This is essentially pass/fail. If you do not get at least 70% your should resubmit the problems you got wrong.
Do not give me raw print-outs or a huge amount of numbers. For example I dont want a list of every homologous protein. Rather tell me how many their are. Do they fall into interesting classes-how many from bacteria or higher animals? Are they from different organs? Are there lots of mutants? If you are lost for how to organize your findings ask each other or ask me in person or by email.
If you want me to look at the output from a particular site or program email me the file or the site address.
What's the point?
Before you look at the atomic coordinates of your protein.
Find some papers that will describe the function of your protein and some that
connect function to the structure.
How is your protein fold classified.
Compare the classification in different systems. What proteins have similar
folds. Again compare this assignment in different systems. (e.g. SCOP, CATH,
FSSP, ...)
How many structures are available for your protein or related proteins? What
can you learn by comparing different structures?
What is the function of your protein? What proteins with similar function have
structures available?
Do a search of the sequence data bank.
Doing sequence analysis (BLAST, HSSP) what sequences of homologous proteins
are known? What regions of the protein are best conserved?
Use tools to start analyzing the structure of your protein
Topology (TOP, I'll run a DSSP analysis to get phi/psi if you email me the
pdb code for your protein
Compare the topology of proteins with the same fold. Is the fold conserved for
proteins with the same function?
Ligands. What residues bind the ligand? Where are these in the structure?
Structure conservation. Use the sequence analysis to identify the most conserved
residues. Where are they in the
structure?
Consider the 'forces in proteins' section and your protein. I will expect you to do something numerical in your paper connecting some homework problems to some property of your protein. Possible examples: The pH dependence of the protien; the electrochemistry, groups that can make hydrogen bonds, the desolvation cost of ion binding.
A topic of your choosing. 30% of your paper should be on a topic of your choosing. It should be related to your protein but can go in any direction you want - explore the physics of electron tunneling; making nanodevices that use what we learn in biology, tell us about some metabolic problem or a disease; apoptosis, teach me something I don't know.
1) Do a medline search to
find papers that describe the structure and function of your protein. Look at
reviews to start with
2) Folds: do for SCOP and
CATH
How is you protein classified?
CATH Class; Architecture;
Topology; Homologous superfamily
SCOP: class; fold; superfamily,
family
What other proteins are related (e.g. are the proteins in the CATH homologous
superfamily; what proteins are in the same SCOP family? Are they the same proteins.
What is the description of the fold of your protein?
3) Look in A Library of Protein Family Cores
to find proteins with similar cores (Use the PDB structure List to search for
your structure). This seems a good place to start since you will move to the
other data bases already keyed to your pdb file..
Move down to search in Swiss Prot for your entry. Now do a DIRECT BLAST submission
to find homologous protein sequences.
Report on one other data base info for your protein. (e.g. HSSP or DALI or ...)
Report on what information you are getting for one of the data bases. You may
need to read references. If you give you summary by email so I can pass this
on to others in the class). .
Alternately use the PDB report page on your protein to look for other information.
4) Find a PDB file of your protein.
How many other crystal structures are available of your protein? What is the difference between them (resolution; organism that it is isolated from; mutant; ligand bound)?
Make a topology map and compare this with the protein 3 d structure.
5) What ligand is bound to your protein. What is its function? What amino acids are in contact with your ligand. See if you can find the HSSP analysis for your protein. Is the part of the protein near the ligand highly conserved?
IF you put your 4 letter PDB code in the xxxx you will get an HSSP report on your protein http://srs.ebi.ac.uk:5000/srs5bin/cgi-bin/wgetz?-e+[HSSP-ID:'xxxx']
Look for the SEQUENCE PROFILE AND ENTROPY listings if available for your protein.