Proteins: they have an unbelievable range of functions, and each function relates directly to their shape and size. The Protein Data Bank provides extensive information about the structure. But what about the size? This blog entry will address one of the features provided by the PDB for visualizing proteins, and show you can use it to get the size info.
Let’s start with a molecule that may be familiar: kinesin. Kinesin is a protein that “walks” along microtubules, carrying vesicles and other organelles along with it. It is a dimer with two globular heads that bind to the tubulin subunits, each with a neck linker that catalyzes ATP, and a long helical chain with an organelle-binding domain at the top. The molecule is about 30 nm tall altogether (I read most of that in this book: Bittar, E. E. (1991). Structural biology (1st ed.). London, England: JAI Press LTD; some of it was told to me in a cell biology class here at UIC).
The PDB can be accessed at http://www.pdb.org . Going to “advanced search” and entering the word Kinesin, with the query type “molecule name” yields 23 structure hits. The PDB tends to break complicated molecules like kinesin down into their functional subunits, and I was not able to find a crystal structure for the entire kinesin molecule. Additionally, confusion can arise from the availability of mutated structures to view. So, use caution in selecting which entry to use as a reference. The abstract from the original article is linked to the PDB, so if you’re not sure about the structure, read that for more information.
I chose the structure “2kin” which is the structure of part of a monomer of rat kinesin. It is the neck and globular head domain. Jmol: takes you a page with an embedded JAVA applet. The molecule, by default, is shown with the ribbon model. This model can be rotated by dragging with the left mouse button. The mouse wheel enables zooming in and out; hovering reveals a text box telling you which amino acid residue you are hovering over.
Let’s start with a molecule that may be familiar: kinesin. Kinesin is a protein that “walks” along microtubules, carrying vesicles and other organelles along with it. It is a dimer with two globular heads that bind to the tubulin subunits, each with a neck linker that catalyzes ATP, and a long helical chain with an organelle-binding domain at the top. The molecule is about 30 nm tall altogether (I read most of that in this book: Bittar, E. E. (1991). Structural biology (1st ed.). London, England: JAI Press LTD; some of it was told to me in a cell biology class here at UIC).
The PDB can be accessed at http://www.pdb.org . Going to “advanced search” and entering the word Kinesin, with the query type “molecule name” yields 23 structure hits. The PDB tends to break complicated molecules like kinesin down into their functional subunits, and I was not able to find a crystal structure for the entire kinesin molecule. Additionally, confusion can arise from the availability of mutated structures to view. So, use caution in selecting which entry to use as a reference. The abstract from the original article is linked to the PDB, so if you’re not sure about the structure, read that for more information.
I chose the structure “2kin” which is the structure of part of a monomer of rat kinesin. It is the neck and globular head domain. Jmol: takes you a page with an embedded JAVA applet. The molecule, by default, is shown with the ribbon model. This model can be rotated by dragging with the left mouse button. The mouse wheel enables zooming in and out; hovering reveals a text box telling you which amino acid residue you are hovering over.
Now for the exciting part: the right-click functions. There are many features here, and I’m just going to go over the ones that, at first glance, seem most useful to the scientific artist community. One of these menu items is Save with the option to create a JPEG or PNG, or – 3 D modelers, take notice—a VRML or Maya 3D model. I haven’t yet tried bringing either of these into 3DS Max or Maya, but it may prove to be fast and convenient.
As for size info, this can be obtained pretty painlessly. Here’s how: right-click, go to Measurements > Distance units nanometers. Then, right-click and choose “Click for distance measurement.” You can still left-click and drag to rotate. Once you pick the dimension you want to measure, just click once at one location, and again at the other location. A dashed line will be drawn from the first point to the second, and the distance between them will be displayed in white text, in nanometers. (The nanometer is the unit of choice for me, when talking about protein dimensions like these. The Angstrom is something of an out-dated term, and picometers will usually be quite a high number because they are very small units, at 10^-12.) In this case, measuring two points at the widest part of the globular subunit reveals that it is 6.4 nm wide. Easy, right?And now for the weird part: right click and choose Style>Stereographic>Cross Eyed Viewing. This splits the image into two views, and I kid you not, if you cross your eyes and play around with the distance your head is away from your monitor, you will see a 3D image, that can be rotated by clicking and dragging. It’s kinda like those Magic Eye posters from the 90’s, only with those I know you were supposed to look “through” them. Good times.
I hope this entry has given you a useful tool for your workflow; I know it will fit right in to mine.
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