Quantum mechanical studies of residue-specific hydrophobic interactions in p53-MDM2 binding

The Journal of Physical Chemistry. B
Yun DingJohn Z H Zhang

Abstract

Quantum chemistry calculations at the levels of MP2/cc-pVDZ and MP2/cc-PVTZ have been carried out to study residue-specific interactions at the hydrophobic p53-MDM2 binding interface. The result of the calculation, based on structures from nanosecond molecular dynamics simulation, revealed that (19)Phe, (22)Leu, and (23)Trp of p53 have the strongest binding interaction with MDM2 followed by (26)Leu and (27)Pro. The specific residues of MDM2 that have dominant binding interactions with p53 are specifically identified to be (51)Lys, (54)Leu, (62)Met, (67)Tyr, (72)Gln, (94)Lys, (96)His, and (100)Tyr. The p53-MDM2 binding interaction is dominated by van der Waals interaction and to a lesser degree by electrostatic interaction. The MP2 results are in generally good agreement with those from the force field calculation while the DFT/B3LYP calculation failed to give attractive interaction energies for certain residue-residue interactions due to the lack of dispersion energy.

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Citations

May 22, 2010·Journal of Computer-aided Molecular Design·Guodong HuQinggang Zhang
Nov 23, 2013·Journal of Computer-aided Molecular Design·Jianzhong ChenGuohui Li
Sep 6, 2012·International Journal of Molecular Sciences·Ting FuGuohui Li
Jan 7, 2015·Journal of Biomolecular Structure & Dynamics·Jianzhong ChenWeiliang Zhu
Apr 15, 2016·Chemical Reviews·Ulf Ryde, Pär Söderhjelm
Aug 10, 2010·Journal of Chemical Theory and Computation·Jiali GaoYirong Mo

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