390: Unsolved monkey virus protein

Closed since about 15 years ago

Summary

• Created: December 17, 2010
• Expires: January 07, 2011 at 23:00 UTC
• Max points: 100

Description

The Folded monomer of protease from Mason-Pfizer monkey virus is currently unsolved by protein crystallographers. It was solved in 2003 by NMR, but there is a great deal of variation in those models and they don't fit perfectly with the X-ray crystallographic data. We are giving you these 10 NMR models to work on for 3 weeks, so that you have plenty of time to try out each model. We hope you can help us solve this structure! Please see the puzzle comments for more info.

Top groups

• 1. Void Crushers 100 pts. 10,550
• 2. Anthropic Dreams 89 pts. 10,426
• 3. Contenders 78 pts. 10,412
• 4. Russian team 68 pts. 10,312
• 5. Deleted group pts. 10,275
• 6. Richard Dawkins Foundation 52 pts. 10,268
• 7. Deleted group pts. 10,226
• 8. Go Science 39 pts. 10,221
• 9. Mojo Risin' 33 pts. 10,201
• 10. Deleted group pts. 10,183

Top evolvers

• 1. TheGUmmer 100 pts. 10,550
• 2. Dolichwier 91 pts. 10,547
• 3. HillObserver 83 pts. 10,544
• 4. Madde 75 pts. 10,500
• 5. bzipitidoo 68 pts. 10,500
• 6. spmm 61 pts. 10,500
• 7. firejuggler 55 pts. 10,429
• 8. Steve001 49 pts. 10,426
• 9. anthunk 44 pts. 10,426
• 10. Stardancer 39 pts. 10,426

Comments

[gramps]

I didn't mean to judge the protein, it's the desperate recipe code to indirectly find which model is which in the random resets that only a parent could love.

[GaryForbis]

gstart={
{0, -2166.368},
{1, -4012.627},
{2, -2844.162},
{3, -5740.560},
{4, -470.150},
{5, -3847.070},
{6, -2499.297},
{8, -3134.391},
{9, -4259.601}
}
gss={}
for j=1,get_segment_count() do
gss[j]={[L]=0,[H]=0,[E]=0,[M]=0}
end
local startsFound=0
repeat
reset_puzzle()
local i = 0
repeat
i=i+1
until (gstart[i]%1)==(get_score(true)%1)
if gstart[i][3] == nil then
startsFound=startsFound+1
gstart[i][3]='found'
for j=1,get_segment_count() do
ss=get_ss(j)
gss[j][ss]=gss[j][ss] + 1
end
until startsFound=10
– Now if my code is correct
– you have a vote on secondary structure.
– you don't need to have the scores preloaded
– but what the heck. Do you want a vote on
– segment distances as well? You might be
– able to band to those distances.

[prot-bustr]

You tell us the NMR data does not fit perfectly with the X-ray data, and give us the NMR templates and graph, but no information about the X-ray data. I believe, depending on the resolution in Angstroms of the X-ray data, it is possible to determine secondary structure, but that loops tend to be undetermined. Can you tell us the resolution of the X-ray data and what secondary structure information was extracted from it, or any other information you can give us to help fold this mysterious protein?

[beta_helix]

In general, secondary structure composition can't be determined from unphased crystal data. There are some exceptions with all-helical proteins (http://www.nature.com/nmeth/journal/v6/n9/full/nmeth.1365.html)

What we are hoping will work with Foldit is what was done previously using Rosetta: (http://www.nature.com/nature/journal/v450/n7167/abs/nature06249.html).

Most likely, the topology & secondary structure of the protein is pretty similar in the X-ray structure as in the NMR structure. Molecular replacement generally fails above 2A RMS so the target may not be very far from the NMR ensemble. That said, there may be some reorganization due to crystal contacts … but sadly we really don't know.

[apple.muncy]

Links requiring monetary payment are not helpful to me.
What might be helpful would be a link to X-ray structure.

[beta_helix]

Sorry about that, you can download the pdf from the Baker Lab webpage:

http://depts.washington.edu/bakerpg/drupal/node/115

You'll find the Foldit nature paper there as well, if you didn't get a chance to read it:

http://depts.washington.edu/bakerpg/drupal/node/16

If you want to look at some X-ray structures that might be familiar to you, you can go to the CASP9 target page:
http://predictioncenter.org/casp9/targetlist.cgi

and click on the blue PDB code on the right for any of the targets that have been solved using X-ray crystallography (those are denoted by the 4th column on the CASP page saying "X-RAY")