Modulation of p53 binding to
MDM2: computational studies
reveal important roles of Tyr100
Shubhra G Dastidar, David P Lane, Chandra S Verma
p53 network
Vogelstein, B., Lane, D. P., and Levine, A. J. (2000). Surfing the p53 network. Nature 408: 307-310.
Transactivation
domain of p53: 17-29
MDM2: 25-109
Kussie et al., Science 1996
Vassilev et al., Science 2004
L26
• P27S mutation
Δ ΔG = -2.3kcal/mol
F19
P27
W23
E17TFSD LWKLL PEN29
Zondlo et al. Biochemistry 2006
Crystallographically observed
binding mode of WT is retained
S27
Δ ΔG = -4.2 kcal/mol
Δ ΔH = -0.8
-T Δ ΔS = -3.4
Δ ΔG = -4.2
α-helix is propagated by
another turn
Δ Δ G = -4.7 kcal/mol
Δ Δ H = -3.6
-T Δ ΔS = -1.1
Δ Δ G = -4.7
Dastidar, S.G., Lane D.P., Verma C.S., J. Am. Chem. Soc. 2008
S27
Ligand with extended C-terminus
Y100 orients as in wild type
Dastidar, S.G., Lane D.P., Verma C.S., J. Am. Chem. Soc. 2008
Ligand with helical conformation
Y100 flips in
Modulation of binding site of MDM2 while
binding to a variety of ligands in PDB
p53
Nutlin
Optimized peptide
β-hairpin
Optimized peptide
IC50 ~ 10-2000nM
12/1 peptide
L26
Y100
Y100
E17
K70
E28
R65
K51
K70
K94
R97
Y100
K51
K94
R97
K51
p53 binding
pocket
Apo
After MD in presence of p53
N-terminal lid
Y100
C-terminal end,
connects other domains of
MDM2
p53 binding
pocket
Conclusions
• Plasticity of the binding pocket of MDM2 allows the
binding of ligands of widely varying shapes and sizes
• Modulation of binding pocket leads to varying
thermodynamics origin of the stability
• Y100 acts as a gatekeeper
• Lid-dynamics is correlated with Y100 orientation
• K51, K70, K94, R97 have role to steer the ligand towards
binding pocket
Acknowledgement
•
•
•
•
•
•
Chandra S. Verma
David P. Lane
Sebastian Maurer-Stroh
BMAD Group
BII, A*STAR
INCOB organizers
K70
K94
K51
K70
R97
K94 R97
Y100
K51
Y100
H-bond !!
p53 binding
pocket
*Uhrinova et al., JMB 2005