYP functional and the 6-311 + G(d,p) basis set and including the D3 dispersion correction. On this basis, the generation mechanisms of CO and CO2, two important indicator gases in the process of CSC, were explored. The calculation results show that the Gibbs free energy changes and enthalpy changes in the two reaction systems are both of negative values. Accordingly, it is judged that the reactions belong to spontaneous exothermic reactions. In the reaction processes, the activation energy of CO is less than that of CO2, indicating that CO is formed more easily in the above-two reaction processes. In addition, the variations in concentrations of important oxidation products (CO and CO2) and main active functional groups (such as methyl, carboxyl and carbonyl) with temperature were revealed through a low-temperature oxidation experiment. The experimental results verify the accuracy of the above quantum chemical reaction path. Moreover, it is also found that the generation mechanisms of CO and CO2 in coal samples with different metamorphic degrees are different. To be specific, for low-rank coal (HYH), CO and CO2 mainly come from the oxidation of alkyl side chains; for high-rank coal (CQ), CO is produced by the oxidation of alkyl side chains, and CO2 is attributed to the inherent oxygen-containing structure.
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Ilyin, Daniil V., William A. Goddard, Julius J. Oppenheim, and Tao Cheng. "First-principles–based reaction kinetics from reactive molecular dynamics simulations: Application to hydrogen peroxide decomposition." Proceedings of the National Academy of Sciences 116, no. 37 (September 21, 2018): 18202–8. http://dx.doi.org/10.1073/pnas.1701383115.
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This paper presents our vision of how to use in silico approaches to extract the reaction mechanisms and kinetic parameters for complex condensed-phase chemical processes that underlie important technologies ranging from combustion to chemical vapor deposition. The goal is to provide an analytic description of the detailed evolution of a complex chemical system from reactants through various intermediates to products, so that one could optimize the efficiency of the reactive processes to produce the desired products and avoid unwanted side products. We could start with quantum mechanics (QM) to ensure an accurate description; however, to obtain useful kinetics we need to average over ∼10-nm spatial scales for ∼1 ns, which is prohibitively impractical with QM. Instead, we use the reactive force field (ReaxFF) trained to fit QM to carry out the reactive molecular dynamics (RMD). We focus here on showing that it is practical to extract from such RMD the reaction mechanisms and kinetics information needed to describe the reactions analytically. This analytic description can then be used to incorporate the correct reaction chemistry from the QM/ReaxFF atomistic description into larger-scale simulations of ∼10 nm to micrometers to millimeters to meters using analytic approaches of computational fluid dynamics and/or continuum chemical dynamics. In the paper we lay out the strategy to extract the mechanisms and rate parameters automatically without the necessity of knowing any details of the chemistry. We consider this to be a proof of concept. We refer to the process as RMD2Kin (reactive molecular dynamics to kinetics) for the general approach and as ReaxMD2Kin (ReaxFF molecular dynamics to kinetics) for QM-ReaxFF–based reaction kinetics.
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Couture, Christiane, and Anthony James Paine. "Mechanisms and models for homogeneous copper mediated ligand exchange reactions of the type: CuNu + ArX → ArNu + CuX." Canadian Journal of Chemistry 63, no. 1 (January 1, 1985): 111–20. http://dx.doi.org/10.1139/v85-019.
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The title reactions are an important class of copper mediated nucleophilic aromatic substitution processes, which constitute a useful tool in the molecular design and synthesis of small molecules. We report the results of extensive investigation of these processes, primarily focussing on cyanodeiodination (ArI + CuCN → CuI + ArCN). Among the interesting features of these processes are: (a) an unusual rate equation involving autocatalysis by CuI product; (b) retardation by both excess nucleophile (as KCN) and excess leaving group (as KI), which compete with ArX to complex with CuNu; (c) only cuprous nucleophiles are active (ligand exchanged products from cupric salts arise from prior redox equilibria which form CuNu); (d) the halogen effect is large (kI ~ 40–100 kBr ~ 300–5000kCl) but the Hammett ρ value is zero; (e) ortho-alkyl groups do not hinder the reaction (and actually cause mild acceleration by relief of steric strain). Finally, the introduction of an ortho-COO− group accelerates the reaction by a factor of 104–105, but the general features of the accelerated reactions are also the same, again indicating a common mechanism, with entropic acceleration by ortho-carboxylate. Both kinetic and thermodynamic factors were considered in detail, the latter apparently for the first time. Applications to practical syntheses are considered, and novel mechanistic models for these interesting processes are discussed.
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Miller, RJ Dwayne. "2000 John C. Polanyi Award LectureMother Nature and the molecular Big Bang." Canadian Journal of Chemistry 80, no. 1 (January 1, 2002): 1–24. http://dx.doi.org/10.1139/v01-199.
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Biological molecules are mesoscopic systems that bridge the quantum and classical worlds. At the single molecule level, there are often more than 1 × 104 degrees of freedom that are involved in protein-mediated processes. These molecules are sufficiently large that the bath coordinate convolved to the reaction at an active site is defined by the surrounding protein tertiary structure. In this context, the very interatomic forces that determine the active protein structures create a strongly associated system. Thus, the bath fluctuations leading to reactive crossings involve highly hindered motions within a myriad of local minima that would act to cast the reaction dynamics into the high viscosity limit appropriate to glasses. However, the time scales observed for biological events are orders of magnitude too fast to meet this anticipated categorization. In this context, the apparent deterministic nature of biological processes represents an enormous challenge to our understanding of chemical processes. Somehow Nature has discovered a molecular scaffolding that enables minute amounts of energy to be efficiently channeled to perform biological functions without becoming entrapped in local minima. Clearly, energy derived from chemical processes is highly directed in biological systems. To understand this problem, we must first understand how energy is redistributed among the different degrees of freedom and fully characterize the protein relaxation processes along representative reaction coordinates in relation to these dissipative processes. This paper discusses the development of new nonlinear spectroscopic methods that have enabled interferometric sensitivity to protein motions on femtosecond time scales appropriate to the very fastest motions (i.e., bond breaking or the molecular "Big Bang") out to the slowest relaxation steps. This work has led to the Collective Mode Coupling Model as an explanation of the required reduced dimensionality in biological systems. Within this model, the largest coupling coefficients of the reaction coordinate are to the damped inertial collective modes of the protein defined by the strongly correlated secondary structures. These modes act to guide the reaction along the correct seam(s) in an otherwise highly complex potential energy surface. The mechanism by which biological molecules have been able to harness chemical energy over meso-length scales represents the first step towards higher levels of organization. The new insight afforded by the collective mode mechanism may prove important in understanding this larger issue of scaling in biological systems.Key words: biodynamics, energy transduction, ultrafast spectroscopy, nonlinear spectroscopy, primary processes in biology.
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Kubař, Tomáš, and Marcus Elstner. "A hybrid approach to simulation of electron transfer in complex molecular systems." Journal of The Royal Society Interface 10, no. 87 (October 6, 2013): 20130415. http://dx.doi.org/10.1098/rsif.2013.0415.
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Electron transfer (ET) reactions in biomolecular systems represent an important class of processes at the interface of physics, chemistry and biology. The theoretical description of these reactions constitutes a huge challenge because extensive systems require a quantum-mechanical treatment and a broad range of time scales are involved. Thus, only small model systems may be investigated with the modern density functional theory techniques combined with non-adiabatic dynamics algorithms. On the other hand, model calculations based on Marcus's seminal theory describe the ET involving several assumptions that may not always be met. We review a multi-scale method that combines a non-adiabatic propagation scheme and a linear scaling quantum-chemical method with a molecular mechanics force field in such a way that an unbiased description of the dynamics of excess electron is achieved and the number of degrees of freedom is reduced effectively at the same time. ET reactions taking nanoseconds in systems with hundreds of quantum atoms can be simulated, bridging the gap between non-adiabatic ab initio simulations and model approaches such as the Marcus theory. A major recent application is hole transfer in DNA, which represents an archetypal ET reaction in a polarizable medium. Ongoing work focuses on hole transfer in proteins, peptides and organic semi-conductors.
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Bunik, Victoria I., and Alisdair R. Fernie. "Metabolic control exerted by the 2-oxoglutarate dehydrogenase reaction: a cross-kingdom comparison of the crossroad between energy production and nitrogen assimilation." Biochemical Journal 422, no. 3 (August 27, 2009): 405–21. http://dx.doi.org/10.1042/bj20090722.
