28 results on '"Hanan L. Messiha"'
Search Results
2. KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways.
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Irena Spasic, Evangelos Simeonidis, Hanan L. Messiha, Norman W. Paton, and Douglas B. Kell
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- 2009
- Full Text
- View/download PDF
3. From Bugs to Bioplastics: Total (+)‐Dihydrocarvide Biosynthesis by EngineeredEscherichia coli
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Hanan L. Messiha, Gabriel A. Ascue Avalos, Helen S. Toogood, Shirley Tait, and Nigel S. Scrutton
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engineering ,Reductase ,010402 general chemistry ,medicine.disease_cause ,Proof of Concept Study ,01 natural sciences ,Biochemistry ,Chemical synthesis ,Bioplastic ,Lactones ,chemistry.chemical_compound ,Synthetic biology ,Biosynthesis ,Manchester Institute of Biotechnology ,Escherichia coli ,medicine ,Molecular Biology ,chemistry.chemical_classification ,Full Paper ,010405 organic chemistry ,Organic Chemistry ,(+)-dihydrocarvide monomer ,Stereoisomerism ,Full Papers ,Ribosomal RNA ,ResearchInstitutes_Networks_Beacons/manchester_institute_of_biotechnology ,0104 chemical sciences ,bioplastics ,Glucose ,Baeyer–Villiger monooxygenases ,Enzyme ,Metabolic Engineering ,chemistry ,Monoterpenes ,Molecular Medicine ,Synthetic Biology - Abstract
The monoterpenoid lactone derivative (+)‐dihydrocarvide ((+)‐DHCD) can be polymerised to form shape‐memory polymers. Synthetic biology routes from simple, inexpensive carbon sources are an attractive, alternative route over chemical synthesis from (R)‐carvone. We have demonstrated a proof‐of‐principle in vivo approach for the complete biosynthesis of (+)‐DHCD from glucose in Escherichia coli (6.6 mg L−1). The pathway is based on the Mentha spicata route to (R)‐carvone, with the addition of an ′ene′‐reductase and Baeyer–Villiger cyclohexanone monooxygenase. Co‐expression with a limonene synthesis pathway enzyme enables complete biocatalytic production within one microbial chassis. (+)‐DHCD was successfully produced by screening multiple homologues of the pathway genes, combined with expression optimisation by selective promoter and/or ribosomal binding‐site screening. This study demonstrates the potential application of synthetic biology approaches in the development of truly sustainable and renewable bioplastic monomers., Sustainable, renewable bioplastic monomers: The monoterpenoid (+)‐ DHCD can be polymerised to form shape‐memory polymers. We have demonstrated a proof‐of‐principle approach to the complete biosynthesis of (+)‐ DHCD from glucose in E. coli, based on a modified M. spicata biosynthetic pathway. This route from a simple, inexpensive carbon source is more attractive than the alternative chemical synthesis from (R)‐carvone.
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- 2019
4. A Biological Route to Conjugated Alkenes: Microbial Production of Hepta-1,3,5-triene
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Hanan L. Messiha, Nigel S. Scrutton, David Leys, and Karl A. P. Payne
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0106 biological sciences ,Carboxy-Lyases ,Biomedical Engineering ,Polyenes ,Conjugated system ,01 natural sciences ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,Fungal Proteins ,03 medical and health sciences ,010608 biotechnology ,Escherichia coli ,Pyrroles ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,Escherichia coli Proteins ,General Medicine ,Polymer ,Combinatorial chemistry ,Anti-Bacterial Agents ,chemistry ,Metabolic Engineering ,Biocatalysis ,Fatty Acids, Unsaturated ,Aspergillus niger ,Polyketide Synthases - Abstract
Conjugated alkenes such as dienes and polyenes have a range of applications as pharmaceutical agents and valuable building blocks in the polymer industry. Development of a renewable route to these compounds provides an alternative to fossil fuel derived production. The enzyme family of the UbiD decarboxylases offers substantial scope for alkene production, readily converting poly unsaturated acids. However, biochemical pathways producing the required substrates are poorly characterized, and UbiD-application has hitherto been limited to biological styrene production. Herein, we present a proof-of-principle study for microbial production of polyenes using a bioinspired strategy employing a polyketide synthase (PKS) in combination with a UbiD-enzyme. Deconstructing a bacterial iterative type II PKS enabled repurposing the broad-spectrum antibiotic andrimid biosynthesis pathway to access the metabolic intermediate 2,4,6-octatrienoic acid, a valuable chemical for material and pharmaceutical industry. Combination with the fungal ferulic acid decarboxylase (Fdc1) led to a biocatalytic cascade-type reaction for the production of hepta-1,3,5-triene
