BIOC 530: Homework 4 (20 Points)

BIOC530: Homework 4

Name:

Student ID:
1. Use PSI-BLAST (http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi) to search for sequences related to the C chain of the 1KCG crystal structure (you can find its sequence on the RCSB PDB).

Q1. What protein is this?

Q2. To what class of proteins is homology revealed with PSI-BLAST?

Q3. How do the identity and ordering of results change after a second and third iteration of the PSI-BLAST algorithm? (Do this by clicking on the ‘Go’ button.) With what you know about PSI-BLAST from the lectures, why do you think this change occurs?

2. Identify two proteins with SH3 domain-like folds that are not in the SH3 domain sequence family using the SCOP database (http://scop.mrc-lmb.cam.ac.uk/scop/). Use PSI-BLAST to determine whether the structure similarity is detectable using sequencing based searching.

3. A group of researchers at the Protein Design Institute designed an ideal repeat protein. Below is the sequence:

DKDEAWKCVEQLRREGATQIAYRSDDWRDLKEAWKKGADILIVDAT

DKDEAWKQVEQLRREGATQIAYRSDDWRDLKEAWKKGADILIVDAT

DKDEAWKQVEQLRREGATQIAYRSDDWRDLKEAWKKGADILICDAT

They are curious if it matches anything found in nature.

Q1: Use blastp<http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins> to search against the pdb database. Are there any significant PDB hits?

Now try using each of the following foldrecognitionsoftware:

SPARKS-X http://sparks-lab.org/yueyang/server/SPARKS-X/

HHpred http://toolkit.tuebingen.mpg.de/hhpred

RaptorX http://raptorx.uchicago.edu/StructurePrediction/predict/(raptor-X can take some time to run)

Q2: What do you find from those servers?

Q3: For HHpred: Look at the first 10 aligned residues between your chosen target and the matched PDB file. Is there much sequence similarity? Explain. What SCOPfamilydoes this PDB hit belong to?

4. This problem is to learn about distributed computing and how it can be used for protein folding problems. You will enroll at least one computer into Rosetta@home (http://boinc.bakerlab.org/rosetta/) and join our class team.
First you must install BOINC software and open a BOINC account. Then join our class team (team name: BIOC530_2015; website: http://boinc.bakerlab.org/rosetta/team_display.php?teamid=13548) and start folding. Your answer to this problem should include your username and an explanation of one of your results (from the “results” link on the project home page after you’ve logged in). Have fun!

5. For this problem, download and install the protein folding computer game FoldIt from http://fold.it (it is available for PC, Mac, and Linux). Create an account (please specify your username in your answer) and play at least the first four ‘Intro Puzzles’. What concepts from the class do these intro puzzles incorporate? After you’re familiar with the game, go to the ‘Science Puzzles’ section and pick one of the posted puzzles. Use the tools (pulling, shaking, wiggling, and possibly mutating) to improve your score. Explain what the scientific purpose of the puzzle is, and what you did to improve your score. Next, click on the ‘Social’ menu at the bottom of the screen, and then click on ‘Exploration Map’. How is this different and similar to the results plot you saw on the last question? What does this graph show, and how does it change as you play the game?