Systems Biology and Protein Homology Modeling

Theme: MRSA Acetate Kinase and Metabolic Network Modeling

Lab #2

Etienne Z. GnimpiebaBRIN WS 2013

Mount Marty College – June 24th 2013 Etienne.gnimpieba@usd.edu

Context

0. Specification & Aims

Lab #2

Statement of problem / Case study:

MRSA Acetate Kinase ( SAV 1711 from MRSA Mu50 strain) was found in our preliminary study on Silico. It is essential to bacteria growth and absent in humans. Currently, there is no FDA approved antibiotics targeting bacterial central metabolism, these bacterial sites have not yet been exposed to antibacterial agents and therefore will be less likely to develop a drug resistance.

Modeling

Keywords: Bio: MRSA, Acetate Kinase Informatics: programing, bioinformatics tools, getting and exporting data. Validating models.

16 Korean Bioinformation Center, 2010

Reduced expression of frataxin is the cause of Friedrich's ataxia (FRDA), a lethal neurodegenerative disease, how about liver cancer?

Aim: The purpose of this lab is to understand how Protein, Chemical, and Metabolic Network Modeling can be used for research topics. This process will allow researchers more information to have more information available.

Acquired skillsOnline and server tools: - Protein Homology Modeling - Model Evaluation on ERRAT - Chemical Modeling through OCHEM server - Metabolic Network Modeling using BioModels and Virtual Cell.

Biological Hypothesis

2

Resolution Process

T2. Chemical Modeling Objective: Use of OCHEM and PubChem to extract information about the desired chemical models.

T3. Metabolic Network Modeling Objective: Use of BioModels and Virtual Cell to extract data about Metabolic Networking.

T2.1. Using OCHEM and PubChem

T3.1. Finding a model using BioModelsT3.2. Validating the ModelT3.3. Virtual Cell

T1. Protein Homology Modeling (PMP) Objective: Use of PMP website to evaluate different protein models via the ERRAT website.

T1.1 Template SelectionT1.2. Model Evaluation on ERRAT

Protein Modeling Systems Biology and Protein Modeling T1. Protein Modeling

Objective: Use of PMP website to evaluate different protein models via the ERRAT website.

T1.1. Template SelectionOn the Protein Modeling Portal website: http://www.proteinmodelportal.org 1) Click on “interactive modeling” and put in your Name and E-Mail address (results will be

sent to your e-mail)2) Copy and paste the amino acid sequence from the word document “Amino Acid Sequence”3) Check all six boxes below (the different Databases used) Be sure to select the first option

under ModWeb and the check the box under M4T.4) Submit Query5) Once execution has gone through, select the different Database results. Because this query

takes a long time we have the finished results available.6) Open jmol, then go to “File”, “Open” and open the file in your student folder called “Swiss

Model Result” (a pdb file)

Etienne Z. GnimpiebaBRIN WS 2013

Mount Marty College – June 24th 2013

T1.2. Model Evaluation on ERRAT Will have many models, in order to select best fitting model we use model evaluation tools such as ERRAT.On ERRAT website: http://nihserver.mbi.ucla.edu/ERRATv2/ 1) Click “browse” (or “choose file”) and select the PDB file “Swiss Model Result.pdb” in your

folder and click “send file”2) The results will open and you can look at the information provided such as the quality of the

model chosen. 3) Open the PDF version by clicking on “PDF file here” and save.4) You can do this with all of the models you receive in your e-mail and compare the quality of

each in order to chose the best model

Chemical ModelingT2. Chemical Modeling

Objective: Use of OCHEM and PuubChem to extract information about the desired chemical models.

T2.1. Using OCHEM and PubChemOn the OCHEM website: http://www.ochem.eu/home/show.do o Click on “Run predictions” and “login as guest”. Accept the “Terms and Agreements” formo Then select all the boxes under the “What would you like to predict?”o Then open a new tab and go to the PubChem website: http://pubchem.ncbi.nlm.nih.gov/ o Search under the “Compound” tab for “protein kinase” and select the “protein kinase

inhibitor M (6-24)”o Scroll down and copy the sequence from “canonical SMILES” and paste to the “Provide

Name/CAS-RN/SMILES” on OCHEM websiteo Select the “Provide Name/CAS-RN/SMILES” and click “Run predictions”o Once results show up you can read and deduce the information provided.

Etienne Z. GnimpiebaBRIN WS 2013

Mount Marty College – June 24th 2013

Systems Biology and Protein Modeling

Metabolic Network ModelingT3. Metabolic Network Modeling Objective: Use of BioModels and Virtual Cell to extract data about Metabolic

Networking.

T3.1. Finding a model using BioModelsOn the BioModels website: http://www.ebi.ac.uk/biomodels-main/o Search “acetate kinase” select the 3rd, “Cell Cycle 6var”o Place your mouse over “Download SBML” in the top left of the screen, and select “SMBL L2

V4 (curated)” and save the file. This file will already be in your Student Folder as “AcetateKinaseModel.xml”

Etienne Z. GnimpiebaBRIN WS 2013

Mount Marty College – June 24th 2013

T3.2. Validating the ModelOn the SMBL Validator website: http://sbml.org/validator/o Click “Browse” and open the “AcetateKinaseModel.xml”o Click “Validate Now” and check its validity

Systems Biology and Protein Modeling

T3.3. Virtual Cello Go to your Student Folder in “Tools” and run “vcell”. Exit the boxes that pop upo Click on “Reactions” tab and double click “add new here” in the centero On the left side of the arrow put an “S” (for substrate) and on the right side put a “P” (for

product) [S -> P]o Push enter to create your reactiono Make sure you are still on the new reaction and pull down “Kinetic Type” at the bottom and

select “Henri-Michaelis-Menten (Irreversible)..”o Edit the “Expression” for “Km” to be “0.01” as well as the “Vmax” to be “10.0” by double clicking

under “Expression”o Click on the “Applications” on the left, pull down “Add New” in the middle and select

“Deterministic”o Click on “Application: Application0” o Click “New Simulation” [ ] then click “Edit” [ ]o A window will pop up, adjust value under “Default” by clicking the box under “Scan” for;

“P_init_uM” to min “0.1” and max “100”; “S_init_uM” to min “0.1” max “100”o Click “ok”o Push the play button [ ] in the upper right corner to simulate the modelo The results will pop up in a new window. You can choose which results you see by selecting them

on the left