Make a sequence alignment in Cn3D. |
| Sample User Question |
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Align the Apolipoprotein IV sequence (NP_000473) with the structure of chain
A of Apolipoprotein I (1AV1) using the import and align features of
Cn3D.
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| Analysis/Comments |
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While interposing a sequence alignment onto a known structure does not
give a true, exact structure for the sequence of interest, it does
give an initial model from which the researcher may be able to form
testable hypotheses. It is absolutely vital to remember that this is
solely a sequence alignment, based on BLAST. However, where the sequences
are identical, it is possible that the structure may be similar as well.
Remember that this is an assumption which may not always be correct.
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| Flow Chart |
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MMDB - MMDB is a database of experimentally determined three-dimensional
biomolecular structures
- Cn3D
- Cn3D is a helper application for your web browser that allows you to view
3-dimensional structures from NCBI's MMDB
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| Step By Step Guide |
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MMDB
- Go to Entrez Structure and search MMDB for PDB ID# 1AV1 (Apolipoprotein
I chain A). Locate and view the structure summary.
- Click on 'display structure' to open Cn3D.
Cn3D
- Go to the Sequence/Alignment Viewer (text window) and click on
Imports-Show Imports and a new Import Viewer Window will pop up.
- Click on Edit-Import Sequences and a window will pop up asking for you to select a chain to align the imported sequence to
- select chain A.
- The next option asks you to either select a FASTA file or enter Network GI/Accession ID (from Entrez via an internet connection). Choose
the Network option, then enter the accession number for Apo IV (NP_000473) for the sequence to be imported.
- After the sequence comes up in the Import Viewer Window, click on
Algorithms-BLAST single, then immediately click on the imported sequence when
the mouse cursor becomes a cross. When the alignment is made, some of the amino
acid codes will become capital letters.
- Next, click on Alignments-Merge All (Or Aligments-Merge Single). This will put the alignment
in the Sequence/Alignment Viewer for visualization. Close the now-empty Import window.
- View the structure. Note the coloring change. The alignment is shown in one color (usually
red) and the unligned regions of the ApoAI structure are in another color (usually purple).
- Go to the style menu and choose the coloring shortcut under
'sequence conservation' for 'identity'. See that it shows the identities in red
and non-identities in blue.
- Try some of the other style and coloring options.
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| Additional Notes |
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When you look at the alignment, identify areas of higher similarity, lesser
similarity? How useful might this alignment be? How could it be used?
Note that this is a sequence alignment imposed over ONE structure only.
It gives hints to the structure of Apo IV, but doesn't predict it with any certainty.
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