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- 2021
5. Systematic integration of experimental data and models in systems biology.
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Peter Li, Joseph O. Dada, Daniel Jameson, Irena Spasic, Neil Swainston, Kathleen Carroll, Warwick B. Dunn, Farid Khan, Naglis Malys, Hanan L. Messiha, Evangelos Simeonidis, Dieter Weichart, Catherine Winder, Jill Wishart, David S. Broomhead, Carole A. Goble, Simon J. Gaskell, Douglas B. Kell, Hans V. Westerhoff, Pedro Mendes 0001, and Norman W. Paton
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- 2010
- Full Text
- View/download PDF
6. Biocatalytic Routes to Lactone Monomers for Polymer Production
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Syed T. Ahmed, Gabriel A. Ascue Avalos, Adrian J. Mulholland, Reynier Suardíaz, Natalie Fey, Vijaykumar Karuppiah, Hanan L. Messiha, Stephen G. Yeates, Helen S. Toogood, and Nigel S. Scrutton
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EP/ K014714/1 ,biocatalysis ,ring-opening polymerization ,biopolymers ,EP/K014706/1 ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Ring-opening polymerization ,Catalysis ,Mixed Function Oxygenases ,chemistry.chemical_compound ,Lactones ,Bacterial Proteins ,Manchester Institute of Biotechnology ,Pseudomonas ,Structural isomer ,Rhodococcus ,EP/K014668/1 ,crystallography ,EP/K014854/1 ,chemistry.chemical_classification ,biology ,010405 organic chemistry ,RCUK ,Regioselectivity ,Active site ,molecular dynamics simulations ,ResearchInstitutes_Networks_Beacons/manchester_institute_of_biotechnology ,EP/M022609/1 ,Baeyer-Villiger monooxygenases (BVMOs) ,Combinatorial chemistry ,0104 chemical sciences ,EPSRC ,Monomer ,chemistry ,BBSRC ,Biocatalysis ,biology.protein ,Monoterpenes ,EP/M013219/1 ,Organic synthesis ,Lactone ,DFT mechanistic study - Abstract
Monoterpenoids offer potential as biocatalytically derived monomer feedstocks for high-performance renewable polymers. We describe a biocatalytic route to lactone monomers menthide and dihydrocarvide employing Baeyer-Villiger monooxygenases (BVMOs) from Pseudomonas sp. HI-70 (CPDMO) and Rhodococcus sp. Phi1 (CHMOPhi1) as an alternative to organic synthesis. The regioselectivity of dihydrocarvide isomer formation was controlled by site-directed mutagenesis of three key active site residues in CHMOPhi1. A combination of crystal structure determination, molecular dynamics simulations, and mechanistic modeling using density functional theory on a range of models provides insight into the origins of the discrimination of the wild type and a variant CHMOPhi1 for producing different regioisomers of the lactone product. Ring-opening polymerizations of the resultant lactones using mild metal-organic catalysts demonstrate their utility in polymer production. This semisynthetic approach utilizing a biocatalytic step, non-petroleum feedstocks, and mild polymerization catalysts allows access to known and also to previously unreported and potentially novel lactone monomers and polymers.
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- 2018
7. A new regulatory principle for in vivo biochemistry: pleiotropic low affinity regulation by the adenine nucleotides--illustrated for the glycolytic enzymes of Saccharomyces cerevisiae
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Hans V. Westerhoff, Barbara M. Bakker, Fred C. Boogerd, Hanan L. Messiha, Pedro Mendes, Frédéric Crémazy, Femke I. C. Mensonides, Center for Liver, Digestive and Metabolic Diseases (CLDM), Lifestyle Medicine (LM), Synthetic Systems Biology (SILS, FNWI), Molecular Cell Physiology, and AIMMS
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Biochemistry ,GLUCOSE ,chemistry.chemical_compound ,Structural Biology ,Adenine nucleotide ,Models ,Glycolysis ,NETWORK ,Non-U.S. Gov't ,chemistry.chemical_classification ,0303 health sciences ,biology ,Adenine Nucleotides ,Research Support, Non-U.S. Gov't ,Systems Biology ,YEAST HEXOKINASE ,CHEMOSTAT ,RESPIRATION ,Thermodynamics ,Phosphofructokinase ,Subcellular Fractions ,Yeast glycolysis model ,Saccharomyces cerevisiae Proteins ,Allosteric regulation ,Saccharomyces cerevisiae ,Biophysics ,Research Support ,Models, Biological ,03 medical and health sciences ,Allosteric Regulation ,Energetics ,Genetics ,Journal Article ,Enzyme kinetics ,Molecular Biology ,KINETICS ,030304 developmental biology ,030306 microbiology ,Cell Biology ,biology.organism_classification ,Biological ,ATP ,Kinetics ,Enzyme ,chemistry ,Fermentation ,Glyceraldehyde 3-phosphate - Abstract
Enzymology tends to focus on highly specific effects of substrates, allosteric modifiers, and products occurring at low concentrations, because these are most informative about the enzyme's catalytic mechanism. We hypothesized that at relatively high in vivo concentrations, important molecular monitors of the state of living cells, such as ATP, affect multiple enzymes of the former and that these interactions have gone unnoticed in enzymology.We test this hypothesis in terms of the effect that ATP, ADP, and AMP might have on the major free-energy delivering pathway of the yeast Saccharomyces cerevisiae. Assaying cell-free extracts, we collected a comprehensive set of quantitative kinetic data concerning the enzymes of the glycolytic and the ethanol fermentation pathways. We determined systematically the extent to which the enzyme activities depend on the concentrations of the adenine nucleotides. We found that the effects of the adenine nucleotides on enzymes catalysing reactions in which they are not directly involved as substrate or product, are substantial. This includes effects on the Michaelis-Menten constants, adding new perspective on these, 100 years after their introduction. (C) 2013 Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies.
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- 2013
8. Enzyme kinetics informatics: from instrument to browser
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Norman W. Paton, Hanan L. Messiha, Olga Krebs, Heidrun Sauer-Danzwith, Isabel Rojas, Sylvestre Kengne, Pedro Mendes, Andreas Weidemann, Neil Swainston, Saqib Mir, Naglis Malys, Ulrike Wittig, Douglas B. Kell, Renate Kania, Kieran Smallbone, Wolfgang Müller, and Martin Golebiewski
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Data element ,Data collection ,Database ,Computer science ,business.industry ,Experimental data ,Cell Biology ,computer.software_genre ,Biochemistry ,Metadata repository ,Metadata ,Software ,Web service ,business ,Raw data ,Molecular Biology ,computer - Abstract
A limited number of publicly available resources provide access to enzyme kinetic parameters. These have been compiled through manual data mining of published papers, not from the original, raw experimental data from which the parameters were calculated. This is largely due to the lack of software or standards to support the capture, analysis, storage and dissemination of such experimental data. Introduced here is an integrative system to manage experimental enzyme kinetics data from instrument to browser. The approach is based on two interrelated databases: the existing SABIO-RK database, containing kinetic data and corresponding metadata, and the newly introduced experimental raw data repository, MeMo-RK. Both systems are publicly available by web browser and web service interfaces and are configurable to ensure privacy of unpublished data. Users of this system are provided with the ability to view both kinetic parameters and the experimental raw data from which they are calculated, providing increased confidence in the data. A data analysis and submission tool, the kineticswizard, has been developed to allow the experimentalist to perform data collection, analysis and submission to both data resources. The system is designed to be extensible, allowing integration with other manufacturer instruments covering a range of analytical techniques.
