Subject: MD of non-globular proteins - answers

From: Peter Grootenhuis <[email-masked]>
Date: Tue, 12 Mar 1996 09:29:44 +0000 (WET)

CCL-ers,

My original questions concerned MD of non-globular proteins where I observed
both in gas-phase and aqueous simulations a rather strong tendency of the 
system to adopt conformations that result in more globular shapes. 
Questions:
(1) Is anybody aware of (published) MD simulations of non-globular proteins ?
(2) Does anybody has (preferably computationally inexpensive) suggestions on 
	how to handle such a system ? 

Thanks for your suggestions! Here is a summary:
-------------------------------------------------------------------------------
From: [email-masked] (Soaring Bear)

	Sounds like you ought to use more gentle methods, like
lower temp, ramp gradient, shorter times, higher dielectric.
-------------------------------------------------------------------------------
From: Willy Wriggers <[email-masked]>

The problems you mentioned have also been observed by us. We carry  
out MD simulations of calmodulin, a dumbbell shaped protein of only  
148 aa residues, in solution (see "calmodulin" on my homepage at  
http://www.ks.uiuc.edu/~wriggers/). Earlier simulations by our  
collaborators at CUNY (see Pascal-Ahuir, Mehler, Weinstein: Molecular  
Engineering 1, 231-247, 1991 for review) had a limited solvent model  
(only explicit surface waters) and it could not be ruled out that  
observed structural changes were caused by the protein "sticking it's  
tongue out" of the water molecules, which tend to diffuse to the  
center of the protein.
The way we solve the problem now is by placing the protein in a 44 A  
radius sphere of water, which brings the total system size to 33,000  
atoms. Since the explicit solvent model and salt ions slow down the  
movement of calmodulin's domains, we need to simulate for 3 ns. I  
know such a calculation may not be feasible in every case. If you  
have limited resources, it's better to simulate only parts of the  
protein which are of interest, i.e. use stochastic boundary  
conditions (Brooks, Karplus, Pettitt: Proteins. (1988) Wiley  
Interscience Pub.). I would not recommend using a distance-dependent  
dielectric constant to model the solvent because it gives you the  
wrong electrostatics. Depending on your problem, you may also want to  
look at other newer "in vacuo" simulation techniques which use  
constraints (Collins, Burt, Erickson: Flap opening in HIV-1  
protease... (1995) Nature Struct. Biol. 2:334-338). 
-------------------------------------------------------------------------------
From: [email-masked] (Howard Alper)

  In your simulations, how do you treat the nonbonded interactions.  In
particular, do you use switching functions?  The reason I ask is that
while these functions do smooth away discontinuities in the energy, they
can create artificial maxima and minima in the interatomic, interresidue,
or intermolecular forces that could trap the particles at particular
separations from each other.  This can be seen by looking at the way the
switching function varies in the region where it goes from 1 to 0, and
considering what the derivative of the function would look like.
  I have seen this for simulations of neat water (K. Lau. H. E. Alper,
T. Thacher, and T. R. Stouch, J. Phys. Chem. 98, 8785 (1994)), as well as
in simulations of lipid bilayer systems.  Switching functions can decrease
the degree of motion a system undergoes, compared to other cutoff methods...
-------------------------------------------------------------------------------
From: Vincent Collura <[email-masked]>

I am not surprised about " a tendency" to fold into a globular (more compact)
shape in the gas-phase, the reason is certainly the electrostatics term of the
nonbonded energy. The best is to increase the dielectric constant (distance
dependent or not in your case?) close to the value of water. In your case, it
will be a good approximation because if it is not globular or compact it can be
deduced that it has certainly a substantial part of the surface in contact with
the solvent unless it is a membrane protein.
I am slightly more surprised that you observed this effect with the explicit
description of the solvent. Normally it should be more "rigid". If it is not a
compact protein ( higher % of hydrophilic residues? Is there a well defined
hydrophobic core in your protein ?) it is normal that it undergoes larger
average fluctuation at room temperature in the solvent, but it should'nt lead
to a more compact protein. Are you using Periodic Box conditions or only a
water shell around the protein ?
Have a look in the way the electrostatics terms are parameterized in your force
field....
 ______________________________________________________________________________
 Dr. Peter D.J. Grootenhuis       |
 N.V. Organon / CMC Dept. RK2337  | Phone  : +31-412-661920
 P.O. Box 20 / 5340 BH Oss        | Fax    : +31-412-662539
 The Netherlands                  | E-mail : [email-masked]
 _________________________________|____________________________________________