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Interpretation of Program Output
The program, peptide-serum-stability, produces three kinds of fragment output (1) linear, (2) branched and (3) cyclic fragments. Each of the fragment output has its unique format.
For this guide, we will a cyclic peptide with a disulfide linker CGYEQDPWGVRYWYGCkkk(K-Biotin) which is represented in the program as CGYEQDPWGVRYWYGCKKKKB
. The amino acids where the linker connects are emphasized.
We will represent the peptide as follows for illustrative purposes:
- | - | - | - | - | - | - | S | S | - | - | - | - | - | - | - | |||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| | | | |||||||||||||||||||
C | G | Y | E | Q | D | P | W | G | V | R | Y | W | Y | G | C | K | K | K | K | B |
Here is a sample output from the program using the cyclic peptide above:
The sample output will be referenced throughout the guide.
The first suggested fragment from the sample output above, YEQDPWGVRY
, corresponds to the fragment
CGYEQDPWGVRYWYGCkkk(K-Biotin)
or
- | - | - | - | - | - | - | - | - | - | - | - | - | - | |||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| | | | |||||||||||||||||||
Y | E | Q | D | P | W | G | V | R | Y |
Linear fragment outputs do not have any special characters in their fragments.
For cyclic peptides, linear fragments that contain the linker are possible. For example we can have an output: WYGCSSCGYE
. Notice that the linear fragment now includes amino acids from the first and second position. This linear fragment is illustrated as:
- | - | - | - | - | - | - | S | S | - | - | - | - | - | - | - | |||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| | | | |||||||||||||||||||
C | G | Y | E | W | Y | G | C |
The second output from the sample output is: CG#SS#RYWYGCK
Branched fragment outputs will always have the linker surrounded by the symbol #
.
To understand the output format for branched peptide, first let's look at what this output represents:
- | - | - | - | - | - | - | S | S | - | - | - | - | - | - | - | |||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| | | | |||||||||||||||||||
C | G | R | Y | W | Y | G | C | K |
The current illustration of the branched fragment is difficult to print in a program due to the branching structure. Thus, we must come up with a convention to convert this branched illustration into a one line String of characters.
Let us re-arrange the branched fragment illustration such that the linker is oriented vertically and each side of the linker is on the top and the bottom horizontally:
C | G | |||||
| | ||||||
S | ||||||
S | ||||||
| | ||||||
R | Y | W | Y | G | C | K |
For the convention for this program, we replace the connection between the linker and the peptide with the #
symbol. We have labeled the horizontal parts of the illustration for convenience.
(1) | C | G | |||||
# | |||||||
S | |||||||
S | |||||||
# | |||||||
(2) | R | Y | W | Y | G | C | K |
Lastly, we flatten this representation into one line. It will have the following form (1)#SS#(2). In other words:
- We first take the horizontal linear fragment (1) and write it down:
CG
- Then take the vertical segment that contains the linker, flip it to become horizontal and append to the linear fragment (1):
CG#SS#
- Take the horizontal linear fragment (2) and append it to the end:
CG#SS#RYWYGCK
Now we have the output we obtained from the program: CG#SS#RYWYGCK
.
Let's explore another example for further clarification of the branched fragment convention.
Suppose we have the output CGYE#SS#WYGCKKKB
.
The illustration for this branch as follows:
- | - | - | - | - | - | - | S | S | - | - | - | - | - | - | - | |||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| | | | |||||||||||||||||||
C | G | Y | E | W | Y | G | C | K | K | K | K | B |
We re-arrange this illustration such that the linker is vertical. Then we replace the connection with the linker with #
and label the horizontal linear fragments for convenience.
(1) | C | G | Y | E | |||||
# | |||||||||
S | |||||||||
S | |||||||||
# | |||||||||
(2) | W | Y | G | C | K | K | K | K | B |
Then let's follow the branched fragment convention step by step.
- We first take the horizontal linear fragment (1) and write it down:
CGYE
- Then take the vertical segment that contains the linker, flip it to become horizontal and append to the linear fragment (1):
CGYE#SS#
- Take the horizontal linear fragment (2) and append it to the end:
CG#SS#WYGCKKKB
Now we have the output we obtained from the program: CGYE#SS#WYGCKKKB
.