Documentation
Overview
The Bionamic platform consists of a server side code base and a client UI that runs in the browser. The components of the Bionamic platform will be described in this documentation. Currently the documentation is incomplete.
Physical properties of proteins
Molecular weight
The molecular weight of a protein is calculated as where is the mass of waterAmino acid | Molecular weight(g/mol) |
---|---|
A | 71.08 |
R | 156.19 |
N | 114.11 |
D | 115.09 |
C | 103.15 |
E | 129.12 |
Q | 128.13 |
G | 57.05 |
H | 137.14 |
O | 113.11 |
I | 113.16 |
L | 113.16 |
K | 128.18 |
M | 131.2 |
F | 147.18 |
P | 97.12 |
U | 121.09 |
S | 87.08 |
T | 101.11 |
W | 186.22 |
Y | 163.18 |
V | 99.13 |
Isoelectric point
The equilibrium charge of a protein is a function of pH. We use the following formula as an approximation of the charge. where the first sum is over the N terminal and the amino acids with positively charged side chains, and the second sum is over the C terminal and the amino acids with negatively charged side chains. The list of amino acids and their pK values are given in the tables below.
As seen from the formula, the charge is a decreasing function of pH. At small pH, the protein is positively charged, and at large pH, the protein is negatively charged. There is one value in the middle where the protein is neutral. This value is easily found numerically by repeated bisection. The isoelectric point is by definition that particular value of pH where the protein is neutral.
Contributions from the N and C terminal
Amino acid | ||
---|---|---|
A | 2.34 | 9.69 |
R | 2.17 | 9.04 |
N | 2.02 | 8.8 |
D | 1.88 | 9.6 |
C | 1.96 | 10.28 |
E | 2.19 | 9.67 |
Q | 2.17 | 9.13 |
G | 2.34 | 9.6 |
H | 1.82 | 9.17 |
O | 1.82 | 9.65 |
I | 2.36 | 9.6 |
L | 2.36 | 9.6 |
K | 2.18 | 8.95 |
M | 2.28 | 9.21 |
F | 1.83 | 9.13 |
P | 1.99 | 10.6 |
U | 5.6 | 5.2 |
S | 2.21 | 9.15 |
T | 2.09 | 9.1 |
W | 2.83 | 9.39 |
Y | 2.2 | 9.11 |
V | 2.32 | 9.62 |
Positive charge side chain contributions
Amino acid | |
---|---|
R | 12.48 |
H | 6.0 |
K | 10.53 |
Negative charge side chain contributions
Amino acid | |
---|---|
D | 3.65 |
E | 4.25 |
Y | 10.07 |
C | 8.18 |
References
The values of the pK constants are taken from Amino Acids Reference Chart and from protein isoelectric point calculator
Extinction coefficient
Molar extinction coefficient
The molar extinction coefficient of a molecule is calculated by where , and is the number of amino acids of type W, Y and C repectively in the protein. The unit of the molar extinction coefficient is
Mass extinction coefficient
The mass extinction coefficient is given by The unit of the mass extinction coefficient is
Reference
The extinction coefficient formula originates from the Thermo Fisher Application-Notes
Aliphatic index
The aliphatic index is calculated for proteins using the formula
whereReference
The aliphatic index is introduced in
GRAVY
The grand average of hydropathy (GRAVY) of a protein sequence is calculated as the average of the hydropathy values of the amino acids.
Amino acid | Hydropathy |
---|---|
A | 1.8 |
R | -4.5 |
N | -3.5 |
D | -3.5 |
C | 2.5 |
E | -3.5 |
Q | -3.5 |
G | -0.4 |
H | -3.2 |
I | 4.5 |
L | 3.8 |
K | -3.9 |
M | 1.9 |
F | 2.8 |
P | -1.6 |
S | -0.8 |
T | -0.7 |
W | -0.9 |
Y | -1.3 |
V | 4.2 |
Reference
The GRAVY value is introduced in