SIGNAL TRANSDUCTION

PSF HW8 by Jenny Jiou

QUESTION 1
Superimpose RasGTP and RasGDP. Identify and label
secondary structural elements (1, 2,...., 1, 2......) of
both proteins.

RasGTP and RasGDP aligned

Secondary Structure Assignments

D

6
5
4
E
1

A
3
2

QUESTION 2
Identify regions of the proteins that show conformational
differences when bound to the 2 different nucleotides.

Classic GTPase Switches

RasGTP
RasGDP
Switch 2

Switch 1

QUESTION 3
Identify Ras residues that contact the different portions
of both nucleotides - the base, the sugar, the alpha-,
beta- and gamma-phosphates, and the cation that binds
the nucleotide.

Contacts of RasGTP

Contacts of RasGDP

QUESTION 4
Are contacts to the base and sugar moieties of the two
nucleotides similar or different? Are contacts to the alpha
phosphates of the two nucleotides similar or? Are contacts to
the beta phosphates of the two nucleotides similar or
different?

Aligned Measurements

Magnesium Coordination

QUESTION 5
Where are the Ras residues that contact the gammaphosphate of GTP located? Are they on the switch
regions? If yes, which one(s)?

Gamma Phosphate
Switch 2

Switch 1

QUESTION 6
Show interactions between Ras and the Raf RBD. Separate
side chain interactions from main chain-main chain
interactions. Which parts of Ras are contacting Raf RBD?
Are the contact residues on Ras located in the switch
regions?

Backbone Interactions RAF:RAS

Side Chain Interactions RAF:RAS

QUESTION 7
Superimpose 4G0N with Ras bound to GTP (121P). Are the
contact residues of Ras in 4G0N in similar conformations as
in 121P? What does that say about RasGTP alone is it in
a conformation suitable for binding the Raf RBD?

121P align with 4Q0N

Is RasGTP a right fit for Raf?

Switch 1

QUESTION 8
Superimpose 4G0N with Ras bound to GDP (4Q21). Is
RasGDP suitable for binding the Raf RBD?

RasGDP and Complex Aligned

Clash!