Practical Approaches to Biological Inorganic Chemistry

Preface

Shrouded in the mists of scientific antiquity (things move so quickly that even a decade or two seems a long time), in reality a little less than 30 years ago – the Federation of European Biochemical Societies, better known by its acronym FEBS, invited the Belgian Biochemical society to organise their annual Congress in Belgium. For the first time in the history of these meetings (since the inaugural Congress, in London in 1964), two half day symposia were organised on the subject of metalloproteins. At the end of the second of these, a group of what in those days were called inorganic biochemists met to enjoy a drink together in the bar of the Sheraton Hotel. The outcome was that two of those present, one of whom is co-editor of the present volume, together with Cees Veeger were entrusted with the task of organising a FEBS Workshop Course on Inorganic Biochemistry. The first of these was held at the Hotel Etap in Louvain-la Neuve at the end of April, 1985. The origins of this book can be traced back to the long series of Advanced Courses which have followed that pioneering start.

At that very first Course, the pattern was established of organising lectures to introduce the subject and to present a theoretical background to the methods which could be used to study metals in biological systems, together with practical sessions in smaller groups. The final lectures were then devoted to specific examples. It is interesting, and perhaps not too surprising, that after an introduction to ligand field theory by Bob Williams, and metal coordination in biology by Jan Reedijk, X-ray, EPR, NMR, Mössbauer and EXAFS spectroscopy of metalloproteins were on the programme. The practicals included NMR, EPR and Mössbauer as well as Cees Veeger’s favourite, biochemical analysis of Fe and S in Fe–S proteins. There was an evening lecture by Helmut Beinert (then on sabbatical in Konstanz) entitled ‘Limitations of Spectroscopic Studies on Metalloproteins and Chemical Analysis of Metals in Proteins’. While the lecturers were shuffled around from year to year, Fred Hagen, Antonio Xavier, Alfred Trautwein, and Dave Garner represented the cornerstone of the spectroscopic part of the course over the early years.

Since then, over the period from 1985 until now we have organised some 20 courses, and trained over 800 students, most of whom were doctoral or post-doctoral students when they came on the course. It is a source of great pride and satisfaction that many of the former students still enjoy active and distinguished careers in the area of Biological Inorganic Chemistry, as we now call the subject. Even more rewarding are the number of former participants who now form the staff of the course, notably the other co-editor, who has also taken on the mantle of co-organiser of the most recent courses. Indeed, with the exception of Rob Robson, who taught the Molecular Biology lectures and practical for many years, the other authors contributing to this book, Frank Neese, Fred Hagen, Eckhard Bill, Martin Feiters, Christophe Leger and Margarida Archer are all alumni of the ‘Louvain-la-Neuve’ course.

Our intention in editing this volume is that it can serve as a starting point for any student who wants to study metals in biological systems. The presentations by the authors represent a distillation of what they have taught over a number of years in the advanced course. We begin with an overview of the roles of metal ions in biological systems, which we hope will serve as taster for the reader, who will find a much more detailed account in the companion work to this volume (Crichton, 2012). Thereafter, after an introduction to that most erudite of discipline (at least for non-inorganic chemists) ligand field theory, augmented by a good dose of how molecular orbital theory can predict the properties of catalytic metal sites. This leads naturally into a sequence which describes the physicochemical methods which can be used to study metals in biology, concluding with an overview of the application of the powerful methods of modern genetics to metalloproteins.

The considerations expressed by that pioneer of analytical precision Helmut Beinert in his 1985 evening lecture in Louvain-la-Neuve are as relevant today as they were then. Use as many techniques as possible to analyse your sample – the more information from different approaches you have, the better we will understand your protein. Do not waste expensive and sensitive methods on shoddy impure samples, and conversely do not employ primitive technical means to analyse highly purified samples, which have required enormous investment to obtain them. And above all recognise that the key to metalloprotein characterisation is collaboration. Do not think you can simply phagocytise a technique from the laboratory of a colleague who knows the method inside out – it is much richer to collaborate, incorporating his or her know-how into your research. And you will be the richer for it.

Bonne chance, good luck, boa sorte – and we look forward to greet you on one of the courses which will, we hope, continue into the future. Hopefully, this little introductory text will not only whet your appetite, but help you to find your way about the myriad practical methods which can be used to study metals in biological systems.

Robert R. Crichton and Ricardo O. Louro, Louvain-la-Neuve, July, 2012

Chapter 1

An Overview of the Roles of Metals in Biological Systems

Robert R. Crichton, Batiment Lavoisier, Université Catholique de Louvain, Louvain-la-Neuve, Belgium

Chapter Outline

Introduction: Which Metals Ions and Why?

