Download or read book Computational Studies of Electron Transfer in Multi Heme Proteins written by Xiuyun Jiang and published by . This book was released on 2019 with total page 162 pages. Available in PDF, EPUB and Kindle. Book excerpt: Multi-heme proteins are fascinating biomolecules that bind several redox-active heme cofactors in close distance to shuttle electrons across the bacterial membrane. Yet, the kinetics and time scales on which these electron transfer (ET) events occur is not well known and difficult to probe experimentally. The central aim of this thesis is to compute and to quantify heme-heme ET rate constants and electron flux through solvated multi-heme proteins. To this end, density functional theory and molecular dynamics simulation are deployed to compute heme-heme ET parameters in the framework of (non-adiabatic) Marcus theory, the central theory underlying such ET events. Three ubiquitous multi-heme proteins have been studied, which bind 4 and 10 heme cofactors. Our calculations revealed that electron transfer through these proteins is strongly enhanced by cysteine side chains that are inserted in the space between heme groups. We believe this to be a general design principle in this family of proteins for acceleration of ET steps that would otherwise be too slow for biological respiration. Our computational protocol has been verified via comparing our predicted time scale of heme-heme ET with the corresponding ET rate constant measured from pump-probe spectroscopy. The maximum, protein-limited electron flux is ≈ 10^5 - 10^6 s^-1. Such efficiency in long-range electron transfer indicates that multi-heme proteins are promising candidates for biological nano-electronic devices.
Download or read book Electron Transfer Proteins written by Toshiko Ichiye and published by CRC Press. This book was released on 2015-02-01 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt: A molecular understanding of electron transfer is crucial to understanding the molecular basis of metabolic processes in which electron transfer is essential, diseases involving these processes, and drug design targeting these processes. This book provides a cohesive and comprehensive discussion of computational methods used for electron transfer proteins and what has been learned from such studies for the first time in a book. It also gives an overview of results from theory, computation, and experiment about electron transfer proteins. This resource also includes strategies for studying metal sites that have not been examined computationally.
Download or read book Computational Studies of Electron Transfer Proteins written by Yan Luo and published by . This book was released on 2011 with total page 205 pages. Available in PDF, EPUB and Kindle. Book excerpt: Iron-sulfur proteins are an important class of electron transfer proteins found universally in living organisms, serving vital roles in the electron transport chains of cellular energy utilization. Determining the molecular basis of electron transfer properties of these proteins is important in understanding how they promote fast and efficient energy flow in the cell.
Download or read book Characterization of Electron transfer Proteins written by Kathryn Duffy Bewley and published by . This book was released on 2013 with total page 436 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: Electron-transfer proteins that are responsible for redox homeostasis and long-range electron transfer are vital to intracellular and extracellular processes. In this thesis, several examples of electron-transfer proteins are studied in order to determine the emergent properties of multi-electron transfer chemistry.Thioredoxin (Trx) is a small redox-active protein that functions via its disulfide bond. These disulfides, characterized by a CXXC motif, are found to have a range of redox potentials that are often linked to function. Chapter 2 uses a set of archaeal thioredoxins from Thermoplasma acidophilum and Archaeoglobus fulgidus to test the current hypotheses using protein film voltammetry and solution-based experiments that examine folding energies.Thioredoxin reductase (TrxR) functions to provide reducing equivalents to Trx to keep it active in the cell. The TrxR from Thermoplasma acidophilum has been noted to be unusual in that it does not use NADPH as a reductant, as found in most TrxRs. The reaction between T. acidophilum Trx and TrxR is explored in Chapter 3 and a bioinformatic analysis of Ta TrxR is included in Chapter 4 to better understand its relationship in the TrxR protein family, as well as attempt to identity its native reductant.In Chapter 5, the periplasmic decaheme cytochrome DmsE from Shewanella oneidensis is biochemically characterized. This protein is part of the dimethyl sulfoxide reduction pathway and is compared with MtrA, the well-studied decaheme protein from the dissimilatory metal reduction pathway in Shewanella. Additionally, a Cytoscape analysis of the MtrA/DmsE and OmcA protein families is presented.Finally, Chapter 6 explores the electrochemical properties of two multi-heme proteins from Nitrosomonas europaea: cytochrome c 554 and hydroxylamine oxidoreductase (HAO). Cytochrome c554, a tetraheme cytochrome, has been shown to have cooperativity between two of its heme groups and gating has been observed in protein film voltammetry (PFV) experiments. This gating is further explored in this Chapter. The enzymatic hydroxylamine reduction by HAO, a reverse reaction, is also presented.
Download or read book Computation of Electron Transfer in Proteins written by Dmitry Medvedev and published by . This book was released on 2002 with total page 506 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Computational Studies on Electron Transfer by Iminium Ions written by Chris Van Dyke and published by . This book was released on 1991 with total page 186 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Protein Electron Transfer written by D.S. Bendall and published by Garland Science. This book was released on 1996-06 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book melds theory and experiment together in a fundamental aspect of protein biology to develop a framework of ideas that can be applied to a variety of systems. It discusses the crystal structures of electron transfer proteins and complexes.
