Molecules: A Very Short Introduction - Ball Philip 2001

Delivering the message: molecular communication

Each of us is a new world. The molecular view of life reveals that the appropriate analogy for a cell is a city, teeming with molecular inhabitants. Our many-celled bodies are thus collaborations between communities. One cell communicates with another as London does with Liverpool, New York with Philadelphia: messages are passed down wires or carried from place to place by courier. Goods are transported hither and thither along the transportation network of the blood and lymph circulatory systems. It is just as Berzelius said: ’This power to live [is] the result of the mutual operation of the instruments and rudiments on one another.’

Molecular biology has long been content merely to document the social webs of the cell: deducing which molecules speak to which, and how they come and go. But ultimately this is not enough. We need to know also what is said, and how the messages are passed on one to another. This is information that a pharmaceutical chemist can use to develop drugs. The fundamental challenge for medical science is to learn how to take part in the body’s molecular conversations: to intercept harmful or unpleasant messages, to send out new warning messages, to prevent undesirable interactions.

It is largely as a result of these efforts in the field of biochemistry that chemistry itself is undergoing something of a reinvention. The imagination of chemists is fired up by what they see to be possible in biology. Although much of the chemicals industry is devoted to the manufacture of ’passive’ products — new plastics, cement, glue, paint, synthetic fibres — drug molecules were always a little different. For their task is to partake in a dynamic process, to engage in the active life of the cell. They are like actors primed for a dramatic role; indeed, they often play their part by impersonation. Now chemists are beginning to appreciate that this kind of dynamism can be achieved in purely synthetic chemical systems too. And so chemistry is becoming less about the properties of individual molecules and more about how groups of different molecules behave together — forging and breaking relationships, modifying each other’s tendencies, sending out signals. Chemistry is becoming a science of process.

This is the attitude that underpins much of the work I discuss in this book: the development of molecular solar cells, of chemical sensors, of a molecular nanotechnology, and of molecular devices that process information. Much of the research in this area is gathered under the umbrella of supramolecular chemistry, which means chemistry beyond the molecule: the science of molecules in communication.

In this chapter I shall explore a few of the ways in which molecules communicate in biology, before providing a glimpse of how a similar gregariousness can be encouraged in synthetic molecules. As ever, we must remember that, while nature is inspirational, it is also parsimonious and blind. Biology uses a limited range of materials, and has a tendency to adapt a good solution endlessly for new purposes rather than exploring a completely new avenue each time. Just as the Jumbo jet is not a scaled-up pigeon, so the wise molecular engineer takes from nature principles but not blueprints.

Molecular mail

Italy and Germany became countries when their patchworks of small kingdoms and city states agreed to respect a central authority — to collaborate towards a greater good for all. The body cannot behave as a coherent entity unless cells do likewise. This means that there must be mechanisms for sending commands, edicts, and calls to action throughout the entire realm. Nerve signals from the brain are one means by which the body coordinates its actions. They are the body’s telephone system.

But general messages sent globally throughout the body are posted like a mass mail shot into the bloodstream, in the form of molecules called hormones. These are diverse both in form and in function. Some hormones are large proteins; others are small organic molecules. Some are soluble in water, others insoluble (which means that courier molecules are required to carry them through the bloodstream). Some convey urgent, immediate messages such as ’Run away!’ Others have long-term effects, promoting growth or the development of sexual characteristics.

All hormones are the product of the endocrine system, a series of glands that constitutes the overarching regulatory system for the whole body (Fig. 33). We have seen already how the hormones insulin and glucagon, produced in the pancreas, control the blood’s sugar content (see page 78). Similarly, the rate of metabolic processes in cells is regulated by the hormones thyroxine and triiodothyronine released from the thyroid gland. These hormones affect energy production and oxygen consumption, in part by altering the heart-beat rate.

The control centre of the endocrine system is the hypothalamus, a gland in the brain. The hypothalamus is connected to the pituitary gland, which sits just below it, from where hormones are dispatched to other glands. For example, a fall in metabolic rate prompts the hypothalamus to send a molecule called thryotropin-releasing hormone to the pituitary. This gland in turn starts to send out thyroid-stimulating hormone, which triggers the thyroid gland into action.

