VMD-L Mailing List

From: Eduard Schreiner (eduard.schreiner_at_gmail.com)
Date: Sun Jan 24 2010 - 15:38:54 CST

Hi Khaled,

I think your observation can be explained considering the following.

Consider a sphere as your molecule. Now calculate the SASA.
To my understanding, in the calculation of SASA a probe sphere of a
specified radius is used to "roll" over your molecule and the calculated
surface is determined from the center of this rolling sphere
(this is not completely true, but demonstrates it rather pictorially. For
the algorithm in VMD, check:
 http://www.ks.uiuc.edu/Research/vmd/doxygen/Measure_8C-source.html#l01058
and
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/15227.html
).
Now, if you choose a larger probe radius, the calculated area will be
larger
(try it in VMD using only one atom as your molecule).
This is true for a sphere. However, it is not true in general, e.g. consider
a cylinder.
In this case, the SASA will depend on the radius of your probe and the
diameter of the cylinder.

I hope this explanation helps you.

eddie

On Sun, Jan 24, 2010 at 2:44 PM, Khaled Barakat
<kbarakat_at_phys.ualberta.ca>wrote:

> Hello,
>
> I am trying to calculate the solvent accessible/excluded surface area (SASA
> and SESA) using MSMS for different probe
> radii. I noticed that the SASA increases with increasing the probe radius,
> while the SESA decreases. My question is:
> Does these results make sense?! I was expecting opposite results ( i.e. the
> SASA decreases with increasing the probe
> radius, because a larger solvent molecule will not be able to touch the
> surface of the protein as much as a smaller solvent
> molecule).
>
> I will appreciate if someone can help me understand these results.
>
> Thanks in advance.
> Khaled
>
> My numbers are:
>
> Radius SASA SESA
> 2.5 7869.7254 5957.5241
> 2.8 7936.7443 5832.3499
> 3.0 7990.4262 5782.2308
> 4.25 8535.3977 5491.1256
>
> 

-- 
--
=============================================================================
Eduard Schreiner
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
Phone: 217-244-4361
Fax: 217-244-6078
http://www.ks.uiuc.edu/~eschrein/
=============================================================================