Professor Chunying Chen received her Bachelor's degree in chemistry (1991) and obtained her PhD degree (1996) in Biomedical engineering from Huazhong University of Science and Technology of China. She held postdoctoral positions at the Key Laboratory of Nuclear Analytical Techniques, Institute of High Energy Physics of Chinese Academy of Sciences (1996-1998) and at the Medical Nobel Institute for Biochemistry of Karolinska Institute, Sweden (2001-2002). Dr. Chen currently is a principal investigator at CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety in National Center for Nanoscience and Technology of China. She has authored or co-authored over 70 peer-reviewed papers or book chapters and three patents. She is a member of the International Union of Pure and Applied Chemistry (IUPAC), and Chinese Society of Toxicology. Her current research interests include the development of analytical approaches for metallomics and metalloproteomics such as isotopic labeling and synchrotron radiation based techniques that allow the detection of interaction of metal and molecular species; the potential toxicity of nanoparticles used for nanotechnology applications; the therapy for malignant tumor using nanoparticles for their immunomodulatory effects, drug delivery and tumor targeting; extensive in vitro and in vivo studies in cellular uptake and intracellular trafficking of nanoparticles and tissue and cellular targeting for cancer treatment; the improvement of HIV vaccine treatment by novel nanotechnology using nanomaterials as potential non-viral vectors; public health impact of long-term exposure of metals in susceptible population strata.

Professor Zhifang Chai is a radiochemist working at the Multidisciplinary Initiative Centre, Institute of High Energy Physics, the Chinese Academy of Sciences. He graduated from Fudan University, China, in 1964. As a fellow of the Alexander von Humboldt Foundation, Germany, he worked at Cologne University from 1980 to 1982 in the field of nuclear technology and its applications. Later, he worked in France, the USA, the Netherlands and Japan. He has long been involved in the methodology of nuclear analytical techniques and their multidisciplinary applications, especially in the study of the chemical speciation of trace elements in environmental and biological systems. He has authored or co-authored over 332 papers in peer-reviewed journals, 6 Chinese books and 3 English books. He is a titular member of Analytical Chemistry Division, International Union for Pure and Applied Chemsitry, Fellow of Royal Society of Chemistry, UK, and many domestic and international scientific societies. He is a member of editorial board or advisory committee of 10 international and national journals. In 2005 he was awarded the George von Hevesy Award - the premier international award of excellence to honour outstanding achievements in radioanalytical and nuclear chemistry. In 2007 he was elected as a member (Academician) of the Chinese Academy of Sciences. His present interest is to develop novel nuclear analytical methods for the study of metallomics.

Yuxi Gao is an associate professor at Institute of High Energy Physics, Chinese Academy of Sciences. He obtained his PhD degree in environmental sciences in 2000 from Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences. His current research focuses on the methodology of metallomics and metalloproteomics based on the nuclear analytical techniques; the applications of metallomics and metalloproteomics tourniquets on the environmental and biomedical research; the homeostasis of trace elements and their regulatory mechanism; the structure, function and structure-function relationship of important metalloproteins.

Nuclear Analytical Techniques for Metallomics and Metalloproteomics

By Chunying Chen, Zhifang Chai, Yuxi Gao

The Royal Society of Chemistry

Copyright © 2010 Royal Society of Chemistry
All rights reserved.
ISBN: 978-1-84755-901-2

Contents

List of Abbrevations, xix,
About the Editors, xxv,
List of Contributors, xxvii,
Chapter 1 Introduction Ying Qu, Yu-Feng Li, Ru Bai, Chunying Chen and Zhifang Chai, 1,
Chapter 2 Neutron Activation Analysis Zhiyong Zhang, 44,
Chapter 3 X-ray Fluorescence Yuxi Gao, 62,
Chapter 4 Isotopic Techniques Combined with ICP-MS and ESI-MS Meng Wang, Weiyue Feng and Zhifang Chai, 95,
Chapter 5 Mössbauer Spectroscopy Yang Qiu and Chunying Chen, 128,
Chapter 6 X-ray Absorption Spectroscopy Yu-Feng Li and Chunying Chen, 163,
Chapter 7 Protein Crystallography for Metalloproteins Zengqiang Gao, Haifeng Hou and Yuhui Dong, 212,
Chapter 8 Applications of Nuclear Analytical Techniques for Iron-omics Studies Guangjun Nie, Motao Zhu and Bo Ning, 239,
Chapter 9 Nuclear-based Metallomics in Metal-based Drugs Ruiguang Ge, Ivan K. Chu and Hongzhe Sun, 265,
Chapter 10 Application of Integrated Techniques for Micro-and Nano-imaging Towards the Study of Metallomics and Metalloproteomics in Biological Systems Lili Zhang and Chunying Chen, 299,
Chapter 11 Nuclear-based Metallomics in Metallic Nanomaterials: Nanometallomics Yu-Feng Li, Liming Wang, Lili Zhang and Chunying Chen, 342,
Subject Index, 385,