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- 2010
9. Systems Biology: the elements and principles of life
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Evangelos Simeonidis, Catherine L. Winder, Hans V. Westerhoff, Hanan L. Messiha, Warwick B. Dunn, Frank J. Bruggeman, Malgorzata Adamczyk, Malkhey Verma, Evolutionary Intelligence, and Molecular Cell Physiology
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Flux balance analysis ,Occam’s razor ,Energy (esotericism) ,media_common.quotation_subject ,Systems biology ,Biophysics ,Efficiency ,occam ,Biochemistry ,Occam's razor ,symbols.namesake ,Life ,Structural Biology ,Yeasts ,Control ,Genetics ,Simplicity ,Complex systems biology ,Control (linguistics) ,Molecular Biology ,Biological computation ,computer.programming_language ,media_common ,Physics ,Genome ,Management science ,Systems Biology ,Complexity ,Cell Biology ,Yeast ,Minimum energy ,symbols ,Thermodynamics ,Philosophy of Systems Biology ,computer ,Organization ,Regulation - Abstract
Systems Biology has a mission that puts it at odds with traditional paradigms of physics and molecular biology, such as the simplicity requested by Occam's razor and minimum energy/maximal efficiency. By referring to biochemical experiments on control and regulation, and on flux balancing in yeast, we show that these paradigms are inapt. Systems Biology does not quite converge with biology either: Although it certainly requires accurate 'stamp collecting', it discovers quantitative laws. Systems Biology is a science of its own, discovering own fundamental principles, some of which we identify here. Crown Copyright © 2009.
- Published
- 2009
10. Probing the Dynamic Interface between Trimethylamine Dehydrogenase (TMADH) and Electron Transferring Flavoprotein (ETF) in the TMADH−2ETF Complex: Role of the Arg-α237 (ETF) and Tyr-442 (TMADH) Residue Pair
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Gergely Katona, Selena G. Burgess, Stephen E. J. Rigby, Nigel S. Scrutton, David Leys, and Hanan L. Messiha
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Models, Molecular ,Semiquinone ,Electron-Transferring Flavoproteins ,Mutant ,Crystal structure ,Arginine ,Crystallography, X-Ray ,Biochemistry ,Electron-transferring flavoprotein ,Catalysis ,Cofactor ,Electron transfer ,Protein Structure, Quaternary ,biology ,Chemistry ,Electron Spin Resonance Spectroscopy ,Titrimetry ,Oxidoreductases, N-Demethylating ,Electron transport chain ,Protein Structure, Tertiary ,Crystallography ,Methylophilus methylotrophus ,Mutation ,biology.protein ,Tyrosine ,Trimethylamine dehydrogenase ,Oxidation-Reduction ,Protein Binding - Abstract
We have used multiple solution state techniques and crystallographic analysis to investigate the importance of a putative transient interaction formed between Arg-alpha237 in electron transferring flavoprotein (ETF) and Tyr-442 in trimethylamine dehydrogenase (TMADH) in complex assembly, electron transfer, and structural imprinting of ETF by TMADH. We have isolated four mutant forms of ETF altered in the identity of the residue at position 237 (alphaR237A, alphaR237K, alphaR237C, and alphaR237E) and with each form studied electron transfer from TMADH to ETF, investigated the reduction potentials of the bound ETF cofactor, and analyzed complex formation. We show that mutation of Arg-alpha237 substantially destabilizes the semiquinone couple of the bound FAD and impedes electron transfer from TMADH to ETF. Crystallographic structures of the mutant ETF proteins indicate that mutation does not perturb the overall structure of ETF, but leads to disruption of an electrostatic network at an ETF domain boundary that likely affects the dynamic properties of ETF in the crystal and in solution. We show that Arg-alpha237 is required for TMADH to structurally imprint the as-purified semiquinone form of wild-type ETF and that the ability of TMADH to facilitate this structural reorganization is lost following (i) redox cycling of ETF, or simple conversion to the oxidized form, and (ii) mutagenesis of Arg-alpha237. We discuss this result in light of recent apparent conflict in the literature relating to the structural imprinting of wild-type ETF. Our studies support a mechanism of electron transfer by conformational sampling as advanced from our previous analysis of the crystal structure of the TMADH-2ETF complex [Leys, D. , Basran, J. , Sutcliffe, M. J., and Scrutton, N. S. (2003) Nature Struct. Biol. 10, 219-225] and point to a key role for the Tyr-442 (TMADH) and Arg-alpha237 (ETF) residue pair in transiently stabilizing productive electron transfer configurations. Our work also points to the importance of Arg-alpha237 in controlling the thermodynamics of electron transfer, the dynamics of ETF, and the protection of reducing equivalents following disassembly of the TMADH-2ETF complex.
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- 2008
11. The photochemical mechanism of a B12-dependent photoreceptor protein
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Roger J, Kutta, Samantha J O, Hardman, Linus O, Johannissen, Bruno, Bellina, Hanan L, Messiha, Juan Manuel, Ortiz-Guerrero, Montserrat, Elías-Arnanz, S, Padmanabhan, Perdita, Barran, Nigel S, Scrutton, and Alex R, Jones
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Models, Molecular ,Chromatography ,Light ,Protein Conformation ,Spectrum Analysis ,Thermus thermophilus ,Gene Expression Regulation, Bacterial ,Photochemical Processes ,Article ,Bacterial Proteins ,Models, Chemical ,polycyclic compounds ,Computer Simulation ,Cobamides - Abstract
The coenzyme B12-dependent photoreceptor protein, CarH, is a bacterial transcriptional regulator that controls the biosynthesis of carotenoids in response to light. On binding of coenzyme B12 the monomeric apoprotein forms tetramers in the dark, which bind operator DNA thus blocking transcription. Under illumination the CarH tetramer dissociates, weakening its affinity for DNA and allowing transcription. The mechanism by which this occurs is unknown. Here we describe the photochemistry in CarH that ultimately triggers tetramer dissociation; it proceeds via a cob(III)alamin intermediate, which then forms a stable adduct with the protein. This pathway is without precedent and our data suggest it is independent of the radical chemistry common to both coenzyme B12 enzymology and its known photochemistry. It provides a mechanistic foundation for the emerging field of B12 photobiology and will serve to inform the development of a new class of optogenetic tool for the control of gene expression., Coenzyme B12 traditionally acts as cofactor to light-independent metabolic enzymes in bacteria and humans. Here, Kutta et al. present a time-resolved photochemical description of a B12-dependent photoreceptor protein, which represents a mechanistic foundation for B12 photobiology.
