Download MendeleyPredicting the Conformational Variability of Abl Tyrosine Kinase using Molecular Dynamics Simulations and Markov State Models.
Meng, Y., Gao, C., Clawson, D.K., Atwell, S., Russell, M., Vieth, M., Roux, B.(2018) J Chem Theory Comput 14: 2721-2732
- PubMed: 29474075
- DOI: https://doi.org/10.1021/acs.jctc.7b01170
- Primary Citation of Related Structures:
6BL8 - PubMed Abstract:
Understanding protein conformational variability remains a challenge in drug discovery. The issue arises in protein kinases, whose multiple conformational states can affect the binding of small-molecule inhibitors. To overcome this challenge, we propose a comprehensive computational framework based on Markov state models (MSMs). Our framework integrates the information from explicit-solvent molecular dynamics simulations to accurately rank-order the accessible conformational variants of a target protein. We tested the methodology using Abl kinase with a reference and blind-test set. Only half of the Abl conformational variants discovered by our approach are present in the disclosed X-ray structures. The approach successfully identified a protein conformational state not previously observed in public structures but evident in a retrospective analysis of Lilly in-house structures: the X-ray structure of Abl with WHI-P154. Using a MSM-derived model, the free energy landscape and kinetic profile of Abl was analyzed in detail highlighting opportunities for targeting the unique metastable states.
Organizational Affiliation:
Department of Biochemistry and Molecular Biology , University of Chicago , Chicago , Illinois 60637 , United States.
