LIGAND COMPLEXES AND THEIR BIOCHEMICAL SIGNIFICANCE

Introduction

Coordinate bonds are a special case of covalent bonds where the electrons for sharing are supplied by one
atom. There is often a fractional positive charge on the donor atom and a fractional negative charge on the
acceptor atom. CoBr3・3NH3, for instance, exhibits such type of bonding and hence traditionally referred to as a
coordination compound.

Ligand complexes (Coordination compounds) consist of a central atom or ion, such as Co 3+, surrounded by
electron-rich groups (ligands), such as NH3. The ligands are directly bound (coordinated to) to the central atom
or ion; they are usually between 2 and 9 in number and may be single atoms, ions or molecules. The ligands
directly bound to the metal are said to be in the inner coordination sphere, and the counter-ions that balance out
the charge are said to be outer sphere ions. Coordination compounds are usually referred to as complexes; they
can be charged or uncharged and their structure is defined by the coordination number (the number of ligand
atoms bonded to the central atom) and their coordination geometry (the geometrical arrangement of the ligands
and the symmetry of the entire complex). The central ion can be in any oxidation state, which remains
unchanged in the coordination complex.

The metal ions can be empirically sorted into two groups on the basis of their preference for various ligands:
the large and polarizable ions that prefer large, polarizable ligands and the smaller, compact and less-
polarizable ones that prefer compact, less-polarizable ligands. Such a correlation, coupled to the broader
definition of acid– base, led to the concept of ‘hard’ and ‘soft’ acids and bases that can be useful in classifying
and to some extent predicting the strength of metal–ligand bonds, and hence the stability of complexes.

A. Classification of biologically important metal ions and ligands according to the ‘hard–soft acid–base’
concept and their general characteristics
Acid/acceptor (metal ions) Base/donor (ligands)
Hard High charge density Low polarizability
Small ionic radius High electronegativity
No easily excited outer shell electrons Vacant, high-energy orbitals
Na_, K_, Mg2_, Ca2_, Cr3_, Fe3_, Co3_ Hard to oxidize
H2O, OH-, CO2-, CO32_,
NO3-,PO43-, ROPO32-
PO43-, ROPO32-,(RO)2PO2-, ROH, RO-,
R2O,
NH3, RNH2, Cl-
Intermediate Fe2+, Co2+, Ni2+, Cu2+, Zn2+ NO2-, SO32-, Br-, N3-, imidazole

Soft Low-charge density High polarizability

Large ionic radius Low electronegativity
Easily excited outer shell electrons Low-energy vacant orbitals
Cu+ Easily oxidized RSH,
RS-, CN-, CO
Concept of Hard and Soft - Acid and Base (HSAB concept)

This is a Lewis concept in which metal ions are regarded as acids because they accept electrons while ligands
are bases because they donate electrons
•Hard acids tend to form complexes with hard bases (ionic bonds)
•Soft acids tend to form complexes with soft bases (covalent bonds)
•Hard acids: H+, Li+ (> Na+…), Cr6+(> Cr3+)
•Intermediate acids: Fe2+, Mn2+, Cu2+, Zn2+
•Soft acids: Au+ (> Ag+, Cu+), Hg2+, Pt2+
•Hard bases: F-, OH-, NH3, PO43- (> HPO42-), MoO42- •Intermediate
bases: Cl-
•Soft bases: I- (> Br-…), S2-(> HS-, > H2S), AsS2-

In general ‘hard’ acids prefer ‘hard’ ligands whereas ‘intermediate’ and ‘soft’ acids form more stable complexes
with ‘soft’ bases. Hard–hard interactions will be primarily ionic in nature whereas soft–soft interactions will be
governed by ‘orbital’ interactions. A number of more specific ligand–metal ion interactions are hidden within
Table for example, Mg2+ is often associated with phosphate ligands while Ca 2+ is most commonly coordinated
by carboxylate ligands as in proteolytic enzymes of the blood coagulation cascade where Ca 2+ is often bound to
_carboxyglutamate residues, Cu2+ is often bound to histidine residues.

