Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking

Mukherjee, Sudipto; Pantelopulos, George A.; Voelz, Vincent A.

doi:10.1101/053603

Cited by 4 publications

(4 citation statements)

References 56 publications

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“…13,14,21,22 Moreover, the NMR structure of free MDM2 shows that it must adjust upon TAD binding to accommodate the peptide. 23 Other NMR experiments 24,25 and simulations 26 interpreted in the light of the crystal structure 11 demonstrate that residues 19−23 in MDM2 partially covers the p53 TAD-binding site and obstructs the interaction. The opening and closing of this helix were detected in NMR experiments at 25 °C.…”

Section: ■ Resultsmentioning

confidence: 99%

Binding Kinetics of the Intrinsically Disordered p53 Family Transactivation Domains and MDM2

et al. 2018

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Because of their prominent roles in cell-cycle regulation and cancer, the interaction between MDM2 and the intrinsically disordered transactivation domain (TAD) of p53 is exceptionally well-studied. However, although there are numerous computational studies on the interaction mechanism, there is a paucity of experimental data regarding the kinetics and mechanism. We have used stopped flow fluorescence to investigate the binding reaction between MDM2 and TAD from p53 as well as from its paralogs p63 and p73, and in particular, focused on the salt dependence of the interaction. The observed kinetics are consistent with a two-state mechanism within the time frame of the stopped flow methodology; thus, any conformational changes including the previously identified MDM2 lid dynamics must occur on a time scale <5 ms at 10 °C. The association rate constants are similar for the three TADs, and differences in the dissociation rate constants determine the various affinities with MDM2. In contrast to previous studies, we found a relatively small ionic-strength dependence for all three interactions, highlighting the large variation in the role of electrostatics among binding reactions of intrinsically disordered proteins (IDPs). The basal association rate constants in the absence of electrostatic interactions were relatively high (≥2 × 10 M s at 10 °C), suggesting that a large number of initial contacts may lead to a productive complex. Our findings support an emerging picture of "conformational funneling" occurring in the initial stages of interactions involving IDPs and that these early binding events can rely on hydrophobic as well as charge-charge interactions.

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Section: ■ Resultsmentioning

confidence: 99%

Binding Kinetics of the Intrinsically Disordered p53 Family Transactivation Domains and MDM2

et al. 2018

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“…Thus, to tackle the challenges of inefficient CDR loop sampling and capturing relevant backbone conformations, we used a wellestablished protocol to kinetically define CDR loop structures by capturing conformational transitions in the micro-to millisecond timescale. The combination of molecular dynamics simulation protocols with Markov-state models has already been shown to sample kinetically relevant binding competent conformations, which are suitable for docking and drug design (Amaro et al, 2018;Mukherjee et al, 2016;Salmaso and Moro, 2018;Torchala et al, 2013). We also observe that these kinetically dominant antibody conformations are indeed chosen by the antigen with the highest probability.…”

Section: Discussionmentioning

confidence: 66%

Paratope states in solution improve structure prediction and docking

et al. 2022

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“…46 Previous studies with this forcefield have also given a reasonable description of the MDM2 lid IDR dynamics. 38,39,47…”

Section: Resultsmentioning

confidence: 99%

Energetics of a protein disorder-order transition in small molecule recognition

Mendoza-Martinez

Papadourakis

Llabrés

et al. 2021

Preprint

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Many proteins recognise other proteins via mechanisms that involve the folding of intrinsically disordered regions upon complex formation. Here we investigate how the selectivity of a drug-like small molecule arises from its modulation of a protein disorder-to-order transition. Binding of the compound AM-7209 has been reported to confer order upon an intrinsically disordered ‘lid’ region of the oncoprotein MDM2. Calorimetric measurements revealed that truncation of the lid region of MDM2 increases the dissociation constant of AM-7209 250-fold. By contrast, lid truncation has little effect on the binding of the ligand Nutlin-3a. Insights into these differential binding energetics were obtained via a complete thermodynamic analysis that featured adaptive absolute alchemical free energy of binding calculations with enhanced-sampling molecular dynamics simulations. The simulations reveal that in apo MDM2 the ordered lid state is energetically disfavoured. AM-7209, but not Nutlin-3a, shows a significant energetic preference for ordered lid conformations, thus shifting the balance towards ordering of the lid in the AM-7209/MDM2 complex. The methodology reported herein should facilitate broader targeting of intrinsically disordered regions in medicinal chemistry. Graphical TOC

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Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking

Cited by 4 publications

References 56 publications

Binding Kinetics of the Intrinsically Disordered p53 Family Transactivation Domains and MDM2

Binding Kinetics of the Intrinsically Disordered p53 Family Transactivation Domains and MDM2

Paratope states in solution improve structure prediction and docking

Energetics of a protein disorder-order transition in small molecule recognition

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