Download or read book Spectroscopic and Computational Studies of Heme and Nonheme Iron dependent Enzymes written by Jessica D. Gardner and published by . This book was released on 2010 with total page 153 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Spectroscopic and Computational Studies of Peroxo Intermediates in Mononuclear Non heme Iron Enzymes and Their Model Complexes written by Lei Liu and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Mononuclear non-heme iron enzymes catalyze wide varieties of important biological reactions with industrial, medical, and environmental applications. These enzymes can be classified into two classes, O2 activating FeII enzymes and substrate activating FeIII enzymes. This thesis focuses on understanding the geometric and electronic structures of the peroxo level intermediates and their reactivities in two O2 activating FeII enzymes, bleomycin and Rieske dioxygenases related model complexes, by using a combination of spectroscopic and computational methods. Bleomycin is a glycopeptide anticancer drug capable of effecting single- and double-strand DNA cleavage. The last detectable intermediate prior to DNA cleavage is a low spin S = 1/2 FeIII--OOH species, termed activated bleomycin (ABLM). The DNA strand scission is initiated through the abstraction of the C-4' hydrogen atom of the deoxyribose sugar unit. Nuclear resonance vibrational spectroscopy (NRVS) aided by extended X-ray absorption fine structure (EXAFS) spectroscopy and density functional theory (DFT) calculations are applied to define the natures of FeIIIBLM and ABLM as (BLM)FeIII--OH and (BLM)FeIII([eta]1--OOH) species, respectively. The NRVS spectra of FeIIIBLM and ABLM are strikingly different because in ABLM the Fe--O--O bending mode mixes with, and energetically splits, the doubly degenerate, intense O--Fe--Nax trans-axial bends. DFT calculations of the reaction of ABLM with DNA, based on the species defined by the NRVS data, show that the direct H-atom abstraction by ABLM is thermodynamically favored over other proposed reaction pathways. Previously, the rate of ABLM decay had been found, based on indirect methods, to be independent of the presence of DNA. In this thesis, we use a circular dichroism (CD) feature unique to ABLM to directly monitor the kinetics of ABLM reaction with a DNA oligonucleotide. Our results show that the ABLM + DNA reaction is appreciably faster, has a different kinetic isotope effect, and has a lower Arrhenius activation energy than does ABLM decay. In the ABLM reaction with DNA, the small normal kH/kD ratio is attributed to a secondary solvent effect through DFT vibrational analysis of reactant and transition state (TS) frequencies, and the lower Ea is attributed to the weaker bond involved in the abstraction reaction (C--H for DNA and N--H for the decay in the absence of DNA). The DNA dependence of the ABLM reaction indicates that DNA is involved in the TS for ABLM decay and thus reacts directly with (BLM)FeIII([eta]1--OOH) instead of its decay product. Oxygen-containing mononuclear iron species, FeIII--peroxo, FeIII--hydroperoxo and FeIV--oxo, are key intermediates in the catalytic activation of dioxygen by iron-containing metalloenzymes. It has been difficult to generate synthetic analogues of these three active iron--oxygen species in identical host complexes, which is necessary to elucidate changes to the structure of the iron center during catalysis and the factors that control their chemical reactivities with substrates. Here we report the high-resolution crystal structure of a mononuclear non-haem side-on FeIII--peroxo complex, [Fe(III)(TMC)(OO)]+. We also report a series of chemical reactions in which this iron(III)--peroxo complex is cleanly converted to the FeIII--hydroperoxo complex, [Fe(III)(TMC)(OOH)]2+, via a short-lived intermediate on protonation. This iron(III)--hydroperoxo complex then cleanly converts to the ferryl complex, [Fe(IV)(TMC)(O)]2+, via homolytic O--O bond cleavage of the iron(III)--hydroperoxo species. All three of these iron species--the three most biologically relevant iron--oxygen intermediates--have been spectroscopically characterized; we note that they have been obtained using a simple macrocyclic ligand. We have performed relative reactivity studies on these three iron species which reveal that the iron(III)--hydroperoxo complex is the most reactive of the three in the deformylation of aldehydes and that it has a similar reactivity to the iron(IV)--oxo complex in C--H bond activation of alkylaromatics. These reactivity results demonstrate that iron(III)--hydroperoxo species are viable oxidants in both nucleophilic and electrophilic reactions by iron-containing enzymes. The geometric and electronic structure and reactivity of an S = 5/2 (HS) mononuclear non-heme (TMC)FeIII-OOH complex was studied by spectroscopy, calculations, and kinetics for comparison to our past study of an S = 1/2 (LS) FeIII-OOH complex to understand their mechanisms of O-O bond homolysis and electrophilic H-atom abstraction. The homolysis reaction of the HS [(TMC)FeIII-OOH]2+ complex is found to involve axial ligand coordination and a crossing to the LS surface for O-O bond homolysis. Both HS and LS FeIII-OOH complexes are found to perform direct H-atom abstraction reactions but with very different reaction coordinates. For the LS FeIII-OOH, the transition state is late in O-O and early in C-H coordinates. However, for the HS FeIII-OOH, the transition state is early in O-O and further along in the C-H coordinate. In addition, there is a significant amount of electron transfer from substrate to HS FeIII-OOH at transition state, but does not occur in the LS transition state. Thus in contrast to the behavior of LS FeIII-OOH, the H-atom abstraction reactivity of HS FeIII-OOH is found to be highly dependent on both the ionization potential and C-H bond strength of substrate. LS FeIII-OOH is found to be more effective in H-atom abstraction for strong C-H bonds, while the higher reduction potential of HS FeIII-OOH allows it be active in electrophilic reactions without the requirement of O-O cleavage. This is relevant to the Rieske dioxygenases, which are proposed to use a HS FeIII-OOH to catalyze cis-dihydroxylation of a wide range of aromatic compounds. S K-edge XAS is a direct experimental probe of metal ion electronic structure as the pre-edge energy reflects its oxidation state, and the energy splitting pattern of the pre-edge transitions reflects its spin state. The combination of sulfur K-edge XAS and DFT calculations indicates that the electronic structures of {FeNO}7 (S = 3/2) (SMe2N4(tren)Fe(NO), complex I) and {FeNO}7 (S = 1/2) ((bme-daco)Fe(NO), complex II) are FeIII(S=5/2)--NO-- (S = 1) and FeIII(S=3/2)--NO-- (S = 1), respectively. When an axial ligand is computationally added to complex II, the electronic structure becomes FeII(S = 0)--NO[*] (S = 1/2). These studies demonstrate how the ligand field of the Fe center defines its spin state and thus changes the electron exchange, an important factor in determining the electron distribution over {FeNO}7 and {FeO2}8 sites.

