Front Matter

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METALLOPROTEINS Theory, Calculations, and Experiments

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METALLOPROTEINS Downloaded by [115.249.130.56] at 21:46 21 May 2015

Theory, Calculations, and Experiments

Edited by

Art E. Cho

Korea University, Korea

William A. Goddard III

California Institute of Technology, Pasadena, USA

Boca Raton London New York

CRC Press is an imprint of the Taylor & Francis Group, an informa business

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CRC Press Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2015 by Taylor & Francis Group, LLC CRC Press is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S. Government works Version Date: 20150316 International Standard Book Number-13: 978-1-4398-1319-5 (eBook - PDF) This book contains information obtained from authentic and highly regarded sources. Reasonable efforts have been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the validity of all materials or the consequences of their use. The authors and publishers have attempted to trace the copyright holders of all material reproduced in this publication and apologize to copyright holders if permission to publish in this form has not been obtained. If any copyright material has not been acknowledged please write and let us know so we may rectify in any future reprint. Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any information storage or retrieval system, without written permission from the publishers. For permission to photocopy or use material electronically from this work, please access www.copyright.com (http://www.copyright.com/) or contact the Copyright Clearance Center, Inc. (CCC), 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400. CCC is a not-for-profit organization that provides licenses and registration for a variety of users. For organizations that have been granted a photocopy license by the CCC, a separate system of payment has been arranged. Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used only for identification and explanation without intent to infringe. Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com

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We dedicate this volume to the authors who took time from their very busy fundamental research activities to provide an up-todate summary of the recent advances in both the experimental and theoretical understanding of the fundamental processes in Metalloproteins. We hope that this will help engage new generations in the ongoing adventure of explaining and harnessing the powerful life processes mediated by these systems.

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Contents Preface.......................................................................................................................ix Editors........................................................................................................................xi Contributors............................................................................................................ xiii Chapter 1 Advanced Electron Paramagnetic Resonance Studies of the Oxygen-Evolving Complex................................................................... 1

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Troy A. Stich and R. David Britt Chapter 2 Radical SAM Enzymes and Their Roles in Complex Cluster Assembly............................................................................................. 59 Jeremiah N. Betz, Eric M. Shepard, and Joan B. Broderick Chapter 3 Density Functional Theory-Based Treatments of Metal-Binding Sites in Metalloenzymes: Challenges and Opportunities................... 95 Mercedes Alfonso-Prieto and Michael L. Klein Chapter 4 Catalysis of Methane Oxidation by the Tricopper Cluster in the Particulate Methane Monooxygenase and Biomimetic Tricopper Complexes......................................................................................... 117 Suman Maji, Steve S.-F. Yu, and Sunney I. Chan Chapter 5 Oxygen-Evolving Complex of Photosystem II: Insights from Computation and Synthetic Models.................................................. 165 Jacob S. Kanady, Jose Mendoza-Cortes, William A. Goddard III, and Theodor Agapie Chapter 6 Electrifying Metalloenzymes............................................................205 Fraser A. Armstrong Chapter 7 Iron Uptake Mechanism in Ferritin from Helicobacter pylori......... 223 Sella Kim and Kyung Hyun Kim

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Chapter 8 Multiple-Step Electron Flow in Proteins........................................... 235 Jeffrey J. Warren, Maraia E. Ener, Jay R. Winkler, and Harry B. Gray Chapter 9 Modeling of Ligand Binding to Metalloproteins.............................. 253 Art E. Cho

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Index....................................................................................................................... 267

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Preface Metalloproteins play essential critical functional roles in enzymatically catalyzing reactions difficult to achieve without metals, in signal transduction, and in storage and transport of proteins constituting over 1/3 of the proteome of living organisms. Recent breakthroughs in crystallography have provided insights into understanding their mechanisms, but challenges remain in identifying the particularly redox states of the metals and in the chemical mechanisms for the complex reactions they catalyze. With these advances in structural information, theory and computation are starting to play a more significant role, particularly in identifying the reaction mechanism. This volume summarizes some of the recent progresses in both experiment and theory/computation showing the synergy that is now developing. Two papers review the progress in understanding the Oxygen Evolution Reaction (OER) accomplished by Photosystem II (PSII), where four thrusts have converged to provide something close to an atomistically based mechanism: • X-ray structures of some (but unfortunately not all) of the intermediate states in the catalytic reactions and characterization of the active sites through techniques such as EXAFS and XANES • Model systems synthesized to reproduce the active states to enable clear-cut experimental studies of the details of the structures and redox states of the metals • EPR and NMR studies of many of the active states to clarify the steps • Quantum mechanical calculations of the active states to determine the structures and reaction barriers This remarkable progress is summarized in the papers from the Britt and Agapie groups. A driving force in trying to understand the mechanisms of the metalloenzymes is to use them as a model for developing biomimics that catalyze such important reactions as CH4 activation and the OER. The paper by Chan and coworkers describes the Odyssey from characterizing the complex structures and chemistry in methane monooxygenase (pMMO) to determining its unique structure involving three distinct Cu sites and then to developing a functioning biomimic catalyst that is very effective for selective oxidation of CH4 and alkanes. A particularly important class of metalloenzymes is the radical S-adenosyl-lmethionine (SAM) superfamily in which 4Fe–4S complexes carry out important anaerobic transformations as explained in the paper by Betz, Shepard, and Broderick. With the development of accurate structural models, it has become possible to use first principle quantum mechanics (DFT) to develop an understanding of the electron processes of the catalytic and electron transfer reactions involved as summarized by the Klein group. Cho then shows how to model the binding of ligands to metalloproteins by including the role of the more remote parts of the protein on these ix