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- 2015
12. Magnetic field effects as a result of the radical pair mechanism are unlikely in redox enzymes
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Hanan L. Messiha, Alex R. Jones, Pimchai Chaiyen, Thanyaporn Wongnate, and Nigel S. Scrutton
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Dinitrocresols ,ResearchInstitutes_Networks_Beacons/photon_science_institute ,Radical ,Biomedical Engineering ,Biophysics ,Flavoprotein ,Bioengineering ,Flavin group ,Reaction intermediate ,Photon Science Institute ,Photochemistry ,Biochemistry ,Catalysis ,Fungal Proteins ,Biomaterials ,Chemical kinetics ,hydride transfer ,magnetic field effects ,Research Articles ,flavoproteins ,biology ,Chemistry ,Basidiomycota ,radical pair mechanism ,Environmental exposure ,equipment and supplies ,environmental magnetic fields ,Magnetic field ,Kinetics ,Magnetic Fields ,Models, Chemical ,Chemical engineering ,biology.protein ,Carbohydrate Dehydrogenases ,Oxidation-Reduction ,human activities ,Biotechnology - Abstract
Environmental exposure to electromagnetic fields is potentially carcinogenic. The radical pair mechanism is considered the most feasible mechanism of interaction between weak magnetic fields encountered in our environment and biochemical systems. Radicals are abundant in biology, both as free radicals and reaction intermediates in enzyme mechanisms. The catalytic cycles of some flavin-dependent enzymes are either known or potentially involve radical pairs. Here, we have investigated the magnetic field sensitivity of a number of flavoenzymes with important cellular roles. We also investigated the magnetic field sensitivity of a model system involving stepwise reduction of a flavin analogue by a nicotinamide analogue—a reaction known to proceed via a radical pair. Under the experimental conditions used, magnetic field sensitivity was not observed in the reaction kinetics from stopped-flow measurements in any of the systems studied. Although widely implicated in radical pair chemistry, we conclude that thermally driven, flavoenzyme-catalysed reactions are unlikely to be influenced by exposure to external magnetic fields.
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- 2015
13. Role of Active Site Residues and Solvent in Proton Transfer and the Modulation of Flavin Reduction Potential in Bacterial Morphinone Reductase
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Benedict M. Sattelle, Hanan L. Messiha, Andrew W. Munro, Nigel S. Scrutton, Neil C. Bruce, and Michael J. Sutcliffe
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Stereochemistry ,Oxidative phosphorylation ,Flavin group ,Biochemistry ,Redox ,Catalysis ,Bacterial Proteins ,Flavins ,Coenzyme binding ,Molecular Biology ,chemistry.chemical_classification ,Morphinone reductase ,Binding Sites ,biology ,Cyclohexanones ,Active site ,Cell Biology ,NAD ,Recombinant Proteins ,Kinetics ,Enzyme ,Amino Acid Substitution ,Catalytic cycle ,chemistry ,Mutation ,Solvents ,biology.protein ,Protons ,Oxidoreductases ,Oxidation-Reduction - Abstract
The reactions of several active site mutant forms of bacterial morphinone reductase (MR) with NADH and 2-cyclohexen-1-one as substrates have been studied by stopped-flow and steady-state kinetic methods and redox potentiometry. The enzymes were designed to (i) probe a role for potential proton donors (Tyr-72 and Tyr-356) in the oxidative half-reaction of MR; (ii) assess the function of a highly conserved tryptophan residue (Trp-106) in catalysis; (iii) investigate the role of Thr-32 in modulating the FMN reduction potential and catalysis. The Y72F and Y356F enzymes retained activity in both steady-state and stopped-flow kinetic studies, indicating they do not serve as key proton donors in the oxidative reaction of MR. Taken together with our recently published data (Messiha, H. L., Munro, A. W., Bruce, N. C., Barsukov, I., and Scrutton, N. S. (2005) J. Biol. Chem. 280, 4627-4631) that rule out roles for Cys-191 (corresponding with the proton donor, Tyr-196, in the structurally related OYE1 enzyme) and His-186 as proton donors, we infer solvent is the source of the proton in the oxidative half-reaction of MR. We demonstrate a key role for Thr-32 in modulating the reduction potential of the FMN, which is decreased approximately 50 mV in the T32A mutant MR. This effects a change in rate-limiting step in the catalytic cycle of the T32A enzyme with the oxidizing substrate 2-cyclohexenone. Despite the conservation of Trp-106 throughout the OYE family, we show this residue does not play a major role in catalysis, although affects on substrate and coenzyme binding are observed in a W106F enzyme. Our studies show some similarities, but also major differences, in the catalytic mechanism of MR and OYE1, and emphasize the need for caution in inferring mechanism by structural comparison of highly related enzymes in the absence of solution studies.