Ligands are also classified electronically (according to the number of electrons donated to the central atom) and
structurally (by the number of connections they make to the central atom). The structural classification of the
ligands refers to their denticity i.e. the number of donor atoms from each molecule. A ligand attached by one
atom is described as monodentate, by two bidentate, by three tridentate and so on. Multi-dentate ligands bound
directly to one atom are known as chelating agents and a central metal atom bound to one or more ligands is
called a chelate.

Chelation is important in medicine. Treatment of the hereditary disease thalassaemia requires regular blood
transfusion and the excess iron can be removed by the hexadentate chelator desferrioxamine (DesferalR, DFO)
with pFe of the order of 27, depicted in Figure 1.

Figure 1: (a) the metal chelator desferrioxamine (DFO) and (b) its complex with iron.

DFO loses three protons when it binds to Fe 3+. This llustrates an important aspect of coordination chemistry,
namely that the positive charge on the metal ion stabilizes the acid anion (i.e. the conjugate base) of protonated
ligands. The same thing is true for other biologicalligands, such as water, alcohols, carboxylic acids, imidazole,
phenols, phosphoric acid and thiols. In the articular case of water, deprotonation to form a hydroxy ligand is
presumed to be involved in a number of metalloenzyme-catalysed hydrolytic reactions (e.g. the role of Zn 2+_ in
carbonic anhydrase).
The corrins and porphyrins are another important class of natural chelator molecules. They are
thermodynamically very stable and have four nearly coplanar pyrrole rings, the nitrogen atoms of which can
accommodate a number of different metal ions in different oxidation states like Fe 2+ in haem, Mg2+ in
chlorophyll and Co3+ in vitamin B12.
Ligands in Biological System

In biochemistry, a ligand is any molecule or atom which binds reversibly to a protein. A ligand can be an
individual atom or ion. It can also be a larger and more complex molecule made from many atoms. A ligand
can be natural, as an organic or inorganic molecule. A ligand can also be made synthetically, in the laboratory.
This is because the key properties of a ligand are found in its chemical structure. If that structure can be
recreated in the laboratory, the synthetic ligand will be able to interact in the same ways a natural ligand acts.

How a Ligand Works

The ligand travels through the watery fluids of an organism, within the blood, tissues, or within a cell itself.
The ligand travels at random, but once the concentration is high enough, a ligand will eventually reach a
protein. Proteins receiving ligands can be receptors, channels, and can even be the start of a complex series of
intertwined proteins. When the ligand binds to the protein, it undergoes a conformational change. This means
that while no chemical bonds have been formed or broken, the physical action of the ligand fitting into the
protein changes the overall shape of the entire structure. This can trigger many actions. In most cases, the
movement of the protein itself activates another chemical pathway, or triggers the release of another messenger
ligand, to carry the message to other receptors.

The reversibility of the bond between ligand and protein is a crucial aspect of all forms of life. If ligands bound
irreversibly, they could not serve as messengers, and most biological processes would fall apart. If ligands were
changed, the way an enzyme changes a substrate, the ligand would become something else after the interaction,
and could not be as easily recycled as a messenger. Biologically active proteins are active because of their
shape. This shape interacts with the chemistry of the ligand to create a stable connection between the two
molecules, which will eventually reverse, leaving both molecules the same. In a substrate and enzyme reaction,
the substrate is permanently changed.

It is this ability of the ligand, to activate a protein for a short amount of time and then be recycled, which
allows for the biological control of many interactions. The amount of time a ligand spends attached to its
receptor or specific protein is a function of the affinity between the ligand and the protein. If there is a high
affinity, the ligand will tend to stick to the protein and modify its function for longer. If the ligand has a low
affinity for the protein, it will be less likely to bond in the first place and will release from the receptor faster.

