Protein stability manual

DEVELOPED BY S. PRASANTH KUMAR
Bioinformatics Laboratory,
Department of Botany, University School of Sciences,
Gujarat University,
Ahmedabad-380 009, Gujarat, India.
Website: http://prasanthvirtualbioinfolab.blogspot.com
Email: prasanthbioinformatics@gmail.com Ph.: +91-9909893929

© COPYRIGHTS. ALL RIGHTS RESERVED 2011.

Citation: S.Prasanth Kumar and M. Meenachi. Virtual Quantification of Protein
Stability using Applied Kinetic and Thermodynamic Parameters. IIOAB (In Press).

THIS PROGRAM IS DISTRIBUTED UNDER CREATIVE COMMON LICENSE
PERMITTING EXTENSIVE USAGE, REPRODUCTION AND DISTRIBUTION FOR
ACADEMIC AND NON-ACADEMIC USERS PROVIDED THIS WORK SHOULD
BE PROPERLY CITED.

Protein Stability Program- Developed by S. Prasanth Kumar

PROTEIN STABILITY PROGRAM MANUAL

AT A GLANCE

1. Protein Stability 1
2. Applications of Protein Stability Program 1
3. System Requirements 1
4. Downloading the Program 2
5. Input File 2
6. Running the Program 5
7. Results Interpretation 7
8. Expert Level Analysis of Developed Annex-i
Algorithm

©Copyrights. All Rights Reserved, 2011

Protein Stability Program- Developed by S. Prasanth Kumar 1

1. Protein Stability

Protein stability, the most important aspect of molecular dynamics and
simulations, requires sophisticated instrumentations of molecular biology to
analyze its kinetic and thermodynamic background. Protein stability is
defined by the ability of a protein to retain its structural conformation or its
activity when subjected to physical or chemical manipulations. In other
words, any process involved in maintaining the structure and integrity of a
protein and preventing it from degradation or aggregation. Protein stability
is quantitatively described by the standard Gibbs energy change (∆G). Such
∆G values are important properties for a quantitative comparison of
stabilities of different proteins.

2. Applications of Protein Stability Program

It is developed in a view that one might get a clear understanding of
the protein stability from the sequence itself without the need of its 3D
structure which can help us to study the protein dynamics and folding
pattern which act as a prerequisite for protein characterization
experiments.

This program will serve as a better tool for understanding protein
stability in the context of molecular dynamics and the important amino
acids in the domains driving folding.

Protein Stability, a first program of its kind, was developed which
takes raw amino acid sequence as its input and produces energy
distribution for individual amino acids and its overall stability from
the applied kinetic and thermodynamic parameters.

3. System Requirements

Little knowledge of Terminal (for Linux Users) or Command Line
Prompt (for Windows Users).

MS Excel or Office Spreadsheet for executing statistics



4. Downloading the Program

‘Protein Stability’ program can be freely downloaded from an external mirror
http://depositfiles.com/files/tab23x3xo .

Click “FREE downloading”, then the countdown of 60 seconds will be
displayed and a download button ‘Download the file’ will be displayed
after the completion of countdown.

After clicking the download button, it will pop up with a download
“proteinstability.exe”. Select where you want to save the file (program)
in your system.

5. Input File

The only input file is raw protein sequence. Here ‘raw’ means a string of 20
essential amino acids without any header, comments or other features from
any sequence format. The protein of interest can be downloaded from any
publicly available databases such as NCBI, UniProtKB, PIR, etc. We will
illustrate the sequence retrieval from NCBI with ‘Succinate dehydrogenase of
Mycobacterium tuberculosis’ as an example.



Browse the NCBI homepage in World Wide Web with the following URL:
http://ncbi.nlm.nih.gov.in/

Narrow done your search to ‘Protein’ with the keyword ‘Succinate
dehydrogenase Mycobacterium tuberculosis’ typed in the search box and hit
‘Search’



A search list will be displayed for the above keyword. Select a protein
sequence from Mycobacterium tuberculosis H374a and retrieve it by clicking
its corresponding FASTA link provided below its entry.

Now, copy only the raw sequence, paste in a notepad (or any text editor) and
save it in .txt format. For example, ‘sequence.txt’. It is recommended to save
the sequence file in the same location where you had previously downloaded
the program.

The input file will look like this.



6. Running the Program

Invoke the command line interpreter using ‘Run’ command or simply through
the shortcut “Windows ( )’ + r. Type ‘cmd’ to open command prompt. It will
look like this (for clarity the background color and text has been changed).

In order to get interpreted by command line prompt, specify the full path of
the program with the change directory option.

Change the directory to Desktop by the following command
Type: cd C:UsersprashanthDesktop

Open the program by its filename and its file extension
Type: proteinstability.exe

Now, the program asks you to input the protein sequence file
(remember that we had saved the sequence file in the desktop)
Type: sequence.txt and hit “ENTER or RETURN”



After hitting ENTER key, the result will be displayed.



