Computational Studies of Electron Transfer in Multi-Heme Proteins


Book Description

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.




Electron Transfer Proteins


Book Description

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.




Computational Studies of Electron Transfer Proteins


Book Description

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.




Characterization of Electron-transfer Proteins


Book Description

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.










Protein Electron Transfer


Book Description

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.










Atomic-Scale Modelling of Electrochemical Systems


Book Description

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.