Add Building Blocks to Blueprint Tool for loops turning 90 or 120 degrees

Case number:845813-2005628
Topic:Game: Tools
Opened by:jeff101
Status:Open
Type:Suggestion
Opened on:Sunday, August 26, 2018 - 06:49
Last modified:Monday, June 15, 2020 - 22:47

In recent Monomer Design Puzzles, I have been making
structures composed of loops and parallel B-strands
(see https://fold.it/portal/node/2005553 for details).
These structures are somewhat cylindrical, but they
have triangular or square cross-sections. I want the
loops between the B-strands to bend about 90 degrees
for square cross-sections and about 120 degrees for
triangular cross-sections. In some puzzles with the
Ideal Loops Filter, I have found loops with these odd
angles that also pass the Ideal Loops Filter. Does this
mean that some Ideal Loops can turn 90 or 120 degrees?
Are there certain sequences and sets of phi,psi angles
that occur often in nature and are particularly stable
yet form loops that turn 90 or 120 degrees?

I think most if not all of the Blueprint Tool's Building
Blocks for loops between sheets turn 180 degrees.
Are all of these Building Blocks Ideal Loops? Would it
be possible to add some Building Blocks for loops between
sheets that turn 90 or 120 degrees instead? I think having
such Building Blocks would facilitate designing proteins
like in https://fold.it/portal/node/2005553 that also pass
the Ideal Loops Filter and form reliably in the lab.

Thanks!
Jeff

(Sun, 08/26/2018 - 06:49  |  3 comments)


jeff101's picture
User offline. Last seen 4 hours 48 min ago. Offline
Joined: 04/20/2012
Groups: Go Science

How about providing Building Blocks for loops
between sheets that turn the chain by other
angles, like (360 degrees)/n, where n is an
integer? How about angles like 72, 60, 45,
40, 36, 30, 24, 20, 15, 10, 5, and even
0 degrees?

jeff101's picture
User offline. Last seen 4 hours 48 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
The paper LIN2015: "Control over overall 
shape and size in de novo designed proteins"
by Lin, Koga, Tatsumi-Koga, Liu, Clouser, 
Montelione, and Baker at
https://www.bakerlab.org/wp-content/uploads/2016/04/PNAS-2015-Lin-E5478-85.pdf
or https://www.pnas.org/cgi/doi/10.1073/pnas.1509508112
or https://www.pnas.org/content/112/40/E5478
may be useful here. 

LIN2015's Fig.1 shows 4 "lego blocks" 
labeled A, B, E, or G taken from 
4 different parts of the Ramachandran Map 
with very specific phi,psi dihedral angles. 
These 4 "lego blocks" can pair 16 different 
ways, and each pair gives a net change theta 
in the chain direction and a net twist tau 
in the chain. Fig.1C lists the theta angles 
30, 50, 60, 70, 100, 110, 130, 140, 150, and 
170 degrees for the 16 pairs of the 4 "lego 
blocks". LIN2015 then goes on to discuss 
combinations with 3 or more of these "lego 
blocks", which seem to allow even greater 
variety in the net change in the chain 
direction and the net twist in the chain.
Are there analogs to theta and tau values
for groups of 3 or more "lego blocks"?
How about for single "lego blocks"?

I think it would be useful to have within
Foldit's Blueprint Tool not just the usual 
Ideal Loop Building Blocks but to also have 
the 4 single-residue "lego blocks" A, B, E, 
and G from LIN2015. Then we could make many 
different combinations of these 4 "lego 
blocks" and obtain reliably for each 
combination a different net change in the 
chain direction and a different net twist 
in the chain. It would also help if we could 
select groups of one or more of these "lego 
blocks" within the Blueprint Tool, and Foldit 
would list each group's overall theta and 
tau values.
jeff101's picture
User offline. Last seen 4 hours 48 min ago. Offline
Joined: 04/20/2012
Groups: Go Science

Perhaps a single-residue "lego block" from the Rama Map
region for polyproline helices would help too.

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