The affinity of a particular ligand for a particular protein is determined entirely by its chemical makeup and
that of the binding site of the protein. At the binding site, amino acids will be exposed which tend to
complement the desired ligand. The amino acids will match the ligand in certain aspects. For instance, both
will be hydrophilic or hydrophobic. This increases the attraction between the substances. The amino acids tend
to differ from the ligand in terms of electrical activity. If the ligand is positively charged, the binding site
should be negatively charged. This creates the strongest interaction. In this way, proteins can obtain a certain
degree of specificity for a ligand.

While this is the basis for how cells can begin to tell different molecules apart, it is also at the heart of one of
an organism’s biggest problems. Many poisons and toxic substances are so toxic because of their ability to
interfere with the protein-ligand binding process. Either the toxin directly binds to the protein itself, because it
has a higher affinity, or the toxin otherwise prevents the normal bonding of a ligand to its target protein.
Examples of ligands and some competitive toxins can be seen below.

Examples of Biochemical Ligands

Oxygen: One ligand that people often overlook is oxygen. In the bloodstream and body tissues, oxygen must
reach all the mitochondria in the body if the organism is to survive. But, it is not an easy task to get oxygen
everywhere. If oxygen were left to diffuse through the tissue to the cells, it can only pass a few cell layers
thick. That is why all organisms of a certain size must contain some sort of circulatory system. Even still, it is
hard to move the oxygen ligand where it is needed. Many organisms use specialized proteins for this.
In humans and other mammals, hemoglobin is the major blood protein responsible for transporting oxygen.
The hemoglobin protein first attaches to a ligand called heme, which has an iron atom and can help bind
oxygen. Thus, hemoglobin picks up oxygen in the lungs. As it travels to the body, the carbon dioxide content in
the blood rises. As this occur the pH lowers and the conformation of hemoglobin changes. This forces the
release of the ligand, oxygen, which can then be absorbed by the cells which need it.

A main competitor of oxygen is carbon monoxide. This is because carbon monoxide has a higher affinity for
hemoglobin than oxygen has. In other words, once carbon monoxide is bound to the hemoglobin, it won’t
come off. This means that someone exposed to large amounts of carbon monoxide will soon have all their
hemoglobin saturated by the wrong ligand. Their body will have no ability to transfer oxygen to the brains and
tissues. Even if the person gets oxygen after this, they can still suffocate because of their inability to transport
the oxygen.

Dopamine

Dopamine is a ligand used heavily in the brain. When the brain releases dopamine, it is as a signal of a pleasure
coming from success. In other words, dopamine is tied to the sensation of motivation. The dopamine receptors
in your brain are activated when the ligand dopamine is released by the brain. When the receptors are full of
dopamine, your brain feels as if you’ve done something good. This common reward center can be easily
thrown off by drugs such as cocaine and methamphetamine.

These drugs, instead of being in direct competition with the ligand, actually increase its effectiveness. They do
this by limiting the amount of dopamine which can be recycled. Thus, the brain stays in a constant state of
feeling “rewarded”. This is the dangerous feeling which can easily lead to drug addiction. Even though logic
tells you drugs are bad, the feelings produced by your brain and the extra dopamine feel real, and tell you to
use the drug more.

Ligands are used in many other applications by cells. The proteins they control can range widely in type and
function. Insulin

Some ligands, like insulin, are used to signal various things to the metabolism of each cell.

Acetylcholine

Another ligand, such as acetylcholine, is used by the brain to transfer nerve impulses between nerves. In this
case, it opens an ligand-gated channel, which allows the electrical impulse to flow into the cell and down the
length of it. This cell will then transmit acetylcholine to the next cell, and the signal will continue.

Some enzymes are controlled by regulatory ligands, which effectively turn the enzyme on. Without it, they do
not have the proper shape to transform the molecules they operate on. When the ligand is present, however,
these enzymes spring to life and function properly.

Many ligands are needed for controlling the metabolism and other complex processes. Each ligand has a
certain affinity, which is important, and also a point at which the receptors become saturated. Above this limit,
no higher concentration of ligand will bring a greater reaction.