CHAPTER 1

Introduction

YING QU, YU-FENG LI, RU BAI, CHUNYING CHEN, ZHIFANG CHAI

1.1 Background

The terms "-ome" and "-omics" have been widely adopted by scientists. The "omics" informally refers to the studies in biology, while the related "-omes" addresses the objects of study in such fields. The suffix "-ome" is thought to derive from the Latin prefix "omni-", meaning total or complete. Thus, "-omes" are intended to be a comprehensive description of all of the relevant components, both known and unknown, in a particular biomolecular subset. "Omes" can provide an easy short-hand to encapsulate a field; for example, a proteome refers to the protein complement of an entire organism, tissue type, or cell, and its associated field "proteomics" is clearly recognizable as relating to the study field of proteins on a large scale. The term "-omics" represents the rigorous study of various collections of molecules, biological processes, or physiological functions and structures as systems.

Compared to the well known genomics and proteomics, metallomics and metalloproteomics are relatively new fields. They are receiving great attention in the investigation of trace elements in biology and expected to develop as an interdisciplinary science complementary to genomics and proteomics. In the first chapter of this book, the history and definition of metallomics and metalloproteomics will be introduced. In addition, the current application of nuclear or nuclear-related analytical techniques for metallomics and metalloproteomics will be overviewed.

1.2 Metallomics and Metalloproteomics

1.2.1 Trace Elements, Chemical Species and Speciation Analysis

The term "trace elements" dates back to the early 20th century, in recognition of the fact that many elements occurred at such low concentrations that their presence could only just be detected. In analytical chemistry, a trace element is an element in a sample that has an average concentration of less than 100 parts per million atoms, or less than 100 µg g-1. In biochemistry, a trace element is a chemical element that is needed in minute quantities for the proper growth, development, and physiology of the organism and it is also referred to as a micronutrient. So far, 117 elements in total have been observed, of which 92 occur naturally on Earth. However, living organisms are composed of about 26 elements, and only six of those 26 make up practically all of the weight of most living things. The other 20 elements essential for life are present in very small amounts, some of them are in such tiny amounts that they are correspondingly called "trace elements". Besides their phenotypic and phylogenetic characteristics, only 11 elements appear to be approximately constant and predominant in all biological systems, which are called major elements. In the human body, these constitute 99.9% of the total number of atoms present, but just four of them (C, O, H, and N) correspond to 99% of the total and the other seven elements (Na, K, Ca, Mg, P, S, and Cl) represent only about 0.9%.

Trace elements play an important role in the functioning of life. Essential trace elements, acting as catalytic or structural components of larger molecules, have specific functions and are indispensable for life. In addition to the long-known deficiencies of iron and iodine, signs of deficiency for chromium, copper, zinc, and selenium have been identified in free-living populations. It is considered that marginal or severe trace element imbalances can be risk factors for several diseases of public health importance. However, the cause and effect relationships will depend on a more complete understanding of basic mechanisms of action, and more importantly, on better analytical procedures and functional tests to determine marginal trace element status in human.

The biological effect of an element is not only dependent on the total concentration, but also highly related to its chemical forms present in biological systems, e.g. the oxidation state, the nature of the ligands or even the molecular structure. Dramatic examples are chromium, tin and mercury, to name just a few. Cr(VI) ions are considered far more toxic than Cr(III). Although the inorganic forms of tin and mercury are less toxic or even do not show toxic properties, the alkylated forms are highly toxic. Dialkylmercury derivatives are considered extremely toxic, while mercuric selenide has a relatively low toxicity and accumulates as an apparently benign detoxification product in marine animals, and methylmercury cysteine proves to be much less toxic than methylmercury chloride in a zebra fish larvae model system. Therefore, to produce qualitative and quantitative information on chemical compounds that affect the quality of life, chemical forms of specific element should be considered carefully.

Nowadays, there is increasing awareness of the importance of the chemical form in which an element is present in biological systems. More and more chemical speciation information on a given element is demanded in most fields of research. In fact, many environmental, toxicological, pharmacological, nutritional, and biological issues today require reliable information on the actual chemical species present, rather than total element concentrations as usually provided by atomic techniques in routine laboratories. In recent years, trace element speciation has become a worldwide trend in current analytical chemistry. Often these different chemical forms of a particular element or its compounds are referred to as "species".

