Sent to CCL by: "Konrad Hinsen" [hinsen]~[cnrs-orleans.fr]
On 28.02.2007, at 07:07, Pradipta Bandyopadhyay pradipta:iitg.ernet.in wrote:
Applying GNM to a protein (whose structure is a bit open), I
found that in
some regions B-factors obtained from calculation is different from
experimental one (for the rest other regions these are close). This
probably means using one gamma may not be enough. Does anyone know if
there is any simple way to use more than one gamma in GNM (any other
suggestion would be appreciated also)?
It is certainly possible to use different gammas for the different interacting
pairs, but I am not
aware of anyone having done so in a GNM.
If you are reasonably sure that the experimental B factors are reliable, then my
first suggestion
would be to try an elastic network model, i.e. a model taking into account the
directions of atomic
displacements. This increases the number of coordinates in your system by a
factor of three, but
that difference matters only for huge proteins. You gain in two points:
1) The description with three coordinates per C-alpha atom is in itself more
precise and thus
more realistic.
2) The GNM potential is physically unrealistic in not being invariant under
rotations. This
means that it penalizes global rotations (which you probably don't care about),
but also rotational
domain motions which you may well have in your protein.
There is also a wider choice of potential models that have been published for
elastic network
models. The most widely used variety of elastic network models uses a force
constant that depends
on the interatomic distance in the input configuration, nearby atom pairs
interacting stronger than
more distant ones. In this family we find, in historical order:
1) A exp(-r^2) decrease with distance:
K Hinsen
Analysis of domain motions by approximate normal mode calculations
Proteins 33:417-429 (1998)
http://dirac.cnrs-orleans.fr/plone/publications/all-publications/H_1998
2) A more complex function obtained from fitting to the Amber94 all-atom
potential:
K Hinsen, A J Petrescu, S Dellerue, M C Bellissent-Funel, and G R Kneller
Harmonicity in slow protein dynamics
Chem. Phys. 261(1+2):25-37 (2000)
http://dirac.cnrs-orleans.fr/plone/publications/all-publications/Hinsen2000a
3) A step function: constant up to a cutoff distance, then zero (like for GNM):
A. R. Atilgan, S. R. Durell, R. L. Jernigan, M. C. Demirel, O. Keskin, and I.
Bahar
Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model
Biophys. J. 80, 505515 (2001)
The best model is probably the one described in 2). You can find a ready-to-use
implementation in
the Molecular Modelling Toolkit (http://dirac.cnrs-orleans.fr/MMTK, it's called CalphaForceField
there). There is also a Web server that performs various normal-mode based
calculations (including
B factors) using this model for any PDB file you submit; the address is
http://www.bioinfo.no/tools/normalmodes
I remember having seen a paper that modifies the elastic network model in
choosing the force
constants in a more protein-specific way, but I don't have the reference at
hand.
Konrad.
--
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Molculaire, CNRS Orlans
Synchrotron Soleil - Division Expriences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen||cnrs-orleans.fr
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