The Amazing All-Natural Light Machine

Scientists are using a molecule hidden in pond murk to create sugar like a bacteria.

By Mark Caldwell|Friday, December 01, 1995
Molecules can be useful--a fact you’d probably already gathered, since without them you’d be languishing joylessly as a bodiless intelligence. But did you know they can also be beautiful? One particularly splendid example made its first appearance before human eyes in the fall of 1994, after 12 years of dogged up-and-down pursuit by researchers at Scotland’s University of Glasgow and the Daresbury Synchrotron in England. Its public debut followed quickly, in the pages of Nature last spring, and it’s been wowing biochemists ever since.

LH2, as they call it, takes top honors in the molecular talent competition as well as in the beauty pageant. Delicate little gamin though it is, LH2 plays a key role in a process that, should it ever grind to a halt, would spell the quick end of life on Earth: photosynthesis. LH2 is more than just a molecule; it is a tiny machine, a light-harvesting device (hence the LH in its name). Think of it as a minuscule antenna, designed to capture energy from atmospheric light and channel it into the microscopic factory where a photosynthetic cell first stores it, then uses it to manufacture such indispensable substances as sugars and proteins.

The researchers found their basking beauty not in lacy fern or glamorous Schefflera but in a low-rent bacterium called Rhodopseudomonas acidophila. The microbe dwells in the muck of ponds and streams, soaking up whatever light is left over from the photosynthetic algae that typically live above it. It’s even quite happy at the bottom of polluted ponds, says Glasgow crystallographer Neil Isaacs. As its name implies, it loves acid. But unassuming and obscure though this little reddish purple creature is, it’s a good model system for the photosynthesizing world at large: its light-harvesting mechanism works on the same basic principles as the more complicated devices found in green plant cells, but it is far easier to visualize.

Much of LH2’s beauty arises from the elegant and efficient simplicity of the structure that allows it to do its work. The molecule is tiny--just shy of 3 ten-millionths of an inch across--but into that cramped space it packs a transparently symmetrical, though intricate, design. (It’s okay, by the way, to call LH2 a molecule, though it’s more accurately termed a complex, since many of its subunits, while linked to one another chemically, qualify as molecules.) Basically, LH2 is a hollow cylinder, the shape of a doughnut or a thick rubber washer, slapped down in the cell membrane. While LH2s are far too tiny to appear in full molecular detail under a microscope, if you could gaze down on the cell wall, you’d see them anchored everywhere, like little Cheerios. Their ringlike outer edges and central holes face up into the atmosphere and down into the cell. If you could focus closer, you’d see that R. acidophila’s cell membrane folds in on itself, creating an onionlike structure of LH2-studded membrane several layers deep.

Like many antenna systems, LH2 relies on a structural framework to support and deploy the delicate components that pick up signals. Here the framing elements are proteins rather than flexible steel, but in LH2 these structural proteins behave like the uprights and struts that brace a radar installation. There are 18, each a tight, springlike coil. Nine of them, all leaning about 15 degrees to the right of plumb, form a circle of columns around the outer circumference of LH2. The remaining 9, standing nearly vertical, surround the inner hollow.

Between them, these inner and outer colonnades tightly embrace the works of LH2--the pigment compounds that pick up and transmit light energy. These are versions of chlorophyll (the substance that makes green plants green, by absorbing every color of light but green) and carotenoids (which are typically yellow to orange in hue and appear in those blazing leaves every autumn when the chlorophyll dies out of them). LH2 harbors a configuration of 27 chlorophyll molecules and 13 or 14 carotenoids, again in a strikingly symmetrical and logical arrangement.

To keep things simple, let’s take a closer look at the chlorophylls (which, strictly speaking, should be called bacteriochlorophylls, since they differ slightly from the pigments in algae or green plants). They’re more familiar and more important than the carotenoids, and LH2 has more of them. For reasons that mystify everybody, LH2’s favorite number is 9. Typically, 9 chlorophyll molecules circle the outer wall of the complex, one poised between each pair of the 9 outer columns of support protein. The supports then extend upward to surround the remaining 18 chlorophylls. Inside the loggia-like space between the inward and outward support columns, these chlorophylls overlap to form a ring, which resembles an 18-bladed fan or a turbine.