Species and speciation, words borrowed from the biological sciences originally, have been adopted by those in analytical chemistry and accepted in such diverse fields as toxicology, clinical chemistry, geochemistry, and environmental chemistry, expressing the idea that the specific chemical forms of an element should be considered individually. The concept of "speciation" dates back to 1954 when Goldberg introduced it to improve the understanding of the biogeochemical cycling of trace elements in seawater. Since then, this development has been growing exponentially to the point that research on trace element analysis is being conducted. Today, research is almost exclusively focused on trace element species.

Although the concept of speciation is now widely appreciated in many fields, these terms have been used in a number of different ways and created confusion. In a report on the 1984 workshop "The Importance of Chemical Speciation in Environmental Processes", Bernhard et al. pointed out that the usage of speciation varies among different fields ranging from evolutionary changes to distinctions based on chemical state. The term has been used in no fewer than four different ways including the reaction specificity, transformation of species, the distribution of species, or the analytical activity to determine the concentrations of species. They concluded that authors should either avoid the term altogether or clearly define it.

In an attempt to end the confusion that existed regarding the usage of the term speciation, the International Union of Pure and Applied Chemistry (IUPAC), (three IUPAC Divisions represented by the Commission on Microchemical Techniques and Trace Analysis, the Commission on Fundamental Environmental Chemistry, and the Commission on Toxicology) provided IUPAC Recommendations in 2000 in an attempt to define what is a chemical species, what is speciation and what is speciation analysis. It was agreed that straightforward, standard terminology is important for interdisciplinary communication and also for communication to non-scientists, such as legislators and consumer groups. In their paper, IUPAC provided a clear definition of chemical speciation, distinguishing it from fractionation, and where necessary suggested less ambiguous alternative expressions to those in use.

The IUPAC has defined elemental speciation in chemistry as follows:

1. Chemical species. Chemical elements: a specific form of an element defined with regard to isotopic composition, electronic or oxidation state, and/or complex or molecular structure.

2. Speciation analysis. Analytical chemistry: analytical activities of identifying and/or measuring the quantities of one or more individual chemical species in a sample.

3. Speciation of an element; speciation. The distribution of an element amongst defined chemical species in a system.

Normally, the toxicity of metal ions is described by measuring median lethal dose (LD50) values or median lethal concentration (LC50). However, some authors reported toxicities using IC50 (median inhibitory concentration) and EC50 (median effective concentration) terms. LD50 values of some forms of metal ions are listed in Table 1.1 (The values are taken from the book Instrumental Methods in Metal Ion Speciation).

Thus, it is clear that the metal-associated ligands can profoundly affect their solubility, absorption, bioavailability and the effects of exposure, and then the subsequent toxicity in vivo.

Speciation is essential and in urgent need today. The measurement of the total concentration of a particular element cannot provide information about the actual physicochemical form of the element. It is required for the understanding of its toxicity, biotransformation and so forth. Also, new developments in analytical instrumentation and methodology now often allow us to identify and measure the species present in a particular system. Elemental speciation analysis has now become a part of everyday life for environmental and analytical chemists; at the same time, it is also important to industry, academia, and governmental and legislative bodies. Therefore, the number of research papers is increasing continuously every year, especially in "metal speciation". The growth of the speciation of the elements over a 30–year period is shown in Figure 1.1 (Information obtained from the ISI website of science: http://apps.isiknowledge.com/CitationReport).

More than six thousand (6132) papers with an emphasis on "metal speciation" have been published during the past 30 years (1979–2008), with the total number of citations approaching a hundred thousand (96 769). Along with the development of advanced nuclear analytical techniques, there has been an obvious boom in the number of papers written since the 1990s (information obtained from ISI website of science http://apps.isiknowledge.com/CitationReport). Growth in the number of research papers on "metal speciation" over a 30-year period (1979–2008) and the number of times they have been cited are shown in Figures 1.2 and 1.3.

For more comprehensive descriptions about speciation, readers are referred to the Handbook of Elemental Speciation: Techniques and Methodology by Cornelis et al., Instrumental Methods in Metal Ion Speciation by Ali and Aboul-Enein, and reviews by Tack and Verloo, and Caruso and Montes-Bayon, respectively.

1.2.2 Metallomics

1.2.2.1 History and Development

In 2001, Williams used the term "metallome" to refer to an element's distribution, equilibrium concentrations of free metal ions or as the free element content in a cellular compartment, cell, or organism. He mentioned that ... the variety of paths which individual elements follow in any organ adds to the specific character of the organisms. Clearly the paths have evolved to create an elemental distribution which we shall call the metallome, to parallel the nomenclature of protein distribution, the proteome.

