Comparative Protein Structure Modelling: Practical exercises

Lorenza Bordoli


Visualization and analysis tool:

DeepView: [tutorial][download]

Download the Prosite patterns in the "spdbv/usrstuff" directory of DeepView.

Web servers:

Databases:

PDB: repository for 3-D biological macromolecular structure data.
Swiss-Prot: Protein knowledgebase.


Part 1: Homology Modelling: getting started.

Modeling of the bacterial methylpurine-DNA glycosylase (AlkD, Uniprot AC: Q2PAD8)

1) First search for suitable templates to model the methylpurine-DNA glycosylase. Please use the "Template identification" from the Tools section of the SWISS-MODEL Workspace. [You are going to run only the Blast]. How many different templates do you find? Do the structures of the templates differ? Visualize the structures of the putative templates in DeepView, superpose (Fit->Iterative Magic Fit) the structures and look at the differences (if any) of the structures. Which template would you use to generate a model for the bacterial methylpurine-DNA glycosylase protein?



Part 2:
Homology Modelling of Cyclin A1

In the first part of the practical exercises, we are going to build an homology model for the human protein, Cyclin A1 (Swiss-Prot entry P78396).
1) First have a look at the Swiss-Prot entry to learn more about the function of this protein. Is there any protein domains described for Cyclin A1? (Hint: you can either look at the InterPro annotations for this entry, or use the "Sequence Feature Scan" from the Tools section of the SWISS-MODEL Workspace
to run "InterPro domain scan".

2) Now we can search for a suitable template for building the model: please use the "Template identification" from the Tools section of the SWISS-MODEL Workspace. [You are going to run only the Blast]. How many templates are available? Can you build a model for the entire protein? How do the different templates differ? How do you judge the alignment between target and template? (Hint: Exhaustive information about the individual templates is available directly from the template selection output as link to the SWISS-MODEL template library and external resources).

3) Build an homology model for the human Cyclin A1 protein using one of the available templates. Since the alignment between target and template is trivial, you can use the "Automated mode" of the Modelling tools of the Swiss-Model Workspace. How is the quality of the obtained model?


Part 3: Homology Modelling of a putative protein kinase C delta from Drosophila.

In this second example we are goind to build a model for the kinase domain of a putative protein kinase C delta from Drosophila (Pkcdelta, UniProt AC: P83099).

The PKC family members can be grouped into three classes: (i) the conventional PKCs (a,g and b1 and b2), which requires diacylgycerol (DAG), phosphatydilserine (PS), and calcium for activation, (ii) the novel PKCs (d, e, h/l,  q) which are activated by DAG and PS but are insensitive to calcium and (iii) the atypical PKCs (z and i/l) which require only PS for full activity.

1) First have a look at the UniProt entry to learn more about the function of this protein. Is there any additional protein domains described for this protein? (Hint: you can either look at the InterPro annotations for this entry, or use the "Sequence Feature Scan" from the Tools section of the SWISS-MODEL Workspace to run "InterPro domain scan".

2) Now you can search for a suitable template for building the model: please use the "Template identification" from the Tools section of the SWISS-MODEL Workspace. [You are going to run only the Blast and the iterative profile Blast]. How many templates are available? Can you in principle build a model for the entire protein? How do the different templates differ? How do you judge the alignment between target and template? (Hint: Exhaustive information about the individual templates is available directly from the template selection output as link to the SWISS-MODEL template library and external resources).

3) Build an homolgy model for the kinase domain of the Pkcdelta protein with DeepView:

DeepView - Swiss-Model Workpsace


Part 4: Model quality evaluation

A 3D model of the Drosophila UDP-glucose 4-epimerase protein has been generated by homology modeling. The structure of the Human homolog protein Q14376 has been used as template. The PDB ID for the template is 1ek5. Two different models, Model1 and Model2 have been obtained: they differ in the alignment between the target and the template.
Evaluate the two models by checking the following criteria:

Which of the model would you trust more and why?

Output and input of the different web based programs (as of 13.05.06):

Bacterial methylpurine-DNA glycosylase, InterPro Scan and template Selection [output]
Human Cyclin A1, InterPro Scan and template Selection [output]
Human Cyclin A1, Modelling using the automated mode [output]
Drosophila protein kinase C delta, Template Identification [output]
Drosophila protein kinase C delta, Modelling using the project mode and template 2JED [output]
ANOLEA and Gromos output for Model1 [output]
ANOLEA and Gromos output for Model2 [output]