Prediction of transmembrane alpha-helices and signal peptides LAMP1 HUMAN

TMHMM

First, we used TMHMM to predict the transmembrane helices of this protein.

Figure 1: Prediction of TMHMM for the transmembrane helices of LAMP1_HUMAN

start position	end position	location
1	10	inside
11	33	TM Helix
34	383	outside
384	406	TM Helix
407	417	inside

TMHMM predicts two transmembrane helices, which are divided by a very long loop which is located at the extracellular space. This prediction result can be seen on Figure 1.

Comparison with the real structure of the protein:

Figure 2: Comparison between real occurring transmembrane helices and the TMHMM result.

The prediction of TMHMM is quite good (compare Figure 2). Only at the beginning of the protein TMHMM predicts one wrong transmembrane helix (which is a signal peptide in real), but the rest of the prediction is correct.

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Phobius and PolyPhobius

Next, we used Phobius and PolyPhobius to predict the transmembrane helices and also the signal peptide.

Figure 3: Prediction of Phobius for the transmembrane helices and signal peptides of LAMP1_HUMAN

Figure 4: Prediction of PolyPhobius for the transmembrane helices and signal peptides of LAMP1_HUMAN

Phobius			PolyPhobius
start position	end position	prediction	start position	end position	prediction
Signal peptide prediction
1	10	N-Region	1	9	N-Region
11	22	H-Region	10	22	H-Region
23	28	C-Region	23	28	C-Region
Summary signal peptide
1	28	secretory signal peptide	1	28	secretory signal peptide
Transmembrane helices prediction
29	381	outside	29	381	outside
382	405	TM helix	382	405	TM helix
406	417	outside	406	417	outside

The results of both methods are quite equal, which can be seen on Figure 3 and Figure 4.

Comparison with the real structure of the protein:

Figure 5: Comparison between the prediction of Phobius and the real protein

Figure 6: Comparison between the prediction of PolyPhobius and the real protein

Both results of the prediction methods are equal and furthermore, the are equal to the real protein (compare Figure 5 and Figure 6).

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OCTOPUS and SPOCTOPUS

We also used OCTOPUS and SPOCTOPUS to predict the transmembrane helices and the signal peptide.

Figure 7: Prediction of OCTOPUS for the transmembrane helices of LAMP1_HUMAN

Figure 8: Prediction of SPOCTOPUS for the transmembrane helices of LAMP1_HUMAN

OCTOPUS			SPOCTOPUS
start position	end position	prediction	start position	end position	prediction
1	10	inside	1	11	N-terminal of a signal peptide
11	31	TM helix	12	29	signal peptide
32	383	outside	30	383	outside
384	404	TM helix	384	404	TM helix
405	417	outside	405	417	outside

As before by HEXA_HUMAN and RET4_HUMAN, OCTOPUS predicts a transmembrane helix, (Figure 7) whereas SPOCTOPUS predicts the signal peptide (Figure 8).

Comparison with the real structure of the protein:

Figure 9: Comparison between the prediction of OCTOPUS and the real protein

Figure 10: Comparison between the prediction of SPOCTOPUS and the real protein

Except of the beginning of the protein, the prediction of both methods is very similar and also very similar to the real occurring structure (compare Figure 9 and Figure 10).

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TargetP

All of our proteins are proteins from human and archaea, so therefore we only use the non-plant option of TargetP.

Location	Probability
mitochondrial targeting SP	0.043
secretory pathway SP	0.953
other	0.017

The prediction of the secretory pathway signal peptide is wrong, because LAMP1_HUMAN is a transmembrane protein.

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SignalP

For our analysis we used the Hidden Markov Model based and also the neuronal network based prediction.
The prediction with the Hidden Markov Model used three different scores. The S-score which is the score for the signal peptide, the C-score which is the score for the cleavage site and the Y-score which is a combination of the S-score and the C-score and is used to predict the cleavage site, because the Y-score is more precise than the C-score.



Result of the neuronal network

Signal peptide		Cleavage site
start position	end position	start position	end position	prediction
1	28	28	29	signal peptide

Result of the hidden markov model

prediction	signal peptide probability	signal anchor probability	cleavage site start	cleavage site end
signal peptide	1.000	0.000	28	29

Figure 11: Result of the SignalP method based on the neuronal network for LAMP1_HUMAN

Figure 12: Result of the SignalP method based on the Hidden Markov Model for LAMP1_HUMAN

Both methods predict a signal peptide for LAMP1_HUMAN, which is not correct, because LAMP1_HUMAN is a transmembrane protein (compare Figure 11 and Figure 12).

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