7. Results Interpretation

First, we have to find the top most 2 residues whose Gibbs free energy of
activation is higher under kinetics column.

Gibbs free energy of activation of Arginine (R) = 140.53 kcal/mol
Gibbs free energy of activation of Leucine (L) = 130.53 kcal/mol

Hence, this two amino acids were probably consumes the energy of activation
to promote folding and contributes more for the protein hydrophobicity.

Gibbs free energy of activation of Glutamate (E) = -123.97 kcal/mol

Noteworthy, this amino acid has negative energy as it compensates the high
energy consumed by the above 2 amino acids.

Second, we have to examine the thermodynamic Gibbs energy otherwise
knowns as Gibbs free energy of denaturation corresponding to the above
mentioned first 2 amino acids.

Gibbs free energy of denaturation of Arginine (R) = -3207.78 kJ/mol
Gibbs free energy of denaturation of Leucine (L) = -3143.53 kJ/mol

As these amino acids reported a very low energy in terms of thermodynamics,
it can promote the thermal stability of the protein in part.

Gibbs free energy of denaturation of Alanine (A) = -3405.12 kJ/mol

Fortunately, another amino acid (alanine) has an energy value near to the
arginines and leucines. Hence, the alanine probably promotes stability as
compared to the rest of the amino acids.

Third, we have to inspect the frequency of amino acid for the above
mentioned 3 amino acids.

Frequency of R in the protein = 47
Frequency of L in the protein = 57
Frequency of E in the protein = 49
Frequency of A in the protein = 66

The frequencies of all the 4 amino acids were comparatively greater.



Finally, the interpretation of protein stability values

The descriptor ‘protein stability’ and its numerical values reflect the
distribution of hydrophobic amino acids across the protein sequence. If the
hydrophobic amino acids were higher in counts, the protein stability value
will also increase. Thus, it is highly recommended that protein stability value
and Gibbs energy in terms of hydrophobic amino acids calculated for both the
kinetic and thermodynamic calculations should be analyzed and compared
simultaneously.

Kinetic calculations
Protein Stability value = 0.3963
Gibbs energy in terms of hydrophobic amino acids = 528.54 kcal/mol

Thermodynamic calculations
Protein Stability value = 0.3947
Gibbs energy in terms of hydrophobic amino acids = -12881.17 kJ/mol

To understand the existance of any linear relationship between the
calculated protein stability values and Gibbs free energy term for
hydrophobic aminoacids from both kinetic and thermodynamic calculations,
Pearson product moment correlation coefficient can be used that ranges from
-1.0 to 1.0.

correlation
Pearson product moment correlation coefficient Type of Correlation
Negative value e.g. -1.0 Negative Correlation
Zero i.e 0 No Correlation
Positive value e.g. 1.0 Positive Correlation



A value of 1 was observed indicating that the protein stability value and the
Gibbs energy term for both the kinetic and thermodynamic calculations
proved a positive correlation. Hence, the energy term for hydrophobic amino
acids in both the calculations contributes hydrophobicity and stability and it
is evident in the table below:

Arginine
Arginine Leucine Total Gibbs energy Contribution
(Arginine + in terms of (%)
Leucine) hydrophobic
amino acids
Gibbs free energy of activation (Kinetic Calcualtions)
140.53 130.53 271.06 528.54 51.28
kcal/mol kcal/mol kcal/mol kcal/mol
denaturation
Gibbs free energy of denaturation (Thermodynamic Calculations)
-3207.78 -3143.53 -6351.31 -12881.17 49.31
kJ/mol kJ/mol kJ/mol kJ/mol

The contribution of Arginine and Leucine was found to be 51.28 % and
49.31 %, respectively.

We can come to a conclusion that

1. Arginine and Leucine promotes hydrophobicity (consumes more Gibbs
free energy of activation) and this more energy is compensated by a
low energy consuming amino acid, Glutamate.
2. Arginine and Leucine also promotes stability as its Gibbs free energy
of denaturation was very low. Comparatively, Alanine also contributes
for the protein stability.
3. The frequencies of the four amino acids were greater and may play an
important role in folding and stabilizing the molecule.
4. A linear relationship was observed between the estimated protein
stability values and Gibbs energy term in both the calculations taken
together.
5. Arginine and Leucine contributed 51.28% for the protein
hydrophobicity and contributed 49.31% for the protein stability. Hence,
it is evident that these two amino acids contributed half of the driving
force for hydrophobicity and stabilization.

From this analysis, one might get an overall idea about the importance of
amino acids in kinetics and thermodynamics point of view and the major
force promoting the protein stability.


Protein Stability Program- Developed by S. Prasanth Kumar Annex-i

8. Expert Level Analysis of Developed Algorithm


Protein Stability Program- Developed by S. Prasanth Kumar Annex-i


Protein stability manual

Recommended

Recommended

More Related Content

Similar to Protein stability manual

Similar to Protein stability manual (20)

More from Prasanthperceptron

More from Prasanthperceptron (20)

Recently uploaded

Recently uploaded (20)

Protein stability manual