I noticed (in the graphics of R@H) that an AA tryptophan looked like it was on the outside of a protein during the full atom relax mode (I'm unsure which WU).

Can someone point me to a PDB that contains a TRP that is not buried within the protein. There are probably lots, I've just never seen one before. Ta

Edit: to make more sense.

I noticed (in the graphics of R@H) that an AA tryptophan looked like it was on the outside of a protein during the full atom relax mode (I'm unsure which WU).

Interesting observation. Here's a post in Vijay Pande's blog at F@H on this subject.

http://folding.typepad.com/news/2007/11/on-turkey-and-t.html

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Interesting observation. Here's a post in Vijay Pande's blog at F@H on this subject.

http://folding.typepad.com/news/2007/11/on-turkey-and-t.html

Thanks for the link svincent.

It turns out that Trp is one of the most bulky amino acids, with its ring structure. Being a bulky ring, Trp is one of the most hydrophobic amino acids, and is thus present in protein cores.

Moreover, Trp has a very important properties in the study of protein folding. Due to its ring structure, Trp fluoresces (i.e. gives off light at a particular frequency, when hit with light of another frequency), and so Trp is a very important probe of protein folding. When a protein is unfolded, usually its Trp residues are exposed to solvent, but when folded, Trp is buried. This difference leads to differences in how it fluoresces, which can be measured very precisely.

Maybe R@H needs a tweak, assuming I'm reading that, and also viewing the structure, correctly.

The WU(s) that contained it should be in this list:

130356009
130163643
130163642
130163641
130163640
130163639
130163491
129312370
129096848
129096485

look

Hi Hugo,

This is a very good observation, and many people have looked at this in the past. On average, tryptophans tend to be buried in the center of proteins due to its hydrophobicity. However this isn't always true, there are many proteins that have tryptophans or other hydrophobic amino acids on their surface. A large amount of the time these hydrophobic amino acids are on the surface for a reason, and one such reason is that tryptophans can sometimes form binding interfaces for proteins to connect to one another.

The idea that some amino acids like to be more on the surface and others like to be more buried is behind one of the terms in our energy function. Good job figuring this out on your own!

Cheers,

James

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If a protein is a trans-membrane protein, would the section that is embedded in the membrane not be in a lipid environment and hence atractive to Tryptophan and other hydrophobic residues?

   |---> <---|
   |---> <---|
   |---> <---|
   |---> <---|
  ++ooooooooo++
   |---> <---|
   |---> <---|
   |---> <---|
   |---> <---|

I tried to draw what I meant above, the BB software limits detail. A lipid bilayer and a transmembrane protein with hydrophilic domains at each end, (+), and a hydrophobic domain, (o), in the middle.

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