Interaction of Metal Ions with Proteins as a Source of Inspiration for Biomimetic Materials

ANDREW M. SMITH

1.1 Introduction

Nature utilises proteins to fulfil a range of functions from catalysing reactions, storage and transfer of energy to acting as structural supports. Proteins are, at the most basic level, polymers made up of a specific sequence of amino acids; this is known as the primary structure. These polymer chains have the potential to form highly complex structures where the individual amino acids interact to form specific folds, such as α-helices and β-sheets, known as the protein's secondary structure. These individual secondary structure units combine to give the protein fold, or tertiary structure. Individual proteins can interact with other proteins and molecules to give the supramolecular structure, which is the quaternary structure. The information that determines how the protein folds and interacts is encoded in the amino acid side chains and these are also responsible for the catalytic function of enzymes. The side chains of the twenty naturally occurring (canonical) amino acids cover a wide swathe of interactions including hydrophobic, hydrophilic, ionic and covalent bonds, however, there is a limit to what can be done using the canonical amino acids; as a consequence, nature has evolved to use inorganic components within the organic proteins to extend their functionality and facilitate reactions that would not be feasible using amino acids alone. For some functions, proteins have evolved to incorporate cofactors to increase the variety or efficiency of their functions. These cofactors can be organic or inorganic; here we are interested in the latter. Inorganic cofactors can be as simple as metal ions that are coordinated by amino acid side chains to complex organic non-protein groups that coordinate the metal ions. These metal ions are used for a variety of functional reasons, from aiding in the formation of the correct protein fold to forming the active site of an enzymatic reaction. The variety of metals incorporated in proteins is also very broad with a range of valences of metals such as iron, copper, zinc, magnesium, nickel, molybdenum, and manganese being seen in humans alone. The degree of variety is also increased when organic groups such as haems are included as well as cases of multiple metal ion clusters.

The first thing to bear in mind with the involvement of metal ions with proteins is that the concentration of each metal ion is maintained in cells and organelles within a specific range dependent on the cells. If metal ions exceed their normal levels then they can bind to additional sites as well as cause the displacement of other metal ions, resulting either in a change in specificity and reactivity or deactivation of the protein. The concentration ranges of free divalent metal ions is roughly based on the binding affinities of the metal ions, with Zn(II) being the strongest binder, and if sufficiently high concentrations are used, it will bind to most proteins. For the purpose of the discussions here, the interactions of physiologically relevant levels will be discussed.

Metal ions are involved in an extremely wide range of proteins, with over half of all proteins being metallo-proteins including all types of enzymatic reactions as well as being involved in electron transport chains. They are also involved in the formation of extracorporeal structures such as holdfast mechanisms, silks, and glues. Additionally, metal ions are also involved in disease states, such as neurodegenerative diseases involving the formation of amyloid plaques. Due to the extremely wide breadth of the involvement of metal ions, this chapter will give a general overview and pick a few examples to go into more detail.

First, we will look at metal ions in the active site of enzymes covering a few examples and cover different metal ions as well as multiple metal ion clusters. We will then move on to the use of metal-containing organic cofactors, such as haem, and the variety of functions such a structure can fulfil. We will then discuss the use of metal ions in structural proteins both in the formation of the structure and also in its interactions. Finally, we will have a look at the influence of metal ions on protein folding and misfolding and its involvement in neurodegenerative diseases as well as anti-microbial peptides.

1.2 Enzymes

Enzymes are the molecular machines of life as they catalyse an extremely wide range of reactions with varying efficiencies and specificities. There are an extremely wide range of proteins that contain metal ions; these can generally be split into two main groups, those which have inorganic cofactors, where the metal ion is directly bound by the protein side chains and those that have an organic cofactor, a non-protein group for example a haem group that coordinates the metal ions.

1.2.1 Single Metal Ion Enzymes

1.2.1.1 Zinc Dependent Enzymes

Zinc was the first of the metal ions to be recognised as essential for life and in 1939 the first enzyme, erythrocyte carbonic anhydrase, was discovered where zinc was essential for activity. There are now in the order of 3000 zinc proteins and they have functionalities across all classes of enzymes. One of the major discoveries was the "zinc finger" which was first identified in the Xenopus laevis transcription factor IIIA, which contains nine repetitive sequences of cysteine and histidine residues that coordinate nine zinc ions in the protein. The characteristic pattern of cysteine and histidine residues separated by spacers of amino acids (X) CXaCXbHXcH which can coordinate metal ions has allowed the identification of these small domains in many proteins. The sequence forms a small elongated domain (Figure 1.1) where the Zn(II) acts as the pinning...