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Mechanism-based inhibitors and both forward and reverse genetics have proved to be essential tools in revealing roles for specific enzymatic processes in cellular function. Here, we review experimental studies aimed at assessing the impact of OG (2-oxoglutarate) oxidative decarboxylation on basic cellular activities in a number of biological systems. After summarizing the catalytic and regulatory properties of the OGDHC (OG dehydrogenase complex), we describe the evidence that has been accrued on its cellular role. We demonstrate an essential role of this enzyme in metabolic control in a wide range of organisms. Targeting this enzyme in different cells and tissues, mainly by its specific inhibitors, effects changes in a number of basic functions, such as mitochondrial potential, tissue respiration, ROS (reactive oxygen species) production, nitrogen metabolism, glutamate signalling and survival, supporting the notion that the evolutionary conserved reaction of OG degradation is required for metabolic adaptation. In particular, regulation of OGDHC under stress conditions may be essential to overcome glutamate excitotoxicity in neurons or affect the wound response in plants. Thus, apart from its role in producing energy, the flux through OGDHC significantly affects nitrogen assimilation and amino acid metabolism, whereas the side reactions of OGDHC, such as ROS production and the carboligase reaction, have biological functions in signalling and glyoxylate utilization. Our current view on the role of OGDHC reaction in various processes within complex biological systems allows us a far greater fundamental understanding of metabolic regulation and also opens up new opportunities for us to address both biotechnological and medical challenges.
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Capurso, Matías, Rodrigo Gette, Gabriel Radivoy, and Viviana Dorn. "The Sn2 Reaction: A Theoretical-Computational Analysis of a Simple and Very Interesting Mechanism." Proceedings 41, no. 1 (November 14, 2019): 81. http://dx.doi.org/10.3390/ecsoc-23-06514.
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Bimolecular nucleophilic substitution (SN2) reaction is one of the most frequently processes chosen as model mechanism to introduce undergraduate chemistry students to computational chemistry methodology. In this work, we performed a computational analysis for the ionic SN2 reaction, where the nucleophile charged (X−; X=F, Cl, Br, I) attacks the carbon atom of the substrate (CH3Cl) through a backside pathway, and simultaneously, the leaving group is displaced (Cl−). The calculations were performed applying DFT methods with the Gaussian09 program, the B3LYP functional, the 6-31+G* basis set for all atoms except iodine (6-311G*), and the solvents effects (acetonitrile and cyclohexane) were evaluated with the PCM model. We evaluated the potential energy surface (PES) for the mentioned reaction considering the reactants, the formation of an initial complex between the nucleophile and the substrate, the transition state, a final complex where the leaving group is still bound to the substrate and the products. We analyzed the atomic charge (ESP) and the bond distance throughout the process. Gas phase and solvent studies were performed in order to analyze the solvation effects on the reactivity of the different nucleophiles. We observed that increasing solvent polarity, decreases reaction rates. On the other hand, we thought it would be enriching, to carry out a reactivity analysis from the point of view of molecular orbitals. Therefore, we analyzed the MOs HOMO and the MOs LUMO of the different stationary states on PES, both in a vacuum (gas phase) and in acetonitrile as the solvent.
Dissertations / Theses on the topic "Complex Reaction Mechanism - Molecular Processes"
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Ishino, So. "Physicochemical studies on reaction mechanism of molecular chaperone GroE." 京都大学 (Kyoto University), 2015. http://hdl.handle.net/2433/199490.
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Etienne, Michel. "Réactivité de complexes dinucléaires hydrure et alcénylidène ponte du fer vis-a-vis d'hydrocarbures cyanes insatures (mono et dicyanoacétylène, tétracyanoethylène)." Brest, 1988. http://www.theses.fr/1988BRES2009.
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Preparation de complexes avec des coordinats cyano-4 butadienyldene portants. On obtient egalement des complexes dinucleaires avec le tricyano-3,4,4 butadienylidene-1,3. Mecanisme ses reactions de migration de l'hydrogene allylique
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Rogueda, Catherine. "Etude comparee de la copolymerisation alternee du styrene et du methacrylate de methyle en solution dans le toluene ou dans le tetrachlorure de carbone." Paris 6, 1987. http://www.theses.fr/1987PA066203.
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Etude cinetique de la copolymerisation du styrene et du methacrylate de methyle en presence d'aletcl::(2) ou alet::(2)cl en solution dans du toluene ou du tetrachlorure de carbone. Analyse d'un mecanisme faisant intervenir des reactions de propagation croisees
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Kontur, Wayne. "Kinetic investigation of the molecular processes involved in the mechanism of open complex formation between E. coli RNA polymerase and the [lambda]Pr promoter." 2006. http://www.library.wisc.edu/databases/connect/dissertations.html.
Full textBook chapters on the topic "Complex Reaction Mechanism - Molecular Processes"
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Nakatani, Naoki, Jia-Jia Zheng, and Shigeyoshi Sakaki. "Approach of Electronic Structure Calculations to Crystal." In The Materials Research Society Series, 209–55. Singapore: Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-99-0260-6_11.
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AbstractNowadays, the importance of molecular crystals and solids with regular structures is increasing in both basic chemistry and applied fields. However, theoretical studies of those systems based on electronic structure theories have been limited. Although density functional theory (DFT) calculations using generalized gradient approximation type functional under periodic boundary condition is effective for such theoretical studies, we need some improvements for calculating the dispersion interaction and the excited state of crystals. Accordingly, in this chapter, two methods for calculating the electronic structures of molecular crystals are discussed: cluster-model/periodic-model (CM/PM)-combined method and quantum mechanics/periodic-molecular mechanics (QM/periodic-MM) method. In the CM/PM-combined method, an infinite crystal system is calculated by the DFT method under periodic boundary condition, and important moieties, which are represented by CMs, are calculated by either DFT method with hybrid-type functionals or wave function theories such as the Møller–Plesset second-order perturbation theory (MP2), spin-component-scaled-MP2, and coupled-cluster singles and doubles theory with perturbative triples (CCSD(T)). This method is useful for gas adsorption into crystals such as metal–organic frameworks. In the QM/periodic-MM method, an important moiety is calculated using a QM method such as the DFT method with hybrid-type functionals and wave function theories, where the effects of the crystal are incorporated into the QM calculation via the periodic MM method using a classical force field. This method is useful for theoretical studies of excited states and chemical reactions. The applications of these methods in the following processes are described in this chapter: adsorption of gas molecules on metal–organic frameworks, chemical reactions in crystals, and luminescence of the crystals of transition metal complexes. To the best of our knowledge, the theoretical calculations conducted in this chapter show one of the successful approaches of electronic structure theories to molecular crystals, because of the reasonable and practical approximations.
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Solomon, Edward I., Christian H. Kjaergaard, and David E. Heppner. "Molecular Properties and Reaction Mechanism of Multicopper Oxidases Related to Their Use in Biofuel Cells." In Electrochemical Processes in Biological Systems, 169–212. Hoboken, NJ: John Wiley & Sons, Inc, 2015. http://dx.doi.org/10.1002/9781118899076.ch8.
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Paro, Renato, Ueli Grossniklaus, Raffaella Santoro, and Anton Wutz. "Chromatin Dynamics." In Introduction to Epigenetics, 29–47. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-68670-3_2.
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AbstractThe nucleus of a eukaryotic cell is a very busy place. Not only during replication of the DNA, but at any time in the cell cycle specific enzymes need access to genetic information to process reactions such as transcription and DNA repair. Yet, the nucleosomal structure of chromatin is primarily inhibitory to these processes and needs to be resolved in a highly orchestrated manner to allow developmental, organismal, and cell type-specific nuclear activities. This chapter explains how nucleosomes organize and structure the genome by interacting with specific DNA sequences. Variants of canonical histones can change the stability of the nucleosomal structure and also provide additional epigenetic layers of information. Chromatin remodeling complexes work locally to alter the regular beads-on-a-string organization and provide access to transcription and other DNA processing factors. Conversely, factors like histone chaperones and highly precise templating and copying mechanisms are required for the reassembly of nucleosomes and reestablishment of the epigenetic landscape after passage of activities processing DNA sequence information. A very intricate molecular machinery ensures a highly dynamic yet heritable chromatin template.