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- 2005
14. Reaction of Morphinone Reductase with 2-Cyclohexen-1-one and 1-Nitrocyclohexene
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Igor L. Barsukov, Hanan L. Messiha, Neil C. Bruce, Andrew W. Munro, and Nigel S. Scrutton
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Morphinone reductase ,biology ,Chemistry ,Stereochemistry ,Active site ,Cell Biology ,Nuclear magnetic resonance spectroscopy ,Flavin group ,Biochemistry ,Cofactor ,chemistry.chemical_compound ,biology.protein ,Nitronate ,Binding site ,Molecular Biology ,Histidine - Abstract
Morphinone reductase (MR) catalyzes the NADH-dependent reduction of alpha/beta unsaturated carbonyl compounds in a reaction similar to that catalyzed by Old Yellow Enzyme (OYE1). The two enzymes are related at the sequence and structural levels, but key differences in active site architecture exist which have major implications for the reaction mechanism. We report detailed kinetic and solution NMR data for wild-type MR and two mutant forms in which residues His-186 and Asn-189 have been exchanged for alanine residues. We show that both residues are involved in the binding of the reducing nicotinamide coenzyme NADH and also the binding of the oxidizing substrates 2-cyclohexen-1-one and 1-nitrocyclohexene. Reduction of 2-cyclohexen-1-one by FMNH(2) is concerted with proton transfer from an unknown proton donor in the active site. NMR spectroscopy and flavin reoxidation studies with 2-cyclohexen-1-one are consistent with His-186 being unprotonated in oxidized, reduced, and ligand-bound MR, suggesting that His-186 is not the key proton donor required for the reduction of 2-cyclohexen-1-one. Hydride transfer is decoupled from proton transfer with 1-nitrocyclohexene as oxidizing substrate, and unlike with OYE1 the intermediate nitronate species produced after hydride transfer from FMNH(2) is not converted to 1-nitrocyclohexane. The work highlights key mechanistic differences in the reactions catalyzed by MR and OYE1 and emphasizes the need for caution in inferring mechanistic similarities in structurally related proteins.
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- 2005
15. Crystal Structure of Bacterial Morphinone Reductase and Properties of the C191A Mutant Enzyme
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Neil C. Bruce, Nigel S. Scrutton, Carlo Petosa, Teréz Barna, Hanan L. Messiha, and Peter C. E. Moody
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Stereochemistry ,Biológiai tudományok ,Reductase ,Codeinone ,Biochemistry ,Cofactor ,Bacterial Proteins ,Természettudományok ,Oxidoreductase ,medicine ,Molecular Biology ,chemistry.chemical_classification ,Morphinone reductase ,Binding Sites ,biology ,Pseudomonas putida ,NADPH Dehydrogenase ,Substrate (chemistry) ,Active site ,Cell Biology ,Kinetics ,Enzyme ,chemistry ,Mutagenesis ,biology.protein ,Crystallization ,Oxidoreductases ,medicine.drug - Abstract
The crystal structure of the NADH-dependent bacterial flavoenzyme morphinone reductase (MR) has been determined at 2.2-A resolution in complex with the oxidizing substrate codeinone. The structure reveals a dimeric enzyme comprising two 8-fold beta/alpha barrel domains, each bound to FMN, and a subunit folding topology and mode of flavin-binding similar to that found in Old Yellow Enzyme (OYE) and pentaerythritol tetranitrate (PETN) reductase. The subunit interface of MR is formed by interactions from an N-terminal beta strand and helices 2 and 8 of the barrel domain and is different to that seen in OYE. The active site structures of MR, OYE, and PETN reductase are highly conserved reflecting the ability of these enzymes to catalyze "generic" reactions such as the reduction of 2-cyclohexenone. A region of polypeptide presumed to define the reducing coenzyme specificity is identified by comparison of the MR structure (NADH-dependent) with that of PETN reductase (NADPH-dependent). The active site acid identified in OYE (Tyr-196) and conserved in PETN reductase (Tyr-186) is replaced by Cys-191 in MR. Mutagenesis studies have established that Cys-191 does not act as a crucial acid in the mechanism of reduction of the olefinic bond found in 2-cyclohexenone and codeinone.
- Published
- 2002
16. Enzyme characterisation and kinetic modelling of the pentose phosphate pathway in yeast
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Pedro Mendes, Neil Swainston, Naglis Malys, Edward Kent, Hanan L. Messiha, Kathleen M. Carroll, and Kieran Smallbone
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chemistry.chemical_classification ,biology ,Metabolite ,Saccharomyces cerevisiae ,Metabolism ,Pentose phosphate pathway ,biology.organism_classification ,Yeast ,chemistry.chemical_compound ,Enzyme ,Biochemistry ,chemistry ,Glycolysis ,Enzyme kinetics - Abstract
We present the quantification and kinetic characterisation of the enzymes of the pentose phosphate pathway in Saccharomyces cerevisiae. The data are combined into a mathematical model that describes the dynamics of this system and allows us to predict changes in metabolite concentrations and fluxes in response to perturbations. We use the model to study the response of yeast to a glucose pulse. We then combine the model with an existing glycolysis model to study the effect of oxidative stress on carbohydrate metabolism. The combination of these two models was made possible by the standardised enzyme kinetic experiments carried out in both studies. This work demonstrates the feasibility of constructing larger network-scale models by merging smaller pathway-scale models.
- Published
- 2014
17. Enzyme characterisation and kinetic modelling of the pentose phosphate pathway in yeast
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Hanan L. Messiha, Edward Kent, Naglis Malys, Kathleen M. Carroll, Pedro Mendes, and Kieran Smallbone
- Abstract
We present the quantification and kinetic characterisation of the enzymes of the pentose phosphate pathway in Saccharomyces cerevisiae. The data are combined into a mathematical model that describes the dynamics of this system and allows for the predicting changes in metabolite concentrations and fluxes in response to perturbations. We use the model to study the response of yeast to a glucose pulse. We then combine the model with an existing glycolysis one to study the effect of oxidative stress on carbohydrate metabolism. The combination of these two models was made possible by the standardized enzyme kinetic experiments carried out in both studies. This work demonstrates the feasibility of constructing larger network models by merging smaller pathway models.
