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In silico study of fragile histidine triad interaction domains with MDM2 and p53.

ABSTRACT: BACKGROUND:Fragile histidine triad (FHIT) is considered as a member of the histidine triad (HIT) nucleotide-binding protein superfamily regarded as a putative tumor suppressor executing crucial role in inhibiting p53 degradation by MDM2. Accumulating evidences indicate FHIT interaction with p53 or MDM2; however, there is no certain study deciphering functional domains of FHIT involving in the interaction with MDM2 and/or p53. In this regard, such evident interaction can spring in mind determining important domains of FHIT binding to MDM2 with regard to p53. MATERIALS AND METHODS:Since there were not any previous studies appraising complete three-dimensional structures of target molecules, molecular modeling was carried out to construct three-dimensional models of full FHIT, MDM2, P53 and also FHIT segments. Truncated structures of FHIT were created to reveal critical regions engaging in FHIT interaction. RESULTS:Given the shape and shape/electrostatic total energy, FHIT structures (?1-5), (?3-7, ?1), and (?5-7, ?1) appeared to be better candidates than other structures in interaction with full MDM2. Furthermore, FHIT structures (?6-7), (?6-7, ?1), (?4-7, ?1) were considered to be better than other structures in interaction with p53. FHIT truncates that interact with MDM2 presented lower energy levels than FHIT truncates interacting with p53. CONCLUSION:These findings are beneficial to understand the mechanism of the FHIT-MDM2-p53 complex activation for designing inhibitory compounds.

SUBMITTER: Eslamparast A

PROVIDER: S-EPMC4162077 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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In silico study of fragile histidine triad interaction domains with MDM2 and p53.

Eslamparast Ameneh A Ghahremani Mohammad Hossein MH Sardari Soroush S

Advanced biomedical research 20140819

<h4>Background</h4>Fragile histidine triad (FHIT) is considered as a member of the histidine triad (HIT) nucleotide-binding protein superfamily regarded as a putative tumor suppressor executing crucial role in inhibiting p53 degradation by MDM2. Accumulating evidences indicate FHIT interaction with p53 or MDM2; however, there is no certain study deciphering functional domains of FHIT involving in the interaction with MDM2 and/or p53. In this regard, such evident interaction can spring in mind de ...[more]

PMID: 25221773

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Project description:Murine double minute 2 (MDM2) proteins are found to be overproduced by many human tumors in order to inhibit the functioning of p53 molecules, a tumor suppressor protein. Thus, reactivating p53 functioning in cancer cells by disrupting p53-MDM2 interactions may offer a significant approach in cancer treatment. However, the structural characterization of the p53-MDM2 complex at the atomistic level and the mechanism of binding/unbinding of the p53-MDM2 complex still remain unclear. Therefore, we demonstrate here the probable binding (unbinding) pathway of transactivation domain 1 of p53 during the formation (dissociation) of the p53-MDM2 complex in terms of free energy as a function of reaction coordinate from the potential of mean force (PMF) study using two different force fields: ff99SB and ff99SB-ILDN. From the PMF plot, we noticed the PMF to have a minimum value at a p53-MDM2 separation of 12 Å, with a dissociation energy of 30 kcal mol-1. We also analyzed the conformational dynamics and stability of p53 as a function of its distance of separation from MDM2. The secondary structure content (helix and turns) in p53 was found to vary with its distance of separation from MDM2. The p53-MDM2 complex structure with lowest potential energy was isolated from the ensemble at the reaction coordinate corresponding to the minimum PMF value and subjected to molecular dynamics simulation to identify the interface surface area, interacting residues at the interface, and the stability of the complex. The simulation results highlight the importance of hydrogen bonds and the salt bridge between Lys94 of MDM2 and Glu17 of p53 in the stability of the p53-MDM2 complex. We also carried out the binding free energy calculations and the per residue energy decomposition analyses of the interface residues of the p53-MDM2 complex. We found that the binding affinity between MDM2 and p53 is indeed high [ΔG bind = -7.29 kcal mol-1 from molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) and ΔG bind = -53.29 kcal mol-1 from molecular mechanics/generalized borne surface area]. The total binding energy obtained using the MM/PBSA method was noticed to be closer to the experimental values (-6.4 to -9.0 kcal mol-1). The p53-MDM2 complex binding profile was observed to follow the same trend even in the duplicate simulation run and also in the simulation carried out with different force fields. We found that Lys51, Leu54, Tyr100, and Tyr104 from MDM2 and the residues Phe19, Trp23, and Leu26 from p53 provide the highest energy contributions for the p53-MDM2 interaction. Our findings highlight the prominent structural and binding characteristics of the p53-MDM2 complex that may be useful in designing potential inhibitors to disrupt the p53-MDM2 interactions.

Dataset Information

In silico study of fragile histidine triad interaction domains with MDM2 and p53.

Publications

In silico study of fragile histidine triad interaction domains with MDM2 and p53.

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