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J Mol Model. 2011 Aug;17(8):1927-34. doi: 10.1007/s00894-010-0897-z. Epub 2010 Nov 26.

Effect of the SH3-SH2 domain linker sequence on the structure of Hck kinase.

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Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität, Fahrstraße 17, 91054 Erlangen-Nürnberg, Germany.


The coordination of activity in biological systems requires the existence of different signal transduction pathways that interact with one another and must be precisely regulated. The Src-family tyrosine kinases, which are found in many signaling pathways, differ in their physiological function despite their high overall structural similarity. In this context, the differences in the SH3-SH2 domain linkers might play a role for differential regulation, but the structural consequences of linker sequence remain poorly understood. We have therefore performed comparative molecular dynamics simulations of wildtype Hck and of a mutant Hck in which the SH3-SH2 domain linker is replaced by the corresponding sequence from the homologous kinase Lck. These simulations reveal that linker replacement not only affects the orientation of the SH3 domain itself, but also leads to an alternative conformation of the activation segment in the Hck kinase domain. The sequence of the SH3-SH2 domain linker thus exerts a remote effect on the active site geometry and might therefore play a role in modulating the structure of the inactive kinase or in fine-tuning the activation process itself.

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