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(Wed, 07/13/2022 - 13:05  |  3 comments)
jeff101's picture
User offline. Last seen 18 hours 48 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
Questions about Trim/Untrim and cis peptide bonds:
Please see the links below for some questions 
about the Trim and Untrim Tools:

https://fold.it/portal/node/2013141#comment-46429
https://fold.it/portal/node/2013246

Also, could some of the pdb's we are trying to
improve in the Reconstruction Puzzles (see 
https://fold.it/portal/node/2013193 for more
details) need that improvement because the 
software used in their original ED-fitting did 
not include cis peptide bonds? I don't think 
Foldit really lends itself to including cis 
peptide bonds right now, but maybe it should. 

https://fold.it/portal/node/2006311
https://fold.it/portal/node/2006311#comment-46377

https://fold.it/portal/node/995580#comment-24061 
says that cis peptide bonds are quite rare 
compared to trans ones (the trans:cis ratio is
usually about 1000:1, but near prolines it can 
be 3:1). This means that near prolines 75% of
peptide bonds are trans while 25% are cis. 25%
is a pretty big population to ignore. Why not 
make it easier for us to consider cis peptide 
bonds in Foldit puzzles? It could lead to better
results.
jeff101's picture
User offline. Last seen 18 hours 48 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
More about cis peptide bonds:

https://fold.it/portal/node/995580#comment-24061 says:
---------------------------------------------------
We warn you about cis because, as it turns out, cis 
bonds are very rare in the natural proteins that we 
have observed (1000 to 1 in favor of trans).

There's a small exception to this in the case of 
prolines - when a proline is the top residue in a 
peptide bond, the ratio is about 3 to 1 in favor of 
trans, and consequently we do not create a warning 
about this.
---------------------------------------------------
What does "proline is the top residue in a peptide
bond" mean? Does this mean that of the 2 adjacent 
segments in a peptide bond, the lower #'d one is 
the bottom residue while the higher #'d one is the 
top residue? Are x-pro cis peptide bonds more 
common than pro-x ones (here I list the lower #'d
segments first, and x is any amino acid)? Do
certain amino acids in the x positions make cis
peptide bonds more likely?

jeff101's picture
User offline. Last seen 18 hours 48 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
Many puzzles should have some cis peptide bonds:
I made a list of some recent puzzles, 
how many segments each one had, and 
how many prolines each one had. Then
I divided the # of prolines in each 
by 4 to estimate how many cis peptide 
bonds each should have:

puzzle #segs #prolines #cis  
2167    129    2        0.5   
2158    588   34        8.5   
2155b   588   34        8.5   
2142/3  124    2        0.5   
2137    143    5        1.25  
2128     69    4        1     
2125     95    3        0.75  
2120    128    4        1     
2116     54    5        1.25  
2114    215   11        2.75  
2110     80    6        1.5   
2108    127    4        1     
2100    124    2        0.5   

In this chart, most puzzles should 
have at least one cis peptide bond. 
Also, puzzles like 2167, 2142/3,
and 2100 each have a 50% chance of 
having a cis peptide bond while 
puzzle 2125 has a 75% chance of 
having a cis peptide bond. 

The above makes me think that many 
of our solutions could be improved 
if it was easier for us to include 
cis peptide bonds in them.
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