ObjectiveTo add another GPCR sequence to the alignment made in the previous lesson and to improve the alignment within the first helix using the ICM alignment editor.

Background Here you will become familiar with sequence .drag and drop. and the ICM Alignment Editor.

Instructions

1. File/Load/Swissprot and enter D2DR_HUMAN (Human Dopamine GPCR)
2. Click on the D2DR_HUMAN sequence in the ICM Workspace and then drag it and drop it into the ICM Alignment. A new alignment will be formed with the 3 sequences (1f88_a, 5HT1A_Human and D2DR_HUMAN).
3. You may need to restore the secondary structure display. Each red bar indicates a helix. There should be 7 in total.

Notes and things to try:

• Helix 1 in GPCRs are notoriously hard to align to the only currently available template structure (bovine rhodopsin . 1f88). The ASN55 (is the only fully conserved residue in helix 1. Shift the sequence of 5HT1A and D2DR along to remove the gaps in this helix. To move a block of sequences there needs to be a gap in front. To do this click and drag over the block and they will be highlighted in blue. Use the right and left arrow cursors to move.
• Try hiding gaps using the menu displayed when right clicking on the Alignment Editor.

Manual References (Web Links) Alignment Editor Align Multiple Sequences