Introduction to Bioinformatics

Introduction to Bioinformatics - COIN81

Protein Structure Exercise Part One

See also the protein_structure_exercise.zip file archive

Instructions for navigating NCBI structure, molecular database (MMDB), and conserved domain databases (CDD)

From http://www.ncbi.nlm.nih.gov choose structure http://www.ncbi.nlm.nih.gov/Structure/

From the Structure main page, we're going to search for a structure file. Let's choose COMT first. Type COMT into the search field and press go.

The page that is returned will have this URL http://www.ncbi.nlm.nih.gov/entrez/query.fcgi On this page you'll see four structure file entries:

1KYZ
1KYW
1JR4
1VID

We will explore 1VID, but make a mental (and physical) note to come back here, as we'll also look at 1KYZ.

Move your mouse down to the 1VID link, select that.

Your URL is now: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?form=6&db=t&Dopt=s&uid=4499

The page will show MMDB Structure Summary

There are three colored lines across the page. One is labeled protein, and the other two are CDs (conserved domains).

Protein
KOG1663
COG4122

Choose the protein link, and click on it. You'll now go to http://www.ncbi.nlm.nih.gov/Structure/vast/vastsrv.cgi?sdid=11590

That page is entitled VAST Structure neighbors. This is a *very* busy page.

This page has roughly 50 structure entries below 1VID. These start with 1HID chain A, and move down to 1EJ6.

From this page you can explore the structure of 1VID, it's neighbors, and the conserved domain database.

We'll do one at a time. First note that there are four rounded / rectangular images, two red, one light blue, and one dark blue. We're going to explore each one of these.

The top red image has a link on either side of it. On the left side, 1VID will take you to the GenPept entry for 1VID. Try that. On the right hand side there is a link to aligned residues.

Press that link to see a very thorough table comparing the alignment of 1VID with the 50 closest structural neighbors. This alignments are based on the same scoring matrix as BLAST.

Now go back to http://www.ncbi.nlm.nih.gov/Structure/vast/vastsrv.cgi?sdid=11590 and press in the middle of the top red image. You'll then see a residues by residue alignment of 1VID with each of the structural neighbors.

Come back to http://www.ncbi.nlm.nih.gov/Structure/vast/vastsrv.cgi?sdid=11590 once again. Scroll down just to the second red image labeled chain.

Chose the link on the left hand side, labeled 3D_domain. It will take you to back to the structure page http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=structure&cmd=Display&dopt=structure_domains&from_uid=4499

Fell like you're going around in circles? You're not - this is simply how all the entries are interconnected.

Go back to the VAST page http://www.ncbi.nlm.nih.gov/Structure/vast/vastsrv.cgi?sdid=11590 and click the second red image with chain marked on it. This *is* essentially the same page.

Go back and now explore the two blue images, but first click the blue link on the left labeled CDs. That take you to:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd&term=19451[pssm]+OR+13404[pssm], which are our two entries in the CDD (Conserved Domain Database).

You can choose either of the links from this page, or from VAST, either of the two images. Explore those two pages so that you are sure of that.

The Conserved Domain Database shows the protein domains closest to 1VID (COMT) but we'll come back and look at 1KYZ later as well.

BTW - if you have time, to a side by side BLAST comparison of 1VID and 1KYZ. Can you remember how to get to 1KYZ? From Structure search 1KYZ and then choose the GenPept link.

As you explore KOG1663 and COG4122, look at Pfam links pfam01596.11, Methyltransf_3 - and make a note to remember to look at Pfam (using COMT sequence) later on.

Now let's go back to NCBI structure at http://www.ncbi.nlm.nih.gov/Structure/ Repeat everything above, but after entering COMT, chose the 1KYZ entry.

Okay - now we've finished with the basic navigation pieces of Structure, Let's dive into Cn3d, RasMol, and SPDBV viewer next.

These will be a lot of fun, although using VAST alignment within Cn3D can be *very* tricky.

So let's try Cn3D next. You'll need to download and install the latest version for PC, Mac, or Linux.

From the main Structure page http://www.ncbi.nlm.nih.gov/Structure/ choose http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml

Then http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dinstall.shtml and choose windows, Macintosh, or Linux

Make *sure* to look through the Cn3D tutorial at http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dtut.shtml as well as

the VAST tool at http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml . We'll be using that for structure alignments.

We'll start by going back into Structure. We're going to download and view the .val and .pdb structures for COMT, focusing on 1VID and 1KYZ

The exact files you'll be looking at will be 1VID.val, 1VID.pdb, 1KYZ.val, and 1KYZ.pdb

In order to view the .pdb files, we'll need to download and install two more software applications. Both are free, and both are pretty stable.

To download RasMol, go to http://www.rasmol.org/ and or go to http://www.informaticus.org/COIN81/files/RASWIN_v2.71.EXE

to download SPDBV go to http://www.expasy.org/swissmod/SWISS-MODEL.html and follow the link in the right hand frames window (Deep View)

The exact pages you'll visit will be http://au.expasy.org/spdbv/ and http://au.expasy.org/spdbv/text/download.htm

You can also go to the COIN81 files directory http://fgamedia.org/faculty/rdcormia/COIN81/files/ and download spdbv37b2.zip (for Windows) If you are nervous about installing software, just try Cn3D and RasMol. SPDBV is pretty cool though.

After you've installed these applications, we'll start downloading some files to investigate.

Go back to http://www.ncbi.nlm.nih.gov/Structure/ and type in 1VID. Follow that link back to:

http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?form=6&db=t&Dopt=s&uid=4499

This time click on the silver button in the lower left hand corner that says 'View 3D Structure' and make sure you have Best Model and Cn#D set.

You can display the file in Cn3D or save the file to your desktop - it's one or the other, but either way you *will* need to save the file, and view it in Cn3D. Try it both ways.

For fun, you should also click the 'view 3D Structure' with 'see file' set. Now you are looking at the actual file.

Spend some time using Cn3D. It's pretty cool. Things to do are to:

1) view different types

2) color and display

3) export image to a .png (Portable Network Graphics) file. From there you can convert to .bmp, .gif, or .jpg in Paint or Photoshop LE etc.

Later we'll do an alignment using VAST, but that's a little trickier.

From the Structure page http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?form=6&db=t&Dopt=s&uid=4499, you should next navigate to save the PDB file.

Follow the PDB 1VID link http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1VID to RCSB

Chose view structure in http://www.rcsb.org/pdb/cgi/explore.cgi?job=graphics&pdbId=1VID&page= to see HTML and JPEG images.

Next chose download file http://www.rcsb.org/pdb/cgi/explore.cgi?job=download&pdbId=1VID&page= to see a page with file and download options

Choose file format PDB, and file compression none to download the file (you can right click) :

http://www.rcsb.org/pdb/cgi/export.cgi/1VID.pdb?format=PDB&pdbId=1VID&compression=None

after you download these files, you can (and should) open them with RasMol, and with SPDBV 3.7

RasMol is very basic, but does let you view pieces of the structure (backbone, side chains etc.) and color them in different ways.

Make sure to go to http://www.rasmol.org/ to look at information related to help files and guides.

Then open in SPDBV 3.7. This application is pretty powerful in what it can do, and as such, it can be used in a basic or advanced mode.

After you have finished that, take a break. Part two of this exercise will focus on alignments of two proteins (1VID and 1KYZ) using VAST.