33. The body’s endocrine system, a series of hormone-producing glands.

All of the hormones released from the pituitary are peptides: small protein-like molecules. Antidiuretic hormone, for instance, controls the body’s water content by regulating the production of urine in the kidneys. Growth hormone provides a stimulus for cell multiplication, and plays a key role during childhood and adolescence. It also stimulates localized growth of tissue when repairs need to be made — for example, during wound healing.

The adrenal glands manufacture some important steroid hormones. These are insoluble molecules with a carbon backbone consisting of several small rings joined together. Some steroids, such as cortisol, regulate the storage and use of the body’s energy resources: the conversion of glucose to glycogen and the breakdown of proteins into amino acids. Bodybuilders and athletes use these hormones (legally or otherwise) to build up body mass and muscle.

As you might anticipate, the hormone adrenaline is also a product of the adrenal glands. Along with noradrenaline, it is released rapidly into the bloodstream in response to stress. Both hormones quicken the heart rate and dilate the blood vessels, increasing the oxygen supply to muscles so that they are prepared for extreme exertion.

The sex glands — ovaries in women, testes in men — release the hormones that differentiate the sexes and trigger changes in growth during puberty. Testosterone stimulates sperm production in men. Oestrogen and progesterone control the female menstrual cycle; their production is regulated by hormones released from the pituitary gland, called follicle stimulating hormone (FSH) and luteinizing hormone (LH).

These two hormones regulate ovulation during the menstrual cycle. In the early days of pregnancy, high levels of oestrogen and progesterone in the bloodstream inhibit the production of FSH and LH and suppress ovulation. Birth-control pills have the same effect: containing oestrogen and progesterone, they persuade the woman’s body that she is already pregnant.

Production of oestrogen declines when a woman is in her thirties, and particularly during the menopause. Side effects of low oestrogen levels include an increased susceptibility to coronary heart disease and to bone loss, which are two of the prime motivations for administering oestrogen in hormone replacement therapy. The treatment remains controversial, because long-term doses of oestrogen can have unwelcome side effects of their own, including an enhanced susceptibility to breast cancer and different forms of heart disease.

Switched on

How is a hormonal message read? This depends on the nature of the message. Some hormones can be posted right through the walls of cells, wherein they bind to some receptor protein. This activates the receptor to stimulate the transcription of a particular gene, making a protein that the cell needs. This so-called direct gene mechanism of hormone action works for hormones that are small and insoluble, so that they can penetrate the fatty cell membrane.

But many hormones, particularly those comprised of peptide and protein molecules, get no further than knocking on the doors of the cell. They are received by butlers at the cell surface — receptor proteins whose job it is to convey the message to others inside the cell.

Like most other molecular communication, the passing of a message from hormone to receptor protein is an intimate affair. Molecules show no inhibitions: they speak to one another through close embraces. Lacking any other means of recognition, molecules identify one another by ’touch’, through binding events in which the receptor latches onto a target (substrate) with precisely the right shape, like a key fitting in a lock. Each hormone-receptor protein on a cell surface has a binding site sculpted to fit around the hormone.

Despite the variety of messages that hormones convey, the mechanism by which the signal is passed from a receptor protein at the cell surface to the cell’s interior is the same in almost all cases. It involves a sequence of molecular interactions in which molecules transform one another down a relay chain. In cell biology this is called signal transduction. At the same time as relaying the message, these interactions amplify the signal so that the docking of a single hormone molecule to a receptor creates a big response inside the cell.

It works like this. The receptor proteins span the entire width of the membrane; the hormone-binding site protrudes on the outer surface, while the base of the receptor emerges from the inner surface (Fig. 34). When the receptor binds its target hormone, a shape change is transmitted to the lower face of the protein, which enables it to act as an enzyme.

The process that the enzyme catalyses is the ’activation’ of a so-called G protein, attached to the inner surface of the membrane. G protein is short for guanine-nucleotide-binding protein: the protein holds onto a molecule of guanosine diphosphate (GDP). When a hormone-charged receptor interacts with a GDP-laden G protein, the G protein first replaces the GDP with guanosine triphosphate (GTP, analogous to energy-rich ATP), and then breaks in two. The half that binds the GTP becomes an enzyme, and travels off to activate another enzyme at the inner surface of the cell wall. Commonly, this other is adenylate cyclase, a protein that converts ATP into cyclic AMP (cAMP).