- Published
- 2014
18. Regulation of the activity of lactate dehydrogenases from four lactic acid bacteria
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Rebecca C. Wade, Anna Feldman-Salit, Nadine Veith, Hanan L. Messiha, Bernd Kreikemeyer, Tomas Fiedler, Hans V. Westerhoff, Antje Sieg, Vlad Cojocaru, Silvio Hering, Molecular Cell Physiology, AIMMS, and Synthetic Systems Biology (SILS, FNWI)
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Static Electricity ,Sodium Chloride ,Crystallography, X-Ray ,Biochemistry ,Models, Biological ,Enterococcus faecalis ,Phosphates ,chemistry.chemical_compound ,Enzyme activator ,Allosteric Regulation ,Lactate dehydrogenase ,Fructosediphosphates ,Enzyme kinetics ,Lactic Acid ,Molecular Biology ,Lactate Dehydrogenases ,chemistry.chemical_classification ,Binding Sites ,biology ,Bacteria ,Lactococcus lactis ,food and beverages ,Computational Biology ,Cell Biology ,Hydrogen-Ion Concentration ,biology.organism_classification ,Lactic acid ,Enzyme Activation ,Isoenzymes ,Kinetics ,Enzyme ,chemistry ,Biocatalysis ,Lactobacillus plantarum - Abstract
Despite high similarity in sequence and catalytic properties, the l-lactate dehydrogenases (LDHs) in lactic acid bacteria (LAB) display differences in their regulation that may arise from their adaptation to different habitats. We combined experimental and computational approaches to investigate the effects of fructose 1,6-bisphosphate (FBP), phosphate (Pi), and ionic strength (NaCl concentration) on six LDHs from four LABs studied at pH 6 and pH 7. We found that 1) the extent of activation by FBP (Kact) differs. Lactobacillus plantarum LDH is not regulated by FBP, but the other LDHs are activated with increasing sensitivity in the following order: Enterococcus faecalis LDH2
- Published
- 2014
19. A model of yeast glycolysis based on a consistent kinetic characterization of all its enzymes
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Hans V. Westerhoff, Pınar Pir, Kieran Smallbone, Ettore Murabito, Joseph O. Dada, John E.G. McCarthy, David S. Broomhead, Kathleen M. Carroll, Naglis Malys, Stephen G. Oliver, Douglas B. Kell, Catherine L. Winder, Irena Spasic, Warwick B. Dunn, Simon J. Gaskell, Jill A. Wishart, Neil Swainston, Farid Khan, Daniel Jameson, Neil W. Hayes, Norman W. Paton, Evangelos Simeonidis, Dieter Weichart, Pedro Mendes, Hanan L. Messiha, BBSRC / EPSRC [sponsor], Manchester Centre for Integrative Systems Biology [research center], Luxembourg Centre for Systems Biomedicine (LCSB): Experimental Neurobiology (Balling Group) [research center], „Wiley' grupė, Synthetic Systems Biology (SILS, FNWI), Molecular Cell Physiology, and AIMMS
- Subjects
Saccharomyces cerevisiae Proteins ,Metabolite ,Systems biology ,Saccharomyces cerevisiae ,Biophysics ,Metabolic network ,Multidisciplinary, general & others [F99] [Life sciences] ,Biochemistry ,Models, Biological ,Article ,Modelling ,Set (abstract data type) ,03 medical and health sciences ,chemistry.chemical_compound ,QH301 ,Multidisciplinaire, généralités & autres [F99] [Sciences du vivant] ,Structural Biology ,Enzyme kinetic ,Genetics ,Computer Simulation ,Enzyme kinetics ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,biology ,030302 biochemistry & molecular biology ,Cell Biology ,biology.organism_classification ,Yeast ,Isoenzyme ,Isoenzymes ,Kinetics ,chemistry ,Biological system ,Flux (metabolism) ,Glycolysis ,Metabolic Networks and Pathways - Abstract
We present an experimental and computational pipeline for the generation of kinetic models of metabolism, and demonstrate its application to glycolysis in Saccharomyces cerevisiae. Starting from an approximate mathematical model, we employ a “cycle of knowledge” strategy, identifying the steps with most control over flux. Kinetic parameters of the individual isoenzymes within these steps are measured experimentally under a standardised set of conditions. Experimental strategies are applied to establish a set of in vivo concentrations for isoenzymes and metabolites. The data are integrated into a mathematical model that is used to predict a new set of metabolite concentrations and reevaluate the control properties of the system. This bottom-up modelling study reveals that control over the metabolic network most directly involved in yeast glycolysis is more widely distributed than previously thought.
- Published
- 2013
- Full Text
- View/download PDF
20. Towards a full quantitative description of yeast metabolism a systematic approach for estimating the kinetic parameters of isoenzymes under in vivo like conditions
- Author
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Hanan L, Messiha, Naglis, Malys, and Kathleen M, Carroll
- Subjects
Isoenzymes ,Kinetics ,Saccharomyces cerevisiae Proteins ,Information Management ,Saccharomyces cerevisiae ,Databases, Protein ,Energy Metabolism ,Glycolysis ,Algorithms ,Enzyme Assays - Abstract
In order to produce a full quantitative description of yeast metabolism, a number of kinetic parameters of enzymes that are important for energy metabolism must be determined experimentally. We aim to determine the prospective in vivo kinetic properties of a range of yeast-purified isoenzymes that are important in energy metabolism, with respect to the concentration of their substrates and products. This endeavor forms part of our systems biology pipeline to facilitate the production of bottom-up models of metabolism. Within this workflow, we implement an infrastructure for medium- to high-throughput determination of the kinetic properties of purified isoenzymes in in vivo like conditions. This includes the use of the KineticsWizard software for data capture and analysis. The captured experimental data are analyzed by the software and subsequently stored in appropriate repositories (MeMo-RK and SABIO-RK). While we focus initially on glycolysis in Saccharomyces cerevisiae, our methodology is generic and can be widely applied to the study of other enzymes and pathways in yeast and other organisms.