Some Physicochemical Considerations on Alkali Metals

Na+ and K+ – Functional Ionic Gradients

Mg²+ – Phosphate Metabolism

Ca²+ and Cell Signalling

Zinc – Lewis Acid and Gene Regulator

Iron and Copper – Dealing with Oxygen

Ni and Co – Evolutionary Relics

Mn – Water Splitting and Oxygen Generation

Mo and V – Nitrogen Fixation

Introduction: Which Metals Ions and Why?

In the companion book to this one, ‘Biological Inorganic Chemistry 2nd edition’ (Crichton, 2011), we explain in greater detail why life as we know it would not be possible with just the elements found in organic chemistry – namely carbon, oxygen, hydrogen, nitrogen, phosphorus and sulfur. We also need components of inorganic chemistry as well, and in the course of evolution nature has selected a number of metal ions to construct living organisms. Some of them, like sodium and potassium, calcium and magnesium, are present at quite large concentrations, constituting the so-called ‘bulk elements’, whereas others, like cobalt, copper, iron and zinc, are known as ‘trace elements’, with dietary requirements that are much lower than the bulk elements.

Just six elements – oxygen, carbon, hydrogen, nitrogen, calcium and phosphorus – make up almost 98.5% of the elemental composition of the human body by weight. And just 11 elements account for 99.9% of the human body (the five others are potassium, sulfur, sodium, magnesium and chlorine). However, between 22 and 30 elements are required by some, if not all, living organisms, and of these are quite a number are metals. In addition to the four metal ions mentioned above, we know that cobalt, copper, iron, manganese, molybdenum, nickel, vanadium and zinc are essential for humans, while tungsten replaces molybdenum in some bacteria. The essential nature of chromium for humans remains enigmatic.

Just why these elements out of the entire periodic table (Figure 1.1) have been selected will be discussed here. However, their selection was presumably based not only on suitability for the functions that they are called upon to play in what is predominantly an aqueous environment, but also on their abundance and their availability in the earth’s crust and its oceans (which constitute the major proportion of the earth’s surface).

FIGURE 1.1 An abbreviated periodic table of the elements showing the metal ions discussed in this chapter.

The 13 metal ions that we will discuss here fall naturally into four groups based on their chemical properties. In the first, we have the alkali metal ions Na+ and K+. Together with H+ and Cl−, they bind weakly to organic ligands, have high mobility, and are therefore ideally suited for generating ionic gradients across membranes and for maintaining osmotic balance. In most mammalian cells, most K+ is intracellular, and Na+ extracellular, with this concentration differential ensuring cellular osmotic balance, signal transduction and neurotransmission. Na+ and K+ fluxes play a crucial role in the transmission of nervous impulses both within the brain and from the brain to other parts of the body.

The second group is made up by the alkaline earths, Mg²+ and Ca²+. With intermediate binding strengths to organic ligands, they are, at best semi-mobile, and play important structural roles. The role of Mg²+ is intimately associated with phosphate, and it is involved in many phosphoryl transfer reactions. Mg-ATP is important in muscle contraction, and also functions in the stabilisation of nucleic acid structures, as well as in the catalytic activity of ribozymes (catalytic RNA molecules). Mg²+ is also found in photosynthetic organisms as the metal centre in the light-absorbing chlorophylls. Ca+ is a crucial second messenger, signalling key changes in cellular metabolism, but is also important in muscle activation, in the activation of many proteases, both intra- and extracellular, and as a major component of a range of bio-minerals, including bone.

Zn²+, which is arguably not a transition element,¹ constitutes the third group on its own. It is moderate to strong binding, is of intermediate mobility and is often found playing a structural role, although it can also fulfil a very important function as a Lewis acid. Structural elements, called zinc fingers, play an important role in the regulation of gene expression.

