Wednesday, September 4, 2013

Three Lefts Make A Right

Biology concepts - chirality, homochiral, enantiomer, stereoisomer, racemic mixture, biofilm, antimicrobial peptide, protein, amino acid

Geordi was the chief engineer on Start Trek; The Next
Generation, but I was partial to Scotty on the original.
They both work on the matter-antimatter reactors that
powered everything from the warp drive to the phasers.
Don’t laugh – NASA is working on a warp drive as we
speak, and we have been able to produce antimatter for
years. Not sure how antimatter will solve our energy
problems though, it takes much more energy to produce
it than we get from a matter-antimatter reactor.
Today we’ll start with a story that may seem to have nothing to do with biology. Hopefully we can draw a parallel later.

For every type of every subatomic particle there is an opposite particle. There are protons and anti-protons, electrons and anti-electrons (positrons), neutrons and anti-neutrons. Together, they make up matter and antimatter – think Star Trek.

So why is our universe made of matter and not antimatter? It turns out that when matter meets antimatter, they obliterate one another. This is bad – Scotty was always trying to prevent a matter/antimatter catastrophe on the Enterprise.

When the universe was young, there was antimatter and matter; lots of annihilations. Scientists hypothesize that there were a few more molecules of matter than antimatter, so when the fireworks were over, only matter remained; so matter matters.

What’s this got to do with protein exceptions, our subject for last week and this? We’ll get to that, a little background first. Remember that the shape of the protein is important for its function, and its shape is dependent on the amino acid order and the structure of those amino acids.

Look at your hands. They’re mirror images of one another, but no matter how you try, you can’t make your left glove fit exactly on your right hand. Unlike a ball reflected in a mirror where the two images will be superimposable on one another, there is no way to do this with say….. your left and right shoes.

If you reflect your right hand in a mirror, you get an
image exactly like your left hand. But your right and
left hands can’t be superimposed – try it, turn one over,
turn the other over, turn them around the over
direction, detach one – you still can’t do it. It is the same
with chiral molecules. The different groups come at you
or away from you, and once you reflect them, no two can
be superimposed – try it, at least one group will be
pointing the wrong direction.
Molecules like this in chemistry are called chiral; the amino acid central carbon (chiral carbon) has four different groups, so no flipping will make the two mirror images look exactly the same. The two different amino acid variations are called stereoisomers, specifically, enantiomers.

The different enantiomers (enantio = opposite) have different chemical properties. Without getting into too much chemistry (nobody wants that), different enantiomers cause light waves to rotate in different directions.

One version of a molecule called gluteraldehyde rotates light to the right (dextrorotary or D, dextra = right), while the other is levorotary (levo = left). Amino acid enantiomers are comparable to the structure of gluteraldehyde, so amino acids that parallel the two gluteraldehydes are assigned a D- or L- label, ie. L-alanine has a structure similar to the gluteraldehyde enantiomer that rotates light to the left.

This is a bit of a misnomer because light rotation depends on many factors. In fact, many amino acids labeled L-type because of their similarity to L-gluteraldehyde actually rotate light to the right –that little factoid won’t be on anyone’s final exam.

Most proteins fold on their own, and they fold the same way every time. But what might happen if the protein sometimes used a certain L-amino acid and sometimes the D-version? The two resulting proteins would fold differently and therefore have different possible functions. Heaven forbid!

To avoid this, nature has devised an ingenious solution - only L-amino acids are used. This assures that all proteins of a specific type assume the same shape, and it turns out that proteins are most stable when they are made of all L- or all D-amino acids. This is the rule of homochirality.

Polarized light has practical implications. Your 3-D movie
glasses may be plane polarizers. The light from the screen
is a mix of right and left polarized light. One lens lets in
one, while the other lets in the opposite light. This splits
the image into two images, one for each eye, and they are
separated by a distance. This gives a stereoptic image, just
like your eyes seeing something in real space.
This is one of the best-known rules of biology, right behind the “form follows function” we talked about last week. But we saw that proteins were exceptions to that rule, so there must be exceptions to this one as well.

One question before the exceptions -just why did life opt for all L-proteins instead of all D-proteins? Do they annihilate one another when they come into contact, like matter and anti-matter? Thankfully, no.