Download or read book Spectroscopic and Computational Studies of Mononuclear Nonheme Iron Enzymes written by Kenneth M. Light and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Mononuclear nonheme iron enzymes (NH Fe enzymes) catalyze a variety of biological reactions. A large group of NH Fe enzymes use a ferrous active site to activate dioxygen towards reaction with substrate, and require an additional cofactor as a source of electrons necessary for catalysis. The main part of this thesis involves the application of a circular dichroism (CD), magnetic circular dichroism (MCD) and variable temperature, variable-field MCD (VTVH MCD) spectroscopic methodology to a series of alpha-ketoglurate-dependent (alpha-KG-dependent) enzymes for the purpose of understanding how this enzyme family and the NH Ferrous enzymes in general induce the dissociation the generation of a 5C site for dioxgyen reactivity, as well as how dioxygen binding is oriented for proper catalysis. In addition to catalyzing oxidation of organic substrates, NH Fe enzymes are also involved in the catalytic hydrolysis and hydration of substrates. A prominent example of this is nitrile hydratases (NHases), unusual low-spin (LS) Ferric or Cobaltic enzymes that catalyze the conversion of nitriles to amides in soil bacteria. Another part of this thesis involves the spectroscopic characterization of a ferric NHase for the determination of its active site geometric and electronic structure, which are used to calibrate a computational model which is extended to explore the NHase catalytic mechanism.