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Varfolomeev, Sergey, Bella Grigorenko, Sofya Lushchekina, Patrick Masson, Galina Mahaeva, and Alexander Nemuchin. "Human cholinesterases." In ORGANOPHOSPHORUS NEUROTOXINS, 69–126. ru: Publishing Center RIOR, 2020. http://dx.doi.org/10.29039/21_069-126.
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The work is devoted to modeling the elementary stages of the hydrolysis reaction in the active site of enzymes belonging to the class of cholinesterases — acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). The study allowed to describe at the molecular level the effect of the polymorphic modification of BChE, causing serious physiolog ical consequences. Cholinesterase plays a crucial role in the human body. AChE is one of the key enzymes of the central nervous system, and BChE performs protective functions in the body. According to the results of calculations using the combined method of quantum and molecular mechanics (KM/MM), the mechanism of the hydrolysis of the native acetylcholine substrate in the AChE active center was detailed. For a series of ester substrates, a method for estimation of dependence of the enzyme reactivity on the structure of the substrate has been developed. The mechanism of hydrolysis of the muscle relaxant of succininylcholine BChE and the effect of the Asp70Gly polymorph on it were studied. Using various computer simulation methods, the stability of the enzyme-substrate complex of two enzyme variants with succinylcholine was studied.
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Varfolomeev, Sergey, Bella Grigorenko, Sofya Lushchekina, and Alexander Nemuchin. "Human cholinesterases." In Organophosphorous Neurotoxins, 63–120. ru: Publishing Center RIOR, 2020. http://dx.doi.org/10.29039/chapter_5e4132b5f22366.15634219.
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The work is devoted to modeling the elementary stages of the hydrolysis reaction in the active site of enzymes belonging to the class of cholinesterases — acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). The study allowed to describe at the molecular level the effect of the polymorphic modification of BChE, causing serious physiolog ical consequences. Cholinesterase plays a crucial role in the human body. AChE is one of the key enzymes of the central nervous system, and BChE performs protective functions in the body. According to the results of calculations using the combined method of quantum and molecular mechanics (KM/MM), the mechanism of the hydrolysis of the native acetylcholine substrate in the AChE active center was detailed. For a series of ester substrates, a method for estimation of dependence of the enzyme reactivity on the structure of the substrate has been developed. The mechanism of hydrolysis of the muscle relaxant of succininylcholine BChE and the effect of the Asp70Gly polymorph on it were studied. Using various computer simulation methods, the stability of the enzyme-substrate complex of two enzyme variants with succinylcholine was studied.
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Frey, Perry A., and Adrian D. Hegeman. "Complex Enzymes." In Enzymatic Reaction Mechanisms. Oxford University Press, 2007. http://dx.doi.org/10.1093/oso/9780195122589.003.0022.
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Most enzymes discussed in the preceding chapters consist of single proteins that catalyze single biochemical reactions. Many of them contain one type of polypeptide chain, although most exist as oligomers of a polypeptide, and some consist of different polypeptides that cooperate to catalyze one reaction. Increasing attention is being focused on enzymes that catalyze more complex processes and are composed of more than one enzyme or enzymatic domain, each of which catalyzes or facilitates a specific biochemical process. These complex enzymes are the subjects of this chapter. Complex enzymes are so numerous and the processes they catalyze so complex that a complete discussion would fill a book. We therefore limit this discussion to a few examples. The first complex enzymes to be discovered were the multienzyme complexes. They included the four terminal electron transport complexes of the respiratory chain: complex I, known as NADH dehydrogenase (formerly DPNH dehydrogenase); complex II, known as succinate dehydrogenase; complex III, known as cytochrome c reductase; and complex IV, known as cytochrome c oxidase. Other multienzyme complexes discovered at about the same time were the pyruvate dehydrogenase and α-ketoglutarate dehydrogenase complexes, the fatty acid synthase complexes, and the glycine reductase complex and the anthranilate synthase complex. Later, the multimodular polyketide synthases and nonribosomal polypeptide synthetases were characterized. The ATP synthases are multiprotein complexes that function as molecular motors in catalyzing a complex reaction, the condensation of ADP with Pi driven by proton translocation to form ATP. The ribosome catalyzes the polymerization of amino acids in defined sequences specified by the nucleotide sequences in species of mRNA, and nitrogenase catalyzes the ATP-dependent reduction of molecular nitrogen to ammonia. Some of the actions of complex enzymes link together common biochemical reactions of the types discussed in preceding chapters. Others catalyze difficult reactions through mechanistic coupling to energy-producing processes that provide driving force for otherwise unfavorable transformations. We present examples of each type. Catalysis by an α-ketoacid dehydrogenase complex is carried out by three physically associated enzymes, a TPP-dependent α-ketoacid dehydrogenase (E1), a dihydrolipoyl transacetylase (E2), and dihydrolipoyl dehydrogenase (E3).
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Ross, John, Igor Schreiber, and Marcel O. Vlad. "Introduction to Chemical Kinetic Processes." In Determination of Complex Reaction Mechanisms. Oxford University Press, 2006. http://dx.doi.org/10.1093/oso/9780195178685.003.0004.
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It is useful to have a brief discussion of some kinetic processes that we shall treat in later chapters. Some, but not all, of the material in this chapter is presented in [1] in more detail. A macroscopic, deterministic chemical reacting system consists of a number of different species, each with a given concentration (molecules or moles per unit volume). The word “macroscopic” implies that the concentrations are of the order of Avogadro’s number (about 6.02 × 1023) per liter. The concentrations are constant at a given instant, that is, thermal fluctuations away from the average concentration are negligibly small (more in section 2.3). The kinetics in many cases, but far from all, obeys mass action rate expressions of the type . . . dA/dt = k(T )AαBβ . . . (2.1) . . . where T is temperature, A is the concentration of species A, the same for B, and possibly other species indicated by dots in the equation, and α and β are empirically determined “orders” of reaction. The rate coefficient k is generally a function of temperature and frequently a function of T only. The dependence of k on T is given empirically by the Arrhenius equation . . . k(T ) = C exp−Ea/RT (2.2) . . . where C, the frequency factor, is either nearly constant or a weakly dependent function of temperature, and Ea is the activation energy. Rate coefficients are averages of reaction cross-sections, as measured for example by molecular beam experiments. The a priori calculation of cross-sections from quantum mechanical fundamentals is extraordinarily difficult and has been done to good accuracy only for the simplest trimolecular systems (such as D + H2). A widely used alternative approach is based on activated complex theory. In its simplest form, two reactants collide and form an activated complex, said to be in equilibrium. One degree of freedom of the complex, a vibration, is allowed to lead to the dissociation of the complex to products, and the rate of that dissociation is taken to be the rate of the reaction.
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Ross, John, Igor Schreiber, and Marcel O. Vlad. "Experimental Test and Applications of Correlation Metric Construction." In Determination of Complex Reaction Mechanisms. Oxford University Press, 2006. http://dx.doi.org/10.1093/oso/9780195178685.003.0010.
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In this chapter we present an experimental test case of the deduction of a reaction pathway and mechanism by means of correlation metric construction from time-series measurements of the concentrations of chemical species. We choose as the system an enzymatic reaction network, the initial steps of glycolysis. Glycolysis is central in intermediary metabolism and has a high degree of regulation. The reaction pathway has been well studied and thus it is a good test for the theory. Further, the reaction mechanism of this part of glycolysis has been modeled extensively. The quantity and precision of the measurements reported here are sufficient to determine the matrix of correlation functions and, from this, a reaction pathway that is qualitatively consistent with the reaction mechanism established previously. The existence of unmeasured species did not compromise the analysis. The quantity and precision of the data were not excessive, and thus we expect the method to be generally applicable. This CMC experiment was carried out in a continuous-flow stirred-tank reactor (CSTR). The reaction network considered consists of eight enzymes, which catalyze the conversion of glucose into dihydroxyacetone phosphate and glyceraldehyde phosphate. The enzymes were confined to the reactor by an ultrafiltration membrane at the top of the reactor. The membrane was permeable to all low molecular weight species. The inputs are (1) a reaction buffer, which provides starting material for the reaction network to process, maintains pH and pMg, and contains any other species that act as constant constraints on the system dynamics, and (2) a set of “control species” (at least one), whose input concentrations are changed randomly every sampling period over the course of the experiment. The sampling period is chosen such that the system almost, but not quite, relaxes to a chosen nonequilibrium steady state. The system is kept near enough to its steady state to minimize trending (caused by the relaxation) in the time series, but far enough from the steady state that the time-lagged autocorrelation functions for each species decay to zero over three to five sampling periods. This long decay is necessary if temporal ordering in the network is to be analyzed.