The other eight transition metal ions, Co, Cu, Fe, Mn, Mo, Ni, V and W form the final group. They bind tightly to organic ligands and therefore have very low mobility. Since they can exist in various oxidation states, they participate in innumerable redox reactions, and many of them are involved in oxygen chemistry. Fe and Cu are constituents of a large number of proteins involved in electron transfer chains. They also play an important role in oxygen-binding proteins involved in oxygen activation as well as in oxygen transport and storage. Co, together with another essential transition metal, Ni, is particularly important in the metabolism of small molecules like carbon monoxide, hydrogen and methane. Co is also involved in isomerisation and methyl transfer reactions. A major role of Mn is in the catalytic cluster involved in the photosynthetic oxidation of water to dioxygen in plants, and, from a much earlier period in geological time, in cyanobacteria. Mo and W enzymes contain a pyranopterindithiolate cofactor, while nitrogenase, the key enzyme of N2 fixation contains a molybdenum–iron–sulfur cofactor, in which V can replace Mo when Mo is deficient. Other V enzymes include haloperoxidases. To date no Cr-binding proteins have been found, adding to the lack of biochemical evidence for a biological role of the enigmatic Cr.

Some Physicochemical Considerations on Alkali Metals

Before considering, in more detail, the roles of the alkali metals, Na+ and K+, and the alkaline earth metals, Mg²+ and Ca²+, it may be useful to examine some of their physicochemical properties (Table 1.1). We can observe, for example that Na+ and K+ have quite significantly different unhydrated ionic radii, whereas, the hydrated radii are much more similar. It therefore comes as no surprise that the pumps and channels which carry them across membranes, and which can easily distinguish between them, as we will see shortly, transport the unhydrated ions. Although not indicated in the table, it is clear that Na+ is invariably hexa-coordinate, whereas K+ and Ca²+ can adjust to accommodate 6, 7 or 8 ligands. As we indicated above, both Na+ and K+ are characterised by very high solvent exchange rates (around 10⁹/s), consistent with their high mobility and their role in generating ionic gradients across membranes. In contrast, the mobility of Mg²+ is some four orders of magnitude slower, consistent with its essentially structural and catalytic. Perhaps surprisingly, Ca²+ has a much higher mobility (3 × 10⁸/s), which explains why it is involved in cell signalling via rapid changes on Ca²+ fluxes.

TABLE 1.1

Properties of Common Biological Cations

(From Maguire and Cowan, 2002).

The selective binding of Ca²+ by biological ligands compared to Mg²+ can be explained by the difference in their ionic radius, as we pointed out above. Also, for the smaller Mg²+ ion, the central field of the cation dominates its coordination sphere, whereas for Ca²+, the second and possibly even the third, coordination spheres have an important influence resulting in irregular coordination geometry. This allows Ca²+, unlike Mg²+ to bind to a large number of centres at once.

The high charge density on Mg²+ as a consequence of its small ionic radius ensures that it is an excellent Lewis acid in reactions notably involving phosphoryl transfers and hydrolysis of phosphoesters. Typically, Mg²+ functions as a Lewis acid, either by activating a bound nucleophile to a more reactive anionic form (e.g. water to hydroxide anion), or by stabilising an intermediate. The invariably hexacoordinate Mg²+ often participates in structures where the metal is bound to four or five ligands from the protein and a phosphorylated substrate. This leaves one or two coordination positions vacant for occupation by water molecules, which can be positioned in a particular geometry by the Mg²+ to participate in the catalytic mechanism of the enzyme.

Na+ and K+ – Functional Ionic Gradients

How, we might ask, do the pumps and channels responsible for transport across membranes distinguish between Na+ and K+ ions? Studies over the last 50 years or so of synthetic and naturally occurring small molecules which bind ions have established the basic rules of ion selectivity. Two major factors appear to be of capital importance, namely the molecular composition and the stereochemistry (essentially the size) of the binding site. Synthetic molecules have been created which selectivity bind Li+ (radius 0.60 Å), Na+ (0.95 Å), K+ (1.35 Å) and Rb+ (radius 1.48 Å) by simply adjusting the cavity size to match the ion (Dietrich, 1985). Now that we have the crystal structures of membrane transport proteins, we can begin to understand how ion selectivity is accomplished (MacKinnon, 2004; Gouax and MacKinnon, 2005). The Na+-selective binding sites in the Na+-dependant leucine transporter LeuT and the K+-selective binding sites in the K+ channel have been determined, providing a direct comparison of selectivity for Na+ and K+. The Na+ and K+ ions are completely dehydrated, both the Na+ and the K+ sites contain oxygen ligands, but by far the most important factor distinguishing Na+ and K+ sites is the size of the cavity formed by the binding site, which agrees well with the rules already learned from host/guest chemistry. What determines alkali metal cation selectivity, similar to that observed in ion binding by small molecules, is that the protein selects for a particular ion, Na+ or K+, by providing an oxygen-lined binding site of the appropriate cavity size.