Download or read book Mononuclear Non heme Iron Dependent Enzymes written by and published by Elsevier. This book was released on 2024-09-01 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mononuclear Non-heme Iron Dependent Enzymes, Volume 703 focuses on methods for studying, characterizing, and leveraging the chemistry of mononuclear non-heme iron dependent enzymes. Chapters in this new release include Photoreduction for Rieske oxygenase chemistry, Insights into the Mechanisms of Rieske Oxygenases from Studying the Unproductive Activation of Dioxygen, Non-heme iron and 2-oxoglutarate enzymes catalyze cyclopropane and azacyclopropane formations, Obtaining precise metrics of substrate positioning in Fe(II)/2OG dependent enzymes using Hyperfine Sublevel Correlation Spectroscopy, Xe-pressurization studies for revealing substrate-entrance tunnels, and much more. Additional chapters cover A tale of two dehydrogenases involved in NADH recycling, Rieske oxygenases and/or their partner reductase proteins, Expression, assay and inhibition of 9-cis-epoxycarotenoid dioxygenase (NCED) from Solanum lycopersicum and Zea mays, Biocatalysis and non-heme iron enzymes, In vitro analysis of the three-component Rieske oxygenase cumene dioxygenase from Pseudomonas fluorescens IP01, Structure and function of carbazole 1,9a-dioxygenase, Characterization of a Mononuclear Nonheme Iron-dependent Mono-oxygenase OzmD in Oxazinomycin Biosynthesis, and much more. Provides detailed articles regarding how to study the structures and mechanisms of mononuclear non-heme iron dependent enzymes Guides readers on how to use partner proteins in non-heme iron enzyme catalysis Includes strategies to employ mononuclear non-heme iron enzymes in biocatalytic applications

Download or read book Mononuclear Non heme Iron Dependent Enzymes Part B written by and published by Elsevier. This book was released on 2024-09-17 with total page 382 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mononuclear Non-heme Iron Dependent Enzymes, Volume 703 PART B focuses on methods for studying, characterizing, and leveraging the chemistry of mononuclear non-heme iron dependent enzymes. Chapters in this new release include Photoreduction for Rieske oxygenase chemistry, Insights into the Mechanisms of Rieske Oxygenases from Studying the Unproductive Activation of Dioxygen, Non-heme iron and 2-oxoglutarate enzymes catalyze cyclopropane and azacyclopropane formations, Obtaining precise metrics of substrate positioning in Fe(II)/2OG dependent enzymes using Hyperfine Sublevel Correlation Spectroscopy, Xe-pressurization studies for revealing substrate-entrance tunnels, and much more. Additional chapters cover A tale of two dehydrogenases involved in NADH recycling, Rieske oxygenases and/or their partner reductase proteins, Expression, assay and inhibition of 9-cis-epoxycarotenoid dioxygenase (NCED) from Solanum lycopersicum and Zea mays, Biocatalysis and non-heme iron enzymes, In vitro analysis of the three-component Rieske oxygenase cumene dioxygenase from Pseudomonas fluorescens IP01, Structure and function of carbazole 1,9a-dioxygenase, Characterization of a Mononuclear Nonheme Iron-dependent Mono-oxygenase OzmD in Oxazinomycin Biosynthesis, and much more. Provides detailed articles regarding how to study the structures and mechanisms of mononuclear non-heme iron dependent enzymes Guides readers on how to use partner proteins in non-heme iron enzyme catalysis Includes strategies to employ mononuclear non-heme iron enzymes in biocatalytic applications

Download or read book Non heme Iron Enzymes Structures and Mechanisms written by and published by Academic Press. This book was released on 2019-09-28 with total page 134 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nonheme Iron Enzymes: Structures and Mechanisms, Volume 117, highlights new advances in the field, with this new volume presenting new and interesting chapters on the topics. Each chapter is written by an international board of authors. Targeted to a very wide audience of specialists, researchers and students Contains timely chapters written by well-renowned authorities in their field Includes a number of high quality illustrations, figures and tables

Download or read book Spectroscopic and Theoretical Studies of Mononuclear Non heme Iron Enzymes written by Adrienne Renee Diebold and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Mononuclear non-heme iron enzymes are an important class with a wide range of medical, pharmaceutical and environmental applications. Within this class, the oxygen activating enzymes use Fe(II) to activate O2 for reaction with the substrate. The focus of this thesis is on understanding two major themes of the oxygen activating enzymes - the role of the (2His/1 carboxylate) facial triad and the initial O2 reaction steps of alpha-keto acid-dependent dioxygenases - using a combination of spectroscopic techniques and DFT calculations. For ferrous systems, abs/CD/MCD/VTVH MCD studies define the geometric and electronic structure of the ferrous site. In combination with DFT calculations, a structure/function picture of the ferrous sites is developed. To extend these studies to the initial steps of O2 binding, studies with NO as an O2 analogue ({FeNO}7/{FeO2}8) utilize EPR/abs/CD/MCD/VTVH MCD spectroscopy with DFT calculations to elucidate important effects of the substrate on the {FeNO}7 bond. These effects are used in the computational extension to the experimentally inaccessible O2 bound complexes giving insight into the initial steps of O2 binding and activation. Taken together, these studies shed light on the rational for facial triad ligation at the Fe(II) site in the oxygen activating enzymes and how the Fe(II) ligand set tunes the specific reactivity of these enzymes.