Were there more L-amino acids available on the early Earth so life made a choice and stuck with it? Maybe – this is one of the hypotheses currently being investigated. It’s also possible that some life developed as D-protein makers, but they were out-competed somehow and we descended from the L-protein winners. It isn’t as easy a question as the physics matter/antimatter issue - more on this biology exception next week. There are so many more exceptions in biology as compared to physics – that’s why I love life more than physics itself.

The most mundane is exception to homochirality is the one amino acid that isn’t chiral. Glycine’s R group is just a hydrogen, so the central carbon has two bound hydrogens, and the mirror images can be superimposed. There’s no L-glycine or D-glycine, just glycine. Don’t worry, the rest of the exceptions are better.

It turns out that the rule of homochirality is more of a guideline - there are examples of important D-amino acids (D-aa) in plants, animals, and prokaryotes. We don’t have time or space to go into many of them, but I will highlight two exceptions that are simply amazing. Let’s start with the bacteria since they own the planet, and we probably inherited our D-amino acid uses from them.

Bacteria use D-amino acids in various ways. First, new research shows that as bacterial numbers go up and resources (food) go down, D-aa-containing proteins might prepare bacteria for the bad times ahead. A 2009 study shows that Bacillus subtilis and Vibro cholerae make large amounts of D-aa as they age, including D-tryptophan, D-tryosine, D-phenylalanine, and D-leucine. As the amounts increase, they start to have an effect on the bacterial cell wall.

A gram positive bacterium has a thick cell wall, which
includes peptidoglycan. The glycan parts are NAM and
NAG. The NAM has a tetrapeptide attached to it, and this
is where the D-aa can be used. This strengthens the cell
wall and makes it even thicker. The lipoteichoic acid in
the outer layer is where change to a D-aa prevents
defensins from sitting in the cell wall and disrupting
the buried plasma membrane.
The D-aa are incorporated into the growing peptidoglycan, the elastic and stress-bearing component of the cell wall, and they also regulate enzymes that control the thickness and structure of the peptidoglycan. By putting D-aa into the cell wall, the bacteria make themselves strong for the lean times ahead.

What is more, a 2010 study showed that in B. subtilis and S. aureus, the increasing numbers of bacteria and their increasing concentration of D-aa’s leads to a breakdown of the extracellular matrix that holds all the bacteria together (the biofilm). D-aa's were able to prevent biofilm formation and degrade existing biofilm, again preparing the bacteria to go off on their own as resources dwindle.

S. aureus also uses D-aa-proteins to avoid being killed. We have antimicrobial peptides (AMP) on our skin and mucosal surface that are always looking to kill bacteria. They often work by poking holes in the bacterial membrane. However, a 2013 study shows that by switching out L-alanine to D-alanine in its cell wall, S. aureus can render the AMP’s ineffective. The D-alanine gives the protein a different shape, so the AMP's can’t fit in and do their job. Smart bacteria.

Animals have gotten into the act, especially the gastropod mollusks, ie. some snails and sea hares (marine slugs). D-tryptophan is their exception of choice. The cone snails (genus Conus), the most predatory and venomous of the marine snails, use D-tryptophan in the active peptides of their venom, called contryphans. Large cone snails have been known to kill humans, but the role of the D-tryptophan in the venom activity is not yet known.

The cone snails use many peptide venoms to incapacitate
their faster prey; they move like snails don’t ya know. The
siphon has the black stripe and tests the water for prey.
Then the proboscis below (kind of pinkish orange at the
tip) sends out the radula that envenomates the victim.
The sea hare, Aplysia kurodai, also uses D-tryptophan in a cardioexcitatory neuropeptide called NdWFamide (it speeds up the slug’s heartbeat). This protein has also been found in terrestrial slugs, so it may be that many mollusks are D-aa users.

How about us? Do humans use D-amino acids? Sure we do. But there are tricksters here. D-alanine is found in all mammals, but we don’t know what it might be doing. Its levels change with the time of day (circadian cycling), so who know what it might be controlling. A 2013 study set out to determine what drove the circadian changes. They tested several things: changing diet or fasting didn’t matter; enzymes that degrade D-alanine didn’t change levels of function either. But when they studied germ-free mice, the D-alanine levels didn’t change.

