Secondary Structure Prediction

PSIPRED

PSIPRED delivers many different kind of output file formats. The pictures show the pdf-output which shows the secondary structure in a graphical kind. It predicts 14 alpha-helices and 15 beta-sheets. The rest are predicted coils.

First part of the PSIPRED output

Second part of the PSIPRED output

Legend for the PSIPRED output

Jpred3

The following alignemt shows the output of Jpred3. The secondary structure elements is marked by ourself. It predicted 14 alpha-helices and 15 beta-sheets.

Jpred output with colored secondary structure elements

DSSP

We started DSSP on the webserver with the PDBB-id. Therefore, we get the secondary structure assignment for the whole protein and not only for the alpha-subunit. The following sequence with the according secondary structure is the output for our sequence (we extracted it from the whole). It assigned 16 alpha-helices and no beta-sheet.

                    10        20        30        40        50
                     |         |         |         |         |
   1 -   52 LWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSVLDEAFQRYRDLLFG
   1 -   52   T  TT    T      TTT      TT TT TT HHHHHHHHHHHHHHH
   1 -   52    * ** *                     *
   1 -   52    A  AAAA AAA   A AA A A  AA   AAA        AA  A   A

                  60        70        80        90       100       110
                   |         |         |         |         |         |
  53 -  112 TLEKNVLVVSVVTPGCNQLPTLESVENYTLTINDDQCLLLSETVWGALRGLETFSQLVWK
  53 -  112       SSSSTT   TTT   TT    SSSSSTTT SSSSSTTHHHHHHHHHHHHHHSSS
  53 -  112           * ***
  53 -  112 AA AA A   AAAA  AAA A A A   A    AAA A A A                AA
                 120       130       140       150       160       170
                   |         |         |         |         |         |
 113 -  172 SAEGTFFINKTEIEDFPRFPHRGLLLDTSRHYLPLSSILDTLDVMAYNKLNVFHWHLVDD
 113 -  172  TT  SSS  SSSSS  T TSSSSSSSTTTT   HHHHHHHHHHHHHTT  SSSSS   T
 113 -  172
 113 -  172  AA      A A A A A A             AAA  AA                   A
                 180       190       200       210       220       230
                   |         |         |         |         |         |
 173 -  232 PSFPYESFTFPELMRKGSYNPVTHIYTAQDVKEVIEYARLRGIRVLAEFDTPGHTLSWGP
 173 -  232 T      TT THHHHHHTT TTTT   HHHHHHHHHHHHHTT SSSSS   TTT TTTTT
 173 -  232
 173 -  232 A      AAA A  AA  A A A    A   AA  AA                  A   A
                 240       250       260       270       280       290
                   |         |         |         |         |         |
 233 -  292 GIPGLLTPCYSGSEPSGTFGPVNPSLNNTYEFMSTFFLEVSSVFPDFYLHLGGDEVDFTC
 233 -  292 TTTT SSSSSTTTTSSSSSSSS TT HHHHHHHHHHHHHHHHH  TTSSS    T  THH
 233 -  292
 233 -  292   AA   A AAAAAAAAAA      AAA  A   A  A   AA A A       A AAA
                 300       310       320       330       340       350
                   |         |         |         |         |         |
 293 -  352 WKSNPEIQDFMRKKGFGEDFKQLESFYIQTLLDIVSSYGKGYVVWQEVFDNKVKIQPDTI
 293 -  352 HHH HHHHHHHHHHT TT THHHHHHHHHHHHHHHHTTT SSSSSHHHHHTT    TT S
 293 -  352         *  ****  *
 293 -  352  AA AA AAA AAAAAAAA AA   A  AA  A  AAAA         A  A A AAA
                 360       370       380       390       400       410
                   |         |         |         |         |         |
 353 -  412 IQVWREDIPVNYMKELELVTKAGFRALLSAPWYLNRISYGPDWKDFYVVEPLAFEGTPEQ
 353 -  412 SSS  TTTTT HHHHHHHHHHTT SSSS TT  TTT  TT THHHHHH  TT TT  HHH
 353 -  412       *
 353 -  412    AAAAAAAAAAA   A  AAA A          A AA A  AA  A   AA A AAA
                 420       430       440       450       460       470
                   |         |         |         |         |         |
 413 -  472 KALVIGGEACMWGEYVDNTNLVPRLWPRAGAVAERLWSNKLTSDLTFAYERLSHFRCELL
 413 -  472 HTTSSSSSSSS TTT TTTTHHHHHTTHHHHHHHHHHT TT   HHHHHHHHHHHHHHHH
 413 -  472                                       * **
 413 -  472 AAA              A   A                AAA AAAAA AA   A  AA
                 480       490
                   |         |
 473 -  492 RRGVQAQPLNVGFCEQEFEQ
 473 -  492 HTT     TTT   TT
 473 -  492
 473 -  492 A A A    AA A AA  AA

Discussion

To determine how succesful our secondary structure prediction with PSIPRED and Jpred are, we had to compare it with the secondary structure assignment of DSSP. First of all, DSSP assigns no beta-sheets whereas both prediction methods predict some beta-sheets. Therefore the main comparison in this case refers to the alpha-helices.

For PSIPRED the prediction of the alpha-helices was good. In the most cases the alpha-helices of DSSP und PSIPRED corrspond. There is only one helix which is predicted by PSIPRED which is not assigned as helix by DSSP. Furthermore there are three helices which are allocated as helices by DSSP which were not predicted by PSIPRED. The most of these helices which were presented only in one output are very small ones.

For Jpred3 the prediction of the alpha-helices was sufficiently good. In the most cases it agrees with DSSP. There are only two helices which are predicted by Jpred and which are not also assigned by DSSP. In contrary there are three small helics which are allocated to an alpha-helices by DSSP but are not predicted by Jpred. There is another special case where DSSP assignes two helices which are separated by a turn and Jpred predicts there only one big helix.

All in all, the prediction of the helices is probably good because they correspond mostly with the assignmet of DSSP. The only negative aspect is, that both prediction methods predict a lot of sheets which were not assigned by DSSP at all.