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Manual

Command Line

Open a command line window and go to the directory where you have put the executable.

Call tango as in the following example (use spaces, not tabs):

Tango P05100 ct="N" nt="N" ph="7.4" te="303" io="0.05" seq="DNEWGYIAYHVSQDP"
  • ct: Protection at the C-terminus: can be N for no or Y for amidated
  • nt: Protection at the N-terminus: can be N for no, A for acetylated or S for succinilated.
  • ph: pH
  • te: Temperature in Kelvin
  • io: Ionic strength

Input File

To be run with an input file, Tango needs a text file that can have any name the user wants as long as it has less than 25 characters. Inside the file the user can place as many sequences to be analyzed as long as the number is less than 1000 sequences.
The format of the sequences to be run is as follows:

Name Cter Nter pH Temp Ionic Sequence
  • Name = name of the sequence (less than 25 characters)
  • Cter = status of the C-terminus of the peptide (amidated Y, free N)
  • Nter = status of the N-terminus of the peptide (acetylated A, succinilated S and free N)
  • pH = pH
  • Temp = temperature in Kelvin
  • Ionic = ionic strength in M
  • sequence = sequence of the peptide in one letter code.

Example

Sup1 N N 7 298 0.1 AMAPVLYLQDKSS
sup2 N N 7 298 0.1 AMASVLYLQDKSS
sup3 N N 7 298 0.1 AMAPVLYLQSKSS
sup4 N N 7 298 0.1 AMASVLYLQSKSS
sup5 N N 7 298 0.1 AMAPVLYLQPKSS
sup6 N N 7 298 0.1 AMARVLYLQDKSS
sup7 N N 7 298 0.1 AMAPVLYLQRKSS

The programme window first asks if the user wants to have the aggregation content by residue.
If the user types Y, then he/she will get a file for each sequence in the text file.

Tango output

The output of TANGO is in text format with the extension .out. You will get two classes of outputs. One with the name of the file you run that will contain the average aggregation per residue for every sequence you had in your file. The other will be a series of files with the names of the sequences you run that will contain the prediction at the residue level.

Those files will have the following columns:

  • Sequence Number
  • Amino acid in one-letter code
  • Percentage of -strand conformation
  • Percentage of -turn conformation
  • Percentage of -helical conformation
  • Percentage of Aggregation
  • Percentage of Helical Aggregation.

Please be aware that the latest is calculated independently of the first four and therefore you could get a number higher than 1 if you sum the 5 columns.

Example of sequence output:

01, M, 0.14, 0.08, 0.00, 0.00, 0.00
02, R, 0.24, 0.11, 0.00, 0.00, 0.00
03, S, 0.44, 0.11, 0.00, 0.00, 0.00
04, L, 0.45, 0.27, 0.00, 0.87, 0.00
05, E, 0.36, 0.19, 0.00, 0.87, 0.00
06, T, 1.14, 0.16, 0.00, 1.40, 0.00
07, F, 1.08, 0.16, 0.00, 1.61, 0.00
08, V, 1.08, 0.62, 0.00, 1.61, 0.00
09, G, 1.03, 0.66, 0.00, 0.74, 0.00
10, D, 0.18, 0.67, 0.00, 0.74, 0.00
11, Q, 0.14, 0.67, 0.00, 0.74, 0.00
12, V, 0.39, 0.05, 0.00, 3.80, 0.00
13, L, 0.64, 0.00, 0.00, 3.80, 0.00
14, E, 0.73, 0.00, 0.00, 3.31, 0.00
15, I, 0.75, 0.00, 0.00, 3.31, 0.00
16, V, 0.48, 0.00, 0.00, 3.31, 0.00
17, P, 0.23, 0.22, 0.00, 3.04, 0.00
18, S, 0.12, 0.24, 0.00, 0.62, 0.00
19, N, 0.00, 0.35, 0.00, 0.00, 0.00
20, E, 0.00, 0.38, 0.00, 0.00, 0.00
21, E, 0.00, 0.17, 0.00, 0.00, 0.00
22, Q, 0.33, 0.15, 0.00, 0.00, 0.00
23, I, 0.39, 0.14, 0.00, 0.00, 0.00
24, K, 0.40, 0.12, 0.00, 0.00, 0.00
25, N, 0.40, 0.12, 0.00, 0.00, 0.00
26, L, 0.11, 0.12, 0.00, 0.00, 0.00
27, L, 0.34, 0.03, 0.00, 0.00, 0.00
28, Q, 0.59, 0.02, 0.00, 0.00, 0.00
29, L, 0.63, 0.04, 0.00, 0.00, 0.00
30, E, 0.62, 0.04, 0.00, 0.00, 0.00
31, A, 0.33, 0.06, 0.00, 0.00, 0.00
32, Q, 0.09, 0.12, 0.00, 0.00, 0.00
33, E, 0.06, 0.10, 0.00, 0.00, 0.00
34, H, 0.16, 0.10, 0.00, 0.00, 0.00
35, L, 0.44, 0.09, 0.00, 0.00, 0.00
36, Q, 0.56, 0.04, 0.00, 0.00, 0.00
37, L, 0.78, 0.03, 0.00, 0.00, 0.00
38, D, 0.82, 0.03, 0.00, 0.00, 0.00
39, F, 0.70, 0.00, 0.00, 0.00, 0.00
40, W, 0.76, 0.00, 0.00, 0.00, 0.00
41, K, 0.54, 0.00, 0.00, 0.00, 0.00
42, S, 0.38, 0.25, 0.00, 0.00, 0.00
43, P, 0.20, 0.25, 0.00, 0.00, 0.00
44, T, 0.05, 0.25, 0.00, 0.00, 0.00
45, T, 0.04, 1.47, 0.00, 0.00, 0.00
46, P, 0.04, 1.36, 0.00, 0.00, 0.00
47, G, 0.04, 1.48, 0.00, 0.00, 0.00
48, E, 0.01, 1.48, 0.00, 0.00, 0.00
49, T, 0.14, 0.27, 0.00, 0.00, 0.00
50, A, 0.20, 0.12, 0.00, 0.00, 0.00
51, H, 0.49, 0.00, 0.00, 0.00, 0.00
52, V, 2.69, 0.00, 0.00, 0.00, 0.00
53, R, 2.57, 0.00, 0.00, 0.00, 0.00
54, V, 2.50, 0.00, 0.00, 6.27, 0.00
55, P, 2.21, 0.00, 0.00, 6.27, 0.00
56, F, 0.00, 0.00, 0.00, 11.61, 0.00
57, V, 0.00, 0.00, 0.00, 11.93, 0.00
58, N, 0.00, 0.00, 0.00, 11.93, 0.00
59, V, 0.00, 0.01, 0.33, 11.69, 0.00
60, Q, 0.00, 0.01, 0.33, 8.01, 0.00
61, A, 0.00, 0.01, 0.33, 7.08, 0.00
62, V, 0.00, 0.01, 0.33, 6.80, 0.00
63, K, 0.00, 0.00, 0.00, 0.00, 0.00
64, V, 0.00, 0.00, 0.00, 4.17, 0.00
65, F, 0.00, 0.00, 0.00, 4.39, 0.00
66, L, 0.00, 0.09, 0.00, 4.39, 0.00
67, E, 0.00, 0.19, 0.00, 4.39, 0.00
68, S, 0.00, 0.38, 0.00, 4.53, 0.00
69, Q, 0.00, 0.40, 0.00, 5.02, 0.00
70, G, 0.00, 0.31, 0.00, 12.27, 0.00
71, I, 0.00, 0.21, 0.00, 64.25, 0.00
72, A, 0.00, 0.02, 0.00, 68.13, 0.00
73, Y, 0.00, 0.01, 0.00, 70.91, 0.00
74, S, 0.00, 0.01, 0.00, 70.91, 0.00
75, I, 0.00, 0.01, 0.00, 70.91, 0.00
76, M, 0.00, 0.01, 0.00, 67.35, 0.00
77, I, 0.00, 0.12, 0.00, 62.97, 0.00
78, E, 0.00, 0.12, 0.00, 4.98, 0.00
79, D, 0.00, 0.12, 0.00, 1.93, 0.00
80, V, 0.00, 0.12, 0.00, 1.85, 0.00
81, Q, 0.00, 0.00, 0.00, 0.00, 0.00

Interpretation of the data

The user must be aware that TANGO considers that the polypeptide sequence is fully denatured and solvent exposed. Thus a globular protein with high stability could have a strong aggregating sequence inside and will aggregate little if it folds fast and under diluted conditions, while the same sequence in a small unfolded peptide will readily aggregate.
Strong aggregation regions in globular proteins could be problematic if the protein is exposed to denaturing conditions, suffers a point mutation that destabilizes it or is at sufficient high concentration that the small percentage of the denatured form can start aggregation.
The user must be aware that aggregation is a concentration dependent process and therefore sequences that at 0.1 mM will be soluble they will precipitate at 1 mM. TANGO assumes a fixed concentration of 1 mM (We have other versions with concentration and stability dependence which are available).
As a rule of the thumb any segment with an aggregation tendency above 5% over 5-6 residues is a potential aggregating segment