In the 2002 international symposium on bio-trace elements held in Japan, Haraguchi proposed the concept and term of "metallomics" as a new scientific field to integrate the research fields related to biometals. The concept was further elucidated in his successive publication, in which metallomics was defined as bio-trace element science, and metalloproteins, metalloenzymes and other metal-containing biomolecules were defined as "metallomes" in a similar manner to genomes in genomics as well as proteomes in proteomics. Subsequently, the term "metallomics" has been used as the name for the study of metallomes. Szpunar defined metallomics as "... comprehensive analysis of the entirety of metal and metalloid species within a cell or tissue type".

Although it is a rather new concept, metallomics has received great attention. Indeed, many of the papers in recent-year issues have bearings on metallomics, and the subject has been the topic of a number of reviews. The Journal of Analytical and Atomic Spectrometry, based at the Royal Society of Chemistry, published two special issues on metallomics in 2004 and 2007 (see Figure 1.4 for the cover of these two special issues), and a new metallomics and biological elemental speciation web page () has been set up. In 2009, RSC published a new journal, Metallomics (see Figure 1.5 for the journal cover), which covers the research fields related to biometals, and is expected to be the core publication for the emerging metallomics community as they strive to fully understand the role of metals in biological, environmental, and clinical systems. This timely new journal is comprised of papers dealing with techniques, applications, and perspectives that address this emerging field of study and show how atomic spectrometry is contributing to the understanding of biological systems.

International symposiums on metallomics have been held in Nagoya, Japan (ISM 2007), and Cincinnati, USA (ISM 2009 ). The symposia brought scientists together from different areas to realize a greater understanding of the role of metals and metal compounds in many biological, chemical, environmental and clinical systems. These meetings included invited presentations by world leaders in the multidisciplinary areas of system biology, bioinorganic chemistry, instrument development, metallomics methods and approaches, environmental and clinical sciences, as well as contributed papers covering the entirety of metallomics. Also, a Metallomics Center of the Americas under the leadership of Professor Joseph A. Caruso, and in partnership with Agilent Technologies () has been established at the University of Cincinnati, which is the first large-scale metallomics research center in the world.

IUPAC is currently working on a project "Metal-focussed -omics: guidelines for terminology and critical evaluation of analytical approaches", and the objectives are (1) the definition of terms related to analytical chemistry of interactions of metals with biomolecules in environmental, nutrition and life-sciences, such as metallome, metalloproteome, and the corresponding -omics; and (2) a critical evaluation of analytical techniques suitable for metallomics, and the validity and pertinence of data obtained.

The project targets the speciation analysis community organized around the European Virtual Institute of Speciation Analysis (EVISA, http://www. speciation.net), structural genomic consortia, clinical biochemistry, medicine and health sciences communities (characterization of metal-related diseases and related areas, heteroatom-containing species as new clinical biomarkers), nutrition and metabolic sciences (molecular targets of metal binding for essential nutrients and toxic metals), and environmental toxicology (toxic metals in life sciences and their environmental effects). It should be of interest to regulatory bodies answering the question on what valid information can be obtained in quantitative and routine ways in the metal-related -omics areas.

1.2.2.2 Definition of Metallomics and Metallomes

Metallomics is the study of metallomes, interactions and functional connections of metal ions and their species with genes, proteins, metabolites, and other biomolecules within organisms and ecosystems, where a metallome is the entirety of metal and metalloid species present in a cell, cell compartment, tissue or organism, defined according to their identity, quantity, and localization.

A metallomics study is expected to imply:

1. A focus on (essential, beneficial or toxic) metals (e.g. Cu, Zn, Fe, Mn, Mo, Ni, Ca, Cd, Pb, Hg) or metalloids (e.g. As, Se, Sb) in a biological context. The extension of the term to biologically important non-metals, such as sulfur or phosphorus, is discouraged.

2. A correlation of the element concentration blueprint or element speciation with the genome. This correlation may be statistical (an enrichment of an element coincides with the presence of a particular gene), structural (sequence of a metalloprotein is traceable to a gene) or functional (the presence of a bioligand is the result of a gene-encoded mechanism).

3. A systematic, comprehensive or global approach. An identification of a metal species, however important, without specifying its significance and contribution to the system is not metallomics.

(Continues...)Excerpted from Nuclear Analytical Techniques for Metallomics and Metalloproteomics by Chunying Chen, Zhifang Chai, Yuxi Gao. Copyright © 2010 Royal Society of Chemistry. Excerpted by permission of The Royal Society of Chemistry.
All rights reserved. No part of this excerpt may be reproduced or reprinted without permission in writing from the publisher.
Excerpts are provided by Dial-A-Book Inc. solely for the personal use of visitors to this web site.