[ Homology Modeling | Kinase Homology Modeling | Loop model tutorial ]

Overview

This lesson will take you through the basics of protein modeling. Topics include:

• Building a homology model.
• Kinase modeling example
• Loop Modeling

Background

ICM has an excellent record in building accurate models by homology. The ICM modeling procedure builds the framework, shakes up the side-chains and loops by global energy optimization. You can also color the model by local reliability to identify the potentially incorrect regions of the model. ICM also offers a fast and completely automated method to build a model by homology and extract the best fitting loops from a database of all known loops. It just takes a few seconds to build a complete model by homology with loops. Some selected publications related to modeling and structure determination are listed here.

Abagyan, R.A., and Totrov, M.M. (1994). Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations for Peptides and Proteins. J. Mol. Biol., 235, 983-1002

Cardozo, T., Totrov, M., and Abagyan, R. (1995). Homology modeling by the ICM method. Proteins: Structure, Function, Genetics, 23, 403-414

Abagyan, R., and Totrov, M. (1999). Ab initio folding of peptides by the optimal-bias Monte Carlo minimization procedure. Journal of Computational Physics, 151, 402-421

Maiorov, V.N., and Abagyan, R.A. (1997). A new method for modeling large-scale rearrangements of protein domains. Proteins, 27, 410-424

Schapira, M., Totrov, M. and Abagyan, R. (2002). Structural Model of Nicotinic Acetylcholine Receptor Isotypes Bound to cetylcholine and Nicotine. BMC Structural Biology 2:1

22.4.1 Homology Modeling

Objective

To make a protein model based on sequence homology.

Instructions

1. Edit/Delete All . let us begin with a clear ICM session!
2. Homology/Load Example
3. Two sequences (ly6,CD59), one template structure (x) and an alignment (sx) should be loaded. Sequence CD59 is the sequence of the template structure called x.
4. Homology/Build Model and fill in the table using the drop down options. Warning minimize side-chains may take a few minutes.

Notes and things to try:

• The four built in loops are shown in red as default.
• Try displaying the model and the template in different colors or representations to observe any siginificant deviations between template and model.

Manual References (Web Links)

Homology Modeling

22.4.2 Kinase Homology Modeling

[ Search for Template | Make Alignment | Build Model | Model Loop ]

22.4.2.1 Search for Template

22.4.2.2 Make Alignment

22.4.2.3 Build Model

22.4.2.4 Model Loop

22.4.3 Loop Modeling Tutorial

In this example we will use the high precision loop modeling method Arnautova et al Proteins. 2010, 79:477 to model a loop region in Anthrax Protective Antigen which contains a proline residue where the cis/trans conformation is not clear from the available X-ray crystal structures. We will determine the most energetically favorable conformation of the proline and the neighboring loop residues.

Step 1: Use the search tab to read in two pdb structures 1acc and 1tzo.

Step 2: Delete everything except for the first molecule of each protein. You can use the command line as suggested to delete the other molecules or you can: -use the CTRL button and click on them - right click and select delete.

Step 3: Extract hte sequences from both receptor by right clicking on the molecule in the ICM workspace. The alignment makes it easier to superimpose the loop and select the loop in both structures.

Step 4: Select the loop region from residues 410-414.

Step 5: Take this opportunity to look at both structures and observe that one is in the trans conformation and the other in the cis.

Step 6: We will re-model the lower resolution structure and so we need to convert it into an ICM object.

Step 7: Select the loop region in 1tzo only - do not select the loop in both proteins.

Step 8: Start the loop modeling using the option in the MolMechanics menu.

Step 9: The docking will run in the background.

Step 10: You will be notified when the simulation is finished.

Step 11: The best energy conformation of the proline in the loop is the cis conformation.