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electronic  processes through coupling of QM with a force field description (QM/ MM). The advances in our understanding of the electrochemical processes essential to metalloproteins through protein film electrolysis (PFE) are summarized by Armstrong, showing how this provides detailed mechanisms underlying how these proteins play essential roles in life. Ferritins play an essential role in storing iron in bioavailable assembly, providing an example of the interplay between metal transport and storage of well-­characterized structural detail as explained in the paper by Kim and Kim showing the unique characteristics that are important in the functioning of Helicobacter pylori. At the heart of essentially all metalloenzymes is the role of electron transfer in controlling the rates of their reactions. The elucidation of how these electron transfer processes are mediated by the structures of the metalloenzymes involves a combination of theory and experiment as explained by the Gray group. We hope that this volume will ignite further collaborations between experiment and theory in elucidating and exploiting the metalloproteins. We envision that the volume will be valuable to researchers in the general field of bioinorganic chemistry and also as a sourcebook for courses at the biology/chemistry interface. We hope that this comprehensive collection of the recent research by top researchers will stimulate accelerated developments in combining experimental and theoretical studies of metalloproteins. William A. Goddard III Materials and Process Simulation Center, California Institute of Technology Art E. Cho Department of Bioinformatics, Korea University

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Editors William A. Goddard III is the Charles and Mary Ferkel Professor of chemistry, materials science, and applied physics, and the director of the Materials and Process Simulation Center at the California Institute of Technology. He earned his BS degree in engineering from the University of California, Los Angeles, in 1960 and his PhD degree in engineering science with a minor in physics from the California Institute of Technology in 1965. After passing his PhD exam in October 1964, he joined the Chemistry department at Caltech in November 1964, where he continues his activities in research and teaching. Dr. Goddard has pioneering methods for quantum mechanics (generalized valence bond theory, first principle pseudo-potentials) and reactive fields molecular dynamics (ReaxFF and eFF), and complete sampling for protein structure predicting and docking (GEnSeMBLE and DarwinDock), which he has applied to many areas of chemical reaction theory, catalysis, materials science, and selective ligand design. He has been a member of the US National Academy of Sciences since 1984 and is a fellow (IAQMS, APS, AAAS, Am Acad, Arts Science) or a member (ACS, MRS, Protein Society) of many other organizations. He was a cofounder of Materials Simulation Inc. (now Accelrys) and Schrodinger Inc., and continues with recent startups in electron etching of semiconductors (Systine) and design of therapeutics (GIRx). Art E. Cho is a professor in the Department of Bioinformatics, Korea University. He graduated from the University of California at Berkeley in 1988, with a double major in physics and mathematics. After completing the master’s program in mathematics at the University of Chicago, he pursued a PhD degree in physics at Brown University. Before finishing his PhD degree, he took time off and returned to his home country of Korea to fulfill mandatory military duty. As a substitution for service in the army, he worked as a senior research scientist at the supercomputing center of Samsung Advanced Institute of Technology affiliated with Samsung Electronics Co. After earning a PhD degree in physics in 2001, he worked as a postdoctoral scholar at Caltech and then as a research scientist at Columbia University. He also worked as an applications scientist at Schrodinger Inc. Since 2007, he has been with Korea University. In 2010, while taking up a departmental duty as the chair, he founded a startup company, named Quantum Bio Solutions, which specializes in computational drug design.

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Contributors Theodor Agapie Department of Chemistry California Institute of Technology Pasadena, California

Harry B. Gray Beckman Institute California Institute of Technology Pasadena, California

Mercedes Alfonso-Prieto Institute for Computational Molecular Science Temple University Philadelphia, Pennsylvania

Jacob S. Kanady Department of Chemistry California Institute of Technology Pasadena, California

Fraser A. Armstrong Department of Chemistry University of Oxford Oxford, United Kingdom Jeremiah N. Betz Department of Chemistry and Biochemistry Montana State University Bozeman, Montana R. David Britt Department of Chemistry University of California Davis, California Joan B. Broderick Department of Chemistry and Biochemistry Montana State University Bozeman, Montana Sunney I. Chan Institute of Chemistry Academia Sinica Taipei, Taiwan Maraia E. Ener Beckman Institute California Institute of Technology Pasadena, California

Kyung Hyun Kim Department of Bioinformatics Korea University Sejong, Korea Sella Kim Department of Bioinformatics Korea University Sejong, Korea Michael L. Klein Institute for Computational Molecular Science Temple University Philadelphia, Pennsylvania Suman Maji School of Physical Sciences Lovely Professional University Punjab, India Jose Mendoza-Cortes Department of Chemical and Biomedical Engineering Florida State University Tallahassee, Florida Eric M. Shepard Department of Chemistry and Biochemistry Montana State University Bozeman, Montana xiii

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Troy A. Stich Department of Chemistry University of California Davis, California

Jay R. Winkler Beckman Institute California Institute of Technology Pasadena, California

Jeffrey J. Warren Beckman Institute California Institute of Technology Pasadena, California

Steve S.-F. Yu Institute of Chemistry Academia Sinica Taipei, Taiwan