This page will allow you to zoom in on the molecular motor dynein. You can explore how it powers transport around the body. On your left you can see a computer representation of the part of dynein which generates movement (the motor). It is about 30 nano-metres long - 330,000 of them stretched end to end would fit into 1cm.
To get an idea of how dynein looks in 3D it is necessary to move it around. You can move your mouse over the
image, press the left mouse button and then drag the mouse gently back and forth. As the protein moves you get a better idea
of its structure. You can return to the original view by pressing this button.
Reset
Alternative you can allow the dynein to spin: try the following buttons:
Spin On
Spin Off
Many foods are rich in protein (milk, eggs, meat etc). The body breaks proteins down into their individual building blocks, called "amino acids"
and then uses the amino acids to build new proteins like dynein. This dynein motor contains a chain of 3150 amino acids. Press the button to zoom in on one.
1 amino acid
Amino acids are built of atoms. We can colour the different atoms: carbon (grey), oxygen (red), nitrogen (blue), sulphur (yellow). Colour Atoms Each type of atom is a slightly different size: move the amino acid around and you will see sulphur is slightly bigger than the others. The carbon atoms are roughly 0.3 nano-meters across.
This atom representation is called "spacefill". It shows each atom as a ball. To see how atoms are joined together we can use two different representations. Try these: Ball&Stick Wireframe
Amino acids are joined together into a chain. To show this the next button will add on 6 more amino acids, one at a time, to show you a length of chain.
Show chain
The amino acid chain is made up of a central "backbone" with "sidechains" sticking off it. First we will colour the sidechains green.
Sidechains
This shows you the repeating structure of the backbone (oxygen-carbon-carbon-nitrogen,oxygen-carbon-carbon-nitrogen, etc).
Next we will color the backbone green. Backbone This shows you how proteins are made up of amino acids with lots of different side chains. Move the chain around to see them better. There are 20 different amino acids in total (there are 6 different types here). The order in which the amino acids are joined together determines the shape of the protein and what it does (a bit like a very complicated code).
Next we will add on some more amino acids to make a longer chain. Longer chain
As you try to show more of the protein it looks a bit too complicated. So we have ways of showing the protein that simplify its structure.
We can replace all the atoms in the backbone with lines that join up the side chains. This is called a C-alpha trace.
C-alpha
To make things simpler we can get rid of the side chains. C-alpha only The amino acid chain folds into three types of structures. Helices and Sheets When it runs in a straight line it is called a beta-sheet (yellow). When the chain wraps round and round it is called an alpha-helix (pink). The rest of the chain is referred to as a coil (white).
A common way to display protein structures is using the "cartoon" format, which has special shapes for helices and sheets. Cartoon . Press the next button to zoom out and see how the dynein is made up of lots of regions of beta sheet and alpha helix. Dynein - helix & sheet Use the mouse to move the structure so you can see this better. Now we will use color to highlight the main parts of the dynein motor. To start colour the whole motor grey.
Colour Grey
The engine of the dynein motor is a ring shaped structure (green). Ring If you look carefully you will see it is divided into six sections, all shaded slightly differently
Dynein walks along a track called a microtubule. The next button will color the part of dynein that binds to the microtubule in orange.
Microtubule Binding
This microtubule binding region is connected to the ring by a 15 nano-meter long stalk (yellow).
Stalk
The most important part of the dynein motor is called the linker. This amplifies the movements in the ring to let dynein take a step. Linker
Dynein is powered by a small molecule called ATP (Adenosine Tri-Phosphate). ATP is your body's universal fuel: it also powers your muscles to move, your brain to compute things and many other functions. Dynein breaks ATP down into ADP (Adenoside Di-Phosphate) and Pi (Phosphate) which releases energy.
The next button shows you where ATP binds the dynein ring. It will use a thin "CA-trace" for dynein, so you can see the ATP molecule in "spacefill". ATP fuel You can use the following buttons to turn the ATP on and off. ATP off ATP on Rotate the molecule around to see how it binds to the ring.
To show how dynein uses ATP we will change its orientation so that stalk is pointing down. Stalk down
When ATP is broken down and released from dynein the linker moves. This is called the "powerstroke". Press the button to see what happens. Power-stroke When another ATP binds, the linker moves back in a recovery stroke. Recovery-stroke
To see how linker movement lets dynein walk play movie below. It show two dynein motors attached together (as they are arranged in your cells). The power-stroke on one moves it forward. Once the forward motor binds to the microtubule (grey tube in the bottom of the movie), it can then do a powerstroke to bring the other motor forwards. Play/Pause
Return to Start