BCB 590

Final Exam

1) Resources and tools (16 pts – 2 pts each)

In the blank preceding each of the following questions/problems and from the list provided, identify the single best software/server to use to answer the question

a) What is the predicted secondary structure of this RNA?

b) Is there a structure for this protein?

c) What is the predicted secondary structure of my protein?

d) Have any characteristic patterns or profiles been identified for my protein family?

e) Are there any predicted genes in my sequence?

f) Is the leptin protein thought to be involved any human diseases?

g) What would server could I use to generate a homology model for this protein?

h) Does this protein interact with other proteins?

GeneMark

3D-Jury

GEPAS

OMIM

SwissProt

Readseq

PyMol

M-Fold

UCSC Genome Browser

PDB

Clustal W

Phylip

PSI-PRED

SWISS MODEL

ProSite

DIP

2) What's that protein? (28 pts)

MEESQSELNIDPPLSQETFSELWNLLPENNVLSSELCPAVDELLLPESVVNWLDEDSDDAPRMPATSAPT
APGPAPSWPLSSSVPSPKTYPGTYGFRLGFLHSGTAKSVTWTYSPLLNKLFCQLAKTCPVQLWVSSPPPP
NTCVRAMAIYKKSEFVTEVVRRCPHHERCSDSSDGLAPPQHLIRVEGNLRAKYLDDRNTFRHSVVVPYEP
PEVGSDYTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNVLGRNSFEVRVCACPGRDRRTEEENFHKK
GEPCPEPPPGSTKRALPPSTSSSPPQKKKPLDGEYFTLQIRGRERYEMFRNLNEALELKDAQSGKEPGGS
RAHSSHLKAKKGQSTSRHKKLMFKREGLDSD

Answer the following questions and be sure to list the software you used, accession or reference numbers for genes/proteins on which you base your conclusions and describe the conclusions you were able to draw from each type of analysis.

(2 pts) What is this protein?

(2 pts) In what organism(s) is this protein found?

(2 pts) What is the accession number for this protein?

(2 pts) What is the NCBI Gene ID for this protein?

(2 pts) What are the conserved domains in this protein?

(2 pts) Are there any related structures for this protein? If so, is the structure of the entire protein?

(2 pts) Does this protein have a homolog(s) in the human genome?

(2 pts) Are any of these genes/homologs associated with known disease(s) in human?

(3 pts) Find a 3-D structure for this protein or one of its homologs. What is the PDB id for this structure?

(3 pts) Predict the structure of this protein. What server did you use? What template structure was used? Is this the same structure you found in the previous section?

(3 pts) What is the predicted secondary structure of this protein?

(3 pts) Does the predicted secondary structure agree with the secondary structure observed in your predicted 3D structure?

3) Pymol (16 pts)

(6 pts) Download the structure file for PDB ID 1AAY and open it in PyMOL. Create separate selections for each of the following (items in parentheses are the residue name(s) for the specified selection):

DNA (DA+DT+DG+DC)

water (HOH)

zinc ions (ZN)

Create an additional selection containing only the protein.

Hide everything, then show the DNA in sticks representation, the protein in cartoon representation, and the zinc ions in spheres representation.

Once you have done this, get the attention of one of the TAs. You will either receive credit for completing this part of the exercise, or be informed that you need to try again until you have everything displayed properly.

(6 pts) Create a selection called interfaceh2o containing molecules that are:

· water and are within 3.5 angstroms of the protein and are within 3.5 angstroms of the DNA. (hint: you will need to use the around selector)

· Show these interface water molecules in spheres representation

Once you have done this, get the attention of one of the TAs. You will either receive credit for completing this part of the exercise, or be informed that you need to try again until you have everything displayed properly.

(4 pts) Create a selection called waterbinding that contain molecules that are:

· Within 3.5 angstroms of the selection you just created. (hint: you will need to use the around selector)

· Use the byres selector to modify your waterbinding selection to contain the entire residue for any atoms involved in binding the water.

· Show this selection in sticks representation

Once you have done this, get the attention of one of the TAs. You will either receive credit for completing this part of the exercise, or be informed that you need to try again until you have everything displayed properly.