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Frey, Perry A., and Adrian D. Hegeman. "Decarboxylation and Carboxylation." In Enzymatic Reaction Mechanisms. Oxford University Press, 2007. http://dx.doi.org/10.1093/oso/9780195122589.003.0012.
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Decarboxylation is an essential process in catabolic metabolism of essentially all nutrients that serve as sources of energy in biological cells and organisms. The most widely known biological process leading to decarboxylation is the metabolism of glucose, in which all of the carbon in the molecule is oxidized to carbon dioxide by way of the glycolytic pathway, the pyruvate dehydrogenase complex, and the tricarboxylic acid cycle. The decarboxylation steps take place in thiamine pyrophosphate (TPP)–dependent α-ketoacid dehydrogenase complexes and isocitrate dehydrogenase. The latter enzyme does not require a coenzyme, other than the cosubstrate NAD+. Many other decarboxylations require coenzymes such as pyridoxal-5'-phosphate (PLP) or a pyruvoyl moiety in the peptide chain. Biological carboxylation is the essential process in the fixation of carbon dioxide by plants and of bicarbonate by animals, plants, and bacteria. Carboxylation by enzymes requires the action of biotin or a divalent metal cofactor, and it requires ATP when the carboxylating agent is the bicarbonate ion. The most prevalent enzymatic carboxylation is that of ribulose bisphosphate carboxylase (rubisco), which is responsible for carbon dioxide fixation in plants. The basic chemistry of decarboxylation is illustrated by mechanisms A to D in fig. 8-1. The mechanisms all require some means of accommodation for the electrons from the cleavage of the bond linking the carboxylate group to the α-carbon. In mechanism A, an electron sink at the β-carbon provides a haven for two electrons. Acetoacetate decarboxylase functions by this mechanism (see chap. 1), as well as PLP- and TPP-dependent decarboxylases (see chap. 3). In mechanism B, a leaving group at the β-carbon departs with two electrons. Mevalonate-5-diphosphate decarboxylate functions by mechanism B and is discussed in a later section. In mechanism C, a leaving group replaces the α-carbon and departs with a pair of electrons. A biological example is formate dehydrogenase, in which the leaving group is a hydride that is transferred to NAD+. In mechanism D, a free radical center is created adjacent to the α-carbon and potentiates the homolytic scission of the bond to the carboxylate group. Mechanism D requires secondary electron transfer processes to create the radical center and quench the formyl radical.
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Ross, John, Igor Schreiber, and Marcel O. Vlad. "Introduction." In Determination of Complex Reaction Mechanisms. Oxford University Press, 2006. http://dx.doi.org/10.1093/oso/9780195178685.003.0003.
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Chemical kinetics as a science has existed for more than a century. It deals with the rates of reactions and the details of how a given reaction proceeds from reactants to products. In a chemical system with many chemical species, there are several questions to be asked: What species react with what other species? In what temporal order? With what catalysts? And with what results? The answers constitute the macroscopic reaction mechanism. The process can be described macroscopically by listing the reactants, intermediates, products, and all the elementary reactions and catalysts in the reaction system. The present book is a treatise and text on the determination of complex reaction mechanisms in chemistry and in chemical reaction systems that occur in chemical engineering, biochemistry, biology, biotechnology, and genomics. A basic knowledge of chemical kinetics is assumed. Several approaches are suggested for the deduction of information on the causal chemical connectivity of the species, on the elementary reactions among the species, and on the sequence of the elementary reactions that constitute the reaction pathway and the reaction mechanism. Chemical reactions occur by the collisions of molecules, and such an event is called an elementary reaction for specified reactant and product molecules. A balanced stoichiometric equation for an elementary reaction yields the number of each type of molecule according to conservation of atoms, mass, and charge. Figure 1.1 shows a relatively simple reaction mechanism for the decomposition of ozone by light, postulated to occur in a series of three elementary steps. (The details of collisions of molecules and bond rearrangements are not discussed.) All approaches are based on the measurements of the concentrations of chemical species in the whole reaction system, not on parts, as has been the practice. One approach is called the pulse method, in which a pulse of concentration of one or more species of arbitrary strength is applied to a reacting system and the responses of as many species as possible are measured. From these responses causal chemical connectivities may be inferred. The basic theory is explained, demonstrated on a model mechanism, and tested in an experiment on a part of glycolysis.
Conference papers on the topic "Complex Reaction Mechanism - Molecular Processes"
1
Tom, Harry W. K., Judith A. Prybyla, and Gary D. Aumiller. "Observation of the Laser-Induced Desorption of CO from Cu(111) with 100 Femtosecond Time-Resolution." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 1992. http://dx.doi.org/10.1364/up.1992.fd5.
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The most promising aspects of ultrafast investigations of chemical systems are the possibility of resolving reactions on the time-scale of bond-formation and bond-breaking and of understanding the microscopic dynamical processes that drive reactions. For molecules adsorbed on solid surfaces, the relevant time-scale is 100 fsec: this time is short enough to resolve molecular bond changes as well as the transfer of energy between the electronic and vibrational degrees of freedom in the substrate and substrate-adsorbate complex. We have used 100 fsec time-resolved second-harmonic generation to probe the departure of adsorbed CO molecules from a Cu(111) surface after the surface is irradiated with a 100 fsec, 2 eV laser pump pulse. The desorption event is >90% completed within the first 325 fsec after the pump pulse. In contrast to techniques that measure the properties of desorbed molecules,[1] SHG allows us to probe the adsorbed molecules and in principle to directly measure the reaction time. Here, the reaction time is so short that we can identify the dynamical processes that drive this reaction. All conventional mechanisms (thermal and direct photochemical) are ruled out and a novel mechanism is proposed. We believe hot electrons, produced by 100 fsec excitation of the substrate, excite the adsorbate electronic state several times during the CO-metal stretch period and cooperatively pump the CO-metal stretch into high enough states to desorb the CO.
2
Wang, Shuicai, Tong Ye, Yan Cui, Yaodong Chen, Jianmin Hou, Kunyun Yang, Zhenbao Yu, Chongqin Tang, Tingyun Kuang, and Xun Hou. "Investigation of the Energy Transfer and Electronic Excitation Transport in Photosystem II Reaction Center Using Time-resolved Fluorescence Spectroscopy." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 1994. http://dx.doi.org/10.1364/up.1994.md.12.
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The energy transfer( ET ) and electronic excitation transport( EET ) are two important ultrafast primary processes in PS II reaction centers. All kinds of ultrafast laser spectroscopy techniques are used in the dynamic study on PS II reaction center1. Although many results have been obtained, much debate still exists on the structure and function of the reaction center, the physical mechanism and rates of the ET and EET2. In this paper we report some experimental results on the ultrafast dynamic study on the ET and EET in the PS II reaction center. The PS II reaction center, D1/D2/cyt-b559 complex, is isolated and purified from the spinach, which contains 4 or 5 Chia molecules, 2 pheoa molecules, 1 β-carotene molecule.
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Bluestein, Danny, João S. Soares, Peng Zhang, Chao Gao, Seetha Pothapragada, Na Zhang, Marvin J. Slepian, and Yuefan Deng. "Multiscale Modeling of Flow Induced Thrombogenicity Using Dissipative Particle Dynamics and Molecular Dynamics." In ASME 2013 2nd Global Congress on NanoEngineering for Medicine and Biology. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/nemb2013-93094.