Mammalian cells maintain a high intracellular K+ (around 140 mM) and low intracellular Na+ (around 12 mM) through the action of the Na+, K+-ATPase present in the plasma membrane. The overall reaction catalysed is:

3Na+(in) + 2K+ (out) + ATP + H2O ⇔ 3Na+ (out) + 2K+ (in) + ADP + Pi

The extrusion of three positive charges for every two which enter the cell, results in a transmembrane potential of 50–70 mV, which has enormous physiological significance, controlling cell volume, allowing neurons and muscle cells to be electrically excitable, and driving the active transport of important metabolites such as sugars and amino acids. More than one-third of ATP consumption by resting mammalian cells is used to maintain this intracellular Na+ − K+ gradient (in nerve cells this can rise to up to 70%).

This thermodynamically unfavourable exchange is achieved by ATP-mediated phosphorylation of the Na+,K+-ATPase followed by dephosphorylation of the resulting aspartyl phosphate residue, which drives conformational changes that allow ion access to the binding sites of the pump from only one side of the membrane at a time. The ATPase exists in two distinct conformations, E1 and E2, which differ in their catalytic activity and their ligand specificity (Figure 1.2). The E1 form, which has a high affinity for Na+, binds Na+, and the E1.3Na+ form then reacts with ATP to form the high-energy aspartyl phosphate ternary complex E1 ~ P.3Na+. In relaxing to its low-energy conformation E2-P, the bound Na+ is released outside the cell. The E2-P, which has a high affinity for K+, binds 2K+, and the aspartyl phosphate group is hydrolysed to give E2.2K+, which then changes conformation to the E1 form, releasing its 2K+ inside the cell. The structures of a number of P-type ATPases, including the Na+ - K+-ATPase and the Ca²+−ATPase of the Sarcoplasmic reticulum have been determined and are shown in Figure 1.3.

FIGURE 1.2 A model for the active transport of Na + and K + by the Na + -K + -ATPase.

FIGURE 1.3 Overall structures and ion-binding site architectures of two P-type ATPases, rabbit sarcoplasmic reticulum Ca ²+- ATPase (SERCA) and pig Na + ,K + -ATPase. The upper panel depicts rabbit SERCA (E1 Protein Data Base [PDB] entry 1T5S) and pig Na + -K + -ATPase (E2:Pi, PDB entry 3KDP). N-, P-, and A-domains are coloured red, blue and yellow, respectively; the β-subunit and γ-subunit of Na + ,K + -ATPase wheat and cyan. The lower panel depicts the ion-binding sites, viewed approximately perpendicular to the membrane plane from the extracytoplasmic side, in the E1 state. Ion liganding residues are shown as sticks, transmembrane helices and calcium ions in SERCA are indicated by numbers and grey spheres, respectively, and the sites superposed as transparent spheres onto the Na + ,K + -ATPase model. Putative binding sites for the third sodium ion in the Na + ,K + -ATPase are indicated as grey ellipses. (From Bublitz et al., 2010. Reproduced Copyright 2010 with permission from Elsevier).

Mg²+ – Phosphate Metabolism

The intracellular concentration of free Mg²+ is about 5 × 10−3 M, so that although Mg²+-binding to enzymes is relatively weak (Ka not more than 10⁵M−1) and most Mg²+-dependent enzymes have adequate local concentrations of Mg²+ for their activity. Mg²+ is the most abundant divalent cation in the cytosol of mammalian cells, binds strongly to ATP and ADP, and is therefore extensively involved in intermediary metabolism and in nucleic acid metabolism. However, like Zn²+, it is a difficult metal ion to study, since it is spectroscopically silent, with the consequence that many spectroscopic studies on Mg²+ enzymes utilise Mn²+ as a replacement metal ion.

Of the five enzymes selected in the Enzyme Function Initiative, recently established to address the challenge of assigning reliable functions to enzymes discovered in bacterial genome projects, but for which functions have not yet been attributed (Gerlt et al., 2011), three of them are Mg²+-dependent. We discuss two of them briefly here.

The haloalkanoic acid dehalogenase superfamily (HADSF) (>32,000 nonredundant members) catalyse a diverse range of reactions that involve the Mg²+-dependent formation of a covalent intermediate with an active site Asp. Despite being named after a dehalogenase, the vast majority are involved in phosphoryl transfer reactions (Allen and Dunaway-Mariano, 2004, 2009). While ATPases and phosphatases are the most prevalent, the haloacid dehalogenase (HAD) family can carry out many different metabolic functions, including membrane transport, signal transduction and nucleic-acid repair. Their physiological substrates cover an extensive range of both size and shape, ranging from phosphoglycolate, the smallest organophosphate substrate, to phosphoproteins, nucleic acids, phospholipids, phosphorylated disaccharides, sialic acids and terpenes.

