ABC-INT-Homology modelling

Integrator Unit: Homology Modelling

(Integrator unit: create a homology model and assess the role of sequence conservation)

 

Abstract:

This page integrates material from the learning units for working with multiple sequence alignments and structure data in a task for evaluation.

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Deliverables:

Integrator unit: Deliverables can be submitted for course marks. See below for details.

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Prerequisites:
This unit builds on material covered in the following prerequisite units:

• BIN-SX-Homology_modelling (Homology Modeling)

 

 

 

Evaluation

This "Integrator Unit" should be submitted for evaluation for a maximum of 13 marks if one of the written deliverables is chosen, resp. 24 marks if you choose this for your oral test.

Please note the evaluation types that are available as options for this unit.

Be mindful of the Marking rubrics.

If this is submitted for your oral test, please read the Oral test instructions before you begin.

If your submission includes R code, please read the Code submission instructions before you begin.

Once you have chosen an option ...

1. Create a new page on the student Wiki as a subpage of your User Page.
2. Put all of your writing to submit on this one page.
3. When you are done with everything, go to the Quercus Assignments page and open the appropriate Integrator Unit assignment. Paste the URL of your Wiki page into the form, and click on Submit Assignment.

Your link can be submitted only once and not edited. But you may change your Wiki page at any time. However only the last version before the due date will be marked. All later edits will be silently ignored.

 

Report option

• Work through the tasks described in the scenario below.
• Document your results in a short technical report on a subpage of your User page on the Student Wiki. Describe your methods (R-code!) in an appendix linked from your report;
• When you are done, submit the link to your page via Quercus as described above.

 

Publication Image option

• Work through the tasks described in the scenario below.
• Produce the image as described and "publish" it on a subpage of your User page on the Student Wiki. Describe your methods (R-code! ChimeraX commnds!) in an appendix linked from your report;
• When you are done, submit the link to your page via Quercus as described above.

 

Oral test option

• Work through the tasks described below. Remember to document your work in your journal, but there is no need to format this specially as a report.
• Part of your task will involve writing an R script; refer to the Code submission instructions and link to your page from your Journal.
• Note that the work must be completed before your actual test date.

 

R code option

• Work through the tasks described in the scenario below and develop code as required.
• Put your code and other documentation on a subpage of your User page on the Student Wiki;
• When you are done, submit the link to your page via Quercus as described above.

Contents

 

Scenario background

You have collected the APSES domain proteins of MYSPE in your protein database and this is now a pretty nice collection of widely distributed sequences with a shared fold. We can be very confident about our APSES domain alignments, since there are hardly any indels in these sequences - and given a confident alignment we can arrive at a very reasonable structural model. This, for example would allow us to look at residues in the APSES recognition domain that are conserved among known Mbp1 orthologues, but vary between paralogues - you have all the tools to try this at some point.

For this assignment however we are going to look at conservation in the ankyrin domains and their identification and alignment is a bigger challenge. Interestingly, an ankyrin domain structure is known for one of the homologues in this set- although it is not in our set of sequences. This is the structure of yeast Swi6, a homologue of Mbp1 that has a non-functional APSES domain; it too is involved in cell-cycle regulation since it dimerizes with Mbp1 in the MBF complex (as well as dimerizing with Swi4 in the SBF complex).

 

Task:

Your common taks for this scenario are as follows. Execute them and document.

• Produce a multiple sequence alignment of the yeast Swi6 sequence from PDB 1SW6. Make sure you include all MBP1 homologues from the database, not just the Mbp1 orthologues.
• Following the procedures of the Homology Modelling unit, prepare a homology model of the MBP1_MYSPE ankyrin domains based on the 1SW6 structure.

 

Task:

For the report option...

Considering the columns of your multiple sequence alignment, discuss and document with reference to your homology model whether the model has solvent exposed residues that are highly conserved. Take particular note whether there are any such residues where MBP1_MYSPE differs from the consensus of the other, aligned sequences. (Such outliers could point to functionally significant residues.)

 

Task:

For the Oral Test option...

Prepare to discuss during the test, with specific reference to your homology model, whether the model has solvent exposed residues that are highly conserved. Take particular note whether there are any such residues where MBP1_MYSPE differs from the consensus of the other, aligned sequences. (Such outliers could point to functionally significant residues.) Make sure the data upon which you base your conclusions is available in summary on a page of the Student Wiki before your test.

 

Task:

For the publication image option...

Create a two-panel publication-quality image to illustrate whether conserved residues of the model form a putative interaction surface. Panel (a) contains a stereo image of your modelled domain with a transparent surface enclosing a cartoon representation of your model. Highly conserved residues are colored red, and their side-chains are shown. Panel (b) shows the plot of conservation scores (per residue, not rolling averages) with a horizontal line that indicates your cutoff of what you have considered "highly conserved". Include informative figure captions. Don't forget to describe your methods and submit your code and commands in an appendix.

 

Task:

For the R-code option

Referring to the User Documentation of the ChimeraX commands color byattribute ..., and defattr ..., write the msa conservation scores for your model to a text file in the format of a ChimeraX attribute assignment file (cf. the examples linked from the ChimeraX User Documentation). Read the attribute file into ChimeraX using the remotecontrol rest ... command and appropriate scripted commands sent via the CX() function as demonstrated in the RPR-ChimeraX-remote.R script. Structure your code so that you can switch a defined constant at the beginning that defines whether the commands are applied to your homology model, or to the original 1SW6 coordinate set. Produce a stereo scene that shows your model as a cartoon image enclosed by a transparent surface, where both model as well as surface are colored by conservation values. Briefly interpret the results.

To evaluate your code, I need to be able to reproduce the scene from your code.

Document your work clearly, and discuss the process of computing attributes in R and mapping them to 3D models with ChimeraX. Can the process be significantly improved?

 

Notes

 

About ...
 
Author:

Boris Steipe <boris.steipe@utoronto.ca>

Created:

2017-08-05

Modified:

2020-10-07

Version:

1.3

Version history:

• 1.3 Edit policy update
• 1.2 2020 updates. Full rewrite of tasks and evaluation: model ankyrin domains and focus on conservation scores.
• 1.1 Corrected posted marks, which were not consistent with the description in the syllabus.
• 1.0 Live 2017
• 0.1 First stub

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