The tyrosinekinases of the Src family are highly conserved signaling proteins involved in the regulation of cell growth whose catalytic activity can be modulated in response to specific cellular signals. The key role that the Src-family kinases play in the onset of many human diseases, particularly cancer, makes them important targets for therapeutic intervention. All nine members of the Src family are formed by a catalytic domain which is preceded by two peptide binding modules, the Src-homology domains SH2 and SF13. Phosphorylation of two tyrosines (Tyr527 and Tyr416) has opposing effects on catalytic activity: dephosphorylation of Tyr527 in the C-terminal tail results in the activation of the enzyme, while phosphorylation of Tyr416 which is located in a central activation loop"""""""" of the kinase domain opens the catalytic site and activates the enzyme. The available crystallographic structures do not, however, show readily how the catalytic activity is regulated by these two sites. To refine our understanding of the factors responsible for the regulation of Src tyrosine kinases, John Kuriyan and myself initiated a theoretical investigation using molecular dynamics simulations. Motivated by our preliminary results, we now seek to extend our collaborative effort. The goal of this research proposal is to characterize quantitatively the importance of conformational flexibility in the activation of Src tyrosine kinases. To overcome the sampling and timescale difficulties and obtain meaningful results, we will use special computational strategies based on molecular dynamics potential of mean force techniques with biased sampling. In particular, we will calculate the free energy barrier associated with the opening of the activation loop of the catalytic domain for various states of the tyrosine kinase. Lastly, the results of the computations based on atomic models will be contrasted and compared with a statistical analysis of the sequence patterns of members of the Src family.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Research Project (R01)
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Molecular and Cellular Biophysics Study Section (BBCA)
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Knowlton, John R
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Weill Medical College of Cornell University
Schools of Medicine
New York
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Pond, Matthew P; Blachowicz, Lydia; Roux, Benoît (2018) 1H, 15N, and 13C resonance assignments of the intrinsically disordered SH4 and Unique domains of Hck. Biomol NMR Assign :
Meng, Yilin; Gao, Cen; Clawson, David K et al. (2018) Predicting the Conformational Variability of Abl Tyrosine Kinase using Molecular Dynamics Simulations and Markov State Models. J Chem Theory Comput 14:2721-2732
Meng, Yilin; Pond, Matthew P; Roux, Benoît (2017) Tyrosine Kinase Activation and Conformational Flexibility: Lessons from Src-Family Tyrosine Kinases. Acc Chem Res 50:1193-1201
Fajer, Mikolai; Meng, Yilin; Roux, Benoît (2017) The Activation of c-Src Tyrosine Kinase: Conformational Transition Pathway and Free Energy Landscape. J Phys Chem B 121:3352-3363
Meng, Yilin; Roux, Benoît (2016) Computational study of the W260A activating mutant of Src tyrosine kinase. Protein Sci 25:219-30
Meng, Yilin; Shukla, Diwakar; Pande, Vijay S et al. (2016) Transition path theory analysis of c-Src kinase activation. Proc Natl Acad Sci U S A 113:9193-8
Martin, Eric; Knapp, Stefan; Engh, Richard A et al. (2015) Perspective on computational and structural aspects of kinase discovery from IPK2014. Biochim Biophys Acta 1854:1595-604
Meng, Yilin; Lin, Yen-lin; Roux, Benoît (2015) Computational study of the ""DFG-flip"" conformational transition in c-Abl and c-Src tyrosine kinases. J Phys Chem B 119:1443-56
Meng, Yilin; Roux, Benoît (2014) Locking the active conformation of c-Src kinase through the phosphorylation of the activation loop. J Mol Biol 426:423-35
Lin, Yen-Lin; Meng, Yilin; Huang, Lei et al. (2014) Computational study of Gleevec and G6G reveals molecular determinants of kinase inhibitor selectivity. J Am Chem Soc 136:14753-62

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