The lovely structure almost seems more like the impeccable work of a human engineer with classical taste than a messy, improvised product of nature. But why has nature waxed so lavishly arty when LH2’s sole purpose is to gather and transmit light energy? That, as it turns out, is the scheme’s real beauty. The elegant circular fretwork into which the proteins weave the chlorophylls makes those pigments adept at catching and transmitting light energy. The protein columns hold them in a chemical grip that helps determine what sort of light energy they pick up, and also place them in a configuration that helps them pass that energy from molecule to molecule, down into the cell’s reaction center, where the final steps in photosynthesis take place.

Let’s start with that all-sustaining light as it filters down through the pond murk to R. acidophila. Chlorophyll and carotenoids in algae floating in the water above have soaked up much of the visible light, leaving only light in the infrared range available for absorption by the humble neighbor downstairs. How do the proteins in LH2 tweak the chlorophyll so it absorbs light at the available wavelengths rather than at wavelengths the algae have already grabbed? Steve Prince, a member of the Glasgow team who trained as a physicist, says no one yet knows the answer. But the columns of support protein are somehow involved. These proteins, bonded chemically to the chlorophylls, hold them in positions that alter the configuration of electrons surrounding them. Since a molecule’s electrons store and release energy, changing the configuration of electrons might also change the wavelengths of light to which the chlorophyll will respond.

It’s a little like a string in a musical instrument, Prince explains. There are a hundred things you could do to it--like pinching or stretching it--that would change the frequency it resonates at. Significantly, in LH2 the circle of 9 chlorophylls arrayed lower down in the complex is tuned to absorb light with a wavelength of 800 nanometers (800 billionths of a meter); the 18 packed more closely together near the upper surface absorb at a slightly longer wavelength--850 nanometers. Why two forms? Really, Neil Isaacs says, the ring of 800-nanometer bacteriochlorophylls is just an additional energy source. They’re packed into available space in the complex, and they conveniently increase the range of light energy it can respond to. But, Prince points out, the proteins hold the bacteriochlorophylls far apart from one another and in such a way that they don’t easily transmit energy back and forth to one another. Instead they’re configured to flash it up to the tightly packed ring of 850-nanometer chlorophylls above, a feat that they achieve with blazing speed: the mad rush upstairs takes less than a trillionth of a second.

LH2 transacts its real business in this closely packed ring of 850-nanometer chlorophylls toward the top of the complex. The 850s pick up light energy on their own, of course, in addition to what they get from the 800s below. But unlike the 800s, they are held close together by the proteins, in a pattern that enables them to transmit energy to one another at a speed that surges beyond blazing to blinding: within 2 or 3 ten- trillionths of a second they flash any light energy they’ve snagged around the entire ring, which briefly pulsates with it.

Now pan out a bit, and imagine eight LH2s, each with its circle of 850-nanometer chlorophylls, suspended at a precisely calibrated level in the complex, and glowing with stored energy. The story would end there except that these eight LH2s surround--and touch--a similar but considerably larger antenna device called, unsurprisingly, LH1. Its exact structure hasn’t been fully determined yet. Like LH2, LH1 seems to be a hollow cylinder, but larger in size, probably because it has to be big enough to surround the reaction center, the submicroscopic dynamo in which the energy gathered by LH1 and LH2 is put to final use. The ring of 850- nanometer chlorophylls in each LH2 unit is aligned with a ring of 875- nanometer chlorophylls circling LH1--which allows light energy to hop easily aboard LH1 from any LH2 (in fact, the transfer takes no more than 20 trillionths of a second).

Are you getting the overall picture? It’s simply elegant and elegantly simple, says Prince, like an antenna dish, with the LH2s on the outer edges, the LH1 in the middle, and the reaction center in the middle of that. Like an antenna dish, the array captures and focuses incoming signals. Prince explains: Imagine you’re an exciton--the quantum physics term for a burst of energy stored in an electron when it jumps up to a higher energy level because it’s excited, and discharged when the electron slips back to its normal state. If you find yourself in a circular orbit, as soon as you touch a nearby circle, you can jump over. In other words, if any chlorophyll molecule anywhere in an LH2 picks up light energy, it instantly disperses it around the entirety of the 850 ring. So wherever the 850 ring comes close to the LH1’s adjacent 875 ring, the energy can handily leap across.

