In this tutorial, we’ll cover the basics of molecular modelling by setting up a protein in complex with a ligand and uploading the structure to Galaxy. This tutorial will make use of CHARMM-GUI. Please note that the follow-up to this tutorial (located in Running molecular dynamics simulations using NAMD) requires access to NAMD Galaxy tools, which can be accessed using the Docker container but are currently not available on any public Galaxy server.

Comment: Audience

This tutorial is intended for those who are new to the computational chemistry tools in Galaxy.

Agenda

In this tutorial, we will cover:

1. Cellulase and cellulose
   1. Get data
2. Modelling with CHARMM-GUI
   1. CHARMM
   2. NAMD
3. Conclusion

Cellulase and cellulose

To start we’ll look at the PDB and find the entry for a fungal enzyme that cleaves cellulose. The enzyme is 7CEL, a hydrolase as seen in the figure.

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In this section we’ll access the PDB, download the correct structure, import it and view in Galaxy.

Details: Background: What is the PDB (Protein Data Bank) and format?

The Protein Data Bank (PDB) format contains atomic coordinates of biomolecules and provides a standard representation for macromolecular structure data derived from X-ray diffraction and NMR studies. Each structure is stored under a four-letter accession code. For example, the PDB file we will use is assigned the code 7CEL).

More resources:

• Multiple structures are stored and can be queried at https://www.rcsb.org/
• Documentation describing the PDB file format is available from the wwPDB at http://www.wwpdb.org/documentation/file-format.php.

Details: Background: Why choose a cellulase?

Using enzymes to break down abundant cellulose into disaccharide units (cellobiose) is a method to optimise the biofuel process. Barnett et al. 2011

More resources:

• https://en.wikipedia.org/wiki/Cellulase
• https://en.wikipedia.org/wiki/Biofuel
• Payne et al. 2015
• Barnett et al. 2010

Get data

The 7CEL PDB does not include a complete 8 unit substrate and some modelling is required. The correctly modelled substrate is provided for this tutorial.

Details: More details about the modelling done

• VMD (visualisation software) was used for atomic placement and CHARMM was used for energy minimisation.
• The PDB structure contains a mutation at position 217 (glumatate to glutamine). Our structure reverses this.
• The ligand was modelled separately and inserted into the binding site.

Hands On: Data upload

1. Create a new history for this tutorial.

   Tip: Creating a new history

   To create a new history simply click the new-history icon at the top of the history panel:

   

2. Import the files from the Zenodo link provided.

   https://zenodo.org/record/2600690/files/7cel_modeled.pdb?download=1
   

   Tip: Importing via links

   • Copy the link location

   • Click galaxy-upload Upload Data at the top of the tool panel

   • Select galaxy-wf-edit Paste/Fetch Data

   • Paste the link(s) into the text field

   • Press Start

   • Close the window

   Tip: Importing data from a data library

   As an alternative to uploading the data from a URL or your computer, the files may also have been made available from a shared data library:

   1. Go into Libraries (left panel)
   2. Navigate to the correct folder as indicated by your instructor.
      • On most Galaxies tutorial data will be provided in a folder named GTN - Material –> Topic Name -> Tutorial Name.
   3. Select the desired files
   4. Click on Add to History galaxy-dropdown near the top and select as Datasets from the dropdown menu

   5. In the pop-up window, choose

      • “Select history”: the history you want to import the data to (or create a new one)
   6. Click on Import

3. Rename the datasets.

4. Check that the datatype is correct. The file should have the PDB datatype.

   Tip: Changing the datatype

   • Click on the galaxy-pencil pencil icon for the dataset to edit its attributes
   • In the central panel, click galaxy-chart-select-data Datatypes tab on the top
   • In the galaxy-chart-select-data Assign Datatype, select pdb from “New type” dropdown
     • Tip: you can start typing the datatype into the field to filter the dropdown menu
   • Click the Save button

Modelling with CHARMM-GUI

It is convenient to set up the molecular system outside Galaxy using a tool such as CHARMM-GUI. Alternative methods are possible - see the GROMACS tutorial for an example. Jo et al. 2016

Tip: Viewing figures

• Some of the figures are screenshots and it may be difficult to make out details
• Right-click on the image and choose ‘Open image in new tab’ to view
• Zoom in and out as needed to see the content

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Go to the correct section depending on which MD engine you will be using.

