Using structure alignment tools

1. Using structure alignment tools

2. Structure alignment • View a structural alignment of the P53 1T4F protein with Catalytic And Tetramerization Domains From Rat 2TOH protein. Look at the similarities and differences between these two proteins.

3. Structure alignment with VAST • VAST (Vector Alignment Search Tool) • structural alignment is based on similarities in 3-dimensional form rather than linear sequence. As such, it is a much more complicated alignment and requires more extensive computing power. This is why the structure alignments are precalculated and stored for retrieval instead of being generated upon user demand like sequence alignments.

4. What do structure alignments look like

5. Using Structure neighbors • From MMDB's structure summary pages, lists of structure neighbors are available by clicking on the chain itself in the graphical portion of the structure summary page. The VAST-result page then presents a graphical representation of the neighboring structures sorted by VAST similarity scores. This is particularly useful when searching for related structures to a structure of interest. • Method for viewing an alignment using structure neighbors: • 1. Open the structure summary of interest. • 2. Click on one chain or domain in the graphical representation. • 3. View the structure neighbors list. • 4. Select a structure (or structures) to align with the first structure by clicking the checkboxes. • 5. Click on the "View 3-D Structure" button. • 6. There is also an option ("Find") to search for a specific structure.

6. Do It • P53 1T4F protein with • align Rat 2TOH as neighbor • http://www.ncbi.nlm.nih.gov/Structure/

7. Importing Structures • Just as the Import Window in Cn3D allows the user to import sequences and make BLAST alignments, the Import Window also provides the option of importing structures and VAST structure alignments. • 1. Determine the PDB and MMDB identifier numbers for the structures in advance. It may be helpful to write them down. • 2. Open one of the structures in Cn3D.3. From the Sequence Window's Imports Menu select "Show Imports." This will open the Import Window. • 4. From the Import Window's Edit Menu, select "Import Structures." From the dialog box that opens up, select "Via Network.” • 5. Enter the MMDB identifier number for the structure to import. • 6. If it asks which chain, select the one(s) to align. • 7. It will create an alignment in the Import Window, but also it will provide a warning that is is necessary to save the alignment to a file and then re-open it in Cn3D. Click on "OK.” • 8. From the Import Window's Alignment Menu, select either "Merge Single" or "Merge All" depending on how many structures have been imported. • 9. Close the Import Window. • 10. From the Structure Window's File Menu, select "Save." Give it a file name and say "yes" to any queries. • 11. From the Structure Window's File Menu, select "Open." Choose the file that was just saved. • 12. It should open in Cn3D and show the structural alignment.

8. Do It • View a structural alignment of the human Leptin protein (MMDB: 9153; PDB: 1AX8) with the human Ciliary Neurotrophic Factor protein (MMDB: 5903; PDB: 1CNT). • Look at the similarities and differences between these two proteins. • Can you add the structure for human prolactin (MMDB: 22679; PDB: 1N9D) to the alignment?