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Updated: Aug 5, 2026
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Development and Application of Rapamycin-regulated Tyrosine Phosphatases
Published on: September 6, 2024
A model for PIP2/3 and Rnd1 effects on Plexin-B1 GAP activity on Rap1b GTPase derived from molecular dynamics
Biorxiv : the Preprint Server for Biology
|July 29, 2026
Summary
The cell membrane
Area of Science:
- Molecular and Cellular Biology
- Biophysics
- Computational Biology
Background:
- Plexin-B1 is a receptor that controls cell processes by integrating signals from GTPases.
- Understanding how membrane composition affects Plexin-B1 structure and function is crucial.
Purpose of the Study:
- To investigate the impact of phosphoinositides (PIP2 and PIP3) and GTPases on Plexin-B1.
- To explore the allosteric effects of membrane lipids on Plexin-B1 structure and dynamics.
Main Methods:
- Performed 1 μs all-atom molecular dynamics simulations of Plexin-B1-GTPase complexes.
- Simulated complexes on membranes containing PIP2 and PIP3 lipids.
- Analyzed contact maps and allosteric communication networks.
Main Results:
- PIP2 enhanced Rap1b-Plexin-B1 interactions, while PIP3 strengthened Rnd1-Plexin contacts.
- Lipids influenced Plexin-B1's orientation and interactions with activation switch loops.
- Identified lipid-dependent shifts in allosteric communication pathways.
Conclusions:
- Membrane phosphoinositides (PIP2, PIP3) and GTPase context synergistically modulate Plexin-B1 signaling.
- The cell membrane actively influences Plexin-B1 receptor structure, dynamics, and allosteric signaling.
- Proposed a model for Plexin-B1 activation involving membrane-mediated regulation.
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