Systematic simulation of the interactions of pleckstrin homology domains with membranes

Huray, Kyle I P Le; Wang, He; Sobott, Frank; Kalli, Antreas C.

doi:10.1126/sciadv.abn6992

Cited by 17 publications

(30 citation statements)

References 82 publications

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“…Recent coarse-grained molecular dynamics simulations of the BTK PH domain support this interpretation (Le Huray et al, 2022). Consistent with this, many substitutions of Glu 41 confer a fitness advantage, not just the lysine.…”

Section: High-throughput Assays For Btk Function In B Cells and T Cellsmentioning

confidence: 65%

“…One explanation for the activating effect of the E41K mutation is the removal of a negatively charged residue (Glu 41 ) from the vicinity of the membrane, and its replacement by a positively charged residue (lysine). Recent coarse-grained molecular dynamics simulations of the BTK PH domain support this interpretation (Le Huray et al, 2022). Consistent with this, many substitutions of Glu 41 confer a fitness advantage, not just the lysine.…”

Section: Resultsmentioning

confidence: 86%

“…We find that many substitutions of Glu 41 confer a fitness advantage, not just the lysine, consistent with the principal activating effect being the loss of the negatively charged residue, rather than addition of the positively charged one. Recent coarse-grained molecular dynamics simulations of the BTK PH domain support this interpretation [51]. Not all substitutions at position 41 confer a fitness advantage, however.…”

Section: High-throughput Assays For Btk Function In B Cells and T Cellsmentioning

confidence: 99%

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Conditional Requirement for Dimerization of the Membrane-Binding Module of BTK

Eisen,

Ghaffari-Kashani,

Groves

et al. 2023

Preprint

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Bruton’s tyrosine kinase (BTK) functions in many types of immune cells and is a major chemotherapeutic target. BTK is activated at the plasma membrane and can dimerize through its pleckstrin-homology and contiguous tec-homology domains (the PH–TH module). The features that support dimerization of the PH–TH module are unique to BTK among the Tec kinases and appeared relatively recently in evolutionary history. Previous studies suggest that dimerization enhances kinase activity by promotingtransautophosphorylation, but whether BTK dimerizes in cells via the PH–TH module, and whether this dimerization controls signaling, is unknown. To address this question, we developed a high-throughput mutagenesis assay for BTK function in B cells and T cells. We measured the fitness costs for thousands of point mutations in the PH–TH module and kinase domain, allowing us to assess whether dimerization of the PH–TH module and BTK kinase activity are necessary for function. In Ramos B cells we find that neither dimerization nor kinase activity is required for BTK signaling. Instead, in Ramos cells, BTK signaling is enhanced by mutations that increase membrane adsorption, even at the cost of reduced PH–TH dimerization. In contrast, in Jurkat T cells, we find that BTK signaling depends on PH–TH dimerization and also on kinase activity. These results provide a framework for understanding why PH–TH dimerization is a more recent evolutionary innovation that is not conserved across the Tec family.

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Section: High-throughput Assays For Btk Function In B Cells and T Cellsmentioning

confidence: 65%

Section: Resultsmentioning

confidence: 86%

Section: High-throughput Assays For Btk Function In B Cells and T Cellsmentioning

confidence: 99%

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Conditional Requirement for Dimerization of the Membrane-Binding Module of BTK

Eisen,

Ghaffari-Kashani,

Groves

et al. 2023

Preprint

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“…Little is known about the atomistic-level mechanisms by which LTPs extract and release lipids from cellular membranes -or even from simpler in vitro vesicle models -because these events do not lend themselves well to experimental investigations. Molecular dynamics simulations have the potential to provide mechanistic models and generate hypotheses testable experimentally (13,(17)(18)(19)(20)(21)(22)(23).…”

Section: Discussionmentioning

confidence: 99%

A Mechanistic Model for the Release of Ceramide from the CERT START Domain

Moqadam,

Gartan,

Talandashti

et al. 2023

Preprint

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Ceramide transfer protein CERT is the mediator of non-vesicular transfer of ceramide from ER to Golgi. In CERT, START is the domain responsible for the binding and transport of ceramide. A wealth of structural data has revealed a helix-grip fold surrounding a large hydrophobic holding the ceramide. Yet little is known about the mechanisms by which START releases the ceramide through the polar region and into the packed environment of cellular membranes. As such events do not lend themselves easily to experimental investigations we used multiple unbiased microsecond-long molecular simulations. We propose a membrane-assisted mechanism in which the passage of the ceramide acyl chains is facilitated by the intercalation of a single phosphatidylcholine lipid in the cavity, practically greasing the ceramide way out. We verify using experimental lipidomics data that CERT forms stable complexes with phosphatidylcholine lipids, in addition to ceramide, thus providing a validation for the proposed computational model.

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“…The simulation methodology however, designed for identifying key lipid interaction sites, does not provide a good quantitative estimate of the overall PH domain-membrane binding free energy. It is therefore common practice to instead examine the normalized contact frequency, where the contacts are normalized relative to the amino acid with the highest number of contacts for the protein (49,50,66,67):…”

Section: Dataset Selection and Feature Processingmentioning

confidence: 99%

Rapid Prediction of Lipid Interaction Sites on Pleckstrin Homology Domains Using Deep Graph Neural Networks and Molecular Dynamics Simulations

Le Huray,

Sobott,

Wang

et al. 2023

Preprint

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Interactions between membrane proteins and specific lipid molecules play a major role in cellular biology, but characterizing these interactions can be challenging due to the complexity and physicochemical properties of membranes. Molecular dynamics (MD) simulations allow researchers to predict protein-lipid interaction sites and generate testable models. MD simulations are however computationally expensive and require specialist expertise. In this study, we demonstrate that graph neural networks trained on coarse-grained MD simulation data can predict phosphoinositide lipid interaction sites on Pleckstrin Homology (PH) domain structures, a large family of membrane binding domains. The predictions are comparable to the results of simulations and require only seconds to compute. Comparison with experimental data shows that the model can predict known phosphoinositide interaction sites and can be used to form hypotheses for PH domains for which there is no experimental data. This model is a next generation tool for predicting protein-lipid interactions of PH domains and offers a basis for further development of models applicable to other membrane protein classes.

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Systematic simulation of the interactions of pleckstrin homology domains with membranes

Cited by 17 publications

References 82 publications

Conditional Requirement for Dimerization of the Membrane-Binding Module of BTK

Conditional Requirement for Dimerization of the Membrane-Binding Module of BTK

A Mechanistic Model for the Release of Ceramide from the CERT START Domain

Rapid Prediction of Lipid Interaction Sites on Pleckstrin Homology Domains Using Deep Graph Neural Networks and Molecular Dynamics Simulations

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