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:
I am taking a normal protein (figure 1)
Then I take the phi and psi torsion angles of each residue
Then I assemble a totally new flat amino acid chain, a primary structure, with the same original amino acid sequence (figure 2)
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...
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?
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
How are you doing about omega? https://en.wikipedia.org/wiki/Dihedral_angle#Proteins
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?
: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).