Download or read book Iron containing Enzymes written by Sam P. De Visser and published by Royal Society of Chemistry. This book was released on 2011 with total page 463 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mononuclear iron containing enzymes are important intermediates in bioprocesses and have potential in the industrial biosynthesis of specific products. This book features topical review chapters by leaders in this field and its various sub-disciplines.

Download or read book Spectroscopic and Computational Studies of the Intradiol and Extradiol Dioxygenases written by Monita Yuen-Ming Pau and published by . This book was released on 2007 with total page 458 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book 2 Oxoglutarate Dependent Oxygenases written by Christopher J Schofield and published by Royal Society of Chemistry. This book was released on 2015-05-06 with total page 508 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the discovery of the first examples of 2-oxoglutarate-dependent oxygenase-catalysed reactions in the 1960s, a remarkably broad diversity of alternate reactions and substrates has been revealed, and extensive advances have been achieved in our understanding of the structures and catalytic mechanisms. These enzymes are important agrochemical targets and are being pursued as therapeutic targets for a wide range of diseases including cancer and anemia. This book provides a central source of information that summarizes the key features of the essential group of 2-oxoglutarate-dependent dioxygenases and related enzymes. Given the numerous recent advances and biomedical interest in the field, this book aims to unite the latest research for those already working in the field as well as to provide an introduction for those newly approaching the topic, and for those interested in translating the basic science into medicinal and agricultural benefits. The book begins with four broad chapters that highlight critical aspects, including an overview of possible catalytic reactions, structures and mechanisms. The following seventeen chapters focus on carefully selected topics, each written by leading experts in the area. Readers will find explanations of rapidly evolving research, from the chemistry of isopenicillin N synthase to the oxidation mechanism of 5-methylcytosine in DNA by ten-eleven-translocase oxygenases.

Download or read book Comprehensive Coordination Chemistry III written by and published by Elsevier. This book was released on 2021-07-29 with total page 6948 pages. Available in PDF, EPUB and Kindle. Book excerpt: Comprehensive Coordination Chemistry III describes the fundamentals of metal-ligand interactions, provides an overview of the systematic chemistry of this class of compounds, and details their importance in life processes, medicine, industry and materials science. This new edition spans across 9 volumes, 185 entries and 6600 printed pages. Comprehensive Coordination Chemistry III is not just an update of the second edition, it includes a significant amount of new content. In the descriptive sections 3-6, emphasis is placed upon material that has appeared in primary and secondary review literature since the previous edition published. The material in other sections is newly written, with an emphasis on modern aspects of coordination chemistry and the latest developments. The metal-ligand interaction is the link between the award of the 1913 Nobel Prize in Chemistry to Alfred Werner, the father of Coordination Chemistry, the 1987 prize for supramolecular chemistry and the 2016 award for molecular machines. The key role of coordination chemistry in the assembly of hierarchical nano- and micro-dimensioned structures lies at the core of these applications and so this Major Reference Work bridges several sub-disciplines of chemistry, thus targeting a truly interdisciplinary audience. Provides the go-to foundational resource on coordination chemistry research, providing insights into future directions of the field Written and edited by renowned academics and practitioners from various fields and regions this authoritative and interdisciplinary work is of interest to a large audience, including coordination, supramolecular and molecular chemists Presents content that is clearly structured, organized and cross-referenced to allow students, researchers and professionals to find relevant information quickly and easily

