Exploring Metalloproteins

Introduction

Metals are crucial participants in many areas of biology and across all types of organisms. They play roles in myriad biological functions including membrane potential maintenance, nucleic acid stabilization, protein stabilization, signaling, electron transport, oxygen transport, and catalysis that organic molecules alone could not perform. Along with their natural functions, metals are also powerful tools for drug development.

Occupying the majority of the periodic table, metals have diverse properties and their incorporation in biological systems requires a carefully-tuned environment. Certain metals such as the alkali and alkaline earth metals are soluble under physiological conditions. Other metal ions, including the transition metals, must be coordinated by biomacromolecules such as proteins and nucleic acids in order to be bioavailable.

As metals cannot be synthesized by living organisms, they must be acquired from the environment. For humans, this occurs through dietary sources.

Exploring the Structure of Metalloproteins

Iron

In vertebrates, iron is necessary for oxygen transport and storage through its stable coordination in heme groups. Biological iron is most commonly found in two oxidation states: ferrous and ferric. Ferrous iron (Fe2+ or Fe(II)) is soluble under physiological conditions, but it is readily oxidized to the insoluble ferric iron (Fe3+ or Fe(III)). As shown in Figure 1, iron is coordinated in heme groups in the ferrous form. Thus, iron that is not bound to a heme-group (non heme iron) is broadly considered to have low bioavailability. In contrast, heme iron that is coordinated in a heme group as Fe(II) is considered to be highly bioavailable. The heme group coordinates iron via multiple points of attachment, making heme a “polydentate” ligand to iron. Denticity refers to the number of donor groups that bind to the central metal atom. In a heme group, each of the four pyrrole nitrogen atoms acts as a donor, making the heme a “tetradentate” ligand (Figure 1). Due to the manner in which heme provides multiple interactions with the metal center, heme is known as a “chelator”.

Figure 1: Iron is an essential element for humans, yet “free” or non-heme iron readily oxidizes to the insoluble ferric Fe(III) form. Heme iron is robustly coordinated by the heme molecule, preventing iron oxidation and precipitation. The heme molecule provides tetradentate coordination through the four pyrrole nitrogens, colored in blue.

Proteins and Nucleic Acids As Metal Chelators

Larger molecules such as proteins and nucleic acids may also act as metal chelators, providing coordination through amino acid residues and nucleotides, respectively. Metals bind to amino acid residues such as cysteine, histidine, aspartate, glutamate, asparagine, glutamine, tyrosine, serine, and threonine through their ionizable sidechains. The main chain of the protein may also coordinate metals through the carbonyl oxygen. Nucleotides can provide coordination through various moieties within the molecule including the phosphate oxygens, sugar hydroxyls, and nitrogens within the nitrogenous base.

Each metal has its own “preferences” for type and number of donors. For example, sodium tends to accept oxygen-based donors such as main chain carbonyl oxygens or side chain oxygens from aspartate, glutamate, serine, or threonine to complete a 6-coordinate octahedral geometry (Figure 2). In contrast, zinc prefers a 4-coordinate tetrahedral geometry but has greater flexibility on donor atoms, frequently accepting nitrogen-based coordination from histidine, sulfur-based coordination from cysteine, and oxygen-based coordination from aspartate and glutamate (Figure 2).

Figure 2: Metals have unique coordination geometry preferences. Left: sodium with octahedral coordination by oxygen ligands, including a serine hydroxyl group, main chain carbonyls, and water molecule (pdb_00001ewn). Right: zinc with tetrahedral coordination by cysteine and histidine (pdb_00001cz0).

Alkali Metals

Alkali metal ions such as sodium and potassium are soluble under physiological conditions and do not require chelators, making them suitable for maintaining membrane potential as they can reside stably on either side of the cell membrane as hydrated ions. However, as charged ions cannot freely diffuse across the membrane, the flow of ions in and out of the cell is controlled by channels and pumps.