The participants of all these processes are stuck to the cell wall. But cAMP floats freely in the cell’s cytoplasm, and is able to carry the signal into the cell interior. It is called a ’second messenger’, since it is the agent that relays the signal of the ’first messenger’ (the hormone) into the community of the cell. Cyclic AMP becomes attached to protein molecules called protein kinases, whereupon they in turn become activated as enzymes. Most protein kinases switch other enzymes on and off by attaching phosphate groups to them — a reaction called phosphorylation. The action of a protein kinase initiates a cascade of reactions, since each activated kinase can act on several enzyme molecules, each of which in turn can do its job many times. In this way docking of one hormone to its receptor can affect many molecules inside the cell: the signal becomes amplified.

34. How G proteins work.

The process might sound rather complicated, but it is really nothing more than a molecular relay. The signal is passed from the hormone to its receptor, then to the G protein, on to an enzyme and thence to the second messenger, and further on to a protein kinase, and so forth.

The G-protein mechanism of signal transduction was discovered in the 1970s by Alfred Gilman and Martin Rodbell, for which they received the 1994 Nobel Prize for medicine. It represents one of the most widespread means of getting a message across a cell membrane. Some hormones attenuate rather than stimulate cell processes; in such cases the activated G proteins might exert an inhibitory effect on their target enzymes rather than activating them. In other cases the second messenger might be a small molecule other than cAMP: certain activated G proteins trigger the release of calcium ions from the calcium-binding protein calmodulin, for instance.

And it is not just hormonal signalling that makes use of the G-protein mechanism. Our senses of vision and smell, which also involve the transmission of signals, employ the same switching process. The roof of the nasal cavity is lined with smell sensors called olfactory hairs, which are attached to the ends of nerve cells that carry signals to the olfactory bulb — the ’smell centre’ of the brain. The cell walls of the olfactory hairs are studded with receptor proteins designed to bind particular odorant molecules that enter the nose.

There are several hundred different kinds of odorant receptors, each one with a binding site shaped to accommodate a specific common odorant. We can, however, discriminate between a wider range of odours than this, because each odour is typically the result of a complex blend of different odorant molecules. The olfactory bulb forms an ’image’ of the smell from the mixture of impulses that it receives from different receptors, much as we recognize a person’s face from the sum of the different component parts.

In smell signalling, the cAMP produced by G proteins binds to a membrane protein called a sodium channel, whereupon the channel opens up and lets sodium ions flow into the cell. This triggers a nerve impulse, which passes to the olfactory bulb. The same basic process generates visual signals in the optic nerve when stimulated by light.

Our sense of taste is due largely to our olfactory system. The taste buds in our tongues can distinguish only relatively crude signifiers of taste: sweetness, bitterness, saltiness, and sourness. The full delight of a matured cheese or freshly baked bread comes mostly from the odorant molecules they release.

All in the mind

Hormones can trigger complex webs of biochemical action, but the messages they bear are pretty crude, related to the exigencies of growth and survival. It is quite another matter that communication between molecules gave birth to the Sistine Chapel, to The Magic Flute, to the theory of relativity. Yet the mind is, after all, made of molecules.

At the same time, the mind is still a mystery — one of the great remaining mysteries of science. Some scientists argue that the mind will never be able fully to comprehend itself, that the self-referential nature of the problem will always create blind spots. Others believe that a scientific explanation of consciousness is on the horizon. Either way, it is likely that the secrets of the mind lie far beyond the molecular realm, embedded in questions about the behaviour of complex, highly connected information networks. Here we see the limitations of reductionism — for the molecular processes of thought are now fairly well mapped out, yet their collective consequences are barely sketched.

