Structure of influenza NP protein determined

Compared to other viruses, the influenza virus is relatively simple, although its biology is not. To date, the eight genetic segments in the viral genome (the totality of its genetic information) has been shown to code for only eleven proteins. A virus can get away with this because it hijacks the host cell's extensive protein making machinery and doesn't use its own. But we are still learning about those eleven proteins, what their role is, how they work and even what they look like. A paper that just appeared in Nature (.pdf, subscription only) is the first to reveal what one of these proteins, the nucleoprotein or NP, looks like. The paper has two features we have seen aplenty with flu science. It presents intriguing and hopeful information for new ways to attack influenza therapy and/or vaccine technology. And whatever benefits might ensue, there are are many, many steps away from this paper. They are not in the near future.

So what was involved here?

These proteins are big molecules, long chains of amino acids. Like an actual chain, they can be folded in many different ways, although unlike an actual chain whose fold is somewhat arbitrary, protein amino acid chains tend to assume one or just a few of the possible folded shapes. Trying to figure out how proteins are folded is the Holy Grail of modern bioinformatics and it remains unsolved, even with the world's most powerful supercomputers. If you know the genetic or protein sequence as given in GenBank, you still have a long way to go before you know what the protein actually looks like. That shape is critical to its function.

If you can't figure out the shape from the sequence, then what? You need to use laboratory methods. The Gold Standard here is something called x-ray crystallography. As the name implies, it involves shooting x-rays into a crystal of the protein and looking at the pattern the x-rays produce when they are scattered. In order to use this method you need a pure crystal of the protein. Since proteins don't exist in nature as crystals, the first step is to purify the protein and then crystalize it, often a tedious and difficult task and one reason we know what only a few of the influenza proteins look like. One of the authors of the paper, Yizhi Jane Tao of Rice University, described the process to Science Daily:

Tao said it was a challenge to growing NP protein crystals. The method used was the hanging drop vapor diffusion method, which involves suspending a liquid droplet of concentrated protein solution on the underside of a glass slide that is sealed inside a jar. As the liquid in the droplets evaporates, the proteins become supersaturated, and in some cases they form tiny crystals of a few hundred microns in size. Tao estimates that postdoctoral research associate Qiaozhen Ye prepared about 1,000 jars, with multiple droplets per jar, to get the 100 or so crystals that were needed for the experiments. (ScienceDaily)

NP forms the protein scaffold for the screw-shaped ribbon of viral genetic material and replicating enzyme. It is therefore important for viral RNA replication. The scaffold is formed by units of the NP protein lining up with each other in a specific fashion:

Once the virus has hijacked a host cell, and converted it into a virus-replicating factory, the NPs come together in small rings as building blocks. Many NP rings stack one atop the other in a slightly off-registered fashion, forming long helical-shaped columns. The virus's RNA genome is twisted around this column and shipped out to infect other cells.

NP's structure also has a tail loop, consisting of only about 30 of the more than 500 amino acids. This tail loop, however, seems critical to allowing the NP units to come together in the right way. Small changes in the loop prevent NP from carrying out its function and hence replication of the virus. The structure also reveals a possible drug target.

A single change in some amino acids in this tail can cause the NP to fail in its function. This is another way to see that the same fallible replication that is the source of genetic variation and evolution can also produce a non viable virus. It is likely that most such replication mistakes lead to defective viruses.

As we learn more, things don't always become clearer. Sometimes we find that what we thought we knew was wrong or that there is much more to something than we thought. In this case we have learned more. What it will mean in the long run, only time (and effort) will tell.