Task 3 (MSUD)
Contents
Secondary structure
Result
Secondary structure prediction and assignment
The results for ReProf and PsiPred predictions and the DSSP assignments are in the following folders:
/mnt/home/student/schillerl/MasterPractical/task3/reprof/
/mnt/home/student/schillerl/MasterPractical/task3/psipred/
/mnt/home/student/schillerl/MasterPractical/task3/dssp/
For P10775, ReProf was run with the protein sequence fasta file and position specific scoring matrices (PSSM) derived from big_80 and SwissProt (see /mnt/home/student/schillerl/MasterPractical/task3/pssm/) as input. The following tables show the comparison of the prediction results to the secondary structure assignment of DSSP. The f-measure is the harmonic mean of recall and precision, it gives a good indication for the quality of a classificator.
| secondary structure element | recall | precision | f-measure |
|---|---|---|---|
| H | 0.719 | 0.585 | 0.645 |
| E | 0.211 | 0.500 | 0.296 |
| L | 0.616 | 0.654 | 0.635 |
| secondary structure element | recall | precision | f-measure |
|---|---|---|---|
| H | 0.944 | 0.889 | 0.916 |
| E | 0.649 | 0.685 | 0.667 |
| L | 0.826 | 0.866 | 0.846 |
| secondary structure element | recall | precision | f-measure |
|---|---|---|---|
| H | 0.923 | 0.914 | 0.919 |
| E | 0.807 | 0.523 | 0.634 |
| L | 0.719 | 0.859 | 0.782 |
Predictions using a PSSM instead of a simple sequence have a considerably better quality. All methods predict helices better than loops and these better than beta sheets. The results of the run with the big_80 PSMM are better for E and L and only slightly worse than those using the SwissProt PSMM.
The percentages of correctly identified secondary structure (H, E or L) for the three methods are 61 %, 86 % and 82 %. So for the remaining sequences, the method with the best performance (usage of PSSM derived from big_80 as input for ReProf) is used.
Information from UniProt and PDB
A summary of interesting features for the proteins:
P12694, 2BFD:
- name: 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial
- EC: 1.2.4.4
- gene: BCKDHA
- organism: Homo sapiens (Human)
- sequence length: 445 AA
- subunit structure: heterotetramer of alpha and beta chains
- subcellular location: mitochondrion matrix
- secondary structure: 42% helical, 10% beta sheet
- 3D similarity: pyruvate dehydrogenase E1
- ligands: chloride ion, glycerol, potassium ion, manganese (II) ion, (4S)-2-methyl-2,4-pentanediol, thiamin diphosphate
P10775, 2BNH:
- name: ribonuclease inhibitor
- gene: RNH1
- organism: Sus scrofa (Pig)
- sequence length: 456 AA
- subcellular location. cytoplasm
- sequence similarities: contains 15 LRR (leucine-rich) repeats
- secondary structure: alternating helix and strand, 42% helical, 12% beta sheet
Q08209, 1AUI:
- name: serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
- EC: 3.1.3.16
- gene: PPP3CA
- organism: Homo sapiens (Human)
- sequence length: 521 AA
- subunit structure: heterodimer of alpha and beta chain (human calcineurin heterodimer)
- subcellular location: nucleus
- secondary structure: 27% helical, 11% beta sheet
- ligands: calcium ion, Fe (III) ion, zinc ion
Q9X0E6, 1KR4:
- name: divalent-cation tolerance protein CutA
- gene: cutA
- organism: Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
- sequence length: 101 AA
- subunit structure: homotrimer
- subcellular location: cytoplasm
- secondary structure: great fraction of strands, 29% helical, 35% beta sheet
Discussion
The prediction of secondary structure is much better if a PSSM is used instead of the sequence. The reason is that a PSSM describes the requirements for each position better than the amino acid sequence, because it uses evolutionary information. So it identifies for each position alternatives for the residues in the primary sequence, that don't alter the overall structure of the protein. The difference between the usage of big_80 or SwissProt for generating the PSSM is not that obvious, but we decided to take big_80 because it showed a slightly better performance in our test with the example protein P10775.
