Bioinformatics I

Graham Kemp > Teaching > Bioinformatics I

Practical: Molecular Graphics 2

Aims

To reinforce the basic concepts of protein structure described in the lectures.
To give practice in using molecular visualisation software.

Objectives

After this practical you will:

be familiar with examples of different protein structure classes;
be familiar with examples of protein super-secondary structure;
be aware of the distribution of hydrophobic and hydrophilic residues in protein domains;
understand how main chain conformation is represented on a Ramachandran plot.

Introduction

We shall use RasMol to view protein structures taken from the Protein Data Bank (PDB). If you need help during the practical, please ask. If you need help when working on your own, a useful starting point is the RasMol Manual.

Exercises

Myoglobin

Protein Data Bank entry 1MBN is an X-ray structure of sperm whale myoglobin. What is the structural class of this protein (CATH and/or SCOP)?
Start with a wireframe representation of the whole molecule, then highlight the helix between residues 20 and 34 as follows:
```
      RasMol> select 20-34
      RasMol> cartoons
      RasMol> select 20-34 and sidechain
    
```
and select "Ball & Stick" from the "Display" menu.

Looking along the axis of this helix, describe the distribution of charged and uncharged residues.

You might find it convenient to reset the center of rotation by typing "set picking center" then clicking on an atom, and to colour the residues according to their properties e.g. by typing "colour amino".

Next, highlight the same helix as follows:
```
      RasMol> select all
      RasMol> colour white
      RasMol> spacefill
      RasMol> select 20-34
      RasMol> colour amino
    
```
Which side chains of this helix are accessible to solvent?
Again, start with a wireframe representation of sperm whale myoblobin (1MBN). Highlight the region between residues 20 and 42 as follows:
```
      RasMol> select all
      RasMol> cartoons
      RasMol> select 20-42
      RasMol> colour red
    
```
Describe the conformation of this region. Explain what happens to the conformation after position 34.
Measure the phi and psi angles of some residues in the middle of alpha helices. Where are these located on a Ramachandran plot?
This protein contains four proline residues. Where are these located on a Ramachandran plot?
Where are the residues at positions 80 and 150 located on a Ramachandran plot?
Read the description of Ramachandran plots by residue type in the PROCHECK Operating Manual. Discuss whether the residues examined in Questions 5 and 6 have favourable main chain conformations.

Immunoglobulin

Protein Data Bank entry 1HZH is an X-ray structure of the human antibody IgG1 b12. What is the structural class of this protein (CATH and/or SCOP)?
When viewing a large protein it is often convenient to display only a part of the structure. As examples of how to restrict the set of atoms displayed, the following RasMol commands display the following atoms: all atoms in chain H; all atoms in the first domain of chain H; all atoms in beta-sheets in the first domain of chain H.
```
      RasMol> restrict *h
      RasMol> restrict *h and 1-113
      RasMol> restrict *h and 1-113 and sheet
    
```
The first domain of chain H contains several beta-hairpins and a three-strand meander. Where is the meander?
Measure the phi and psi angles of some residues in the middle of strands. Where are these located on a Ramachandran plot?
The loop between residues 146 and 152 in chain H contains two residues that have a cis conformation. Identify these residues and measure their omega angles.

Triose Phosphate Isomerase

Protein Data Bank entry 1TIM is an X-ray structure of triose phosphate isomerase. What is the structural class of this protein (CATH and/or SCOP)?
How many examples of beta-alpha-beta super-secondary structure are in chain A of this protein? Are these examples left-handed or right-handed?
Describe the distribution of changed and uncharged residues in chain A. In particular, what residues are in the beta-barrel?

Structural Classifications

Browse through the CATH and SCOP classifications and view some other structures.

Supplementary Material

The immunolobulin structure examined in the practical exercise is an antibody against HIV-1. For more information about the structure of this antibody, and its potential value in vaccine design, see:

Saphire, E.O., Parren, P.W.H.I., Pantophlet, R., Zwick, M.B., Morris, G.M., Rudd, P.M., Dwek, R.A., Stanfield, R.L., Burton, D.R. and Wilson, I.A. (2001) Crystal Structure of a Neutralizing Human IgG Against HIV-1: A Template for Vaccine Design. Science, 293, 1155-1159