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Spidermonkey's Sporadic Lab Stuff

by Spidermonkey

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Hello World from the lab!

Part spider - part lab monkey, will do science for cash, strawberries, or for a place to be that's out of the rain (but preferably for cash).

The rest of what I get up to goes into the Tunnel of Goats :)

Urgent Science Stuff:

Please help reform English libel law
Current UK libel laws are very bad for science and free speech.

Cool science stuff:

RCSB Protein data bank: Molecule of the Month in alphabetical order

The PCR Song It's the little things that keep you going...

NCBI's Entrez Gene My favourite starting point for finding out what is known about any gene of interest.

NCBI's PubMed Where to go to find pretty much all research published in the last 30 years or so (may go back a lot further now). All newly published research is quickly added to the site.

The Genetic Code - table of the DNA/RNA triplet codes for amino acids. This is how DNA codes for protein.

Another PCR song Disco frenzy :)

Recent visitors

A bit more of this and that.

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This being docking and that being gels.
I think I'm getting the hang of displaying the protein so you can see how the ligands fit inside, but I'm not happy with it yet. I think I'm missing something...

Got nice bright bands to cut out on the gel though, and only 2 of them so was relatively quick and painless to process. The gel is made with a tiny amount of ethidium bromide in it which slots nicely into the DNA molecules and glows fluorescent orange when you shine UV light through the gel. It's a bit carcinogenic but easily the best way to see where your DNA is on a gel, you just have to handle with care (like everything else in the lab really). The blue dyes are so you can keep an eye on how far your sample has run when it is still in the electrophoresis tank.
This was taken from behind a perspex screen to keep me safe from burns and eye damage.

Got new ligase today so have set up more ligations overnight. Will find out if these have worked Thursday morning.
25th Nov 2009, 03:06   | tags:,,,


Viv says:

not sure whether to make an attempt tp try and understand it or wether just to be in awe of nature and you scientists and how pretty it all is!

25th Nov 2009, 09:20

Spidermonkey says:

I'm attempting to understand all the time, this is still pretty new to me too, so by all means please join me :) I never cease to be in awe of nature, it always has something more amazing than the last thing up it's sleeve.
If you want to find out more about protein structures and how to look at them a good place to start is the RCSB Protein data bank. On their home page they feature a molecule of the month, with cool pictures and a good summary explanation in layman's terms.

There are various free to use programs that will take crystal structure files (text files of coordinates giving an x,y,z position to every atom in a protein crystal, usually derived from x-ray crystalography) and render them as 3D images that you can rotate on the screen to see from all angles. That is what I have got in the top image. Mostly, only the secondary structure of the protein is being displayed (that is the overall shape the sequence of amino acids adopts when it is folded properly, the red coils are alpha helices and the blue-green ribbons at the back are bit of beta sheet). The blue, purple and orange structures in the centre are different positions that can be occupied by the same small molecule in the binding pocket of the protein. The bright pink bits are any atoms of the protein that happen to be within 2 Angstrom (0.2 nanometers) distance of any conformation of the small molecule.

As you can see I have a long way to go before I find the least complicated way to display this. It's much easier to see what's what when you have it on your screen and can spin it round.

If you want to have a play with any of this yourself please do and drop me a line if you get stuck/want more explanation on anything. It does me good to try to explain things - shows me what I need to learn (i.e. lots!).

26th Nov 2009, 02:56

Caine says:

The top image is amazing.

26th Nov 2009, 04:36

Viv says:

Thanks SB I will return to this when I am not cold/flu ridden!

26th Nov 2009, 08:54

Spidermonkey says:

Oh poor you! This one's for you then: Influenza neuraminidase, that's the bit that tamiflu is supposed to work against I think.
Get well soon.

26th Nov 2009, 15:40