posted on 2020-03-31, 20:30authored byDuy Phuoc Tran, Akio Kitao
Here,
we investigate the association and dissociation mechanisms
of a typical intrinsically disordered region (IDR), transcriptional
activation subdomain of tumor suppressor protein p53 (TAD-p53), with
murine double-minute clone 2 protein (MDM2). Using a combination of
cycles of association and dissociation parallel cascade molecular
dynamics, multiple standard molecular dynamics (MD), and the Markov
state model, we were successful in obtaining the lowest free energy
structure of the MDM2/TAD-p53 complex as the structure closest to
the crystal structure without prior knowledge of the crystal structure.
This method also reproduced the experimentally measured standard binding
free energy, and the association and dissociation rate constants,
requiring only an accumulated MD simulation cost of 11.675 μs
even though that actual dissociation occurs on the order of seconds.
We identified few complex intermediates with similar free energies;
yet TAD-p53 first binds MDM2 as the second lowest free energy intermediate
kinetically with >90% of the flux, adopting a conformation similar
to that of one of these few intermediates in its monomeric state.
Even though the mechanism of the first step has a conformational-selection-type
aspect, the second step shows induced-fit-like features and occurs
as concomitant dehydration of the interface, side-chain π–π
stacking, and main-chain hydrogen-bond formation to complete binding
as an α-helix. In addition, dehydration is a key process for
the final relaxation process around the complex interface. These results
demonstrate that TAD-p53 kinetically selects its initial binding form
and then relaxes to complete the binding.