CHARMM

Upload the PDB to CHARMM-GUI

Navigate to CHARMM-GUI and use the Input Generator, specifically the PDB Reader tool and upload the Cellulase PDB file. Press ‘Next Step: Select Model/Chain’ in the bottom right corner.

Hands On: Upload the PDB to CHARMM-GUI

1. Retrieve the modelled PDB structure from Zenodo.
2. Upload the PDB and choose CHARMM format.

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Select both protein and ligand models

Hands On: Generate PDB file

Two model chains are presented for selection: the protein (PROA) and the hetero residue, which is the ligand or glycan in this case (HETA). Select both, and press ‘Next Step: Generate PDB’ in the bottom right corner.

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Manipulate the system

Hands On: Make necessary modifications

Rename the hetero chain to BGLC and add ten disulfide bonds to the protein, as shown in the figure. Then press ‘Next Step: Generate PDB’ in the bottom right corner.

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Download the output

Hands On: Download CHARMM output

The output is a .tgz file (a tarball or zipped tarball). Inside the archive you will see all inputs and outputs from CHARMM-GUI.

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Tip: What is a .tgz file?

This is a compressed file which contains all the output files created by the CHARMM-GUI. To access them, the .tgz file needs to be decompressed. There should be a tool available on your operating system for this. If you prefer to use the command line, tar will work fine on Linux or Mac tar -zxvf example.tgz. On Windows use 7zip, or download Git for windows and use Git Bash.

Upload to Galaxy

Hands On: Upload files to Galaxy

Upload the step1_pdbreader.psf and step1_pdbreader.crd files to your Galaxy instance and run the system setup tool.

NAMD

Upload the PDB to CHARMM-GUI

Hands On: Upload the PDB to CHARMM-GUI

Retrieve the modelled PDB structure from Zenodo. Navigate to CHARMM-GUI and use the Input Generator, specifically the Solution Builder tool. Upload the PDB file, selecting ‘CHARMM’ as the file format. Press ‘Next Step: Select Model/Chain’ in the bottom right corner.

Open image in new tab

Select both protein and ligand models

Hands On: Generate PDB file

Two model chains are presented for selection: the protein (PROA) and the hetero residue, which is the ligand or glycan in this case (HETA). Select both, and press ‘Next Step: Generate PDB’ in the bottom right corner.

Open image in new tab

Manipulate the system

Hands On: Make necessary modifications

Rename the hetero chain to BGLC and add disulfide bonds.Press ‘Next Step: Generate PDB’ in the bottom right corner.

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Set up the waterbox and add ions

Hands On: Solvate the protein

Set up a waterbox. Use a size of 10 angstroms and choose a cubic box (‘rectangular’ option).

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Question

Why is 10 angstrom a fair choice for the buffer? Why choose 0.15M NaCl?

Solution

Under periodic boundary conditions, we need to ensure the protein can never interact with its periodic image, otherwise artefacts are introduced. Allowing 10 angstroms between the protein and the box edge ensures the two images will always be at minimum 20 angstroms apart, which is sufficient.

Some of the residues on the protein surface are charged and counter-ions need to be present nearby to neutralise them. Failure to explicitly model salt ions may destabilise the protein.

Generate the FFT automatically

Hands On: Generate the FFT

Particle Mesh Ewald (PME) summation is the method being used to calculate long-range interactions in this system. To improve the computational time a Fast Fourier Transform (FFT) is used. A detailed discussion of FFT will not be presented here; there are many articles on the subject. Try Wikipedia and Toukmaji and Board 1996.