- Published
- 2011
21. Building a kinetic model of trehalose biosynthesis in Saccharomyces cerevisiae
- Author
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Kieran, Smallbone, Naglis, Malys, Hanan L, Messiha, Jill A, Wishart, and Evangelos, Simeonidis
- Subjects
Saccharomyces cerevisiae Proteins ,UTP-Glucose-1-Phosphate Uridylyltransferase ,Systems Biology ,Glucose-6-Phosphate Isomerase ,Trehalose ,Saccharomyces cerevisiae ,Models, Biological ,Kinetics ,Phosphoglucomutase ,Glucosyltransferases ,Stress, Physiological ,Gene Expression Regulation, Fungal ,Computer Simulation ,Glycolysis ,Algorithms ,Metabolic Networks and Pathways ,Enzyme Assays - Abstract
In this chapter, we describe the steps needed to create a kinetic model of a metabolic pathway based on kinetic data from experimental measurements and literature review. Our methodology is presented by utilizing the example of trehalose metabolism in yeast. The biology of the trehalose cycle is briefly reviewed and discussed.
- Published
- 2011
22. Building a Kinetic Model of Trehalose Biosynthesis in Saccharomyces cerevisiae
- Author
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Evangelos Simeonidis, Hanan L. Messiha, Jill A. Wishart, Naglis Malys, and Kieran Smallbone
- Subjects
Trehalose biosynthesis ,chemistry.chemical_compound ,Metabolic pathway ,biology ,chemistry ,Biochemistry ,Kinetic model ,Systems biology ,Trehalose metabolism ,Saccharomyces cerevisiae ,biology.organism_classification ,Trehalose ,Yeast - Abstract
In this chapter, we describe the steps needed to create a kinetic model of a metabolic pathway based on kinetic data from experimental measurements and literature review. Our methodology is presented by utilizing the example of trehalose metabolism in yeast. The biology of the trehalose cycle is briefly reviewed and discussed.
- Published
- 2011
23. Towards a Full Quantitative Description of Yeast Metabolism
- Author
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Kathleen M. Carroll, Hanan L. Messiha, and Naglis Malys
- Subjects
Biochemistry ,In vivo ,Systems biology ,Saccharomyces cerevisiae ,Experimental data ,Biology ,biology.organism_classification ,Kinetic energy ,Biological system ,Isozyme ,Yeast metabolism ,Yeast - Abstract
In order to produce a full quantitative description of yeast metabolism, a number of kinetic parameters of enzymes that are important for energy metabolism must be determined experimentally. We aim to determine the prospective in vivo kinetic properties of a range of yeast-purified isoenzymes that are important in energy metabolism, with respect to the concentration of their substrates and products. This endeavor forms part of our systems biology pipeline to facilitate the production of bottom-up models of metabolism. Within this workflow, we implement an infrastructure for medium- to high-throughput determination of the kinetic properties of purified isoenzymes in in vivo like conditions. This includes the use of the KineticsWizard software for data capture and analysis. The captured experimental data are analyzed by the software and subsequently stored in appropriate repositories (MeMo-RK and SABIO-RK). While we focus initially on glycolysis in Saccharomyces cerevisiae, our methodology is generic and can be widely applied to the study of other enzymes and pathways in yeast and other organisms.
- Published
- 2011
24. Systematic integration of experimental data and models in systems biology
- Author
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Hanan L. Messiha, Evangelos Simeonidis, Dieter Weichart, Farid Khan, David S. Broomhead, Peter Li, Pedro Mendes, Simon J. Gaskell, Catherine L. Winder, Neil Swainston, Warwick B. Dunn, Daniel Jameson, Irena Spasic, Carole Goble, Douglas B. Kell, Norman W. Paton, Jill A. Wishart, Naglis Malys, Kathleen M. Carroll, Hans V. Westerhoff, Joseph O. Dada, Molecular Cell Physiology, and AIMMS
- Subjects
Databases, Factual ,Interface (Java) ,Computer science ,Systems biology ,Q1 ,computer.software_genre ,lcsh:Computer applications to medicine. Medical informatics ,Biochemistry ,Models, Biological ,QA76 ,Interoperation ,QH301 ,Structural Biology ,Biochemical reactions ,Enzyme kinetics ,SBML ,QA ,Molecular Biology ,lcsh:QH301-705.5 ,business.industry ,Applied Mathematics ,Methodology Article ,Systems Biology ,Experimental data ,Data science ,Computer Science Applications ,Metabolic pathway ,Workflow ,lcsh:Biology (General) ,lcsh:R858-859.7 ,Software engineering ,business ,computer ,Metabolic Networks and Pathways ,Data integration - Abstract
Background The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions, and corresponding parameters. Automating the assembly and use of systems biology models is dependent upon data integration processes involving the interoperation of data and analytical resources. Results Taverna workflows have been developed for the automated assembly of quantitative parameterised metabolic networks in the Systems Biology Markup Language (SBML). A SBML model is built in a systematic fashion by the workflows which starts with the construction of a qualitative network using data from a MIRIAM-compliant genome-scale model of yeast metabolism. This is followed by parameterisation of the SBML model with experimental data from two repositories, the SABIO-RK enzyme kinetics database and a database of quantitative experimental results. The models are then calibrated and simulated in workflows that call out to COPASIWS, the web service interface to the COPASI software application for analysing biochemical networks. These systems biology workflows were evaluated for their ability to construct a parameterised model of yeast glycolysis. Conclusions Distributed information about metabolic reactions that have been described to MIRIAM standards enables the automated assembly of quantitative systems biology models of metabolic networks based on user-defined criteria. Such data integration processes can be implemented as Taverna workflows to provide a rapid overview of the components and their relationships within a biochemical system.
