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 8 marks if one of the written deliverables is chosen, resp. 16 marks for the oral test.

Please note the evaluation types that are available as options for this unit. Choose one evaluation type that you have not chosen for another Integrator Unit. (Each submitted Integrator Unit must be evaluated in a different way and one of your evaluations - but not your first one - must be an oral test).

 

Report option

• Work through the tasks described in the scenario.
• Document your results in a short report on a subpage of your User page on the Student Wiki. Describe your methods (R-code!) in an appendix;
• When you are done with everything, add the following category tag to the end of page:

[[Category:EVAL-INT-Homology_modelling]].

Once the page has been saved with this tag, it is considered "submitted". Do not change your submission after this tag has been added. The page will be marked and the category tag will be removed by the instructor.

 

Publication Image option

• Work through the tasks described in the scenario.
• Document your results in a short report on a subpage of your User page on the Student Wiki. Describe your methods (R-code!, ChimeraX commands!) in an appendix;
• When you are done with everything, add the following category tag to the end of page:

[[Category:EVAL-INT-Homology_modelling]].

Once the page has been saved with this tag, it is considered "submitted". Do not change your submission after this tag has been added. The page will be marked and the category tag will be removed by the instructor.

 

Oral test option

• Work through the tasks described in the scenario. Remember to document your work in your journal.
• Your work must be complete before 21:00 on the day before your exam.
• Schedule an oral test by editing the signup page on the Student Wiki. Enter the unit that you are signing up for, and your name. You must have signed-up for an exam slot before 21:00 on the day before your exam.

 

R code option

• Work through the tasks described in the scenario and develop code as required.
• Put your code on a subpage of your User page on the Student Wiki;
• When you are done with everything, add the following category tag to the end of page:

[[Category:EVAL-INT-Homology_modelling]].

Once the page has been saved with this tag, it is considered "submitted". Do not change your submission after this tag has been added. The page will be marked and the category tag will be removed by the instructor.

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 alignment 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 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 described. Write your code so that you can switch a defined constant at the beginning that defines whetehr the commands are applied to your homology model, or to the original 1SW6 coordinates. 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. To evaluate your code, I need to be able to reproduce the scene from your code.

 

Notes

 

About ...
 
Author:

Boris Steipe <boris.steipe@utoronto.ca>

Created:

2017-08-05

Modified:

2020-10-02

Version:

1.2

Version history:

• 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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