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4-Feb 9 -> Hand in Feb 14 Lecture:
Protein Motifs; 1°,2°,3° structures; visualization
I strongly encourage you to look at the section on protein geometry at Birbeck and at the first chapter of our text book. A very complete site for Ramachandran plots
(1) Go to the The protein data bank (PDB) site.
I'd suggest using the new
version as well. It seems slower though.
1a) How many entries are currently in the protein data bank?
(2) You have each been given a protein from the list: Actin, Tubulin, Dynein,
Kinesin, Myosin, F1/F0 ATPase (either F1 or F0). Look up your protein the protein
databank
2a) How many entries do you get?
Each protein structure has a unique 4-letter code. This search may give you
proteins that interact with your but are that protein. Also there may be multiple
copies of the same protein - from different organisms, with different mutations,
or with different bound molecules.
Try looking for your protein in 'text serch' in the Macromolecular Structure Database, I like the quick link to the abstract of the paper for each structure. This can help you figure out what PDB file you actually want. SCOP actually does the best key word search - It seems to be the best way to seperate all the 'protein X' binding proteins (which you don't want) from 'protein X' itself'. 2b) Using SCOP how many structures of your protein are available - get a list of them. Another way to go is to use PubMed and go to STRUCTURE. A keyword search will get you the PDB file you want.
Actin. 1J6Z
Tubulin. 1JFF
Dynein. 1F3C
Kinesin, 2KIN
Myosin. 1BR2
F1 part of ATPase. 1BMF
F0 part of ATPase. 1C17
For your protein. - Start with the pdb file I
gave you above. Also find one other pdb file for your protein (using SCOP or
PUBMED) and answer question 3.
You can answer these questions from The
protein data bank (PDB) site. their new
version or Macromolecular
Structure Database. In each case just type your 4 letter code in and play
around.
3a) Is this a wild type protein or a mutant?
3b) What is the 'source'. What's the common name for this organism?
3c) How many atoms in the protein?
3e) How many residues?
3f) How many polypeptide chains (subunits)?
3g) What is the resolution?
Low values of resolution are better. Below 2 Å is not too bad.
3h) What non-amino acid groups are bound to this protein (list the ligands and
prosthetic groups)?
4) Look up the function of your protein using GOOGLE and using a cell biology
text book.
4a) What does your protein do?
4b) Give me the reference to a review article about your protein.
Try using PubMed,
Google Scholar, (or when on campus
ISI web of knowledge or Science
Direct). You can use the citation for your pdb file or use 'related articles'
in pubmed to find some papers. Use keyword 'review' to narrow your seach.
For 5-7 use the pdb file I gave you for your protein.
5) Find the Ramachandran plot for your protein. I'd go to
old (PDB) site in the geometry section.
5a) Make a sketch pointing out the helical and sheet regions. Are all residues
at the optimum position for the 2° structure type?
6) Look at the MOTIF SUMMARY in old
(PDB) site.
6a) How many chains do you have?
6b) For one chain how many helices and b-sheets do you have.
6c) Use one of the visualization tools. Can you find the helices and sheets?
Which tool are you using? You can use a host of downloadable tools
like RASMOL or SwissPDB viewer (see below) or a number of simple click tools
from PDB or MSD site.
7) Look at the Ligand-Protein Contacts
for your protein. MDS LIGAND site does this well.
7a) What ligands are bound.
7b) For one ligand. Draw its structure. Go to view the interactions of __ with
__. What residues interact with the ligand?
(Swiss PDB viewer is also a good free viewer).
*** I encourage those of you who want to get the very most out of this
course to download Rasmol
onto your computer (Don't bother with Protein Explorer). Start with Rasmol
Quick Start. There is an excellent RASMOL
tutorial (work through the 'Questions & Answers about 1d66.pdb'. This
will let you look at any molecule on your computer. RASMOL runs on MACS, WINDOWS,
LINX.
**Swiss-Prot is a more sophisticated program which does what RASMOL does and
more.
**The CHIME requiring displays are GREAT but unfortunately the newer browsers
don't support CHIME. This has just happened this year and I'm not sure what
the future will bring.
LOOK AT DOWNLOAD
HELP on the PDB View Structure Site for more information.
To get the x,y,z coordinate for all atoms in this protein!
Go to www.rcsb.org
Use Search the Archive
(eg 2KIN is a pdb id for kinesin - if you look for this as an example you should
end up here
Go to Download/Display structure (left of screen)
you should end up here
Use Download the Structure File: with no
compression in PDB format
At this point the data bank will put the file 2KIN.pdb somewhere on your computer.
The file will be in TEXT format. (although the .pdb extension may confuse your
computer). Use Open in Rasmol - hopefully Rasmol will see the file. If it doesn't
let me know - the problems are computer specific and have to do with the file
not being saved as text on your machine.
**************************************************************************
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January 30, 2005