The brain contains somewhere in the region of a billion to a hundred billion brain cells or neurons. That is nothing to write home about — other organs are comparably populous. But the distinguishing feature of the brain is the complexity of the communication network between these cells. Each neuron makes around a thousand links, so there may be up to a hundred trillion interconnections in the brain — about the same as the number of stars in a thousand galaxies like our own. On such a transportation network, you would be lost in an instant. The degree of connectivity in the integrated circuits of computers is nowhere near so great, and it is no surprise that computers, for all their literal-minded speed, fail miserably at some tasks that a child can do in a flash.

Neurons send nerve signals — in essence, electrical pulses — to one another along tubular channels called axons. The axon ends in a series of branches whose tips push up against the membranes of other neurons. At these junctions, called synapses, a nerve signal is transmitted from one neuron to another. Neurons also sprout many shorter, bushy branches called dendrites, which collect information from the axons of other cells. The axons are, if you like, the motorways of the brain, stretching from one neuronal city to the next. They end in slip roads that connect up at synapses to the city road system of the dendrites.

Although axon signals are electrical, they differ from those in the metal wires of electronic circuitry. The axon is basically a tubular cell membrane decorated along its length with channels that let sodium and potassium ions in and out. Some of these ion channels are permanently open; others are ’gated’, opening or closing in response to electrical signals. And some are not really channels at all but pumps, which actively transport sodium ions out of the cell and potassium ions in. These sodium-potassium pumps can move ions ’uphill’ — from regions of low to high concentration — because they are powered by ATP.

In its ’resting’ state, the axon has an imbalance of sodium and potassium ions inside and outside that sets up a charge difference, or voltage, across the membrane: the fluid inside has a small negative charge (the ’resting potential’) relative to that outside. When a signal is sent down the axon, some of the gated sodium channels open up, altering the distribution of ions and reversing the imbalance: the inside becomes positively charged relative to the outside. This region of reversed voltage opens up sodium channels ahead of it, so that it moves along the axon. At the same time, the channels behind close up and the resting potential is restored. In this way, a voltage pulse or ’action potential’ travels down the axon (Fig. 35).

35. Electrical pulses are sent down the axon by the opening and closing of ion channels.

At a synapse, this nerve impulse is transmitted from the axon to another neuron. The signal is generally first converted from electrical to chemical form. A small molecular messenger called a neurotransmitter conveys the signal across the space (called the synaptic cleft) between the terminal membrane of the axon and the membrane of the other neuron. The neurotransmitter is packaged up inside a bubble-like membrane that merges with the axon’s cell wall, releasing the molecular message into the synaptic cleft. It travels to the outer surface of the other neuronal membrane, where it becomes bound to receptor proteins.

A diverse array of molecules serve as neurotransmitters. Some are simple amino acids — glycine and glutamate — or molecules derived from them, such as serotonin and dopamine. The molecule acetylcholine is a neurotransmitter that carries messages between the central nervous system and muscle cells at neuromuscular junctions (see page 103). When acetylcholine binds to its receptor on a muscle cell, the receptor is transformed to an open sodium channel. Sodium ions rush into the cell, changing the voltage across the cell membrane and opening up a voltage-controlled calcium channel. This triggers a rise in calcium ion concentration inside the cell, which stimulates muscle contraction.

Acetylcholine illustrates the general function of a neurotransmitter: to open or close an ion channel, thereby altering the voltage across the membrane in which the receptor sits. This converts a chemical message back to an electrical one. Acetylcholine does the job directly, since its receptor is itself an ion channel. Some other neurotransmission pathways function rather differently: they use a second messenger to transfer the message from the neurotransmitter to an ion channel, again with the mediation of G proteins.

Is it surprising that the G-protein signal transduction mechanism appears in so many different contexts? Not really. As the complexity of multicelled organisms evolved, cells with ever more specialized functions arose from common ancestors with more general functions. Tried-and-tested mechanisms for certain tasks would be retained, though adapted where necessary. That, after all, is why we share genes with yeast and bacteria. The G-protein pathway is an effective way of passing a chemical message from the outside to the inside of a membrane, and amplifying it in the process. The cell’s motto is: if it works, find a way to use it.

Pleasure and pain

Neurotransmission is a common target for drugs — beneficial, harmful, pleasurable, or, depending on the dose, all three. The nervous system is one of the most vulnerable parts of the body: if nerve impulses are blocked, we cannot move. Many animals make toxins that cause paralysis in their prey by attacking the sodium-potassium pumps or the voltage-gated ion channels in axons, blocking the progress of action potentials.