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The coagulation cascade of blood may be initiated by flow induced platelet activation, which prompts clot formation in prosthetic cardiovascular devices and arterial disease processes. While platelet activation may be induced by biochemical agonists, shear stresses arising from pathological flow patterns enhance the propensity of platelets to activate and initiate the intrinsic pathway of coagulation, leading to thrombosis. Upon activation platelets undergo complex biochemical and morphological changes: organelles are centralized, membrane glycoproteins undergo conformational changes, and adhesive pseudopods are extended. Activated platelets polymerize fibrinogen into a fibrin network that enmeshes red blood cells. Activated platelets also cross-talk and aggregate to form thrombi. Current numerical simulations to model this complex process mostly treat blood as a continuum and solve the Navier-Stokes equations governing blood flow, coupled with diffusion-convection-reaction equations. It requires various complex constitutive relations or simplifying assumptions, and is limited to μm level scales. However, molecular mechanisms governing platelet shape change upon activation and their effect on rheological properties can be in the nm level scales. To address this challenge, a multiscale approach which departs from continuum approaches, may offer an effective means to bridge the gap between macroscopic flow and cellular scales. Molecular dynamics (MD) and dissipative particle dynamics (DPD) methods have been employed in recent years to simulate complex processes at the molecular scales, and various viscous fluids at low-to-high Reynolds numbers at mesoscopic scales. Such particle methods possess important properties at the mesoscopic scale: complex fluids with heterogeneous particles can be modeled, allowing the simulation of processes which are otherwise very difficult to solve by continuum approaches. It is becoming a powerful tool for simulating complex blood flow, red blood cells interactions, and platelet-mediated thrombosis involving platelet activation, aggregation, and adhesion.
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Zhang, Peng, Jawaad Sheriff, João S. Soares, Chao Gao, Seetha Pothapragada, Na Zhang, Yuefan Deng, and Danny Bluestein. "Multiscale Modeling of Flow Induced Thrombogenicity Using Dissipative Particle Dynamics and Coarse Grained Molecular Dynamics." In ASME 2013 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/sbc2013-14187.
Full textAbstract:
The coagulation cascade of blood may be initiated by flow induced platelet activation, which prompts clot formation in prosthetic cardiovascular devices and arterial disease processes. While platelet activation may be induced by biochemical agonists, shear stresses arising from pathological flow patterns enhance the propensity of platelets to activate and initiate the intrinsic pathway of coagulation, leading to thrombosis. Upon activation platelets undergo complex biochemical and morphological changes: organelles are centralized, membrane glycoproteins undergo conformational changes, and adhesive pseudopods are extended. Activated platelets polymerize fibrinogen into a fibrin network that enmeshes red blood cells. Activated platelets also cross-talk and aggregate to form thrombi. Current numerical simulations to model this complex process mostly treat blood as a continuum and solve the Navier-Stokes equations governing blood flow, coupled with diffusion-convection-reaction equations. It requires various complex constitutive relations or simplifying assumptions, and is limited to μm level scales. However, molecular mechanisms governing platelet shape change upon activation and their effect on rheological properties can be in the nm level scales. To address this challenge, a multiscale approach which departs from continuum approaches, may offer an effective means to bridge the gap between macroscopic flow and cellular scales. Coarse Grained Molecular dynamics (CGMD) and discrete/dissipative particle dynamics (DPD) methods have been employed in recent years to simulate complex processes at the molecular scales, and various viscous fluids at low-to-high Reynolds numbers at mesoscopic scales. Such particle methods possess important properties at the mesoscopic scale: complex fluids with heterogeneous particles can be modeled, allowing the simulation of processes which are otherwise very difficult to solve by continuum approaches. It is becoming a powerful tool for simulating complex blood flow, red blood cells interactions, and platelet-mediated thrombosis involving platelet activation, aggregation, and adhesion.
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Bluestein, Danny, João S. Soares, Peng Zhang, Chao Gao, Seetha Pothapragada, Na Zhang, Marvin J. Slepian, and Yuefan Deng. "Multiscale Modeling of Flow Induced Thrombogenicity With Dissipative Particle Dynamics (DPD) and Molecular Dynamics (MD)." In ASME 2013 Conference on Frontiers in Medical Devices: Applications of Computer Modeling and Simulation. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/fmd2013-16176.
Full textAbstract:
The coagulation cascade of blood may be initiated by flow induced platelet activation, which prompts clot formation in prosthetic cardiovascular devices and arterial disease processes. While platelet activation may be induced by biochemical agonists, shear stresses arising from pathological flow patterns enhance the propensity of platelets to activate and initiate the intrinsic pathway of coagulation, leading to thrombosis. Upon activation platelets undergo complex biochemical and morphological changes: organelles are centralized, membrane glycoproteins undergo conformational changes, and adhesive pseudopods are extended. Activated platelets polymerize fibrinogen into a fibrin network that enmeshes red blood cells. Activated platelets also cross-talk and aggregate to form thrombi. Current numerical simulations to model this complex process mostly treat blood as a continuum and solve the Navier-Stokes equations governing blood flow, coupled with diffusion-convection-reaction equations. It requires various complex constitutive relations or simplifying assumptions, and is limited to μm level scales. However, molecular mechanisms governing platelet shape change upon activation and their effect on rheological properties can be in the nm level scales. To address this challenge, a multiscale approach which departs from continuum approaches, may offer an effective means to bridge the gap between macroscopic flow and cellular scales. Molecular dynamics (MD) and dissipative particle dynamics (DPD) methods have been employed in recent years to simulate complex processes at the molecular scales, and various viscous fluids at low-to-high Reynolds numbers at mesoscopic scales. Such particle methods possess important properties at the mesoscopic scale: complex fluids with heterogeneous particles can be modeled, allowing the simulation of processes which are otherwise very difficult to solve by continuum approaches. It is becoming a powerful tool for simulating complex blood flow, red blood cells interactions, and platelet-mediated thrombosis involving platelet activation, aggregation, and adhesion.
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Gupta, Ashwani K. "Challenges and Opportunities for Solid Wastes (Invited)." In ASME 2005 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2005. http://dx.doi.org/10.1115/detc2005-84607.
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Incineration of plastic and other waste has provided energy recovery opportunities, together with associated challenges on the environmentally benign energy recovery. Most of the wastes have significant energy potential, the utilization of which can save millions of dollars on the national scale. However difficulties exist for their utilization in propulsion and power systems in an environmentally acceptable manner. It is anticipated that the amount of waste generated will continue to grow in the new millennium, along with associated changes in its composition. Incineration (thermal destruction) of wastes to the molecular level allows one to more cleanly convert into usable energy. The challenges provide opportunities for combustion engineers, whose research has expanded significantly in recent years, particularly in areas related to fossil fuels and wastes being used as fuels. The field of combustion is further diversified by the complex nature of most reaction processes. Fuel chemistry, fluid mechanics, convective and radiative heat transfer, gas-phase elementary reactions, turbulence, and particle kinetics and dynamics are relevant processes that often have a direct, and sometimes controlling influence, on the behavior of a particular combustion system. Sensors, diagnostics and miniaturization of the system continue to be of major importance for successful implementation of this new technology.
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Zinth, W., U. Finkele, C. Lauterwasser, K. Dressier, E. Umlauf, S. Schmidt, and W. Kaiser. "Molecular Processes in the Primary Reaction of Photosynthetic Reaction Centers." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 1992. http://dx.doi.org/10.1364/up.1992.wa3.
Full textAbstract:
The primary electron transfer (ET) is the key process in photosynthesis. It occurs in a membrane bound pigment protein complex called reaction center (RC). Fortunately x-ray structure analysis has revealed the arrangement of aminoacids and chromophores of the RC giving the basic information for an understanding of the primary ET on a molecular basis: The important actors in the primary ET are four bacteriochlorphyll (BChl) and two bacteriopheophytin (BPh) molecules. After optical excitation of the primary donor P (which is a "special pair" of BChl molecules) the electron travels to or passes by the accessory BChl B and arrives within less than 4 ps at the BPh H before it finally (on the picosecond time scale) reaches the quinone Q after 200 ps. While the role of quinone Q and BPh H as real electron carriers is well established there is no general agreement about the function of the BChl B. Recently femtosecond absorption data have revealed a weak additional 0.9 ps kinetic component compatible with the assignment that the radical pair state P+B– is a real intermediate in the reaction (see model A in Fig. 1). However, alternative reaction models (B and C) - where the electron does not reside on the BChl B - could not be excluded by experimental data on native RC at room temperature.
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Reddy, N. R. S., and G. J. Small. "Hole Burning of the Exciton Coupled Antenna Complex of Rhodobacter Sphaeroides." In Persistent Spectral Hole Burning: Science and Applications. Washington, D.C.: Optica Publishing Group, 1991. http://dx.doi.org/10.1364/pshb.1991.the14.
Full textAbstract:
Efficient energy transfer in light harvesting (LH) complexes forms an important part of the photosynthetic process that results in the conversion of light energy into chemical free energy. A number of factors are important for understanding the process that directs the optical excitation to the reaction center. Included are the nature of relevant excited states of chlorophylls (e.g. localised or delocalised), bath induced mechanisms for homogeneous broadening of transitions etc. The Qy-absorption (S1) of chlorophyllic molecules in protein complexes appears as inhomogeneously broadened bands with ΓI ~ 50 - 200cm-1 at liquid helium temperatures.