- Published
- 2010
25. Enzyme kinetics informatics: from instrument to browser
- Author
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Neil, Swainston, Martin, Golebiewski, Hanan L, Messiha, Naglis, Malys, Renate, Kania, Sylvestre, Kengne, Olga, Krebs, Saqib, Mir, Heidrun, Sauer-Danzwith, Kieran, Smallbone, Andreas, Weidemann, Ulrike, Wittig, Douglas B, Kell, Pedro, Mendes, Wolfgang, Müller, Norman W, Paton, and Isabel, Rojas
- Subjects
Electronic Data Processing ,Internet ,Kinetics ,Systems Biology ,Data Mining ,Databases, Protein ,Recombinant Proteins ,Software ,Enzymes - Abstract
A limited number of publicly available resources provide access to enzyme kinetic parameters. These have been compiled through manual data mining of published papers, not from the original, raw experimental data from which the parameters were calculated. This is largely due to the lack of software or standards to support the capture, analysis, storage and dissemination of such experimental data. Introduced here is an integrative system to manage experimental enzyme kinetics data from instrument to browser. The approach is based on two interrelated databases: the existing SABIO-RK database, containing kinetic data and corresponding metadata, and the newly introduced experimental raw data repository, MeMo-RK. Both systems are publicly available by web browser and web service interfaces and are configurable to ensure privacy of unpublished data. Users of this system are provided with the ability to view both kinetic parameters and the experimental raw data from which they are calculated, providing increased confidence in the data. A data analysis and submission tool, the kineticswizard, has been developed to allow the experimentalist to perform data collection, analysis and submission to both data resources. The system is designed to be extensible, allowing integration with other manufacturer instruments covering a range of analytical techniques.
- Published
- 2010
26. KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways
- Author
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Norman W. Paton, Evangelos Simeonidis, Douglas B. Kell, Hanan L. Messiha, and Irena Spasic
- Subjects
Statistics and Probability ,Information retrieval ,Computer science ,Systems biology ,Systems Biology ,Computational Biology ,Information needs ,Context (language use) ,Saccharomyces cerevisiae ,Biochemistry ,Yeast ,Computer Science Applications ,Computational Mathematics ,Metabolic pathway ,Computational Theory and Mathematics ,Index (publishing) ,Molecular Biology ,Metabolic Networks and Pathways ,Software ,Information Systems - Abstract
Motivation: Most experimental evidence on kinetic parameters is buried in the literature, whose manual searching is complex, time consuming and partial. These shortcomings become particularly acute in systems biology, where these parameters need to be integrated into detailed, genome-scale, metabolic models. These problems are addressed by KiPar, a dedicated information retrieval system designed to facilitate access to the literature relevant for kinetic modelling of a given metabolic pathway in yeast. Searching for kinetic data in the context of an individual pathway offers modularity as a way of tackling the complexity of developing a full metabolic model. It is also suitable for large-scale mining, since multiple reactions and their kinetic parameters can be specified in a single search request, rather than one reaction at a time, which is unsuitable given the size of genome-scale models. Results: We developed an integrative approach, combining public data and software resources for the rapid development of large-scale text mining tools targeting complex biological information. The user supplies input in the form of identifiers used in relevant data resources to refer to the concepts of interest, e.g. EC numbers, GO and SBO identifiers. By doing so, the user is freed from providing any other knowledge or terminology concerned with these concepts and their relations, since they are retrieved from these and cross-referenced resources automatically. The terminology acquired is used to index the literature by mapping concepts to their synonyms, and then to textual documents mentioning them. The indexing results and the previously acquired knowledge about relations between concepts are used to formulate complex search queries aiming at documents relevant to the user's information needs. The conceptual approach is demonstrated in the implementation of KiPar. Evaluation reveals that KiPar performs better than a Boolean search. The precision achieved for abstracts (60%) and full-text articles (48%) is considerably better than the baseline precision (44% and 24%, respectively). The baseline recall is improved by 36% for abstracts and by 100% for full text. It appears that full-text articles are a much richer source of information on kinetic data than are their abstracts. Finally, the combined results for abstracts and full text compared with the curated literature provide high values for relative recall (88%) and novelty ratio (92%), suggesting that the system is able to retrieve a high proportion of new documents. Availability: Source code and documentation are available at: http://www.mcisb.org/resources/kipar/ Contact: i.spasic@manchester.ac.uk; dbk@manchester.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
- Published
- 2009
27. Chapter 22 Enzyme Kinetics and Computational Modeling for Systems Biology
- Author
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Pedro Mendes, Hanan L. Messiha, Stefan Hoops, and Naglis Malys
- Subjects
chemistry.chemical_classification ,Computational model ,Modeling software ,biology ,Systems biology ,Computational biology ,Enzyme assay ,Biochemical network ,Triosephosphate isomerase ,Enzyme ,Biochemistry ,chemistry ,biology.protein ,Enzyme kinetics - Abstract
Enzyme kinetics is a century-old area of biochemical research which is regaining popularity due to its use in systems biology. Computational models of biochemical networks depend on rate laws and kinetic parameter values that describe the behavior of enzymes in the cellular milieu. While there is a considerable body of enzyme kinetic data available from the past several decades, a large number of enzymes of specific organisms were never assayed or were assayed in conditions that are irrelevant to those models. The result is that systems biology projects are having to carry out large numbers of enzyme kinetic assays. This chapter reviews the main methodologies of enzyme kinetic data analysis and proposes using computational modeling software for that purpose. It applies the biochemical network modeling software COPASI to data from enzyme assays of yeast triosephosphate isomerase (EC 5.3.1.1).
- Published
- 2009
28. Evidence for protein conformational change at a Au(110)/protein interface
- Author
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Nigel S. Scrutton, Hanan L. Messiha, Caroline I. Smith, and Peter Weightman
- Subjects
Protein interface ,Conformational change ,biology ,Chemistry ,General Physics and Astronomy ,Nanotechnology ,Electron ,Electron-transferring flavoprotein ,Cofactor ,Article ,Electron transfer ,Electrode ,biology.protein ,Biophysics ,sense organs ,Spectroscopy ,skin and connective tissue diseases - Abstract
Evidence is presented that reflection anisotropy spectroscopy (RAS) can provide real-time measurements of conformational change in proteins induced by electron transfer reactions. A bacterial electron transferring flavoprotein (ETF) has been modified so as to adsorb on an Au(110) electrode and enable reversible electron transfer to the protein cofactor in the absence of mediators. Reversible changes are observed in the RAS of this protein that are interpreted as arising from conformational changes accompanying the transfer of electrons.
- Published
- 2008
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