ABC-INT-Homology modelling

Integration Unit: Homology Modelling

 

Keywords:  Integration unit: create a homology model and assess the role of sequence conservation

 

 

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Abstract

This page assesses the learning units for working with multiple sequence alignments and structure data.

• Use an Mbp1 orthologue (RBM)
• Find all orthologues in MYSPE and reference species
• Homology model
• Calculate conservation scores
• Map, visualize
• Interpret with reference to winged HTH domains: 1VTN (canonical), 4UX5 (M. Oryzae Mbp1), 1DP7, 3HTS.

 

This unit ...

Prerequisites

You need to complete the following units before beginning this one:

• BIN-SX-Homology_modelling (Homology Modeling)

 

Objectives

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Outcomes

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Deliverables

• No separate deliverables: This unit collects other units and has no deliverables on its own.

 

Evaluation

Evaluation: Integrated Unit

This unit should be submitted for evaluation for a maximum of 10 marks. Details TBD.

 

Contents

This is a "milestone unit". Its purpose is merely to collect a number of preparatory units into a single, common prerequisite. It has no contents of its own; you are expected to be familiar and competent with all preparatory material at this point.

The DNA binding site

Now, that you know how MYSPE Mbp1 aligns with yeast Mbp1, you can evaluate functional conservation in these homologous proteins. You probably already downloaded the two Biochemistry papers by Taylor et al. (2000) and by Deleeuw et al. (2008) that we encountered in Assignment 2. These discuss the residues involved in DNA binding. In particular the residues between 50-74 have been proposed to comprise the DNA recognition domain.

Task:

1. Using the APSES domain alignment you have just constructed, find the MYSPE Mbp1 residues that correspond to the range 50-74 in yeast.
2. Note whether the sequences are especially highly conserved in this region.
3. Using Chimera, look at the region. Use the sequence window to make sure that the sequence numbering between the paper and the PDB file are the same (they are often not identical!). Then select the residues - the proposed recognition domain - and color them differently for emphasis. Study this in stereo to get a sense of the spatial relationships. Check where the conserved residues are.
4. A good representation is stick - but other representations that include sidechains will also serve well.
5. Calculate a solvent accessible surface of the protein in a separate representation and make it transparent.
6. You could combine three representations: (1) the backbone (in ribbon view), (2) the sidechains of residues that presumably contact DNA, distinctly colored, and (3) a transparent surface of the entire protein. This image should show whether residues annotated as DNA binding form a contiguous binding interface.

DNA binding interfaces are expected to comprise a number of positively charged amino acids, that might form salt-bridges with the phosphate backbone.

Task:

• Study and consider whether this is the case here and which residues might be included.

 

Further reading, links and resources

 

Notes

 

Self-evaluation

 

 

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If in doubt, ask! If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.

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About ...
 
Author:

Boris Steipe <boris.steipe@utoronto.ca>

Created:

2017-08-05

Modified:

2017-08-09

Version:

0.1

Version history:

• 0.1 First stub

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