DSCAM Tutorial and Homework
Dscam molecules are represented in cartoon schematic.
The schematic traces the path of the protein backbone.
Yellow spheres represent sulfurs of cystein residues
Download the PDB file for DSCAM here DSCAM PDB FILE ,
Download the Pymol Script here PYMOL SCRIPT FILE: step01.pml ,
Homework question #1: How many molecules of Dscam are present?
Homework question #2: This oligomeric assembly is called which of the following:
Homework question #3: How many domains are shown in each Dscam molecule?
Homework question #4: How many disulfide bonds are present in each Dscam domain?
Homework question #5: Dscam is composed mainly of which commonly found secondary structure element?
a monomer? dimer? trimer? tetramer? pentamer? hexamer? heptamer?
Imagine each of the domains of the Dscam molecule is replaced with a single arrow with its tail at the N-terminal end and its head at the C-terminal end.
This train of arrows would trace the path of the domains.
There are two places where the path of domains makes a sharp reverse turn.
Homework question #6:
Homework question #7: When a single molecule of Dscam is oriented so that the black line is vertical, the molecule of Dscam resembles which letter of the English alphabet?
Homework question #8: How are the the molecules of Dscam related: by mirror reflection or 180 degree rotation?
Homework question #9: What is the significance of the black line drawn between molecules?
These sharp turns occur between which two pairs of domains:
1st and 2nd? 2nd and 3rd? 4th and 5th? 5th and 6th? 6th and 7th?
Download the Pymol Script here PYMOL SCRIPT FILE: step02.pml ,
Most of the Dscam molecule is composed of invariant residues shown in gray or white. But there are three variable regions that are encoded by one of many alternative exons. The first variable region of Dscam is shown in red colors. The second variable region is shown in blue colors. The third variable region is shown in green colors.
Circle the correct answer:
Homework question #10: The first variable region of Dscam corresponds to which
of the Ig domains? 1st, 2nd, 23rd, 4th, 5th, 6th, 7th?
Homework question #11: The second variable region of Dscam corresponds to which
of the Ig domains? 1st, 2nd, 3rd, 34th, 5th, 6th, 7th?
Homework question #12: The third variable region of Dscam corresponds to which
of the Ig domains? 1st, 2nd, 3rd, 4th, 65th, 6th, 7th?
Homework question #13: The interface between Dscam molecules composed primarily
of which type of residues: variant or invariant?
Download the Pymol Script here PYMOL SCRIPT FILE: step03.pml ,
The side chains of interface residues are shown as sticks.
Homework question #14: How are the the interface residues related to the position
of the black line: close or far?
Homework question #15: What role do the two sharp reverse turns have in producing
this relationship?
Homework question #16: What is the significance of this relationship?
Download the Pymol Script here PYMOL SCRIPT FILE: step04.pml ,
Only Ig domain 2 is shown. The side chains shown in sticks participate in the interface between molecules.
Homework question #17: What amino acids comprise the interface?
Homework question #18: Are these polar or non-polar contacts?
Homework question #19: How many hydrogen bonds are formed between molecules?
The interface shown here is "homophilic" The molecules of Dscam shown here have identical amino acid sequences-- they correspond to identical splice variants.
Specifically, they correspond to splice variant 2.1 (the first variable exon in Ig2) In general, non identical splice variants ("heterophilic") do not form stable dimers. Let us model a heterophilic interface between variant 2.1 and 2.10. to convince yourself that a heterophilic interface would be less stable than a homophilic interface. Mutate side chains in the salmon molecule from variant 2.1 to 2.10. To do so, mutate aspartic acid residue 109 to arginine. Mutate histidine residue 114 to phenylalanine.
Homework question #20: Why do you think this heterophilic interface is unstable?