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[ironduck]

How about an image contest of Particular Pretty Proteins to un-geek things?

Yeah, I was thinking about that too - similar to the astronomy picture thread.

 

[BCLG100]

Tbh i just skipped everything you just said as i immediatly got lost so maybe could refrain from doing it a little?

 

[MjM]

I joined and finished a WU.

 

[Sophie 378]

Shall I spam this thread with pretty protein pics?
I have lots - dissertation on metalloproteins, and lots of lectures and papers! How about this one?

Spoiler :

Calcium binding to the EF-hand domain of Calmodulin, for those of you who aren't as biochemistry-geeky as me.

 

[MjM]

How come yours are so pretty? Mine are all ugly and ball-shaped.

 

[Sophie 378]

That's because it's off the web, rather than a F@H! Cheat! Cheat!
Have you tried playing with the settings? I presume you have it on Space-filling. I often have Wireframe, or Ball-and-stick, so I can more easily go amino-acid spotting.

 

[ironduck]

Here's something about an attempt of creating a 'periodic table' of protein structure, I'm linking it for myself if nothing else

http://www.berkeley.edu/news/media/releases/2003/02/18_table.shtml

 

[ironduck]

Shall I spam this thread with pretty protein pics?
I have lots - dissertation on metalloproteins, and lots of lectures and papers!

I was hoping for actual microscopic images, but I can't seem to find any.. I was looking at articles that describe the equipment used in tracking individual proteins..

http://cellbio.med.harvard.edu/research/facilities/electron_microscopy/molecular.html
http://www.betterhumans.com/News/4896/Default.aspx

Anyway, bring on the protein pron

 

[Sophie 378]

Here we go! I'm posting these pics with an explanation after each; keep checking for updates if you're interested. Spoiler-tagged in case you're not.

Spoiler intro :

Disclaimer: this is my current understanding, and now I realise how patchy and possibly unreliable it is. I recommend Stryer's Biochemistry if anyone wants to check accuracy or scary details. Better yet, do a degree and join me in thinking you don't know very much yet.

The trouble with proteins is that they are too darn small to take pictures of directly. The best you can do is with an electron microscope - unless you want to use a horrendously expensive one, you can just about make out the biggest ones, like ATP Synthase, and ribosomes.

The mRNA is the chain of instructions, telling the little protein factories (ribosomes) which protein to make: what order to put what amino acid in. The peptide chain being made is already starting to fold - visible on right.

Anyway, with electron microscopy - the only way you can sensibly see proteins - you get that sort of grainy black-and-white image. You can have lovely coloured pics of whole cells from fluorescence microscopy, but basically if you want a Pretty Protein Pic, you've got to use crystallography, maths and a computer simulation.

Some pretty pics of actual microscopy to cheer up ironduck:

shows two fluo stains in kidney cells. The field of view is just 134 µm square!

shows a selection of cells undergoing mitosis (division): just a few bits of each cell are showing up in this case due to selective staining.

You can also see slighly freaky-looking 3D structures with scanning electron microscopes (normal ones are transmission: you are looking at electrons that have gone through the sample, not bounced off the outside). These are, iirc, the hair cells that vibrate to sound waves in your ears, allowing you to hear.
And, to round off, a picture of a plant cell: you can make out the vacuole (big pale bit in the middle), several chloroplasts (dark blobby things) and the cell wall.

Spoiler proteins, now! :

So, basically, with microscopy you can only see a blob instead of the detailed protein structure. Yet. As far as I know. Feel free to go and invent a new TEM! But for now, we use protein crystallography. For this, you get a really pure sample of your protein, and collect and concentrate it until you can crystallise it out. Then you do something complicated, and get a pattern like this - a diffraction pattern of how the beam of Xrays is bent and split as it goes through the crystal.

Yah, very helpful. Then you need ... a computer! Anyway, depending on how good your sample was, and how carefully you've done everything, and how good your machine and computer are, you can use that to work out the protein's structure. (This also works for non-proteins; don't think it's a restricted technique.) An okayish sample, computer, machine etc will give you the resolution to maybe 5 angstroms (50nm); a seriously good sample/machine/computer to maybe 1.5 angstroms. These would resolve the rough shape of the protein backbone, and the exact positioning of each side-chain respectively. some info on protein crystallogaphy. Anyway, your nice computer will then start churning out pretty piccies! Like so!

Here's Staphylococcal protein A, F@H projects 111-114.

