Question: Phi/Psi torsion angles replication
0
gravatar for ac.research
9 months ago by
ac.research10
ac.research10 wrote:

So I am trying to fold a primary structure using only the torsion angles from a natural protein's crystal structure. But I found this strange phenomena, which I cannot understand nor explain. My protocol is as follow:

  1. I am taking a normal protein (figure 1)

  2. Then I take the phi and psi torsion angles of each residue

  3. Then I assemble a totally new flat amino acid chain, a primary structure, with the same original amino acid sequence (figure 2)

  4. Then I change each residue's torsion angles to the torsion angles of the original protein from figure 1. I do this sequentially: residue 1, then residue 2, then residue 3 etc...

  5. Theoretically I should be getting the same original structure back right? but I instead get a messed up structure (figure 3) even though all the torsion angles are EXACTLY the same (check the file Angles.txt that shows separate measurements of each structure giving back exactly the same torsion angles).

So the question is why do I get this messed up structure, even though I use EXACTLY the same torsion angles (up to 9 decimal places - though I am only showing 3 decimal places for clarity).

Anyone can help me understand the issue? Is there something else I should include in my build other than torsion angles?

Figure 1 link

Figure 2 link

Figure 3 link

             PHI Angles                  PSI Angles

          BEFORE     AFTER        BEFORE     AFTER

res 1 :       0.0     =  0.0          158.944 =  158.944
res 2 :      -133.036 = -133.036          131.63  =  131.63
res 3 :      -116.506 = -116.506          121.937 =  121.937
res 4 :      -104.034 = -104.034          117.857 =  117.857
res 5 :      -91.88   = -91.88        110.368 =  110.368
res 6 :      -117.482 = -117.482          26.777  =  26.777
res 7 :      -68.934  = -68.934           137.678 =  137.678
res 8 :       87.321  =  87.321          -12.42   = -12.42
res 9 :      -90.092  = -90.092           139.446 =  139.446
res 10 :     -96.65   = -96.65        147.198 =  147.198
res 11 :     -54.743  = -54.743           149.75  =  149.75
res 12 :     -90.664  = -90.664           25.177  =  25.177
res 13 :     -55.218  = -55.218          -51.992  = -51.992
res 14 :     -56.195  = -56.195          -43.852  = -43.852
res 15 :     -64.895  = -64.895          -38.532  = -38.532
res 16 :     -67.613  = -67.613          -45.091  = -45.091
res 17 :     -61.604  = -61.604          -41.244  = -41.244
res 18 :     -65.734  = -65.734          -43.604  = -43.604
res 19 :     -65.9    = -65.9        -39.484  = -39.484
res 20 :     -61.631  = -61.631          -44.855  = -44.855
res 21 :     -63.75   = -63.75       -37.836  = -37.836
res 22 :     -70.554  = -70.554          -43.277  = -43.277
res 23 :     -64.617  = -64.617          -19.429  = -19.429
res 24 :     -87.124  = -87.124          -13.039  = -13.039
res 25 :     -72.555  = -72.555          -6.894   = -6.894
res 26 :      58.615  =  58.615          -169.69  = -169.69
res 27 :     -63.408  = -63.408          -21.517  = -21.517
res 28 :     -72.631  = -72.631          -17.643  = -17.643
res 29 :      66.031  =  66.031          -175.003 = -175.003
res 30 :      158.845 =  158.845         -159.158 = -159.158
res 31 :     -129.889 = -129.889          132.223 =  132.223
res 32 :     -123.581 = -123.581          118.737 =  118.737
res 33 :     -106.945 = -106.945          144.557 =  144.557
res 34 :     -129.689 = -129.689          129.539 =  129.539
res 35 :     -93.157  = -93.157           119.117 =  119.117
res 36 :     -127.144 = -127.144          158.788 =  158.788
res 37 :     -111.018 = -111.018          24.26   =  24.26
res 38 :     -161.233 = -161.233          149.981 =  149.981
res 39 :     -63.585  = -63.585          -31.181  = -31.181
res 40 :     -61.861  = -61.861          -43.522  = -43.522
res 41 :     -64.088  = -64.088          -41.82   = -41.82
res 42 :     -58.27   = -58.27       -46.947  = -46.947
res 43 :     -59.426  = -59.426          -44.655  = -44.655
res 44 :     -62.459  = -62.459          -42.601  = -42.601
res 45 :     -61.049  = -61.049          -41.605  = -41.605
res 46 :     -70.042  = -70.042          -37.405  = -37.405
res 47 :     -64.006  = -64.006          -38.693  = -38.693
res 48 :     -67.632  = -67.632          -40.142  = -40.142
res 49 :     -65.242  = -65.242          -46.877  = -46.877
res 50 :     -61.888  = -61.888          -49.239  = -49.239
res 51 :     -43.502  = -43.502          -50.091  = -50.091
res 52 :     -76.99   = -76.99       -5.108   = -5.108
res 53 :      79.836  =  79.836           34.694  =  34.694
res 54 :     -113.987 = -113.987          150.501 =  150.501
res 55 :     -83.139  = -83.139           150.361 =  150.361
res 56 :     -153.067 = -153.067          160.032 =  160.032
res 57 :     -147.001 = -147.001          168.855 =  168.855
res 58 :     -147.48  = -147.48           151.234 =  151.234
res 59 :     -139.45  = -139.45           131.529 =  131.529
res 60 :     -90.944  = -90.944           106.94  =  106.94
res 61 :     -90.123  = -90.123          -167.692 = -167.692
res 62 :     -76.915  = -76.915           144.776 =  144.776
res 63 :      70.893  =  70.893           32.437  =  32.437
res 64 :      73.321  =  73.321           3.164   =  3.164
res 65 :     -73.523  = -73.523           126.932 =  126.932
res 66 :     -104.475 = -104.475          125.434 =  125.434
res 67 :     -106.295 = -106.295          121.894 =  121.894
res 68 :     -110.618 = -110.618          122.924 =  122.924
res 69 :     -108.151 = -108.151          125.893 =  125.893
res 70 :     -118.674 = -118.674          130.343 =  130.343
res 71 :     -113.385 = -113.385          132.074 =  132.074
res 72 :     -109.435 = -109.435         -34.442  = -34.442
res 73 :      178.142 =  178.142         -3.115   = -3.115
res 74 :     -50.684  = -50.684           0.0     =  0.0
protein sequence math • 292 views
ADD COMMENTlink modified 8 months ago by Biostar ♦♦ 20 • written 9 months ago by ac.research10

How are you doing about omega? https://en.wikipedia.org/wiki/Dihedral_angle#Proteins

ADD REPLYlink written 9 months ago by fishgolden280

hmmm, good idea.

I added the function to include also the Omega angles which helped "a bit" check out the structure: new protein. But it is still corrupted, compare it with the original structure. what other variables would I need to include?

ADD REPLYlink written 9 months ago by ac.research10

:thinking_face_emoticon: I have no idea then.

Try superposition (select N-terminal 5 or 10 residues & A->align in PyMol) and check where discrepancy starts (ribbon mode or line mode will work).

ADD REPLYlink written 8 months ago by fishgolden280
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