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Chiu, Hui-Ling, John Deak, and R. J. Dwayne Miller. "The Primary Processes in Heme Protein Relaxation: The Coupled Reaction Coordinate Problem in Molecular Cooperativity." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 1996. http://dx.doi.org/10.1364/up.1996.fc.3.
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The phenomena of molecular cooperativity involves an interaction between two or more different protein moieties in which the protein's function is controlled synergistically by its neighbor. Changes in state of the adjacent protein, such as changes in ligation of a receptor molecule, affect the reaction rate of its neighbor, often several nanometers away. The reaction rate can be controlled by either changes in the reaction free energy or activation barriers. Our current understanding of this process is based on structural changes at one site affecting the adjacent activation barrier. In order to affect a reaction coordinate at a distance, these structural changes must involve highly correlated atomic displacements coupling thousands of degrees of freedom. The key question then is what is the mechanism by which the reaction forces at one site propagate to adjacent sites, i.e., what is the communication pathway? How do the reaction forces which develop on an atomic length scale couple to mesoscopic dimensions of motion?
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Houle, F. A. "Mechanism of Chemical Etching of doped GaAs by Cl2." In The Microphysics of Surfaces: Beam-Induced Processes. Washington, D.C.: Optica Publishing Group, 1991. http://dx.doi.org/10.1364/msbip.1991.tua2.
Full textAbstract:
Consideration of product volatility and thermodynamic stability have been central to models developed for the thermal etching and deposition of GaAs by Cl21,2 Mass spectrometric studies of the etching chemistry have tended to support some of the basic assumptions of these models: that the thermodynamically most stable product is formed and that product volatility controls the etch rate. Surface analyses, for example, have revealed the presence of a Ga-rich scale after etching, to be expected if the As chlorides arc more volatile and desorb more readily.3-5 Consequently, models of beam modification of GaAs in the presence of Cl2 have focussed on how energetic particles or light might perturb the thermal reaction. In this work the validity of the basis for these models has been examined by investigation of the etching chemistry of doped GaAs by molecular beam mass spectrometry and in situ Auger spectroscopy.
Reports on the topic "Complex Reaction Mechanism - Molecular Processes"
1
Morrison, Mark, and Joshuah Miron. Molecular-Based Analysis of Cellulose Binding Proteins Involved with Adherence to Cellulose by Ruminococcus albus. United States Department of Agriculture, November 2000. http://dx.doi.org/10.32747/2000.7695844.bard.
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At the beginning of this project, it was clear that R. albus adhered tightly to cellulose and its efficient degradation of this polysaccharide was dependent on micromolar concentrations of phenylacetic acid (PAA) and phenylpropionic acid (PPA). The objectives for our research were: i) to identify how many different kinds of cellulose binding proteins are produced by Ruminococcus albus; ii) to isolate and clone the genes encoding some of these proteins from the same bacterium; iii) to determine where these various proteins were located and; iv) quantify the relative importance of these proteins in affecting the rate and extent to which the bacterium becomes attached to cellulose. BARD support has facilitated a number of breakthroughs relevant to our fundamental understanding of the adhesion process. First, R. albus possesses multiple mechanisms for adhesion to cellulose. The P.I.'s laboratory has discovered a novel cellulose-binding protein (CbpC) that belongs to the Pil-protein family, and in particular, the type 4 fimbrial proteins. We have also obtained genetic and biochemical evidence demonstrating that, in addition to CbpC-mediated adhesion, R. albus also produces a cellulosome-like complex for adhesion. These breakthroughs resulted from the isolation (in Israel and the US) of spontaneously arising mutants of R. albus strains SY3 and 8, which were completely or partially defective in adhesion to cellulose, respectively. While the SY3 mutant strain was incapable of growth with cellulose as the sole carbon source, the strain 8 mutants showed varying abilities to degrade and grow with cellulose. Biochemical and gene cloning experiments have been used in Israel and the US, respectively, to identify what are believed to be key components of a cellulosome. This combination of cellulose adhesion mechanisms has not been identified previously in any bacterium. Second, differential display, reverse transcription polymerase chain reaction (DD RT-PCR) has been developed for use with R. albus. A major limitation to cellulose research has been the intractability of cellulolytic bacteria to genetic manipulation by techniques such as transposon mutagenesis and gene displacement. The P.I.'s successfully developed DD RT- PCR, which expanded the scope of our research beyond the original objectives of the project, and a subset of the transcripts conditionally expressed in response to PAA and PPA have been identified and characterized. Third, proteins immunochemically related to the CbpC protein of R. albus 8 are present in other R. albus strains and F. intestinalis, Western immunoblots have been used to examine additional strains of R. albus, as well as other cellulolytic bacteria of ruminant origin, for production of proteins immunochemically related to the CbpC protein. The results of these experiments showed that R. albus strains SY3, 7 and B199 all possess a protein of ~25 kDa which cross-reacts with polyclonal anti-CbpC antiserum. Several strains of Butyrivibrio fibrisolvens, Ruminococcus flavefaciens strains C- 94 and FD-1, and Fibrobacter succinogenes S85 produced no proteins that cross-react with the same antiserum. Surprisingly though, F. intestinalis strain DR7 does possess a protein(s) of relatively large molecular mass (~200 kDa) that was strongly cross-reactive with the anti- CbpC antiserum. Scientifically, our studies have helped expand the scope of our fundamental understanding of adhesion mechanisms in cellulose-degrading bacteria, and validated the use of RNA-based techniques to examine physiological responses in bacteria that are nor amenable to genetic manipulations. Because efficient fiber hydrolysis by many anaerobic bacteria requires both tight adhesion to substrate and a stable cellulosome, we believe our findings are also the first step in providing the resources needed to achieve our long-term goal of increasing fiber digestibility in animals.
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Banin, Amos, Joseph Stucki, and Joel Kostka. Redox Processes in Soils Irrigated with Reclaimed Sewage Effluents: Field Cycles and Basic Mechanism. United States Department of Agriculture, July 2004. http://dx.doi.org/10.32747/2004.7695870.bard.
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The overall objectives of the project were: (a) To measure and study in situ the effect of irrigation with reclaimed sewage effluents on redox processes and related chemical dynamics in soil profiles of agricultural fields. (b) To study under controlled conditions the kinetics and equilibrium states of selected processes that affect redox conditions in field soils or that are effected by them. Specifically, these include the effects on heavy metals sorption and desorption, and the effect on pesticide degradation. On the basis of the initial results from the field study, increased effort was devoted to clarifying and quantifying the effects of plants and water regime on the soil's redox potential while the study of heavy metals sorption was limited. The use of reclaimed sewage effluents as agricultural irrigation water is increasing at a significant rate. The relatively high levels of suspended and, especially, dissolved organic matter and nitrogen in effluents may affect the redox regime in field soils irrigated with them. In turn, the changes in redox regime may affect, among other parameters, the organic matter and nitrogen dynamics of the root zone and trace organic decomposition processes. Detailed data of the redox potential regime in field plots is lacking, and the detailed mechanisms of its control are obscure and not quantified. The study established the feasibility of long-term, non-disturbing monitoring of redox potential regime in field soils. This may enable to manage soil redox under conditions of continued inputs of wastewater. The importance of controlling the degree of wastewater treatment, particularly of adding ultrafiltration steps and/or tertiary treatment, may be assessed based on these and similar results. Low redox potential was measured in a field site (Site A, KibutzGivat Brenner), that has been irrigated with effluents for 30 years and was used for 15 years for continuous commercial sod production. A permanently reduced horizon (Time weighted averaged pe= 0.33±3.0) was found in this site at the 15 cm depth throughout the measurement period of 10 months. A drastic cultivation intervention, involving prolonged drying and deep plowing operations may be required to reclaim such soils. Site B, characterized by a loamy texture, irrigated with tap water for about 20 years was oxidized (Time weighted average pe=8.1±1.0) throughout the measurement period. Iron in the solid phases of the Givat Brenner soils is chemically-reduced by irrigation. Reduced Fe in these soils causes a change in reactivity toward the pesticide oxamyl, which has been determined to be both cytotoxic and genotoxic to mammalian cells. Reaction of oxamyl with reduced-Fe clay minerals dramatically decreases its cytotoxicity and genotoxicity to mammalian cells. Some other pesticides are affected in the same manner, whereas others are affected in the opposite direction (become more cyto- and genotoxic). Iron-reducing bacteria (FeRB) are abundant in the Givat Brenner soils. FeRB are capable of coupling the oxidation of small molecular weight carbon compounds (fermentation products) to the respiration of iron under anoxic conditions, such as those that occur under flooded soil conditions. FeRB from these soils utilize a variety of Fe forms, including Fe-containing clay minerals, as the sole electron acceptor. Daily cycles of the soil redox potential were discovered and documented in controlled-conditions lysimeter experiments. In the oxic range (pe=12-8) soil redox potential cycling is attributed to the effect of the daily temperature cycle on the equilibrium constant of the oxygenation reaction of H⁺ to form H₂O, and is observed under both effluent and freshwater irrigation. The presence of plants affects considerably the redox potential regime of soils. Redox potential cycling coupled to the irrigation cycles is observed when the soil becomes anoxic and the redox potential is controlled by the Fe(III)/Fe(II) redox couple. This is particularly seen when plants are grown. Re-oxidation of the soil after soil drying at the end of an irrigation cycle is affected to some degree by the water quality. Surprisingly, the results suggest that under certain conditions recovery is less pronounced in the freshwater irrigated soils.
