normal Solvent Accessible Surface Area on Martini Trajectories

  • z.sichaib
  • z.sichaib's Avatar Topic Author
  • Offline
  • Senior Boarder
More
1 year 3 months ago #8099 by z.sichaib
Hi,

I simulated a protein in a membrane with explicit water molecules using Martini FF.
For the analysis, I would like to see which parts of the protein stay buried inside the membrane and which are not. For this, I thought about calculating the SASA.

By definition, SASA is the locus of the center of the solvent molecule as it rolls over the Van Der Waals surface of the protein, and generally, a sphere of water is assumed to be the solvent molecule with a radius 1.4 Å.

In the Martini CG system, is the VDW surface of the protein comparable to the AA one?
We have 2 variables in SASA calculation: VDW surface of the protein and the radius of the solvent molecule (1.4 Å). Does it make sense to calculate it on a Martini CG system? If yes, should I use the same radius of the solvent molecule (1.4Å)?

Thanks a lot for your opinion and help.

Zeineb

Please Log in or Create an account to join the conversation.

More
1 year 3 months ago #8100 by Pim
Dear Zeineb,

As I understand it, it doesn't make so much sense to measure the CG SASA with a 1.4 nm probe, because the probe can easily go in between two beads that have a contact (although the problem doesn't appear to be too severe if you're looking at relative effects). I have used a 0.4 nm probe in the past.

That also means quantitatively you're not going to find the same value as for an atomistic sasa with a small probe (surface area will be probably smaller at the CG level). Maybe it actually makes the most sense to measure both the atomistic and the CG with the same large probe (e.g. 0.4 nm) if you want to compare the values. There may be literature on this topic if you want to know more, this is where my knowledge stops.

Please Log in or Create an account to join the conversation.

More
1 year 3 months ago #8103 by riccardo
I agree with Pim. I would go for a larger probe: 0.4 nm like Pim suggested or at least 0.26 nm, the latter being the radius of a regular Martini bead ( 2**(1./6)*0.47/2 ~ 0.26 nm, where 0.47 is the Lennard-Jones sigma of regular Martini interactions). Any probe in this 0.26-0.4 nm range should do: from my experience, relative differences will be the same across different probe sizes, *as long as* you compare SASA values obtained with the same probe size.

Please Log in or Create an account to join the conversation.

  • z.sichaib
  • z.sichaib's Avatar Topic Author
  • Offline
  • Senior Boarder
More
1 year 3 months ago #8107 by z.sichaib
Very clear!

Thank you so much @Pim and @Riccardo :)

Please Log in or Create an account to join the conversation.

More
1 year 2 months ago #8135 by xavier
We have used a 0.26 nm probe in our measurement of SASA in the periole-JACS-2012.

X-

Please Log in or Create an account to join the conversation.

  • z.sichaib
  • z.sichaib's Avatar Topic Author
  • Offline
  • Senior Boarder
More
1 year 3 weeks ago #8185 by z.sichaib
Thank you Xavier!

Please Log in or Create an account to join the conversation.

Time to create page: 0.097 seconds