PYMOL

Download the following protein from the PDB within Pymol interactive console using the following command and answer the following questions:

PyMOL> fetch 1yy8 

The structure you have downloaded is cetuximab, a therapeutic antibody in development for cancer treatment.

Antibodies are composed of two heavy chains and two light chains; the particular construct of its upper part is known as a Fab fragment and contains one full light chain (chain A) and the N-terminal half of one heavy chain (chain B). At one end of the Fab fragment are six loops known as the "complementarity determining regions" (CDR), which bind a particular antigen.

For the following problems, we will examine the N-terminal domain of chain A (the light chain). To make this easier, type the following command:

PyMOL> select L, chain A and resi 1-107 

From the right panel controls, hide everything but for selection(L)and clickColorSpectrumRainbow. Alternatively you can hide and color the structure with the following commands:

PyMOL> hide not (L) PyMOL> cmd.spectrum("count",selection="(L)") 

a) Answer following questions

• Looking down the direction of the first strand, which way does it twist?
• Do all strands twist the same direction?

Next, let us analyze a couple strands in the N-terminal domain. Zoom in on strands 3 and 8, (which should be adjacent and colored cyan and marigold, respectively.) What are the residue number ranges for these two strands?

Hint: Click on the strand ends and look in the console window for the residue numbers.

b)

• Strand 3:-
• Strand 8:-

c)

Create a new object for these two strands withselectand hide the rest of the molecule. Display the atoms of the amino acid and color them by their element (ShowSticksandColorByElement).

PyMOL> create L, (L) PyMOL> cmd.show("sticks","L") PyMOL> util.cnc("L",_self=cmd) 

Answer the following questions:

• What color are oxygens?___
• What color are nitrogens?___

d) By looking at the side chains, identify the amino-acid sequence (using 1-letter abbreviations) of these two strands? You may also use the sequence viewer to help identify the residues:

PyMOL> cmd.set('seq_view',1) 

e) What is the pattern in these sequences, and why does it occur?