Tuesday, January 17, 2006

Background science for the Turkish mutations, I.

As stories appear in the news about the "small" mutations in the bird flu virus, it's time to do a little background for those of you who want to know a little of what this is all about. For a lot of you this much more than you want to know, but there are a number of lay and professional (but non-specialist) readers of this blog who have become quite knowledgeable and this is meant to provide some additional background. We'll make a stab at it here. Let is know if we are succeeding or failing.

The influenza (or any) virus needs to get inside a host cell in order to make new copies of itself. Reproducing is essentially its only task in life. We know that viruses and other pathogens don't usually infect all animals (they have a specific host range) and within an animal, usually infect only specific tissues. So cells from different animals and different tissues must somehow look different to the virus. How does a virus "recognize" the right cell? This question goes to the heart of the current concern over the small mutations discovered in the Turkish cases. Although we are leaving out a lot of details, there is still much we need to discuss.

Since the virus first "sees" the cell from the outsid, we start at the cell surface or cell membrane, as it's called. Animal cell membranes have a very complicated structure but essentially they consist of a supporting structure, called a lipid bilayer and various bits and pieces sticking on, in and through it. Below is a picture of a lipid bilayer, the structural stuff. (I copped this from a nice set of 1997 lecture notes by Prof. Steve Downing at the University of Minnesota-Duluth. This is copyrighted material, but I am not making any money from it and if the Regents of the University of Minnesota want me to take it down I will, of course. I doubt they care and are probably grateful for the free publicity.)

You can see the reason it's called a bilayer (it has two layers). Each little building block consists of two long fatty chains (the black bars) joined at the end by one of the colored balls. The fatty chains don't like to mix with water and face each other in the interior of the membrane, while the colored balls don't mind water and line both the interior and exterior of the cell. The reason the diagram has different colored balls is that these building blocks can be of various kinds (called phospholipids).

Besides the phopsholipits, there are also a fair number of glycolipids. They aren't shown above because I wanted to keep the picture clean. Whenever you see the word "glyco-" attached to something you should be thinking sugars (carbohydrates). Lots of the building blocks have sugars on them. Attaching a sugar is called glycosylation, and the thing that has the sugar attached is said to be glycosylated (and often the location of the attachment is given). Here's a closer view of a glycolipd, showing some of the molecules (the long CH chains are the corresponding versions of the black bars in the previous picture):

The previous picture of the bilayer didn't show any of these guys (the round colored balls are all phospholipids), but the membrane has these kinds of building blocks, too, althugh fewer of them. Here is what it looks like when we add these glycolipid building blocks to the structural membrane bilayer:

Those colored hexagons are different kinds of sugars and they are strung together in chains (the little pink squiggles are cholesterol and we don't need to discuss them here). Chains of sugar building blocks (the block units are called monosaccharides) can be oligosaccharides (when there are only a few of them), polysaccharides (when there are many building blocks, often in the form of oligosaccharide units strung together) or, more generically, saccharides, sugar chains, or glycans. The variety of terms can be confusing, so we are taking the trouble to set it out here, as they often appear in the literature. See here, for some (very technical) guidance.

So we have fats and sugars here. What about the third food group, proteins. Yes, lots of them and of various kinds and configurations with respect to the cell membrane. They can be bound either to the inside or outside surfaces, be tethered to the membrane and stick out in either direction, or wind their way back and forth through the membrane surface with loops and ends sticking up on either side or both. The proteins can be globs, oblongs, long threads or other complex shapes, but whatever their shape, they are long strings of amino acids (folded into the various shapes) and have two ends, one called the N-terminal end, here designated NH2, and the other the carboxyterminal end, here designated COOH. And it turns out these protein molecules also have sugars hanging off of them (the colored hexagons again), i.e., they are glycosylated. Here's another cartoon picture illustrating an example:

From this you can see that the cell surface will have a lot of sugars (carbohydrates) studding its surface, some from the glycolipids and some from the glycoproteins. Together they form a dense "canopy" of sugars (like the tops of the trees in the rainforest) called the glycocalyx. The glycocalyx of a cell is usually invisible with usual microscope techniques, but special procedures can bring it out. Here are some examples, taken from a wonderful (but very technical) website of Dr. Kevin J. Yarema at Johns Hopkins:

The picture in the left panel shows a cell surface with a fluorescent tags on the glycans to make them visible. The middle panel has a glycocalyx brush border (the hard to read label with two arrows). The right panel shows the glycocalyx looking like a lot of hairs sticking up from the cell surface.

So we've arrived at this point. The cell surface has a lot of sugar chains of various kinds covering it and sticking up around it. It is this surface various pathogens (including the influenza virus) "see" and which determines which pathogens will glom on to which cells.

We'll press on with more details in subsequent posts.