Recall too the numbers assigned to these chlorophyll molecules: 800 to 850 to 875. They tell an important part of the story, since they represent the wavelengths at which the molecules soak up energy. The longer the wavelength of a ray of light, the lower its frequency, and hence the lower its energy. A molecule can’t store a pulse of energy indefinitely. In this antenna system energy moves naturally from the highest-energy chlorophyll (800) to the lowest (875). There’s a certain probability that the energy can transfer either way, Prince explains, but the probability is much higher that it will transfer to the lower-energy chlorophyll. If it has to go up, it needs to get an extra burst of energy from somewhere-- activation energy--so it’s a natural process to move downward. The system is an energy sink, because energy is lost as it moves through. Isaacs adds, It just makes sense to start from the top and move toward the bottom. (He’s speaking, of course, of the energy levels of the molecules rather than their positions: physically, the energy moves up from 800 to 850, then across to the 875 molecules in LH1, then across again into the reaction center.)

The clever arrangement of the various chlorophylls serves to funnel gathered energy in the right direction--from the LH2 units on the outside of the antenna dish to the LH1 in the middle on down to the reaction center that nestles in LH1’s central hole. That’s where a key step in photosynthesis happens: the energy gathered by LH1 and LH2 pulls an electron out of still another chlorophyll molecule and attaches it to an acceptor molecule. Curiously, the only time anything but energy ever moves in the whole process is the moment when an electron is pulled from its donor and attached to an acceptor. Once that happens, the energy it took to achieve the transfer is stored in chemical form in the acceptor molecule and available for the final work of photosynthesis: the dark reactions, so named because they happen after light has been converted into energy. The dark reactions change carbon dioxide into carbohydrates, for instance, and ultimately make the sugars and proteins the plant lives on.

Major discoveries like LH2, the analogous (if much more confusingly laid out) green plant light-harvesting complex, and the reaction center have been following each other rapidly since the late 1980s. Not only is the photosynthetic task they perform of overwhelming ecological importance, it has great practical potential too. LH2’s fierce efficiency in harvesting and transmitting light energy is no mere parlor trick. The best man-made solar collector, Prince observes, is 15 percent efficient. But LH2 is 90 percent efficient. I’d call that a blueprint for a very effective solar collector. Might someone, someday soon, clone LH2 or imitate its structure with other chemicals, and--just by painting it onto a solar panel--achieve a sixfold improvement in energy collection? Antenna complexes, Prince concludes, might conceivably make solar heating systems work even here in cloudy old Scotland.

True beauty really does warm your heart.

LH2, that coy beauty, led the Glasgow team on a merry chase for over a decade. Snaring it required X-ray crystallography, an exacting technology that involves arduous work even before you get to the X-rays.

First you have to fish the molecules out of the cell membrane, where they reside. You do that by finding, through trial and error, a detergent that will wash them out, then form a protective sheath around them and preserve their original shape.

And even once you isolate your molecules, you can’t simply poke them under a microscope. For one thing, visible light waves are too big to get in among the atoms--but X-rays, with their minuscule wavelengths, can zoom freely in and out of even claustrophobic interatomic spaces. For another, a single molecule is too tiny to place in a machine, and a lump of molecules in helter-skelter order would tell you nothing, because you could never be sure where one LH2 ended and another began. So you have to persuade your molecules to organize themselves into a crystal, a formation in which the molecules line up in a regular, constantly repeating lattice.

That part sounds easy. Proteins will crystallize if you can make them precipitate slowly, says Richard Cogdell, the Glasgow biochemist who inaugurated the quest for LH2. You put the proteins in a solution, then drop them onto a membrane that lets the solvent seep through but leaves the proteins on top. If the solvent goes through too quickly, they come out as an amorphous, cruddy mess, Cogdell says. But if it goes through slowly, they may come out orderly. In theory you can train an acolyte to make crystals, but it’s an art not everyone can master. Actually, it’s a black art, intones Glasgow team member Steve Prince, ruefully displaying trays of spiny, blobby, speckled, and otherwise wayward near crystals to prove it.

