Metal Ions in Life Sciences 12 Series Editors: Astrid Sigel · Helmut Sigel · Roland K.O. Sigel Lucia Banci Editor Metallomics and the Cell Metallomics and the Cell Metal Ions in Life Sciences Volume 12 Guest Editor: Lucia Banci Series Editors: Astrid Sigel, Helmut Sigel, and Roland K.O. Sigel For further volumes: http://www.springer.com/series/8385 and http://www.mils-series.com Astrid Sigel (cid:129) Helmut Sigel (cid:129) Roland K.O. Sigel Series Editors Lucia Banci Editor Metallomics and the Cell Editor Lucia Banci Department of Chemistry Centro Risonanze Magnetiche University of Florence University of Florence Via della Lastruccia 5 Via Luigi Sacconi 6 I-50019 Sesto Fiorentino (Florence), Italy I-50019 Sesto Fiorentino (Florence), Italy [email protected]fi .it Series Editors Astrid Sigel Helmut Sigel Department of Chemistry Department of Chemistry Inorganic Chemistry Inorganic Chemistry University of Basel University of Basel Spitalstrasse 51 Spitalstrasse 51 CH-4056 Basel CH-4056 Basel Switzerland Switzerland [email protected] [email protected] Roland K.O. Sigel Institute of Inorganic Chemistry University of Zürich Winterthurerstrasse 190 CH-8057 Zürich Switzerland [email protected] ISSN 1559-0836 ISSN 1868-0402 (electronic) ISBN 978-94-007-5560-4 ISBN 978-94-007-5561-1 (eBook) DOI 10.1007/978-94-007-5561-1 Springer Dordrecht Heidelberg New York London Library of Congress Control Number: 2013933450 © Springer Science+Business Media Dordrecht 2013 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, speci fi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on micro fi lms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. 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While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) Dedication to Ivano Bertini Ivano Bertini passed away untimely on July 7, 2012, at the age of 71. With him the Bioinorganic Community lost one of its giants. Ivano left his traces all the way from Inorganic Chemistry through Magnetic Resonance and Biochemistry to the Medical Sciences with more than 6 50 papers. He and his group in Florence, known for their pioneering NMR work, solved over 150 protein structures. Thanks to his enthusiasm, driving personality, and the way he viewed international relationships, he was initiator and cofounder of the I nternational Conferences on Bioinorganic C hemistry (ICBICs), the European Biological Inorganic Chemistry Conferences (EuroBICs), the E urasia Conferences on Chemical Sciences (EuAsC2S), the E uropean Conferences on Chemistry for Life Sciences (ECCLS), the C hianti Workshops , and more. Ivano was also one of the founders of the S ociety for Biological Inorganic Chemistry (SBIC) and the fi rst Editor of the J ournal of Biological Inorganic Chemistry v vi (JBIC). To name just a few of his initiatives and impacts, which last but not least included also the foundation of CERM, the Magnetic Resonance Center of the University of Florence. This volume M etallomics and the Cell is devoted to Ivano, who coauthored Chapter 1 of this book, and who was fascinated by the “omics” sciences and the possibilities they offer for understanding life. It is thus no surprise to read in the mentioned chapter …” It is the duty of the bioinorganic chemistry community to convince funding agencies that the research on metallomes and metallomics deserves attention” and support. He was a true protagonist of new ideas! There is no way to list here all the achievements of Ivano Bertini and therefore, we simply close by saying: THANK YOU, Ivano, for what you did for us, the chemical sciences and the scienti fi c community in general – you will never be forgotten! Sesto Fiorentino (Florence) , Italy Lucia Banci Basel , Switzerland Astrid Sigel Basel , Switzerland Helmut Sigel Zürich , Switzerland Roland K. O. Sigel Historical Development and Perspectives of the Series Metal Ions in Life Sciences* It is an old wisdom that metals are indispensable for life. Indeed, several of them, like sodium, potassium, and calcium, are easily discovered in living matter. However, the role of metals and their impact on life remained largely hidden until inorganic chemistry and coordination chemistry experienced a pronounced revival in the 1950s. The experimental and theoretical tools created in this period and their appli- cation to biochemical problems led to the development of the fi eld or discipline now known as B ioinorganic Chemistry , Inorganic Biochemistry , or more recently also often addressed as B iological Inorganic Chemistry . By 1970 B ioinorganic Chemistry was established and further promoted by the book series M etal Ions in Biological S ystems founded in 1973 (edited by H.S., who was soon joined by A.S.) and published by Marcel Dekker, Inc., New York, for more than 30 years. After this company ceased to be a family endeavor and its acquisition by another company, we decided, after having edited 44 volumes of the MIBS series (the last two together with R.K.O.S.) to launch a new and broader minded series to cover today’s needs in the L ife Sciences . Therefore, the Sigels