Sodium-potassium pumps move three sodium ions out of the cell for every two potassium ions that are pumped into the cell. Sodium is retrieved from the cytoplasm and potassium from the extracellular matrix through oxygen-based binding to amino acids (Figure 3). In addition, potassium ion channels allow the flow of potassium into or out of the cell, although potassium ions tend to flow out of the cell following the concentration gradient. Potassium ion channels select specifically for potassium, using main chain carbonyl groups to form the 8-coordinate square antiprismatic coordination preferred by potassium (Figure 3). Although these sodium and potassium ions are soluble, their functions are enabled by the proteins that provide the specific coordination environment required for their transport.

Figure 3: Ion channels and pumps for maintaining the membrane potential. Left: sodium-potassium pump with three sodium ions bound (top; pdb_00008jbk) and with two potassium ions bound (bottom; pdb_00002zxe). Right: In the potassium ion channel (pdb_00001k4c), main chain carbonyl groups coordinate potassium ions in a square antiprismatic geometry.

Transition Metals

Transition metals greatly expand metal functionality because they can access various oxidation states, giving them the ability to participate in electron transport and catalysis. For example, electron transport chain (ETC) complexes utilize transition metal cofactors (Figure 4) with finely-tuned reduction potentials that enable electron transport. Iron-sulfur clusters, iron-centered cytochromes, and copper centers facilitate electron flow to the final oxygen electron acceptor. Each iron-sulfur cluster in the ETC has a different reduction potential due to different 3D environments in the primary coordination sphere (atoms directly coordinating the metal) and the secondary coordination sphere (atoms forming non-covalent interactions with the primary coordination sphere). The diversity of environments that can be formed within proteins allows nature to reuse the same cofactor in different ways to create the various components of the ETC.

Figure 4: All complexes of the ETC utilize metal cofactors for electron transport. Complex I (pdb_00005lnk) uses iron-sulfur clusters, complexes II (pdb_00001zoy) and III (pdb_00001ntm) use iron-sulfur clusters and heme, and complex IV (pdb_00005b1a) uses heme and copper.

Assessing Metal Coordination

The 3D environment of metals is a key feature of metalloproteins that drives metal selectivity and reduction potential. In the process of structure determination, researchers often perform parallel spectroscopic experiments to verify the identity of the metal and its coordination environment. It is crucial that researchers utilize proper refinement restraints to ensure that the refined metal coordination geometry aligns with parallel experiments, prior knowledge, and fundamental principles of metal coordination.

To assess metal coordination geometry in protein structures, it is useful to have reliable and reproducible methods for coordination geometry determination. Researchers have developed software programs (e.g. FindGeo and MetalCoord) for determining coordination geometry (e.g. tetrahedral, octahedral) and a measurement of fit to the reference geometry. To report fit to the reference geometry, FindGeo uses a standard RMSD measurement, whereas MetalCoord uses a Procrustes distance, which measures the difference between two shapes.

For example, in oxyhemoglobin in entry pdb_00001a4f, both FindGeo and MetalCoord were used to determine that the iron has octahedral geometry (Figure 5).

Figure 5: The heme iron (FE) in entry pdb_00001a4f has octahedral geometry, as determined by FindGeo and MetalCoord.

Representing Metals in PDB Entries

Metalloproteins in the PDB have been remediated to ensure that the metals included in the structure are represented in an accurate, consistent manner with sufficient annotation. This effort involved the review of all polyatomic metal-containing components in the Chemical Component Dictionary (CCD) and the review of all PDB entries in which these components are incorporated. The remediated CCD definition of metallic ligands includes additional annotation including metal-bond identification, metal-pi bond designation, unique coordination geometry found in the PDB archive as well as the unique descriptors of the coordination spheres. In addition, the remediated files contain value-added annotations, including coordination geometry annotations from FindGeo and MetalCoord.

References

• FindGeo: Claudia Andreini, Gabriele Cavallaro, Serena Lorenzini (2012) FindGeo: a tool for determining metal coordination geometry Bioinformatics, 28: 1658–1660, https://doi.org/10.1093/bioinformatics/bts246
• MetalCoord: Kaveh H. Babai, Fei Long, Martin Malý, Keitaro Yamashitad, Garib N. Murshudov (2024) Improving macromolecular structure refinement with metal-coordination restraints. Acta Cryst. D80: 821-833. https://doi.org/10.1107/S2059798324011458

Authors: Alison Biester, Chenghua Shao, Rachel Kramer Green