Muscle action is also affected by drug molecules that resemble acetylcholine and so compete with it in binding to the receptor proteins at neuromuscular junctions. Nicotine, the active ingredient of tobacco, is one such: it binds to a certain class of acetylcholine receptors in muscle and causes the associated stimulatory sensations: increase in heart rate and dilated pupils. Why the sensation is pleasurable is not, however, fully understood. Curare is a lethal toxin present in the bark of a South American plant, which was once extracted and used by the indigenous people to poison arrow tips. Curare binds to the same class of acetylcholine receptors as nicotine, but does not activate them — so muscle action is prevented. An animal poisoned with curare will die of asphyxiation, unable to inflate its lungs. The medieval poison hemlock works in the same manner.

Whereas some neurotransmitters stimulate neurons, the role of others is to quieten them: to suppress the firing of action potentials. These are said to be inhibitory, and include glycine and the molecule gamma-aminobutyric acid (GABA). Our thoughts are a complex interplay of stimulation and inhibition, as neurons weigh up the various signals they receive from their neighbours and decide whether or not, on balance, they should fire off a salvo themselves.

Hallucinogenic drugs such as LSD (lysergic acid diethylamide) and mescaline overexcite the brain by enhancing the stimulatory effects of serotonin. The poison strychnine blocks inhibitory signals, leading to uncontrollable muscle spasms and a particularly unpleasant death. Depressants assist the binding of inhibitory neurotransmitters or (like alcohol) interfere with the action of excitory neurotransmitters.

Drugs that relieve pain typically engage with inhibitory receptors. Morphine, the main active ingredient of opium, binds to so-called opioid receptors in the spinal cord, which inhibit the transmission of pain signals to the brain. There are also opioid receptors in the brain itself, which is why morphine and related opiate drugs have a mental as well as a somatic effect. These receptors in the brain are the binding sites of peptide molecules called endorphins, which the brain produces in response to pain. Some of these are themselves extremely powerful painkillers.

Cannabinoids, the active ingredients of cannabis, also bind to inhibitory neuroreceptors in the brain to produce pain relief. The natural target of these receptors is a molecule called anandamide, which, like endorphins, is produced in response to pain signals. A closely related molecule called oleamide seems to be the biochemical trigger that induces natural sleep.

Not all pain-relieving drugs (analgesics) work by blocking the pain signal. Some prevent the signal from ever being sent. Pain signals are initiated by peptides called prostaglandins, which are manufactured and released by distressed cells. Aspirin (acetylsalicylic acid) latches onto and inhibits one of the enzymes responsible for prostaglandin synthesis, cutting off the cry of pain at its source. Unfortunately, prostaglandins are also responsible for making the mucus that protects the stomach lining (see page 78), so one of the side effects of aspirin is the risk of ulcer formation.

One of the surprising recent discoveries in neuroscience was that extremely small inorganic molecules can also act as neurotransmitters. Carbon monoxide and nitric oxide — both of them two-atom molecules — serve this function. They are both poisonous in large doses, because they compete with oxygen in binding to haemoglobin. But ’the poison is in the dose’, and in small amounts nitric oxide does some important things. It triggers the dilation of blood vessels, which can relieve stress on the heart. This is why nitroglycerin, which decomposes to release nitric oxide, is administered to treat heart problems. The improvement in circulation initiated by nitric oxide provides the basis for the drug Viagra, which is used to treat erectile dysfunction in men.

Supramolecular chemistry

In recent decades, scientists have become interested in mimicking, in synthetic systems, some of the molecular communication processes of the cell. There are many motivations for this. Drug development is often a matter of concocting a good disguise, so that a synthetic molecule will pass itself off as a natural one and bind preferentially to a receptor, blocking or initiating a biochemical signal. Signal transduction in the eye’s retinal cells and in the olfactory system suggests the concept of molecular sensors that can detect light or other molecules with high sensitivity. Molecular engineers are looking to the olfactory apparatus for inspiration in designing ’artificial noses’ that can identify complex mixtures of molecular components.