In HAD enzymes, Asp mediates carbon-group transfer to water (in the dehalogenases) and phosphoryl-group transfer to a variety of acceptors. Thus, the HAD superfamily is unique in catalysing both phosphoryl-group transfer (top) and carbon-group transfer (bottom) (Figure 1.4a). The roles of the four loops that comprise the catalytic scaffold are shown in Figure 1.4b. The activity ‘switch’ is located on loop 4 of the catalytic scaffold (yellow) which positions one carboxylate residue to function as a general base for the dehalogenases and either two or three carboxylates to bind the Mg²+ cofactor essential for the phosphotransferases. CO represents the backbone carbonyl oxygen of the moiety that is two residues downstream from the loop 1 nucleophile (red). The side-chain at this position is also used as an acid-base catalyst by phosphatase and phosphomutase HAD members. Loop 2 (green) and loop 3 (cyan) serve to position the nucleophile and substrate phosphoryl moiety. Figure 1.4c presents a ribbon diagram of the fold supporting the catalytic scaffold of phosphonatase.

FIGURE 1.4 The catalytic scaffold in the haloacid dehalogenase (HAD) family of phosphotransferases. (a) In HAD enzymes, Asp mediates carbon-group transfer to water (in the dehalogenases) and phosphoryl-group transfer to a variety of acceptors. Thus, the HAD superfamily is unique in catalyzing both phosphoryl-group transfer (top) and carbon-group transfer (bottom). (b) Schematic of the roles of the four loops that comprise the catalytic scaffold. The activity ‘switch’ is located on loop 4 of the catalytic scaffold (yellow) which positions one carboxylate residue to function as a general base for the dehalogenases and either two or three carboxylates to bind the Mg ²+ cofactor essential for the phosphotransferases. CO represents the backbone carbonyl oxygen of the moiety that is two residues downstream from the loop 1 nucleophile (red). The side-chain at this position is also used as an acid-base catalyst by phosphatase and phosphomutase HAD members. Loop 2 (green) and loop 3 (cyan) serve to position the nucleophile and substrate phosphoryl moiety. (c) Ribbon diagram (core domain: loop 1, red; loop 2, cyan; loop 3, green; loop 4, yellow; cap domain: specificity loop, blue) of the fold supporting the catalytic scaffold of phosphonatase (1FES). (From Allen and Dunaway-Mariano, 2004. Copyright 2004, with permission from Elsevier).

The members of another large superfamily of Mg²+ enzymes, the enolase superfamily (with more than 6000 nonredundant members) catalyse diverse reactions, including β-eliminations (cycloisomerisation, dehydration and deamination) and 1,1-proton transfers (epimerisation and racemisation). The three founder members of the family are illustrated by mandelate racemase, muconate lactonising enzyme and enolase (Figure 1.5). They all catalyse reactions in which the α-proton of the carboxylate substrate is abstracted by the enzyme, generating an enolate anion intermediate. This intermediate, which is stabilised by coordination to the essential Mg²+ ion of the enzyme, is then directed to different products in the enzyme active sites.

FIGURE 1.5 The substrates, enolate anion intermediates, and products of the MR; MLE and enolase reactions (adapted from Gerlt et al., 2005).

Ca²+ and Cell Signalling

Calcium ions play a major role as structural components of bone and teeth, but are also crucially important in cell signalling. To prevent the precipitation of phosphorylated or carboxylated calcium complexes, many of which are insoluble, the cytosolic levels of Ca²+ in unexcited cells must be kept extremely low, much lower than that in the extracellular fluid and in intracellular Ca²+ stores. This concentration gradient gives cells the opportunity to use Ca²+ as a metabolic trigger – the cytosolic Ca²+ concentration can be abruptly increased for signalling purposes by transiently opening Ca²+ channels in the plasma membrane or in an intracellular membrane. These increases in intracellular free Ca²+ concentration can regulate a wide range of cellular processes, including fertilisation, muscle contraction, secretion, learning and memory and ultimately cell death, both apoptotic and necrotic.