Download or read book Biomedical Index to PHS supported Research pt A Subject access A H written by and published by . This book was released on 1992 with total page 1064 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book A Computational Study in the Thermodynamic and Dynamic Properties of Electron Transfer Proteins written by David N. LeBard and published by . This book was released on 2008 with total page 440 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Atomic Scale Modelling of Electrochemical Systems written by Marko M. Melander and published by John Wiley & Sons. This book was released on 2021-09-09 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Atomic-Scale Modelling of Electrochemical Systems A comprehensive overview of atomistic computational electrochemistry, discussing methods, implementation, and state-of-the-art applications in the field The first book to review state-of-the-art computational and theoretical methods for modelling, understanding, and predicting the properties of electrochemical interfaces. This book presents a detailed description of the current methods, their background, limitations, and use for addressing the electrochemical interface and reactions. It also highlights several applications in electrocatalysis and electrochemistry. Atomic-Scale Modelling of Electrochemical Systems discusses different ways of including the electrode potential in the computational setup and fixed potential calculations within the framework of grand canonical density functional theory. It examines classical and quantum mechanical models for the solid-liquid interface and formation of an electrochemical double-layer using molecular dynamics and/or continuum descriptions. A thermodynamic description of the interface and reactions taking place at the interface as a function of the electrode potential is provided, as are novel ways to describe rates of heterogeneous electron transfer, proton-coupled electron transfer, and other electrocatalytic reactions. The book also covers multiscale modelling, where atomic level information is used for predicting experimental observables to enable direct comparison with experiments, to rationalize experimental results, and to predict the following electrochemical performance. Uniquely explains how to understand, predict, and optimize the properties and reactivity of electrochemical interfaces starting from the atomic scale Uses an engaging “tutorial style” presentation, highlighting a solid physicochemical background, computational implementation, and applications for different methods, including merits and limitations Bridges the gap between experimental electrochemistry and computational atomistic modelling Written by a team of experts within the field of computational electrochemistry and the wider computational condensed matter community, this book serves as an introduction to the subject for readers entering the field of atom-level electrochemical modeling, while also serving as an invaluable reference for advanced practitioners already working in the field.
Download or read book Storage Transport Release written by Anna Bauß and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: Using molecular dynamics simulations of the thermodynamic integration type, we study the energetics and kinetics of electron transfer through the nitrite reductase enzyme of Sulfurospirillum deleyianum, Wolinella succinogenes and Campylobacter jejuni. In all of these five-heme proteins, the storage of an even number of electrons within a monomeric chain is thermodynamically favoured. Kinetically, two of these electrons are usually transferred almost simultaneously towards the active site. Although the free energy landscape for charge transfer varies significantly from organism to organism, the heme cofactor closest to the interface of a protein dimer always exhibits a particularly low free energy, suggesting that protein dimerization is functional. Interheme electron interaction effects do not play a significant role
Download or read book Computational Studies of Biological Electron Transfer Cofactors and Electron Donor acceptor Complexes written by Kristopher Eric Wise and published by . This book was released on 1999 with total page 406 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Multiheme Cytochromes written by Carlos A. Salgueiro and published by Springer. This book was released on 2016-10-08 with total page 51 pages. Available in PDF, EPUB and Kindle. Book excerpt: This brief introduces the structural and functional characterization of this important group of proteins. The content of each chapter is aimed at the non-specialist so that key concepts, methodologies and applications can be presented in a "snapshot" style volume. Multiheme cytochromes are ever more important now that it is possible to obtain genome sequences of microorganisms which have major biotechnological and environmental implications. There is a tremendous profusion of multiheme cytochromes which have great potential as targets for bioremediation and bioenergy applications. This brief gives a glimpse of an intriguing and fast-moving field.
Download or read book Atomistic Approaches in Modern Biology written by Markus Reiher and published by Springer Science & Business Media. This book was released on 2007-01-08 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt: With contributions by numerous experts
Download or read book Research Awards Index written by and published by . This book was released on 1989 with total page 776 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Fast Processes in Heme Proteins written by Mark Andrew McLean and published by . This book was released on 1997 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Electron and Proton Transfer in Chemistry and Biology written by Achim Müller and published by Elsevier Publishing Company. This book was released on 1992 with total page 420 pages. Available in PDF, EPUB and Kindle. Book excerpt: Various aspects of electron and proton transfer in chemistry and biology are described in this volume. The joint presentation was chosen for two reasons. Rapid electron and proton transfer govern cellular energetics in both the most primitive and higher organisms with photosynthetic and heterotrophic lifestyles. Further, biology has become the area where the various disciplines of science, which were previously diversified, are once again converging. The book begins with a survey of physicochemical principles of electron transfer in the gas and solid phase, with thermodynamic and photochemical driving force. Inner and outer sphere mechanisms and the coupling of electron transfer to nuclear rearrangements are reviewed. These principles are applied to construct artificial photosynthesis, leading to biological electron transfer involving proteins with transition metal and/or organic redox centres. The tuning of the free energy profile on the reaction trajectory through the protein by single amino acids or by the larger ensemble that determines the electrostatic properties of the reaction path is one major issue.Another one is the transformation of one-electron to paired-electron steps with protection against hazardous radical intermediates. The diversity of electron transport systems is represented in various chapters with emphasis on photosynthesis, respiration and nitrogenases. The book will be of interest to scientists in chemistry, physics and the life sciences.
