Effects of FGFR2 kinase activation loop dynamics on catalytic activity.

Jerome M Karp,David Cowburn,Samuel Sparks,Marc A Marti-Renom

doi:10.1371/journal.pcbi.1005360

Jerome M Karp, David Cowburn + Show 2 more

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https://doi.org/10.1371/journal.pcbi.1005360

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Abstract

The structural mechanisms by which receptor tyrosine kinases (RTKs) regulate catalytic activity are diverse and often based on subtle changes in conformational dynamics. The regulatory mechanism of one such RTK, fibroblast growth factor receptor 2 (FGFR2) kinase, is still unknown, as the numerous crystal structures of the unphosphorylated and phosphorylated forms of the kinase domains show no apparent structural change that could explain how phosphorylation could enable catalytic activity. In this study, we use several enhanced sampling molecular dynamics (MD) methods to elucidate the structural changes to the kinase’s activation loop that occur upon phosphorylation. We show that phosphorylation favors inward motion of Arg664, while simultaneously favoring outward motion of Leu665 and Pro666. The latter structural change enables the substrate to bind leading to its resultant phosphorylation. Inward motion of Arg664 allows it to interact with the γ-phosphate of ATP as well as the substrate tyrosine. We show that this stabilizes the tyrosine and primes it for the catalytic phosphotransfer, and it may lower the activation barrier of the phosphotransfer reaction. Our work demonstrates the value of including dynamic information gleaned from computer simulation in deciphering RTK regulatory function.

Highlights

Receptor tyrosine kinases (RTKs) occupy a central role in cellular regulation, acting as intermediaries in relaying signals from extracellular ligands to major signaling pathways in the cell [1,2,3]
We examined one receptor tyrosine kinase, fibroblast growth factor receptor 2 (FGFR2) kinase, and used computer simulation to identify what conformational changes occur in this protein upon activation
We focus on the FGFR2 kinase, for which a wealth of experimental structural information is available, including crystal structures of the wild type kinase [25, 26], of mutant kinases [15, 26, 27], and NMR chemical shift data [15]

Summary

Introduction

Receptor tyrosine kinases (RTKs) occupy a central role in cellular regulation, acting as intermediaries in relaying signals from extracellular ligands to major signaling pathways in the cell [1,2,3]. The similarities between the various RTKs combined with their divergent behaviors presents a unique challenge in designing drugs to target specific RTKs whose constitutive activity has pathologic consequences, without generating off-target effects caused by reduced activity of other kinases [6, 7]. This endeavor has had profound successes [8] but still requires additional effort, with regard to filling the gaps in our structural knowledge of these proteins. This phosphorylation leads to altered dynamics of the activation loop residues resulting in greater catalytic activity of the kinase [14,15,16,17]

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