Extracellular signals often act by causing a transient rise in cytosolic Ca²+ levels, which, in turn, activates a great variety of enzymes through the action of Ca²+-binding proteins like calmodulin, as we will discuss in detail below: this triggers such diverse processes as glycogen breakdown, glycolysis and muscle contraction. In the phosphoinositide cascade (Figure 1.6), binding of the external signal (often referred to as the agonist² when it provokes a positive response) to the surface receptor R (step 1) activates phospholipase C, either through a G protein which uses the energy of guanosine triphosphate hydrolysis to liberate a subunit capable of activating the next partner in the cascade (2) or alternatively (not shown) by activating a tyrosine kinase. The activated phospholipase C, then hydrolyses phosphatidylinositol-4,5-bisphosphate (PIP2) in the plasma membrane to InsP3 (IP3 in the figure) and diacylglycerol (DG) (3). InsP3 stimulates the release of Ca²+, sequestered in the endoplasmic reticulum (4), and this in turn activates numerous cellular processes through Ca²+-binding proteins, such as calmodulin (CaM) (5). The membrane-associated DG activates protein kinase C (6) to phosphorylate and activate other enzymes, like glycogen phosphorylase. This step also requires Ca²+.

FIGURE 1.6 The phosphoinositide cascade.

Calmodulin is a small, dumbbell-shaped protein, abundant in the cytoplasm of most cells of higher organisms, which has been highly conserved throughout evolution It is made up of two globular domains each of which can bind two Ca²+ ions, connected by a flexible linker. When all four Ca²+ sites are filled, the linker forms a flexible seven turn long α-helix, and the protein undergoes a change in conformation, which does not alter its overall dimensions, but opens up its two Ca²+-binding lobes, exposing previously hidden hydrophobic residues, particularly Met. In Figure 1.7a, the structure on the left shows calmodulin without calcium, while that on the right shows calmodulin after calcium binds. The two hydrophobic regions are represented in green and yellow (C and Met S atoms, respectively), and we can see that with calcium bound, the hydrophobic residues form two grooves (red stars), waiting to grip around the target protein, while the linker (pink) has formed a long alpha-helix separating the two calcium-binding domains. A second, and much more dramatic conformation change then occurs, collapsing the elongated structure of calmodulin to a hairpin conformation, which enables it to wrap around the binding domain of the target enzyme, gripping the target protein between its two globular domains. This is illustrated in Figure 1.7b (left panel) for calmodulin bound to calmodulin-dependent protein kinase II-alpha (top) and myosin light chain kinase (bottom). Only a small piece of the target protein chain (red) is included, with the flexible linker of calmodulin, (purple), allowing it to adopt to the slightly different shapes of the two targets. In the case of the oedema factor toxin from the anthrax bacteria shown in Figure 1.7b (left panel), we see a quite different binding geometry. This time, the whole toxin protein is shown; once calmodulin binds, it induces a conformational change in the toxin which activates its adenylyl cyclase activity, thereby depleting the host cell’s energy stores.

FIGURE 1.7 (a) Calmodulin without calcium (left, PDB 1cfd) and after calcium binds (right, PDB 1cll). The linker region between the two Ca ²+ -binding domains is in pink and the Ca ²+ ions are shown in light blue. (b) Left calmodulin bound to two different target enzymes: calmodulin-dependent protein kinase II-alpha (top, PDB 1cm1) and myosin light chain kinase (bottom, PDB 2bbm). Only a small piece of the target protein chain (in red) is included. Right calmodulin bound to anthrax bacteria oedema factor toxin (PDB 1k93). The entire toxin protein is shown in red.

An unusual feature of calmodulin is that, unlike other Ca²+-binding proteins which usually only interact with a specific target protein, calmodulin interacts with a wide range of targets. A comparison of amino acid sequences of calmodulin-binding domains of target proteins suggests that calmodulin principally recognises positively charged amphipathic helices. Upon binding to the target peptide (compare Figure 1.7a and b), the long central helix of uncomplexed calmodulin unwinds and bends to form a globular structure that encloses the target polypeptide within a hydrophobic tunnel.

Zinc – Lewis Acid and Gene Regulator

After iron, zinc is the second most abundant trace element in the human body: an average adult has about 3 g of Zn. Some 95% of Zn is intracellular. It is essential for growth and development in all forms of life, has been proposed to have beneficial therapeutic and preventative effects on infectious diseases, including a shortening of the length of the common cold in man. Zn is found in more than 300 enzymes, where it plays both a catalytic and a structural role. It is the only metal to have representatives in each of the six fundamental classes of enzymes recognised by the International Union of Biochemistry—oxidoreductases (e.g. alcohol dehydrogenase): transferases (RNA polymerase): hydrolases (carboxypeptidase A): lyases (carbonic anhydrase): isomerases (phosphomannose isomerase): and ligases (pyruvate carboxylase, aminoacyl-tRNA synthases). Zinc is involved in enzymes in both a catalytic and a structural role. Many nucleic acid-binding proteins have essential Zn atoms in characteristic structures called ‘zinc fingers’ which are widely involved in the regulation of the transcription and translation of the genetic message. Figure 1.8 is a representation of the Cys2His2 zinc finger motif, consisting of an α helix and an antiparallel β sheet. The zinc ion (green) is coordinated by two histidine residues and two cysteine residues.