In general chemistry, a ligand may refer to any molecule bound to a transition metal. This is not the case in
biology. In biology, a ligand is any molecule which attaches reversibly to a protein. These are typically used in
cellular signaling and cellular regulation, but have many other uses.
 Protein–ligand complexes
A protein–ligand complex is a complex of a protein bound with a ligand that is formed following molecular
recognition between proteins that interact with each other or with various other molecules. Formation of a
protein-
ligand complex is based on molecular recognition between biological macromolecules and ligands, were ligand
means any molecule that binds the protein with high affinity and specificity. Molecular recognition is not a
process by itself since it is part of a functionally important mechanism involving the essential elements of life
like in selfreplication, metabolism, and information processing. For example DNA-replication depends on
recognition and binding of DNA double helix by helicase, DNA single strand by DNA-polymerase and DNA
segments by ligase. Molecular recognition depends on affinity and specificity. Specificity means that proteins
distinguish the highly specific binding partner from less specific partners and affinity allows the specific
partner with high affinity to remain bound even if there are high concentrations of less specific partners with
lower affinity.

These are examples of membrane receptors. Typically, they are proteins that are embedded in the membrane.
Although there are many different ligands located outside of the cell, membrane proteins are specific, and only
certain ligands will bind to each one. That is why each protein has a different ligand, and also induces a
different cellular response. The response may be transcription of a gene, cell growth, or many other cellular
actions.

The protein-ligand complex is a reversible non-covalent interaction between two biological (macro)molecules.
In non-covalent interactions there is no sharing of electrons like in covalent interactions or bonds. Non-
covalent binding may depend on hydrogen bonds, hydrophobic forces, van der Waals forces, π-π interactions,
electrostatic interactions in which no electrons are shared between the two or more involved molecules.

The molecules (protein and ligand) recognize each other also by stereospecificity i.e. by the form of the two
molecules. Because of this real discriminative if not 'cognitive' property, Werner Loewenstein uses the term
'cognitive demon' or molecular demon referring to Maxwell's demon, the famous thought experiment. In fact,
the proteins that form complexes are able to pick a substrate out of a myriad of different molecules [. Jacques
Monod attributed a teleonomic performance or function to these biological complexes. Teleonomy implies the
idea of an oriented, coherent and constructive activity. Proteins therefore must be considered essential
molecular agents in the teleonomic performances of all living beings

Affinity

The highest possible affinity from a protein towards the ligand, or target molecule, can be observed when the
protein has a perfect mirror image of the shape of the target surface together with a charge distribution that
complements perfectly the target surface. The affinity between protein and ligand is given by the equilibrium
dissociation constant Kd or the inverse of the association constant 1/Ka (or binding constant 1/Kb) that relates
the concentrations of the complexed and uncomplexed species in solution. The dissociation constant is defined
as
 Kd = [L][P] / [LP]

where [L], [P] and [LP] represent molar concentrations of the protein, ligand and complex, respectively.

The lower the Kd value the higher the affinity of the protein for the ligand and vice versa. The K d value is
equivalent to the concentration of the ligand at which one-half of the proteins contain bound ligand [3][8]. Affinity
is influenced also by the properties of the solution, like pH, temperature and salt concentration, that may affect
the stable state of the proteins and ligands and hence also their interaction and by the presence of other
macromolecules that causes macromolecular crowding.
Functions
Protein-ligand complexes can be found in almost any cellular process. Binding of a ligand causes a conformational change
in the protein and often also in the ligand. This change initiates a sequence of events leading to different cellular functions.

The complexes are formed by different molecules like macromolecules as in protein complexes, protein DNA or protein
RNA complexes as well as by proteins that bind smaller molecules like peptides, lipids, carbohydrates, small nucleic acids.
They may have various functions within the cell:

• catalysis of chemical reactions (enzyme-substrate),

• defense of the organism through the immune system (antibodies antigen complexes),
• signal transduction (receptor-ligand complexes) that consists of a transmembrane receptor that upon binding the
ligand activates an intracellular cascade.
• Lipophilic hormonal receptor complexes can pass the nuclear membrane where transcription may be regulated.