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Transmembrane proteins

OPM database

For this task a channelrhodopsin was chosen (PDB ID: 3UG9), since channelrhodopsins are cool and are used in optogenetics by Ed Boyden at MIT (the most attentive readers might notice that this might be Michigan Institute of Technology, but no, you are wrong, go read your frigging books).
Below a table describing some of its properties is presented:

Hydrophobic thickness	31.0±1.2Å
Transmembrane α-helices (coordinates)	1(89-109), 2(121-138), 3(157-175), 4(188-207), 5(214-232), 6(252-271), 7(281-304) (two indentical sets of 7 transmembrane α-helices)
Average number of amino acid residues in transmembrane α-helices	20.14
Membrane type	Eukaryotic plasma membrane

Here the red (upper) side of the membrane represents the extracellular side (p-side) and the blue (lower) side represents the cytoplasmic one (the n-side).

The protein of choice containing a β-barrel was an opacity rhodopsin (PDB ID: 2MAF). Honestly, I chose it because it has a cool name. Below you can find some of its properties:

Hydrophobic thickness	23.8±1.0Å
Transmembrane segments (coordinates)	1(8-15), 2(55-62), 3(65-72), 4(117-124), 5(133-141), 6(191-201), 7(208-215), 8(231-236)
Average number of amino acid residues in transmembrane segments	8.375
Membrane type	Outer membrane of gram-negative bacteria

Here the red (upper) side of the membrane represents the extracellular side, and the blue (lower) side represents the periplasmic one. The terms "p-side" and "n-side" do not apply here because the bacterial outer membrane has no electric potential across itself.

Transmembrane segment prediction

Two web-services were used for prediction based on FASTA sequence: TMHMM and Phobius. Both predictors were run for the channelrhodopsin from the previous task.
Results from TMHMM:

# 3UG9:A|PDBID|CHAIN|SEQUENCE Length: 333
# 3UG9:A|PDBID|CHAIN|SEQUENCE Number of predicted TMHs:  5
# 3UG9:A|PDBID|CHAIN|SEQUENCE Exp number of AAs in TMHs: 96.86798
# 3UG9:A|PDBID|CHAIN|SEQUENCE Exp number, first 60 AAs:  0.24368
# 3UG9:A|PDBID|CHAIN|SEQUENCE Total prob of N-in:        0.46389
3UG9:A|PDBID|CHAIN|SEQUENCE	TMHMM2.0	inside	     1    65
3UG9:A|PDBID|CHAIN|SEQUENCE	TMHMM2.0	TMhelix	    66    88
3UG9:A|PDBID|CHAIN|SEQUENCE	TMHMM2.0	outside	    89   131
3UG9:A|PDBID|CHAIN|SEQUENCE	TMHMM2.0	TMhelix	   132   154
3UG9:A|PDBID|CHAIN|SEQUENCE	TMHMM2.0	inside	   155   166
3UG9:A|PDBID|CHAIN|SEQUENCE	TMHMM2.0	TMhelix	   167   184
3UG9:A|PDBID|CHAIN|SEQUENCE	TMHMM2.0	outside	   185   187
3UG9:A|PDBID|CHAIN|SEQUENCE	TMHMM2.0	TMhelix	   188   207
3UG9:A|PDBID|CHAIN|SEQUENCE	TMHMM2.0	inside	   208   226
3UG9:A|PDBID|CHAIN|SEQUENCE	TMHMM2.0	TMhelix	   227   249
3UG9:A|PDBID|CHAIN|SEQUENCE	TMHMM2.0	outside	   250   333

TMHMM absolutely accurately predicted helix No. 4, but failed to predict the coordinates of the others. After some careful inspection of the results, I noticed that it actually correctly predicted 5 out of 7 helices, but their coordinates are shifted towards the N-end by approximately 23 amino acids relative to the structure from the OPM database. The helices that it failed to predict are No. 2 and No. 7. The shift could be due to the fact that although there are 333 amino acids in the FASTA sequence, there are actually around 360 amino acids in the 3D structure on the PDB website. The ends are largely unstructured, so their position in space is by far not fixed, and they are a difficult target for the NMR machine. As a probable consequence, they were not shown in the FASTA sequence, which caused the shift in the coordinates.
Results from TMHMM:

ID   3UG9:A|PDBID|CHAIN|SEQUENCE
FT   TOPO_DOM      1     65       CYTOPLASMIC.
FT   TRANSMEM     66     88       
FT   TOPO_DOM     89    133       NON CYTOPLASMIC.
FT   TRANSMEM    134    154       
FT   TOPO_DOM    155    165       CYTOPLASMIC.
FT   TRANSMEM    166    185       
FT   TOPO_DOM    186    190       NON CYTOPLASMIC.
FT   TRANSMEM    191    209       
FT   TOPO_DOM    210    229       CYTOPLASMIC.
FT   TRANSMEM    230    249       
FT   TOPO_DOM    250    333       NON CYTOPLASMIC.
//

The results are almost the same as in the previous case, but Phobius did a better job at trying to find helices No. 2 and 7 (although didn't quite found them either).
Interestingly, both websites failed to predict anything for the β-barrel protein, which can be either because they are taylored to be used with α-helices only, or because the 2MAF protein is located in the outer membrane of gram-negative bacteria, which is not polarized. It is possible that both factors affected the results.

TCDB

I beg your pardon, but since my website is in English, I decided to spare myself the burden of translating the TC-code into Russian. If needed, I will do it verbally, in person.
Of the two proteins from this practical, only the channelrhodopsin turned out to be in TCDB, and its TCID is 3.E.1.7.2. It is broken down below:
3 - primary active transporters
3.E - light absorption-driven transporters
3.E.1 - ion-translocating microbial rhodopsin (MR) family
The last two digits correspond to the subfamily and to the specific protein, respectively.