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MDM2 is a negative regulator of p53 activity and an important target for cancer therapeutics. The N-terminal lid region of MDM2 modulates interactions with p53 via competition for its binding cleft, exchanging slowly between docked and undocked conformations in the absence of p53. To better understand these dynamics, we constructed Markov State Models (MSMs) from large collections of unbiased simulation trajectories of apo-MDM2, and find strong evidence for diffuse, yet two-state folding and b…

Proc Natl Acad Sci U S A. 2016 Aug 16;113(33):9193-8. doi: 10.1073/pnas.1602790113. Epub 2016 Aug 1. Meng Y, Shukla D, Pande VS, Roux B. Our results suggest that the combination…

J Am Chem Soc. 2016 Aug 10;138(31):9730-42. doi: 10.1021/jacs.6b06543. Epub 2016 Jul 19. Bhowmick A, Brookes DH, Yost SR, Dyson HJ, Forman-Kay JD, Gunter D, Head-Gordon M, Hura GL, Pande…

The rapidly expanding body of available genomic and protein structural data provides a rich resource for understanding protein dynamics with biomolecular simulation. While computational infrastructure has grown rapidly, simulations on an omics scale are not yet widespread, primarily because software infrastructure to enable simulations at this scale has not kept …

Biophys J. 2016 Apr 26;110(8):1716-9. doi: 10.1016/j.bpj.2016.03.026. Schwantes CR, Shukla D, Pande VS After reanalyzing simulations of NuG2-a designed mutant of protein G-generated by Lindorff-Larsen et al. with time structure-based independent…