new series is entitled Metal Ions in Life Sciences. After publication of the fi rst four volumes (2006–2008) with John Wiley & Sons, Ltd., Chichester, UK, and the next fi ve volumes (2009–2011) with the Royal Society of Chemistry, Cambridge, UK, we are happy to join forces now in this still new endeavor with Springer Science & Business Media B.V., Dordrecht, The Netherlands; a most experienced Publisher in the S ciences . *Reproduced with some alterations by permission of John Wiley & Sons, Ltd., Chichester, UK (copyright 2006) from pages v and vi of Volume 1 of the series Metal Ions in Life Sciences (MILS-1). vii viii Historical Development and Perspectives of the Series The development of B iological Inorganic Chemistry during the past 40 years was and still is driven by several factors; among these are (i) the attempts to reveal the interplay between metal ions and peptides, nucleotides, hormones or vitamins, etc., (ii) the efforts regarding the understanding of accumulation, transport, metabo- lism and toxicity of metal ions, (iii) the development and application of metal-based drugs, (iv) biomimetic syntheses with the aim to understand biological processes as well as to create ef fi cient catalysts, (v) the determination of high-resolution structures of proteins, nucleic acids, and other biomolecules, (vi) the utilization of powerful spectros-copic tools allowing studies of structures and dynamics, and (vii), more recently, the widespread use of macromolecular engineering to create new biologi- cally relevant structures at will. All this and more is and will be re fl ected in the volumes of the series M etal Ions in Life Sciences . The importance of metal ions to the vital functions of living organisms, hence, to their health and well-being, is nowadays well accepted. However, in spite of all the progress made, we are still only at the brink of understanding these processes. Therefore, the series M etal Ions in Life S ciences will endeavor to link coordination chemistry and biochemistry in their widest sense. Despite the evident expectation that a great deal of future outstanding discoveries will be made in the interdisciplinary areas of science, there are still “language” barriers between the historically separate spheres of chemistry, biology, medicine, and physics. Thus, it is one of the aims of this series to catalyze mutual “understanding”. It is our hope that M etal Ions in Life Sciences proves a stimulus for new activities in the fascinating “ fi eld” of Biological Inorganic Chemistry . If so, it will well serve its purpose and be a rewarding result for the efforts spent by the authors. Astrid Sigel and Helmut Sigel Department of Chemistry, Inorganic Chemistry, University of Basel, CH-4056 Basel, Switzerland Roland K.O. Sigel Institute of Inorganic Chemistry, Unversity of Zürich, CH-8057 Zürich, Switzerland October 2005, October 2008, and August 2011 Preface to Volume 12 Metallomics and the Cell In this volume of the Metal Ions in Life Sciences series a broad and complete coverage of the “omics” approach to the fi eld of metal ions in biological systems is presented and discussed in a cellular context, i.e., in the frame of a cell or of living systems, underlining the complexity of the interactions between living systems and inorganic elements. In Chapter 1 general concepts are elaborated and the de fi nition of the metallome is provided, as the ensemble of all the biomolecules in a system which bind a given metal ion or an inorganic element in general, or are affected by that element. The metallome is therefore a dynamic property which depends on the conditions of the system. Metallomics is the systematic study of a metallome and of the functional connections and interactions of the metal ion with the genome, proteome, metabo- lome, and other biomolecules in an organism. The role of bioinformatics and infor- mation technology are also discussed, and this knowledge framed in a cellular context. The need of this perspective is required in order to describe the functional processes. The ultimate goal of reaching a systems biology vision from the know- ledge of the interlinks and connections among the various pathways and processes involving metal ions in the cell is discussed. Chapter 2 presents an overview of the most suitable methods for the analysis of metal distributions in a cell, and how this distribution is affected by the cellular status and conditions. In the following, from Chapter 3 through 15, the metallome relative to various metal ions is described, limited to the essential metal ions for at least one domain of life. So the chapters encompass sodium and potassium and range to magnesium, calcium, and then to manganese, iron, cobalt, nickel, copper, zinc, as well as molyb- denum and tungsten. When needed and/or enough knowledge is available, the metal- lome description has been subdivided based on the type of organism, i.e., bacteria and eukaryotic ones, as well on the type of cofactors, e.g., heme for iron. An overview of the most relevant biomolecules (mostly proteins) functionally interacting with ix