The Barrels from Bacteria

I remember a trick published long back in “SUKTARA Pujabarshiki” written by P. C. Sorcar Jr. It said that if you hold your palm facing you and keep a hollow cylinder side by your palm and then look straight to the assembly so that the cylinder axis is perpendicular to your palm you could see a hole in your palm. Here, a visual illusion let us think that we have a see through palm although there is no space through. But what if the case is reverse? What if there is a space you can see but no way to access it unless the cylinder let you do so.

Although membrane proteins do not like crystallographers at all and initially resisted to make their crystals, a group of scientists leaded by three people Hartmut Michel, Johann Deisenhofer, and Robert Huber perturb that shield. They conquered the unwillingness of the membrane proteins and presented us a all helical membrane protein structure named “Photosynthetic reaction center”. After which Biological Science have seen many revolutions like the recent Nobel Prize on GPCRs. But, here I am concerned about the other membrane proteins that contain all-beta and was evolving parallely with some initial work by J. P. Rosenbusch (1974). He discovered a major E. coli (a bacteria) envelope protein called “Porin”. He took some electron micrograph images and said that the protein exists as trimer, meaning three “Porin” proteins assemble together to make a working-unit (see Fig). With their structural resemblance, this protein is also called a Barrel protein.  Barrel proteins are abundant in bacterial surface and all of them have splendid structures. The elementary construction is based on the specific repeat on the polypeptide backbone called “beta sheet”. Certain 3D arrangements of this conformation have earned some fancy names like “beta-propeller”, “Greek key”, Jelly roll”, “beta helix” etc. Now when Rosenbusch was measuring the conductance (a methodology that let us determine how a channel protein work) through the Proins he found that instead of working as individual unit, the “triplet” (three Porins) is working as “singlet”. He also proved from the electron micrograph sections that when “the trio” merged-into-one in one face, “the trio” remained separated in other face. Later both Rosenbusch together with Johan Jansonius and Georg Schulz independently determined the Porin structures. Some of these cylindrical proteins are very strict to allow something to pass it through. Although there is space through, the membrane, there is no way for the intruders.

Microstructures and Macrointerpretations

Molecular structures of proteins are key players of their specificity. Sometimes their structures are indicative to their functions.

Like, the extracellular domain of a Toll like receptor (Fig a) is responsible for the pattern recognition from pathogens and kick starts the body’s natural defense system. A breed of sheep called “Dorset” has horns and their frontal view looks like a pair of Toll like receptors. A Dorset sheep is shown to be sensitive to people face pattern and always tends to kick the unknown people trying to treat them.

An Ankyrin repeat (Fig b) is repetition of the unit containing “two alpha helices separated by a loop”. In fact the TLRs contain this motif. Such repeats on the receptors mediate anchoring one cell to the other thus the name ankyrin.

People must have foreseen the structure of yeast Fatty acid synthase (Fig c) around 340BC because the beer barrels were developed around those times. Although the history says that the particular shape of the barrels is to ease rolling, stacking and withstanding pressure, I say different. There was an unavoidable connection between the fatty acids and the beer.

Protein structure in a movie

 
Has any movie taken advantage of any protein structure viewer, like Pymol, Rasmol, molmol, etc.? O! I found one. It was released during 2011. The movie “Contagion” which has a rating 6.7 in IMDB, and showed that a deadly virus has the ability to kill human within a day. It has a scene where Dr.Ellis Cheever (played by Laurence Fishburne) was showing the structure of the viral antigen in some protein structure viewer to Dr. Ally Hextall (played by Jennifer Ehle). One could see some multiple sequence alignment behind the viewer. I presume the viewer is Rasmol. However, the interesting fact about the movie is that they have the virus antigen structure within four days after discovering the virus and even before culturing the virus in cell.