FIGURE 1.8 Cartoon representation of the Cys2His2 zinc finger motif, consisting of an α helix and an antiparallel β sheet. The zinc ion (green) is coordinated by two histidine residues and two cysteine residues.

The first zinc enzyme to be discovered was carbonic anhydrase in 1940; it represents the archetype of mono-zinc enzymes, with a central catalytically active Zn²+ atom bound to three protein ligands, and the fourth distorted tetrahedral site occupied by a water molecule. The mechanism of action of mononuclear zinc enzymes depends on the Zn²+-OH2 centre, which can participate in the catalytic cycle in three distinct ways (Figure 1.9) – either by ionisation, to give zinc-bound hydroxyl ion (in carbonic anhydrase), polarisation by a general base (as in carboxypeptidases) or displacement of the −OH2 ligand by the substrate (in alkaline phosphatase). In the case of carbonic anhydrase, the zinc ion functions as a powerful electrophilic catalyst by providing some or all of the following properties: (i) an activated water molecule for nucleophilic attack, (ii) polarisation of the carbonyl of the bond to be cleaved, (iii) stabilisation of the negative charge which develops in the transition state.

FIGURE 1.9 The zinc-bound water can either be ionized to zinc-bound hydroxide, polarised by a general base to generate a nucleophile for catalysis, or displaced by the substrate.

The coordination chemistry and the main features of the mechanism of carbonic anhydrase are illustrated in Figure 1.10, and involve the following steps: (i) deprotonation of the coordinated water molecule with a pKa ~ 7, in a process facilitated by general base catalysis involving His 64. This residue is too far away from the Zn²+-bound water to directly remove its proton, but it is linked to it by two intervening water molecules, forming a hydrogen-bonded network which acts as a proton shuttle, (ii) the zinc-bound hydroxide then carries out a nucleophilic attack on the carbon dioxide substrate to generate a hydrogen carbonate intermediate [(His)3Zn-OCO2H]+ which (iii) is displaced by H2O to release bicarbonate and complete the catalytic cycle. The key to understanding the role of the Zn²+ ion is that its charge makes the bound water molecule more acidic than free H2O, and enables it to act as a source of OH− even at neutral pH values.

FIGURE 1.10 ( a ) The active site of human carbonic anhydrase and ( b ) the main features of the mechanism of action of carbonic anhydrase.

Iron and Copper – Dealing with Oxygen

Both iron and copper play a very important role in the living world, and both seem to be essential for life, although iron may not be essential for lactic acid bacteria. On the basis of their chemistry and biochemistry, it seems probable that the early chemistry of life in an oxygen-free environment used water soluble Fe(II), whereas copper was present essentially as highly insoluble sulfides of Cu(I). The advent of oxygen was a catastrophic event for most living organisms, and can be considered to be the first general irreversible pollution of the earth. The oxidation of iron resulted in the loss of its bioavailability as Fe(II) was replaced by insoluble Fe(III), whereas the oxidation of insoluble Cu(I) led to soluble Cu(II). Further, the advent of an oxidising atmosphere exposed the potential toxicity of both elements through their capacity to generate oxygen-free radicals. A new iron biochemistry became possible after the advent of oxygen, with the development of chelators of Fe(III), which rendered iron once again accessible, and with the control of the potential toxicity of iron by its storage in a water soluble, non-toxic, bio-available storage protein (ferritin). Biology also discovered that whereas enzymes involved in anaerobic metabolism were designed to operate in the lower portion of the redox spectrum (attaining values of close to +0.6 V for iron itself), the arrival of dioxygen created the need for a new redox active metal which could attain higher redox potentials. Copper, now bioavailable, was ideally suited to exploit the oxidizing power of dioxygen. The arrival of copper also coincided with the development of multicellular organisms which had extracellular cross-linked matrices capable of resisting attack by oxygen-free radicals. After the initial ‘iron age’, subsequent evolution moved, not towards a ‘copper age’, but rather to an ‘iron-copper’ age.