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Tzfira, Tzvi, Michael Elbaum, and Sharon Wolf. DNA transfer by Agrobacterium: a cooperative interaction of ssDNA, virulence proteins, and plant host factors. United States Department of Agriculture, December 2005. http://dx.doi.org/10.32747/2005.7695881.bard.
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Agrobacteriumtumefaciensmediates genetic transformation of plants. The possibility of exchanging the natural genes for other DNA has led to Agrobacterium’s emergence as the primary vector for genetic modification of plants. The similarity among eukaryotic mechanisms of nuclear import also suggests use of its active elements as media for non-viral genetic therapy in animals. These considerations motivate the present study of the process that carries DNA of bacterial origin into the host nucleus. The infective pathway of Agrobacterium involves excision of a single-stranded DNA molecule (T-strand) from the bacterial tumor-inducing plasmid. This transferred DNA (T-DNA) travels to the host cell cytoplasm along with two virulence proteins, VirD2 and VirE2, through a specific bacteriumplant channel(s). Little is known about the precise structure and composition of the resulting complex within the host cell and even less is known about the mechanism of its nuclear import and integration into the host cell genome. In the present proposal we combined the expertise of the US and Israeli labs and revealed many of the biophysical and biological properties of the genetic transformation process, thus enhancing our understanding of the processes leading to nuclear import and integration of the Agrobacterium T-DNA. Specifically, we sought to: I. Elucidate the interaction of the T-strand with its chaperones. II. Analyzing the three-dimensional structure of the T-complex and its chaperones in vitro. III. Analyze kinetics of T-complex formation and T-complex nuclear import. During the past three years we accomplished our goals and made the following major discoveries: (1) Resolved the VirE2-ssDNA three-dimensional structure. (2) Characterized VirE2-ssDNA assembly and aggregation, along with regulation by VirE1. (3) Studied VirE2-ssDNA nuclear import by electron tomography. (4) Showed that T-DNA integrates via double-stranded (ds) intermediates. (5) Identified that Arabidopsis Ku80 interacts with dsT-DNA intermediates and is essential for T-DNA integration. (6) Found a role of targeted proteolysis in T-DNA uncoating. Our research provide significant physical, molecular, and structural insights into the Tcomplex structure and composition, the effect of host receptors on its nuclear import, the mechanism of T-DNA nuclear import, proteolysis and integration in host cells. Understanding the mechanical and molecular basis for T-DNA nuclear import and integration is an essential key for the development of new strategies for genetic transformation of recalcitrant plant species. Thus, the knowledge gained in this study can potentially be applied to enhance the transformation process by interfering with key steps of the transformation process (i.e. nuclear import, proteolysis and integration). Finally, in addition to the study of Agrobacterium-host interaction, our research also revealed some fundamental insights into basic cellular mechanisms of nuclear import, targeted proteolysis, protein-DNA interactions and DNA repair.
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Ohad, Nir, and Robert Fischer. Regulation of plant development by polycomb group proteins. United States Department of Agriculture, January 2008. http://dx.doi.org/10.32747/2008.7695858.bard.
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Our genetic and molecular studies have indicated that FIE a WD-repeat Polycomb group (PcG) protein takes part in multi-component protein complexes. We have shown that FIE PcG protein represses inappropriate programs of development during the reproductive and vegetative phases of the Arabidopsis life cycle. Moreover, we have shown that FIE represses the expression of key regulatory genes that promote flowering (AG and LFY), embryogenesis (LEC1), and shoot formation (KNAT1). These results suggest that the FIE PcG protein participates in the formation of distinct PcG complexes that repress inappropriate gene expression at different stages of plant development. PcG complexes modulate chromatin compactness by modifying histones and thereby regulate gene expression and imprinting. The main goals of our original project were to elucidate the biological functions of PcG proteins, and to understand the molecular mechanisms used by FIE PcG complexes to repress the expression of its gene targets. Our results show that the PcG complex acts within the central cell of the female gametophyte to maintain silencing of MEA paternal allele. Further more we uncovered a novel example of self-imprinting mechanism by the PgG complex. Based on results obtained in the cures of our research program we extended our proposed goals and elucidated the role of DME in regulating plant gene imprinting. We discovered that in addition to MEA,DME also imprints two other genes, FWA and FIS2. Activation of FWA and FIS2 coincides with a reduction in 5-methylcytosine in their respective promoters. Since endosperm is a terminally differentiated tissue, the methylation status in the FWA and FIS2 promoters does not need to be reestablished in the following generation. We proposed a “One-Way Control” model to highlight differences between plant and animal genomic imprinting. Thus we conclude that DEMETER is a master regulator of plant gene imprinting. Future studies of DME function will elucidate its role in processes and disease where DNA methylation has a key regulatory role both in plants and animals. Such information will provide valuable insight into developing novel strategies to control and improve agricultural traits and overcome particular human diseases.
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Chamovitz, Daniel, and Albrecht Von Arnim. Translational regulation and light signal transduction in plants: the link between eIF3 and the COP9 signalosome. United States Department of Agriculture, November 2006. http://dx.doi.org/10.32747/2006.7696515.bard.
Full textAbstract:
The COP9 signalosome (CSN) is an eight-subunit protein complex that is highly conserved among eukaryotes. Genetic analysis of the signalosome in the plant model species Arabidopsis thaliana has shown that the signalosome is a repressor of light dependent seedling development as mutant Arabidopsis seedlings that lack this complex develop in complete darkness as if exposed to light. These mutant plants die following the seedling stage, even when exposed to light, indicating that the COP9 signalosome also has a central role in the regulation of normal photomorphogenic development. The biochemical mode of action of the signalosome and its position in eukaryotic cell signaling pathways is a matter of controversy and ongoing investigation, and recent results place the CSN at the juncture of kinase signaling pathways and ubiquitin-mediated protein degradation. We have shown that one of the many CSN functions may relate to the regulation of translation through the interaction of the CSN with its related complex, eukaryotic initiation factor (eIF3). While we have established a physical connection between eIF3 subunits and CSN subunits, the physiological and developmental significance of this interaction is still unknown. In an effort to understand the biochemical activity of the signalosome, and its role in regulating translation, we originally proposed to dissect the contribution of "h" subunit of eIF3 (eIF3h) along the following specific aims: (i) Isolation and phenotypic characterization of an Arabidopsis loss-of-function allele for eIF3h from insertional mutagenesis libraries; (ii) Creation of designed gain and loss of function alleles for eIF3h on the basis of its nucleocytoplasmic distribution and its yeast-two-hybrid interactions with other eIF3 and signalosome partner proteins; (iii) Determining the contribution of eIF3h and its interaction with the signalosome by expressing specific mutants of eIF3h in the eIF3h- loss-of function background. During the course of the research, these goals were modified to include examining the genetic interaction between csn and eif3h mutations. More importantly, we extended our effort toward the genetic analysis of mutations in the eIF3e subunit, which also interacts with the CSN. Through the course of this research program we have made several critical scientific discoveries, all concerned with the apparent diametrically opposed roles of eIF3h and eIF3e. We showed that: 1) While eIF3e is essential for growth and development, eIF3h is not essential for growth or basal translation; 2) While eIF3e has a negative role in translational regulation, eIF3h is positively required for efficient translation of transcripts with complex 5' UTR sequences; 3) Over-accumulation of eIF3e and loss-of-function of eIF3h both lead to cop phenotypes in dark-grown seedlings. These results were published in one publication (Kim et al., Plant Cell 2004) and in a second manuscript currently in revision for Embo J. Are results have led to a paradigm shift in translation research – eIF3 is now viewed in all systems as a dynamic entity that contains regulatory subuits that affect translational efficiency. In the long-term agronomic outlook, the proposed research has implications that may be far reaching. Many important plant processes, including developmental and physiological responses to light, abiotic stress, photosynthate, and hormones operate in part by modulating protein translation [23, 24, 40, 75]. Translational regulation is slowly coming of age as a mechanism for regulating foreign gene expression in plants, beginning with translational enhancers [84, 85] and more recently, coordinating the expression of multiple transgenes using internal ribosome entry sites. Our contribution to understanding the molecular mode of action of a protein complex as fundamental as eIF3 is likely to lead to advances that will be applicable in the foreseeable future.
