From owner-biophysics@net.bio.net Thu Mar 05 22:00:00 1998
Path: biosci!agate!newsfeed.kornet.nm.kr!nntp.kreonet.re.kr!logbridge.uoregon.edu!news.bc.net!news.sfu.ca!beaufort!rstorjoh
From: Rasmus Storjohann <rstorjoh@sfu.ca>
Newsgroups: bionet.biophysics
Subject: Lipari/Szabo calculations
Date: Fri, 6 Mar 1998 11:39:25 -0800
Organization: Simon Fraser University
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I want to use relaxation matrix refinement and the Lipari-Szabo 
model-free approach to improve my under-defined NMR structure. This means 
that I need numbers for my correlation time and my order parameter. I was 
planning to get my correlation time either from T1 relaxation at two 
different field strengths, or from publinshed data based on Trp 
fluorescence. (The correlation time from fluorescence is the correlatioin 
time of overall motion, while the correlation time from T1 relaxation is 
the correlation time of overall+internal motion, is that right?)

I have preliminary structures calculated by distance geometry and 
restrained molecular dynamics. These structures have more and less well 
defined regions, which should correspond to some extent to more and less 
flexible regions of the peptide in solution. I was thinking that if I 
could calculate the order parameter based on my preliminary structures, 
the relaxation matrix calculations should have a pretty accurate motional 
model to start from.

X-plor allowes the specification of different order-parameters (and 
different correlation times) between different parts of the molecule, e.g.:

    taucorrel  DMSO
       model lipari
       vector (name hn or name ha) 
              (name hn or name ha) 0.75e-9 0.85 
       vector (name hn or name ha) 
              (name h* and not (name hn or name ha)) 0.75e-9 0.80 
       vector (name h* and not (name hn or name ha)) 
              (name h* and not (name hn or name ha)) 0.75e-9 0.65
       end

giving a uniform correlation time of 0.75ns, and order parameters of 0.85 
for backbone-to-backbone, 0.80 for backbone-to-sidechain, and 0.65 for 
sidechain-to-sidechain.

I'm using the molecular visualisation program MolMol, which allowes me to 
calculate order parameters for all the dihedral angles of the molecule. 
Is there any way I can convert these order parameters to the ones 
seemingly related to inter-proton distances required for X-plor?

Thanks for your patience!

Rasmus

 ____________________________________________________________________
        __		Rasmus Storjohann
       / /\		Institute of Molecular Biology
      / /  \		and Biochemistry
     / / /\ \		Simon Fraser University
    / / /\ \ \		Burnaby, British Columbia V5A 1S6
   / /_/__\ \ \		e-mail: rstorjoh@sfu.ca
  /________\ \ \	Phone: (604) 291-5657 / 415-0575
  \___________\/	FAX:   (604) 291-3765


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