Biochemistry Lab
Informatics and Pymol Assignment
Name __________________________________________
Each assignment will be conducted independently - no partner. Type your answers, paste in images with
word wrap as indicated.
1)
From your initial investigation of NCBI and RCSB, answer the following (some are questions from the
handout/workshop). (5 points)
a. What is the reaction catalyzed by MDH?
b. What domains or conserved domains of MDH have you identified from your search?
c. What can you find about LDH enzymes with MDH activity?
d. Are there different variants of MDH listed in the nucleotide database?
e. Find an MDH not shown below and identify the nucleotide and protein records (sequences).
For the rest of this exercise, use the gene/protein malate dehydrogenase accession numbers pdb 1SMK, 1SEV,
and the nucleotide sequence M33148 for your problems. Use the databases and the papers you worked with
in steps 1 through 4 in the workshop to answer the questions.
2)
Search the protein, nucleotide and structure databases for malate dehydrogenase. How many hits do
you find? (1 points)
3)
Align the DNA and amino acid sequences for two different MDH records. Capture the image with a
screen shot of the result. Repeat the same for the amino acids. Paste both within your typed answers.
Text wrap and limit the image to no larger than 1/8 page. (2 points)
4)
Pick the 50th nucleotide for the reference MDH and report the corresponding nucleotide in the second
sequence. Do the same thing with the amino acids. (1 points)
5)
Briefly summarize the secondary structure of your protein. Is the structure all alpha helix, all beta strands, or
a mixture of both? Does your protein appear to include multiple domains? (2 points)
6)
Does your protein have an "active site"? If so, which amino acids? Which secondary structures are
included in the active site? (2 points)
NOTE: For the following questions, you will be asked to create and capture images. Use the grab or screen
capture to capture the image. Copy these images into your typed answers. All images should be text wrapped
and annotated with a description of the image composition. Adjust all images to no more than two inches.
7) Create a complete cartoon image of the protein and ligand as shown in the first PyMOL tutorial video.
Capture that image and insert into your typed answer word document using either a “grab” utility, or
some other screenshot capture utility. (2 points)
8) Zoom in on the ligand binding site, remove all but the binding/interacting/interesting amino acid residues
from the screen. Capture and insert this image in your report. (2 points)
9) Highlight and zoom in on all important/interesting amino acids as in the third tutorial video. Capture, insert,
and annotate as before. (2 points)
10) Measure the distance from 4 or 5 of the binding residues in your protein to the bound ligand/small
molecule. Capture, insert, and annotate as before. (2 points)
Biochemistry Lab
Informatics and Pymol Assignment
11) Mutate two of the most interesting or critical amino acids to a conserved amino acid mutation and a
mutation with the opposite chemical characteristic. Describe the changes in structure when you perform
each mutation. Capture one of the more dramatic instances, then insert and annotate as before. (3
points)
12) Using a similar homologous protein, perform an overlay of both structures as shown in the tutorial. Capture,
insert, and annotate as before. (3 points)
13) Create a publication quality image using a white background. Have some fun with this image. Capture,
insert, and annotate as before. (3 points)
14) Create a movie with your protein. If possible, email to your instructor. If the file does not email, post it on
youtube, facebook or some other media and send me the link. Alternatively, place a copy on a clean
USB and submit to your instructor. (5 points)