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Christopher, David A., and Avihai Danon. Plant Adaptation to Light Stress: Genetic Regulatory Mechanisms. United States Department of Agriculture, May 2004. http://dx.doi.org/10.32747/2004.7586534.bard.
Full textAbstract:
Original Objectives: 1. Purify and biochemically characterize RB60 orthologs in higher plant chloroplasts; 2. Clone the gene(s) encoding plant RB60 orthologs and determine their structure and expression; 3. Manipulate the expression of RB60; 4. Assay the effects of altered RB60 expression on thylakoid biogenesis and photosynthetic function in plants exposed to different light conditions. In addition, we also examined the gene structure and expression of RB60 orthologs in the non-vascular plant, Physcomitrella patens and cloned the poly(A)-binding protein orthologue (43 kDa RB47-like protein). This protein is believed to a partner that interacts with RB60 to bind to the psbA5' UTR. Thus, to obtain a comprehensive view of RB60 function requires analysis of its biochemical partners such as RB43. Background & Achievements: High levels of sunlight reduce photosynthesis in plants by damaging the photo system II reaction center (PSII) subunits, such as D1 (encoded by the chloroplast tpsbAgene). When the rate of D1 synthesis is less than the rate of photo damage, photo inhibition occurs and plant growth is decreased. Plants use light-activated translation and enhanced psbAmRNA stability to maintain D1 synthesis and replace the photo damaged 01. Despite the importance to photosynthetic capacity, these mechanisms are poorly understood in plants. One intriguing model derived from the algal chloroplast system, Chlamydomonas, implicates the role of three proteins (RB60, RB47, RB38) that bind to the psbAmRNA 5' untranslated leader (5' UTR) in the light to activate translation or enhance mRNA stability. RB60 is the key enzyme, protein D1sulfide isomerase (Pill), that regulates the psbA-RN :Binding proteins (RB's) by way of light-mediated redox potentials generated by the photosystems. However, proteins with these functions have not been described from higher plants. We provided compelling evidence for the existence of RB60, RB47 and RB38 orthologs in the vascular plant, Arabidopsis. Using gel mobility shift, Rnase protection and UV-crosslinking assays, we have shown that a dithiol redox mechanism which resembles a Pill (RB60) activity regulates the interaction of 43- and 30-kDa proteins with a thermolabile stem-loop in the 5' UTR of the psbAmRNA from Arabidopsis. We discovered, in Arabidopsis, the PD1 gene family consists of II members that differ in polypeptide length from 361 to 566 amino acids, presence of signal peptides, KDEL motifs, and the number and positions of thioredoxin domains. PD1's catalyze the reversible formation an disomerization of disulfide bonds necessary for the proper folding, assembly, activity, and secretion of numerous enzymes and structural proteins. PD1's have also evolved novel cellular redox functions, as single enzymes and as subunits of protein complexes in organelles. We provide evidence that at least one Pill is localized to the chloroplast. We have used PDI-specific polyclonal and monoclonal antisera to characterize the PD1 (55 kDa) in the chloroplast that is unevenly distributed between the stroma and pellet (containing membranes, DNA, polysomes, starch), being three-fold more abundant in the pellet phase. PD1-55 levels increase with light intensity and it assembles into a high molecular weight complex of ~230 kDa as determined on native blue gels. In vitro translation of all 11 different Pill's followed by microsomal membrane processing reactions were used to differentiate among PD1's localized in the endoplasmic reticulum or other organelles. These results will provide.1e insights into redox regulatory mechanisms involved in adaptation of the photosynthetic apparatus to light stress. Elucidating the genetic mechanisms and factors regulating chloroplast photosynthetic genes is important for developing strategies to improve photosynthetic efficiency, crop productivity and adaptation to high light environments.
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Lers, Amnon, and Pamela J. Green. LX Senescence-Induced Ribonuclease in Tomato: Function and Regulation. United States Department of Agriculture, September 2003. http://dx.doi.org/10.32747/2003.7586455.bard.
Full textAbstract:
Natural leaf senescence, which occurs even when growth conditions are near optimal, has a negative influence on yield. Postharvest induced senescence contributes to the losses of quality in flowers, foliage, and vegetables. Strategies designed to control the senescence process in crop plants could therefore have great applied significance. However, the successful design of such strategies requires a better insight into the senescence machinery and control in higher plants. A main feature of senescence is the hydrolysis of macromolecules by hydrolases of various types such as ribonucleases (RNases) and proteases. Previously we had identified and characterized the tomato LX RNase gene demonstrating its transcript to be highly and specifically induced during senescence. This reported study was focused on LX but also had broadened our research to other senescence-associated nucleic acids degrading enzymes to learn about their function and the regulation of their encoding genes. Beside tomato we used parsley and Arabidopsis for the study of: the bi-functional nuclease which has a role in senescence. The study of different senescence- associated nucleases in few plant systems will allow a more general view on function and regulation of these enzymes in senescence. The specific original proposed objectives included: 1. Study the consequences of alterations in LX RNase level on tomato leaf senescence and general development; 2. Analyze stimuli which may participate in senescence-specific activation of the LX gene; 3. Clone the senescence-associated BFNI nuclease gene homologue from tomato. 4. Further characterize the sequences required for senescence-specific gene expression. Homozygous transgenic plants in which LX gene was either inhibited or over-expressed were generated. In both of these LX mutated plants no major phenotypic consequences were observed, which may suggests that LX is not essential for plant growth under optimal growth conditions. Lack of any abnormalities in the LX over-expressing lines suggests that special system exist to allow function of the RNase only when needed. Detailed analyses of growth under stress and consequences to RNA metabolism are underway. We have analyzed LX expression on the protein level demonstrating that it is involved also in petal senescing. Our results suggest that LX is responding to complex regulation involving developmental, organ dependent factors and responds differently to hormonal or environmental stimuli in the different plant organs. The cloned 1.4 kb promoter was cloned and its analysis revealed that probably not all required elements for senescence induction are included. Biochemical analysis of senescence-associated be-functional nucleases in the different plants, tomato, parsley and Arabidopsis, suggests they belong to a sub-class within the type I plant nucleases. The parsley PcNUC1/2 nuclease protein was purified from senescing leaves its and activity was studied in vitro revealing endo-, double strand, nucleolytic activity and exo-nucleolytic activity. Its encoding gene was cloned and found to be induced on the mRNA level. The promoter of the related Arabidopsis BFNI nuclease was shown in both tomato and Arabidopsis to be able and direct senescence-specific expression suggesting that, at least part, the gene is regulated on the transcriptional level and that the mechanism for this senescence-specific regulation is conserved between different plants. Few plants in which the BFNI gene is mutated were identified which are subjected now to detailed analysis. Our results suggest that the senescence-related nucleic acid degrading enzymes share similarities in both function and regulation between different plants and possibly have important functions in processes un-related to senescence. Still, the function of these enzymes, at least in some cases is not essential to plant development under optimal growth conditions. We are now at the stage which permits in depth investigation of the specific functions and mode of molecular regulation of senescence-associated nucleases with the aid of the research tools developed. The isolated senescence-specific promoter, shown to be active in heterologous plant system, could be utilized in agricultural-related biotechnological applications for retardation of senescence.