Each crystal takes about six weeks to grow, and when a new one emerges, it can look deceptively regular. But when bombarded, expensively and time-consumingly, with X-rays, its innards may nonetheless reveal themselves as chaotic. If you took a caseful of tennis balls and looked at them from 20 feet away, the arrangement might seem pretty regular, explains crystallographer Neil Isaacs, but when you got closer in, you’d see that the little seams wouldn’t be in any particular order.

It wasn’t till the fall of 1993 that Gerry McDermott, a chemist working with Prince, Cogdell, Isaacs, and their colleagues, figured out how to produce crystals so orderly that they could use them to deduce LH2’s structure. But that was only the beginning. Next they were faced with the rigors of X-ray diffraction, which are formidable, although the theory is simple. If you shine a beam of light through a screen (which, with its regular lattice of wires, resembles a crystal), you’ll see on the wall behind it a pattern of blobs and bright spots--a faithful image of the screen, distorted into unrecognizability by the deflection of light rays as they pass through it. Optics, however, will rectify the apparent disorder. If you put a lens where the spots are, Cogdell explains, it’ll recombine all that information, and you’ll retrieve a recognizable image of the grid.

X-rays pass through a crystal in the same way, and while the resulting pattern of spots isn’t visible to the eye, you can record it on an electromagnetic X-ray detector. Then you can reconstruct the arrangement of atoms in the molecules, except that instead of an optical device, you deploy a series of calculations called Fourier transforms, which act like a virtual lens. As always, however, there’s a hitch. To resolve scattered light back into an image, an optical lens manipulates three features of light waves--their intensity, their wavelength, and their phase, a measure of how one wave interferes with another. Recording intensity and wavelength in X-ray experiments is relatively easy, but the phase information that an optical lens picks up doesn’t make it to the electromagnetic X-ray detector. So a key piece of information comes up missing.

Scientists solved that problem in the 1950s and 1960s. First, they prescribed, bombard your crystal with X-rays and record the pattern that results. Then make a new crystal, deftly sticking into it a few very heavy new atoms that will nestle in the same spot every time the pattern of the crystal lattice repeats, just as if your room had wallpaper with a hunt scene, and someone drew a mustache on every fox. Without, you hope, displacing or moving the atoms in your mystery molecule, the new atoms will significantly alter the diffraction pattern of the crystal. Carefully measure the differences between the patterns thrown out by the two crystals, feed this diffraction pattern into your computer, and--voilà!-- emerge almost triumphant with a preliminary diagram of your molecule.

The Glasgow group, along with Miroslav Papiz and Anna Hawthornthwaite-Lawless of the Daresbury Synchrotron, duly soaked LH2 crystals in a long list of heavy-metal-saturated solutions, hoping they’d suck up a few atoms without giving the LH2 molecules disfiguring fat lips or dislocated shoulders. But no dice. Every time we put a heavy metal into the crystal, Isaacs recalls, it seemed to distort. For a while, nothing worked. After much labor, the team managed to cram six molecules containing platinum into each repeat of the crystal without distorting it, but that, maddeningly, proved too much of a good thing. Taken all together, the added molecules produced so much information that the numbers were too complex to crunch.

Finally, however, the team had a stroke of luck, using a technique called back soaking. They took a crystal overburdened with six platinum molecules and soaked it in a chemical solution, hoping to rinse out some of the platinum. At last one molecule fell out of each repeat, leaving five. Now they had three crystals: one (let’s call it A) with LH2 alone, one (B) with six added platinum molecules, and one (C) with five. But five was still too many, yielding data too complicated to resolve. The trick? By subtracting C from B, they were left with data identical to what they’d have gotten if they had a crystal with just one added platinum molecule.

After that it was relatively easy. Combining the data from the three crystals, the computer belched out a diagram that showed the clouds of electrons in the molecule rather than the atoms--because X-rays bounce off electrons, not nuclei or whole atoms. Then came the fun part. Different groups of atoms have distinctive electron configurations. Using a workstation and a joystick, the researchers grabbed candidates from an inventory of stick-figure diagrams of components. Turning them this way and that, they determined which ones fit best in each electron cloud. That’s how in September 1994, atom-by-atom and subunit-by-subunit, LH2 made its dramatic appearance on a video display in a cupboard at Glasgow’s chemistry department. --M. C.
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