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

Molecular weight = M_{water} + \sum_{a} M_{a}

where

M_{water} = 18.02 g/mol

is the mass of water

Molecular weight of the amino acids
Amino 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. $Charge(pH) = \sum_{i} \frac{1}{1 + 10^{pH - {pK}_{i}}} + \sum_{i} \frac{-1}{1 + 10^{{pK}_{i} - pH}}$ 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

$pK$ values of the amino acids. The ${pK}_{a}$ value is used for the negative charge contribution of the C terminal of the protein. The ${pK}_{b}$ value is used for the positive charge contribution of the N terminal of the protein.
Amino acid	${pK}_{a}$	${pK}_{b}$
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

The ${pK}_{x}$ value is used for the positive charge contribution of a side chain anywhere in the protein.
Amino acid	${pK}_{x}$
R	12.48
H	6.0
K	10.53

Negative charge side chain contributions

The ${pK}_{x}$ value is used for the negative charge contribution of a side chain anywhere in the protein.
Amino acid	${pK}_{x}$
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 $Molar extinction coefficient = 5500 \times N_{W} + 1490 \times N_{Y} + 125 \times N_{C}$ where $N_{W}$ , $N_{Y}$ and $N_{C}$ is the number of amino acids of type W, Y and C repectively in the protein. The unit of the molar extinction coefficient is $M^{-1} {cm}^{-1}$

Mass extinction coefficient

The mass extinction coefficient is given by $Mass extinction coefficient = \frac{Molar extinction coefficient}{Molar mass}$ The unit of the mass extinction coefficient is $L g^{-1} {cm}^{-1}$

Reference

The extinction coefficient formula originates from the Thermo Fisher Application-Notes

Aliphatic index

The aliphatic index is calculated for proteins using the formula

Aliphatic Index = x_{A} + a x_{V} + b (x_{I} + x_{L})

where

a = 2.9

b = 3.9

x_{A} = 100 \times (mole fraction of alanine)

x_{V} = 100 \times (mole fraction of valine)

x_{I} = 100 \times (mole fraction of isoleucine)

x_{L} = 100 \times (mole fraction of leucine)

Reference

The aliphatic index is introduced in

Ikai, A.J. (1980) Thermostability and aliphatic index of globular proteins. J. Biochem. 88, 1895-1898. [Pubmed: 7462208]

GRAVY

The grand average of hydropathy (GRAVY) of a protein sequence is calculated as the average of the hydropathy values of the amino acids.

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

Kyte, J. and Doolittle, R.F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132. [PubMed: 7108955]