Dec 23, 2024
Steered MD simulations of the inactive-active transition
- Ainara Claveras Cabezudo1,2,3,
- Annan Cook4,3
- 1Max Planck Institute of Biophysics;
- 2IMPRS of Cellular Biophysics;
- 3Aligning Science Across Parkinson's CRN;
- 4University of California, Berkeley
Protocol Citation: Ainara Claveras Cabezudo, Annan Cook 2024. Steered MD simulations of the inactive-active transition. protocols.io https://dx.doi.org/10.17504/protocols.io.eq2ly68drgx9/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: December 19, 2024
Last Modified: December 23, 2024
Protocol Integer ID: 116395
Keywords: ASAPCRN, molecular dynamics simulations of the transition, molecular dynamics simulation, lipid membrane, active transition, active transition this protocol detail, membrane, steered md simulation, rab1a
Funders Acknowledgements:
Aligning Science Across Parkinson's
Grant ID: ASAP-000350
Abstract
This protocol details steered molecular dynamics simulations of the transition from the inactive to the active PI3KC3-C1 complex bound to RAB1A on a lipid membrane.
Troubleshooting
Preparation of membrane-engaged inactive complex
Superimpose the cryo-EM structure of the inactive conformation onto a membrane-engaged active complex after relaxation.
Apply harmonic restraints (force constant: 100 kJ mol⁻¹) to increase the center-of-mass z-distance between residues S249 to K887 of VPS34 and the membrane lipids underneath.
Apply a pulling rate of 0.1 nm ns⁻¹ until the regions of interest are not clashing with the membrane.
Relaxation
Run simulation without any steering force for 117 ns to relax the membrane.
Steered MD of inactive-active transition
Apply a lateral force to increase the distance between the C-terminal region of VPS34 (residues S249 to K887) and the N-terminal region of VPS15 (residues G2 to K300) for 30 ns, with a force constant of 100 kJ mol-1.
Apply a pulling velocity of 0.1 nm ns-1 until the interface between VPS34 and VPS15 breaks.
Steered MD to obtain active, membrane-engaged complex
Pull the center of mass of the myristate at the N-terminus of VPS15 along the z coordinate towards the membrane for 220 ns with a force constant of 100 kJ mol-1.
Apply a negative rate of -0.1 nm ns⁻¹ until the myristate is inserted in the membrane and the catalytic domain of VPS34 reaches the membrane surface.
Relaxation
Allow the complex to relax for 160 ns upon removal of any steering force.