GROMACS version: 2024.4
GROMACS modification: No
Dear GROMACS Community,
I am working on a project that aims to study the interaction between a cell-penetrating peptide (CPP), a membrane model, DNA (Dickerson B-DNA), and the CPP-DNA complex with the membrane using umbrella sampling and steered MD (SMD). To ensure meaningful and unbiased results, I plan to maintain the same temperature across all simulations — peptide, DNA, and membrane — to avoid introducing temperature-dependent artifacts when combining these components.
To identify a stable and biologically relevant membrane model, I performed several 200 ns simulations of different membrane compositions and conditions, followed by area per lipid (APL) and thickness analysis using APL@Voro:
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Pure POPC (128 lipids, 64 per leaflet) at 310 K:
Applied standard PBC corrections (whole + nojump + center).
In VMD, the membrane looked unstable, with excessive lipid diffusion and large gaps between lipids.
APL fluctuated significantly, and the membrane struggled to reach equilibrium. -
Pure DPPC (128 lipids) at 310 K:
This membrane was much more stable than POPC at 310 K.
However, since DPPC’s phase transition temperature is around 315 K, 310 K is close to the gel-fluid transition, raising concerns about capturing biologically relevant behavior.
I increased the temperature to 323 K, but at this higher temperature, the DNA structure showed severe instability, with large RMSD fluctuations. -
Pure POPC at 293 K
To improve POPC stability, I tested lowering the temperature closer to POPC’s phase transition temperature (~271 K).
However, as seen in the blue curve in APL@Voro, this did not significantly improve membrane stability. -
POPC + 15% Cholesterol at 310 K (54 POPC + 10 Chol per leaflet)
This partially improved stability, but APL fluctuations were still larger than desired.
Additionally, I found literature suggesting that adding cholesterol could hinder peptide insertion, which is a concern since CPP penetration is a primary objective.
The attached APL@Voro plot compares these trials:
Black: POPC at 310 K
Red: DPPC at 310 K
Blue:POPC at 293 K
Green: POPC+Chol at 310 K
All simulations used the same parameters, force fields, and conditions, except for temperature.
I also considered adding negatively charged lipids to enhance CPP-membrane interaction, but this could interfere with DNA-membrane interaction, as the DNA itself is negatively charged.
I would greatly appreciate your insights on the following:
Based on your experience, what would be the most suitable membrane composition for modeling a biologically realistic bilayer — one that remains stable over long simulations while still allowing for efficient peptide insertion?
How can I best balance membrane stability and biological relevance, considering that my study focuses not only on peptide insertion but also on DNA-membrane interactions and the interaction of a CPP-DNA complex with the membrane?
Are there any recommended workflows, systematic approaches, or best practices for testing and optimizing lipid compositions in such multi-component systems?
If you have worked on CPP-membrane-DNA simulations using GROMACS, I would be very grateful if you could share any practical advice, key challenges to watch out for, or relevant publications that could guide me in refining my setup.
Looking forward to your valuable suggestions and guidance.
