Ensemble-based computational approach discriminates functional activity of p53 cancer and rescue mutants.
The tumor suppressor protein p53 can lose its function upon single-point missense mutations in the core DNA-binding domain ("cancer mutants"). Activity can be restored by second-site suppressor mutations ("rescue mutants"). This paper relates the functional activity of p53 cancer and rescue mutants to their overall molecular dynamics (MD), without focusing on local structural details. A novel global measure of protein flexibility for the p53 core DNA-binding domain, the number of clusters at a certain RMSD cutoff, was computed by clustering over 0.7 µs of explicitly solvated all-atom MD simulations. For wild-type p53 and a sample of p53 cancer or rescue mutants, the number of clusters was a good predictor of in vivo p53 functional activity in cell-based assays. This number-of-clusters (NOC) metric was strongly correlated (r(2) = 0.77) with reported values of experimentally measured ΔΔG protein thermodynamic stability. Interpreting the number of clusters as a measure of protein flexibility: (i) p53 cancer mutants were more flexible than wild-type protein, (ii) second-site rescue mutations decreased the flexibility of cancer mutants, and (iii) negative controls of non-rescue second-site mutants did not. This new method reflects the overall stability of the p53 core domain and can discriminate which second-site mutations restore activity to p53 cancer mutants.
Department of Pharmaceutical Sciences, University of California, Irvine, California, United States of America.
Özlem
Ö
Demir
Roberta
R
Baronio
Faezeh
F
Salehi
Christopher D
CD
Wassman
Linda
L
Hall
G Wesley
GW
Hatfield
Richard
R
Chamberlin
Peter
P
Kaiser
Richard H
RH
Lathrop
Rommie E
RE
Amaro
D006801:Humans; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009154:Mutation; D009369:Neoplasms / Q000235:genetics*; D011485:Protein Binding / Q000235:genetics; D011487:Protein Conformation; D016159:Tumor Suppressor Protein p53 / Q000235:genetics*
D016159:Tumor Suppressor Protein p53