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Download the output

Hands On: Solvate the protein

The output is a .tgz file (a tarball or zipped tarball). Inside the archive you will see all inputs and outputs from CHARMM-GUI.

Open image in new tab

Tip: What is a .tgz file?

This is a compressed file and needs to be uncompressed using the correct tool. On Linux or Mac: tar will work fine tar -zxvf example.tgz. On Windows use 7zip or download Git for windows and use Git Bash.

Upload to Galaxy

Hands On: Upload files to Galaxy

Upload the following files to your Galaxy instance and ensure the correct datatype is selected:

• step3_pbcsetup.psf -> xplor psf input (psf format)
• step3_pbcsetup.pdb -> pdb input (pdb format)
• Checkfft.str -> PME grid specs (txt format)
• step2.1_waterbox.prm -> waterbox prm input (txt format)

You are now ready to run the NAMD workflow, which is discussed in another tutorial.

Conclusion

trophy Well done! You have started modelling a cellulase protein and uploaded it into Galaxy. The next step is running molecular dynamics simulations (tutorial)

You've Finished the Tutorial

Please also consider filling out the Feedback Form as well!

Key points

• The PDB is a key resource for finding protein structures.

• Using CHARMM-GUI is one way to prepare a protein and ligand system.

• To get data into Galaxy you can upload a file from your computer or paste in a web address.

Frequently Asked Questions

• Tutorial FAQs
• Topic FAQs
• Galaxy FAQs
• GTN Matrix Chat
• Galaxy Help Forum

Useful literature

Further information, including links to documentation and original publications, regarding the tools, analysis techniques and the interpretation of results described in this tutorial can be found here.

References

1. Toukmaji, A. Y., and J. A. Board, 1996 Ewald summation techniques in perspective: a survey. Computer Physics Communications 95: 73–92. 10.1016/0010-4655(96)00016-1
2. Barnett, C. B., K. A. Wilkinson, and K. J. Naidoo, 2010 Pyranose Ring Transition State Is Derived from Cellobiohydrolase I Induced Conformational Stability and Glycosidic Bond Polarization. J. Am. Chem. Soc. 132: 12800–12803. 10.1021/ja103766w
3. Barnett, C. B., K. A. Wilkinson, and K. J. Naidoo, 2011 Molecular Details from Computational Reaction Dynamics for the Cellobiohydrolase I Glycosylation Reaction. Journal of the American Chemical Society 133: 19474–19482. 10.1021/ja206842j
4. Payne, C. M., B. C. Knott, H. B. Mayes, H. Hansson, M. E. Himmel et al., 2015 Fungal Cellulases. Chem. Rev. 115: 1308–1448. 10.1021/cr500351c
5. Jo, S., X. Cheng, J. Lee, S. Kim, S.-J. Park et al., 2016 CHARMM-GUI 10 years for biomolecular modeling and simulation. Journal of Computational Chemistry 38: 1114–1124. 10.1002/jcc.24660

Feedback

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Citing this Tutorial

1. Christopher Barnett, Simon Bray, Nadia Goué, Setting up molecular systems (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/setting-up-molecular-systems/tutorial.html Online; accessed TODAY
2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{computational-chemistry-setting-up-molecular-systems,
author = "Christopher Barnett and Simon Bray and Nadia Goué",
	title = "Setting up molecular systems (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/setting-up-molecular-systems/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol}
}

                   

Do you want to extend your knowledge?

Follow one of our recommended follow-up trainings:

• tutorial Hands-on: Running molecular dynamics simulations using NAMD

Galaxy Administrators: Install the missing tools

You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.

shed-tools install [-g GALAXY] [-a API_KEY] -t <(curl https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/setting-up-molecular-systems/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools: []

Feedback

t{ hist[0] | to_stars }}	3

February 2024

• 5 stars: Liked: Everything is in steps and clearly explained. Very well done.

November 2019

• 5 stars: Liked: The feeling of creating something on my own Disliked: Nothing