The scientists determined that it’s our gut bacteria making D-alanine, and circadian changes in intestinal absorption rates is the reason that the D-alanine levels fluctuate. It doesn’t mean that D-alanine isn’t doing something, but it sure had us fooled for a while.

Mammals don't stop there; D-serine and D-aspartate are so important, we have special enzymes called racemases whose job it is to convert their L-forms to D-forms (racemic mixtures contain both D- and L-versions of a molecule). The most amazing exception must be D-serine. However, we will see that there is a Goldilocks effect to D-aa’s, you don’t want too much or too little.

A certain brain neuron receptor (called NMDAR, important for learning and memory) is activated by an amino acid called L-glutamate, but it needs help from either glycine or D-serine to set off the electrical impulse. It turns out that in Lou Gehrig’s disease (amyotrophic lateral sclerosis), lower motor neurons die because they undergo aberrant excitation. In genetic cases of ALS, patients have too much D-serine!

Most patients with ALS are diagnosed after age 50 and
live about five years. Stephen Hawking- the Nobel
winning cosmologist – was diagnosed at 21 and has
lived with the disease for 50 years! Hawking has round
the clock care, for the only muscles that work for him
are breathing, swallowing an eye movement. Lucky for
him, most people’s breathing and swallowing are not
spared and this is how they die. He uses his eye
movement to run his computer.
A 2012 study showed that D-amino acid oxidase (DAAO) is mutated in these patients and doesn’t do its job of breaking down D-serine. Mice with a mutated DAAO were shown to have decreased lower motor neurons and more ALS signs.

So too much D-Ser is bad, but how about too little? Many studies have shown that schizophrenia patients have low levels of D-Ser. It might be that DAAO is too active, or perhaps a D-Ser racemase is inactive, or maybe there is just too little L-Ser to make D-Ser from – we don’t know yet. 

A 2013 study has also implicated D-aspartic acid in schizophrenia. D-Asp can replace L-glutamate in activating NMDA receptors, and schizophrenic patients have low D-Asp levels in the brain and blood. The D-Ser and D-Asp data implicate glutamergic receptor activation in schizophrenia, so much work is underway to find ways to increase these D-aa’s in our brains - the very things that the rules say we shouldn’t be using in the first place. But let’s not raise them too much, no one wants ALS!

Next week, we switch our attention to carbohydrates, the energy sources in our cells. Every cell on Earth is designed to make ATP from glucose - except for those cells that ONLY use fructose.

Lam H, Oh DC, Cava F, Takacs CN, Clardy J, de Pedro MA, Waldor MK. (2009). D-amino Acids Govern Stationary Phase Cell Wall Re-Modeling in Bacteria Science, 18 (325), 1552-1555 DOI: 10.1126/science.1178123

Kolodkin-Gal I, Romero D, Cao S, Clardy J, Kolter R, Losick R. (2010). D-Amino Acids Trigger Biofilm Disassembly Science, 328 (5978), 627-629 DOI: 10.1126/science.1188628
Sasabe J, Miyoshi Y, Suzuki M, Mita M, Konno R, Matsuoka M, Hamase K, Aiso S. (2012). 

D-amino acid oxidase controls motoneuron degeneration through D-serine. Proc Natl Acad Sci U S A. , 109 (2), 627-32 DOI: 10.1073/pnas.1114639109  

Simanski M, Gläser R, Köten B, Meyer-Hoffert U, Wanner S, Weidenmaier C, Peschel A, & Harder J (2013). Staphylococcus aureus subverts cutaneous defense by d-alanylation of teichoic acids. Experimental dermatology, 22 (4), 294-6 PMID: 23528217

 Errico F, Napolitano F, Squillace M, Vitucci D, Blasi G, de Bartolomeis A, Bertolino A, D'Aniello A, & Usiello A (2013). Decreased levels of d-aspartate and NMDA in the prefrontal cortex and striatum of patients with schizophrenia. Journal of psychiatric research PMID: 23835041

For more information or classroom activities, see:

Chirality –

Bacterial cell wall –

Biofilm –

Antimicrobial peptides –

D-amino acids –

Amyotrophic lateral sclerosis –

Schizophrenia -