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

• P27S mutation Δ ΔG = -2.3kcal/mol

W23

L26

F19

P27

E17TFSD LWKLL PEN29

Zondlo et al. Biochemistry 2006

S27

S27 Δ ΔG = -4.2 kcal/mol

Δ Δ G = -4.7 kcal/mol

Crystallographically observed binding mode of WT is retained

Dastidar, S.G., Lane D.P., Verma C.S., J. Am. Chem. Soc. 2008

α-helix is propagated by another turn

Δ ΔH = -0.8-T Δ ΔS = -3.4 Δ ΔG = -4.2

Δ Δ H = -3.6-T Δ ΔS = -1.1 Δ Δ G = -4.7

Y100 orients as in wild type Y100 flips in

Ligand with extended C-terminus Ligand with helical conformation

Dastidar, S.G., Lane D.P., Verma C.S., J. Am. Chem. Soc. 2008

Modulation of binding site of MDM2 while binding to a variety of ligands in PDB

p53

12/1 peptideOptimized peptide

β-hairpin

Nutlin

Optimized peptide

IC50 ~ 10-2000nM

L26

Y100

Y100

E28K70

E17

K51

R65

K70

K51

R97

K94

Y100

K94

R97

K51

ApoAfter MD in presence of p53

p53 binding pocket

N-terminal lid

p53 binding pocket

C-terminal end,connects other domains of MDM2

Y100

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

K70

K51

K51

R97R97

K94

K94

Y100

Y100

H-bond !!

p53 binding pocket

*Uhrinova et al., JMB 2005