The principle loudly extolled by nature is the ’lock and key’: molecules get together when one fits with the other.* To turn such a ’recognition’ event into a communication process, the binding event should trigger some change in the receptor that allows it to relay the signal downstream. In biology this relay process is commonly catalytic: binding turns the receptor into an active enzyme. But the signal might also be passed on in other ways: by the emission of light or release of an electron, for instance, or (as in the case of the acetylcholine receptor) by the creation of an electrochemical potential.

Building artificial signal-transduction processes at the molecular scale is a common objective in supramolecular chemistry. From its outset, this discipline was biologically inspired. In the 1960s, the French chemist Jean-Marie Lehn investigated so-called crown ether molecules that would recognize and bind specific metal ions. Lehn was interested in transporting ions such as sodium and potassium across lipid membranes. Although this can be mediated by protein channels and pumps, another strategy is to engulf the ion within a molecule that will ’dissolve’ in the fatty interior of the membrane wall. Such molecules exist in nature, and are called ionophores. A typical example is valinomycin, a ring-shaped peptide with a central hole into which a potassium ion will fit. Crown ethers are synthetic mimics of valinomycin: they too are ring-shaped, and will bind a metal in their central cavity. The metal ion is held more or less securely depending on the relative sizes of the ion and the hole. If the hole is too big, the metal ’rattles around’ and is only loosely bound; too small, and it will not fit. So crown ethers can be tailored to fit specific metal ions — to display molecular recognition, in other words.

By the 1970s, Lehn and others were making synthetic receptor molecules of all shapes and sizes, with cavities designed to accommodate a wide range of inorganic and organic targets. These ’guest’ molecules are held in place by interactions with their hosts that are weak relative to the covalent bonds that hold the atoms together in the molecules themselves. In this way the guests can be picked up and released again. That is how valinomycin works as a metal-ion transporter: it captures the ions on one side of the membrane and lets them go again at the other side. Supramolecular chemistry is essentially about bringing molecules together into loose associations that can be disassembled back into their separate components.

When crown ethers take up a metal ion, they change shape. Alone, they are rather loose, floppy rings, like rubber bands. With a metal ion in their core, they become organized into relatively rigid structures in which the ring contains zigzag-like kinks: a crown, in other words (Fig. 36). Shape changes of this sort are common when a receptor binds its target.

If binding alone is the objective, a big shape change is not terribly desirable, since the internal rearrangements of the receptor make heavy weather of the binding event and may make it harder to achieve. This is why many supramolecular hosts are designed so that they are ’pre-organized’ to receive their guests, minimizing the shape change caused by binding.

But if the idea is to use binding as the trigger for relaying some signal, then a shape change is often crucial. A particularly dramatic change in shape induced by host—guest binding was reported in 2000 by Ulrich Koert and colleagues at the Humboldt University in Berlin. They constructed a receptor molecule that can be considered as a series of ’modules’: two arms, two legs, and a ’transducer’ unit like a flexible torso connecting the arms to the legs. When the two arms close around a zinc ion, the transducer unit flips and pulls the two legs far apart (Fig. 37). The legs are tipped with fluorescent groups, which change their emission wavelength — from green to ultraviolet — when the distance between them increases. The researchers pointed out how this molecular receptor shows some of the features of a protein receptor involved in signal transduction, responding to binding of the target at one end by altering its shape, and thus its behaviour, at the other end.

36. A crown ether is a cyclic molecule that captures a metal ion in its central cavity.

37. An artificial transducer molecule that converts binding of a zinc ion into a signalling event, by changing shape and altering its fluorescence properties.

A shape change that alters a molecule’s light-emitting properties has been engineered in several other synthetic receptors. But using recognition and binding to switch a molecule’s catalytic behaviour, as in the G-protein signalling mechanism, is rather more challenging, since this means ensuring that the final shape is exactly what is needed for the catalyst to do its job. Harder still would be the task of organizing several molecules into a relay that would carry a message downstream. All the same, the skill of supramolecular chemists is increasing daily, and it would not be at all surprising if we were soon to see artificially devised molecular communication systems that approach the sophistication of those the body uses to run its realm harmoniously.