AMBER Archive (2004)

Subject: Re: AMBER: Normal Mode Analysis possibility

From: David A. Case (case_at_scripps.edu)
Date: Tue May 04 2004 - 13:25:27 CDT

On Tue, May 04, 2004, myang wrote:
>
> Now I have a multimeric protein, whose shape looks like '00' (put two eggs
> together), and I hope to find out the driving force of its dissociation.
> Experiments have found that during the dissociation process, the two parts
> of this protein are relatively rigid (do not undergo substantial
> conformational change). Can I use NMA in such a case? I couldn't find any
> people who use NMA to study protein dissociation, so I am afraid it maybe
> not a suitable tool here. But still want to hear some advice.
>

You might want to look at recent papers from Tama and Brooks:

%A F. Tama
%A C.L. Brooks
%T The Mechanism and Pathway of pH Induced Swelling in Cowpea Chlorotic Mottle
Virus
%J J. Mol. Biol.
%V 318
%P 733-747
%D 2002

%A F. Tama
%A W. Wriggers
%A C.L. Brooks
%T Exploring Global Distortions of Biological Macromolecules and Assemblies
%from Low-resolution Structural Information and Elastic Network Theory
%J J. Mol. Biol.
%V 321
%P 297-305
%D 2002

This model is similar to that used a lot by Bahar and Jernigan (and others),
for example: (a few papers among many):

%A I. Bahar
%A R.L. Jernigan
%T Cooperative Fluctuations and Subunit Communication in Tryptophan Synthase.
%J Biochemistry
%V 38
%P 3478-3490
%D 1999

%A P. Doruker
%A R.L. Jernigan
%A I. Bahar
%T Dynamics of Large Proteins through Hierarchical Levels of Coarse-Grained
%Structures
%J J. Comput. Chem.
%V 23
%P 119-127
%D 2002

%A O. Keskin
%A R.L. Jernigan
%A I. Bahar
%T Proteins with Similar Architecture Exhibit Similar Large-Scale Dynamic
Behavior
%J Biophys. J.
%V 78
%P 2093-2108
%D 2000

...hope this helps...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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