Download or read book Spectroscopic and Reactivity Studies of Binuclear Non heme Iron Complexes written by Subhasish Mukerjee and published by . This book was released on 1996 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Combined Spectroscopic and Computational Studies of Free and Enzyme bound B12 Species written by Laura Dynan Elmendorf and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Vitamin B12 and its derivatives, known collectively as cobalamins (Cbls) or the B12 family, play an essential role in catalyzing a diverse range of reactions across all areas of life. Understanding the versatile reactivity of these cofactors requires a detailed understanding of their geometric and electronic structures, as well as how these change upon enzyme binding and the addition of substrates. Spectroscopic techniques like electronic absorption, resonance Raman (rRaman), and magnetic circular dichroism spectroscopies are invaluable in this area, particularly when combined with computational techniques such as density functional theory that can bridge the gap between spectral features and structural implications. This dissertation presents a collection of projects that used these methods to delve into the properties and reactivity of free and enzyme-bound B12 species, as well as the mononuclear non-heme iron enzyme cysteamine dioxygenase (ADO). This work includes a study of vibronic coupling in vitamin B12, which afforded new insight into the choice of functional for quantum mechanical modeling of B12 and enabled the identification of the elusive Co-C stretching mode in this molecule's rRaman spectrum. It also includes an investigation of Co-C bond activation in ethanolamine ammonia-lyase (EAL), an adenosylcobalamin (AdoCbl)-dependent enzyme that catalyzes the conversion of ethanolamine to acetaldehyde and an ammonium ion. As with other AdoCbl-dependent enzymes, EAL's catalytic cycle begins with homolytic cleavage of the cofactor's Co-C bond, and the rate of homolysis is increased by 12 orders of magnitude when the cofactor is enzyme-bound in the presence of substrate. We identified conformational changes and cofactor-protein electrostatic interactions that occur upon substrate binding as key factors for promoting controlled and dramatically accelerated Co-C bond homolysis. Finally, two computational studies of PduO-type adenosyltransferases (ATRs), one with the native cobalamin substrate and the other with a rhodium-substituted analogue, explored key steps of the enzyme's catalytic cycle.

Download or read book Magnetic Resonance in Biological Systems written by A. Ehrenberg and published by Elsevier. This book was released on 2013-09-24 with total page 441 pages. Available in PDF, EPUB and Kindle. Book excerpt: Magnetic Resonance in Biological Systems, Volume 9 is a collection of manuscripts presented at the Second International Conference on Magnetic Resonance in Biological Systems, held in Wenner-Gren Center, Stockholm, Sweden on June 1966. The conference is sponsored by International Union of Biochemistry Swedish Medical Research Council Swedish Natural Science Research Council Wenner-Gren Center Foundation for Scientific Research. This book contains 51 chapters, and begins with reviews of NMR investigations of biological macromolecules, including proteins, amino acids, and glycylglycine copper (II). Considerable chapters are devoted to numerous biological studies using the electronic paramagnetic resonance (EPR), thus introducing the branch of science called submolecular biology. This book also explores other applications of NMR and EPR, with special emphasis on blood component analysis and protein-metal complexes. The final chapters survey the principles and applications of Mössbauer spectroscopy. This book will prove useful to analytical chemists and biologists.

Download or read book Inorganic Reaction Mechanisms written by and published by Academic Press. This book was released on 2017-06-30 with total page 346 pages. Available in PDF, EPUB and Kindle. Book excerpt: Inorganic Reaction Mechanisms, Volume 70 is the latest volume in the Advances in Inorganic Chemistry series that presents timely summaries of current progress in inorganic chemistry, ranging from bio-inorganic to solid state studies. Topics covered in this updated volume include The Kinetics and Mechanism of Complex Redox Reactions in Aqueous Solution: The Tools of the Trade, O-O Bond Activation in Cu and Fe-Based Coordination Complexes: Breaking it Makes the Difference, μ-Nitrido Diiron Phthalocyanine and Porphyrin Complexes: Unusual Structures With Interesting Catalytic Properties, and The Role of Nonheme Transition Metal-Oxo, -Peroxo and -Superoxo Intermediates in Enzyme Catalysis and Reactions of Bioinspired Complexes. This acclaimed serial features reviews written by experts in the field, serving as an indispensable reference to advanced researchers. Each volume contains an index and chapters are fully referenced. Features comprehensive reviews on the latest developments in inorganic reaction mechanisms, a subfield of inorganic chemistry Includes contributions from leading experts in the field of inorganic reaction mechanisms Serves as an indispensable reference to advanced researchers in inorganic reaction mechanisms

Download or read book Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes written by Adam Liwo and published by Springer. This book was released on 2018-12-19 with total page 851 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a comprehensive overview of modern computer-based techniques for analyzing the structure, properties and dynamics of biomolecules and biomolecular processes. It is organized in four main parts; the first one deals with methodology of molecular simulations; the second one with applications of molecular simulations; the third one introduces bioinformatics methods and the use of experimental information in molecular simulations; the last part reports on selected applications of molecular quantum mechanics. This second edition has been thoroughly revised and updated to include the latest progresses made in the respective field of research.

Download or read book Natural Product Biosynthesis written by Christopher T. Walsh and published by Royal Society of Chemistry. This book was released on 2017-04-28 with total page 787 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook describes the types of natural products, the biosynthetic pathways that enable the production of these molecules, and an update on the discovery of novel products in the post-genomic era.