Wednesday, 17 January 2007

Protein image

I am sorry, there is no real post either today. Just something to look at. This is the demo protein from PyMOL. You can see the α-helices and the β-sheets. In between you have loops, areas with no ordered secondary structure. These loops make the protein more hydrophilic because O and N can form hydrogen bonds to water when they are not bonded to each other. The active sites are mostly contained in loops because they are easier accessible. Loops are also the places where most mutations occur. Mutations in α-helices or β-sheets may mess up the structure but mutations in loops can stay because there is no structure to mess up [1].



As Mike said, the situation is not quite as easy because there is much more than helices and sheets making up a protein's structure.

7 comments:

Mike said...

but mutations in loops can stay because there is no structure to mess up.
I wouldn't bet my nuts on this assertion.

Felix said...

my biochemistry teacher said that and he seems pretty competent. i don't have a source, though.

Mike said...

Even unordered appearing structure (random coil) is ordered to some extend by specific sidechain interactions. It wouldn't affect the whole folding thermodynamics unless the mutation is in the hydrophobic core, but it has some effect - of course still depending on the context.

GCT said...

Not quite an assertion, the key word here is 'can.' But it's nice that you (mike) elaborated on how the situation can become complicated.

Matt Jenks said...

Can't oxygens and nitrogens hydrogen bond with each other through water molecules, too? Or am I just thinking of inhibitors being bound into the active site and using water to help pick up interactions with backbone carbonyls and nitrogens?

Felix said...

you can have water molecules in between. but it does not seem like you would get a defined rigid secondary structure that way.

Yggdrasil said...

A lot of the time, the functional binding site of a protein are in the loops, so these areas of the loops are often conserved. Plus, the structure is harder to mess up by mutation than a binding interface or catalytic cleft.