The extensive range of biological functions carried out by both of these metal ions, range through oxygen transport by haemoglobins, haemerythrins and haemocyanins, through electron transfer by cytochromes, Fe-S proteins and plastocyanins, to multiple reactions involving oxygen activation and detoxification – the list is seemingly endless. However, here we focus briefly on one enzyme which combines the powerful redox chemistry of iron and copper acting in concert, cytochrome oxidase, CcO, the terminal component of the respiratory chain in aerobic organisms, CcO catalyses the one electron reduction of four reduced cytochrome c (c²+) molecules and the four electron reduction of dioxygen to water:

O2 + 4H+ + 4c²+ → 2H2O + 4c³+

In mammals, CcO spans the mitochondrial inner membrane and catalyses the reduction of molecular dioxygen to water at the rate of up to 250 molecules of O2 per second. The energy released in this process is coupled to the translocation of protons, which in turn contributes to the chemiosmotic gradient required for ATP synthesis. Since the electrons and protons are taken up from the opposite sides of the membrane, the reaction results in a net charge separation across the membrane which, together with the coupled proton pumping, corresponds to the overall translocation of two positive charges across the membrane per electron transferred to O2 from the negative (N) side to the positive (P) side of the membrane.

While the structure of the mammalian enzyme, with between 8 and 13 different subunits has been determined, it presents a very much more complex problem than the enzyme from Rhodobacter sphaeroides. This contains only the two catalytic subunits – subunit I with 3 redox-active centres, containing haem a, and the catalytic site made up of haem a3 and CuB, where dioxygen is reduced, and subunit II with the CuA redox centre made up of two copper ions, together with two other non-catalytic subunits (Qin et al., 2006). Its overall structure and the location of the different electron transfer components are shown in Figure 1.11a.

FIGURE 1.11 (a) The structure of cytochrome c oxidase from R. sphaeroides (PDB code 1M56). The four subunits of the enzyme are coloured as indicated in the figure. Haems a and a 3 are shown in red and the copper centres Cu A and Cu B in yellow. The red spheres are water molecules resolved in the structure. Residues Glu286, Asp132, Lys362, all in SU I, and Glu101 in SU II, are shown in the figure (the subscript indicates the subunit number). The approximate position of the membrane is indicated by the solid lines, where the p - and n -sides are the more positively and negatively charged sides of the membrane, respectively. The purple sphere is a non-redox-active Mg ²+ ion found in the structure. (b) The D and K proton pathways shown in more detail. Also the haem a 3 propionates are indicated. (From Brzezinski and Johansson, 2010. Copyright 2010, with permission from Elsevier).

Electrons coming from cytochrome c enter the CcO complex via the dinuclear copper centre (CuA), and are then transferred consecutively one at a time to haem a, and then to the catalytic site of CcO, the dinuclear haem-copper centre (haem a3-CuA). This is the primary oxygen-binding site, involving a haem iron, haem a3, together with a copper ion, CuB, and it is at this dinuclear metal site that dioxygen is reduced. A tyrosine residue, Y(I-288), which is covalently cross-linked to one of the CuB ligands (His 240), is also a part of the active site. A more detailed view of the redox-active cofactors and amino acid residues involved in the proton transfer pathways is shown in Figure 1.11b (Brzezinski and Johansson, 2010).

The individual steps of oxygen binding and its subsequent reduction by CcO are presented in Figure 1.12 (Brzezinski and Johansson, 2010). In oxidised CcO (designated O⁰), both haem a3 and CuB are oxidised. Transfer of the first and second electrons to the catalytic site results in the formation of states E¹ and R² (Fea3²+ and CuB+), each step associated with proton uptake to the catalytic site and proton pumping, and O2 then binds to haem a3 in the R² state. In the next step, the O-O bond is broken, with four electrons being donated, two from haem a3O2²−, one from CuB with a hydroxide ion bound, and one electron (and a proton) from residue Tyr288, located within the catalytic site, which forms a tyrosyl radical, Tyr288⋅. Formation of this P² state is not linked to any proton uptake from solution and, both the protons and the electrons are only relocated locally within the catalytic site resulting in oxidation of haem a3 and CuB. In the next step, an electron is transferred to the Tyr radical, accompanied by proton uptake to form state F³ and again, protons are pumped. In the final step, the last electron is transferred to the catalytic site, forming state O⁴ also accompanied by proton uptake and proton pumping. The O⁴ state is equivalent to O⁰ as the enzyme becomes fully oxidised when four electrons have been transferred to