Sudden attack of boredom, so here endeth the lesson on two last piccies. 1. Here's my favourite protein: ATP synthase!

The different letters make different subunits of the protein; different bits of it have been resolved (=structure solved) to different resolutions.
2. A random piccie that I can't even remember what it is.

Whee! Look at all those alpha helices! Must be a transmembrane protein!

Is anyone actually remotely interested in this? Or shall I stop blabbering away?

Re Ironduck's post below me: Picture 1: the folding proteins look different for two reasons: 1) they are at different stages of being made, 2) they are 3D beasties and you could well be seeing them from a different angle as they wriggle and jiggle and wander around.

Another edit! Long live the Google! Here's some nice info on x-ray crystallography (the main method of solving protein structure): http://ruppweb.dyndns.org/Xray/101index.html

 

[ironduck]

Yes, I realize that it will be monotone images, although they can be colourized in funky ways - I was just of the understanding that there are high enough resolution images that shows individual proteins reasonably well..

That's a cool picture though - especially the folding of the peptide chain, it looks like each one is folding differently though..?

 

[ranathari]

Sophie378: you're making me feel all warm and gooey inside

How strongly would you recommend Stryer's? I'm a medic so there's more than a little biochem in my course and the biomedsci graduates keep mentioning Stryer's.

 

[MjM]

Im not on the front page?

 

[Perfection]

Shall I spam this thread with pretty protein pics?
I have lots - dissertation on metalloproteins, and lots of lectures and papers! How about this one?

Spoiler :

Calcium binding to the EF-hand domain of Calmodulin, for those of you who aren't as biochemistry-geeky as me.

I'm no good with organometallic compounds. What the heck kind of bonds are between the calcium and the other stuff?

How can there be so many?

 

[ironduck]

Sophie, don't put all that good info in spoilers, I hardly realized you had updated! Just make new posts with more info and pics if you want, this is the exact thread to do so

Also, in that first pic it just looks like they're not folding in a 'set' way but more trying their way around before they end up folded properly.. that's what I meant. I understand they're at different stages and we only see them in 2D, it just looks funny - if you got more pics like this of folding and stuff I'd really like to see!

 

[ironduck]

Im not on the front page?

It just needs to be updated, we have a lot of people joining recently

 

[Strider]

I just plugged in under then name Fallen_Hero..

 

[Maniacal]

I'll pass for now. But maybe sometime in the future I'll try it. It's a good idea.

 

[ironduck]

The more the merrier!

Snoman for Strider

 

[Sophie 378]

@ ranathari: Very strongly: it's my favourite textbook. There are three biochemistry books that get recommended in the first year - Stryer, Voet and Voet, and Campbell. I've never been able to find a Campbell, and I don't get on with Voet and Voet. Stryer is really easy to read, explains things clearly, and the subjects are arranged in blocks similarly to some lectures, so it's nice. A lot of the diagrams are the sort you can sketch in exams. The glossary isn't too good, but I have the Collins Dictionary of Biology as well. It comes with a CD and a website, which is always fun. Stryer, Lippard and Berg do some wonderful collaberations, and are pretty famous for having detailed, understandable and readable books. 5th edition, 2002, is massive, green, ISBN 0716746840.

@ Perfection: evil question! They aren't metallic bonds, or quite covalent, or ionic. It's like bonding in complexes, or H-bonding. The Ca is in aquous 2+, and the polar amino acids can go like a hydration shell.

(Don't ask me why they've got s instead of delta.)
Now I get to use some pics from my dissertation! Amino acids can bind metal ions in these methods:

Copyright Lippard and Berg, Principles of Bioinorganic Chemistry 1994.

The calcium in calmodulin is binding these amino acids:

Copyright Berg, Tymoczko and Stryer, Biochemistry, 2002.
You can skip the question by saying it's coordinating rather than bonding to.

Of course, the fun thing about calmodulin (CaM) is that it has four of these binding sites, and under normal conditions they're not bound! And yet, those little calciums are absolutely aching to be with the CaM! This is because Ca2+ is used as a signal in cells; for example, "Contract muscle!" incoming results in a release of Ca2+ from the places it's locked up in. The little Calciums celebrate, and go and find an apo-calmodulin (nothing bound) to bind to. When four of them bind, they activate it! And then funkyness ensues, as the CaM starts activating other stuff. Biochemistry is fun.

 

[Azadre]

I've been running this without any knowledge my name was brought up in this thread...