Modulation of p53 binding to MDM2: computational studies reveal important roles of Tyr100

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Modulation of p53 binding to MDM2 computational
studies reveal important roles of Tyr100
Shubhra G Dastidar, David P Lane, Chandra S Verma
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p53 network
Vogelstein, B., Lane, D. P., and Levine, A. J.
(2000). Surfing the p53 network. Nature 408
307-310.
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Transactivation domain of p53 17-29 MDM2
25-109
Kussie et al., Science 1996
Vassilev et al., Science 2004
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• P27S mutation
• ? ?G -2.3kcal/mol

P27
E17TFSD LWKLL PEN29
Zondlo et al. Biochemistry 2006
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Crystallographically observed binding mode of
WT is retained
? ?G -4.2 kcal/mol
? ?H -0.8 -T ? ?S -3.4 ? ?G
-4.2
a-helix is propagated by another turn
? ? G -4.7 kcal/mol
? ? H -3.6 -T ? ?S -1.1 ? ? G -4.7
Dastidar, S.G., Lane D.P., Verma C.S., J. Am.
Chem. Soc. 2008
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Ligand with extended C-terminus
Ligand with helical conformation
Y100 orients as in wild type
Y100 flips in
Dastidar, S.G., Lane D.P., Verma C.S., J. Am.
Chem. Soc. 2008
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Modulation of binding site of MDM2 while binding
to a variety of ligands in PDB
p53
Nutlin
Optimized peptide
ß-hairpin
IC50 10-2000nM
12/1 peptide
Optimized peptide
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L26
Y100
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Y100
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E17
K70
E28
R65
K51
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p53 binding pocket
Apo
After MD in presence of p53
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N-terminal lid
Y100
p53 binding pocket
C-terminal end, connects other domains of MDM2
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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

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Acknowledgement

• Chandra S. Verma
• David P. Lane
• Sebastian Maurer-Stroh
• BMAD Group
• BII, ASTAR
• INCOB organizers

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K70
K94
K51
R97
K70
R97
K94
Y100
K51
Y100
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H-bond !!
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p53 binding pocket
Uhrinova et al., JMB 2005