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Molecular dynamics simulations reveal membrane lipid interactions of the full-length lymphocyte specific kinase Lck: dataset

Prakaash, Dheeraj and Cook, Graham and Acuto, Oreste and Kalli, Antreas (2022) Molecular dynamics simulations reveal membrane lipid interactions of the full-length lymphocyte specific kinase Lck: dataset. University of Leeds. [Dataset] https://doi.org/10.5518/1158

Dataset description

The membrane-bound lymphocyte-specific protein-tyrosine kinase (Lck) triggers T cell antigen receptor signalling to initiate adaptive immune responses. Despite many structure-function studies, the mode of action of Lck and the potential role of plasma membrane lipids in regulating Lck’s activity remains elusive. Advances in molecular dynamics simulations of membrane proteins in complex lipid bilayers have opened a new perspective in gathering such information. Here, we have modelled the full-length Lck open and closed conformations available from crystallographic studies and simulated its interaction with the inner leaflet of the T cell plasma membrane. In both conformations, we found that the unstructured unique domain and the structured domains including the kinase interacted with the membrane with a preference for PIP lipids. Interestingly, our simulations suggest that the Lck-SH2 domain interacts with lipids differently in the open and closed Lck conformations, demonstrating that lipid interaction can potentially regulate Lck’s conformation and in turn modulate T cell signalling. Additionally, the Lck-SH2 and kinase domain residues that significantly contacted PIP lipids are found to be conserved among the Src family of kinases, thereby potentially representing similar PIP interactions within the family.

Additional information: This dataset is associated with a journal paper currently undergoing peer review (24/5/2022). The data is subject to change until the completion of the peer review process. The data DOI will be registered once peer review is complete and will then function correctly.
Keywords: Full-length Lck, molecular dynamics simulations, protein-lipid interactions, protein conformation
Divisions: Faculty of Medicine and Health > School of Medicine
License: Creative Commons Attribution 4.0 International (CC BY 4.0)
Date deposited: 24 May 2022 20:08
URI: http://archive.researchdata.leeds.ac.uk/id/eprint/968

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