Subject: Correlation time estimation

From: [email-masked] (Mark J Forster )
Date: Thu, 23 Mar 1995 09:17:24 -0800

Dear Chyh-Chong

The most accurate method of correlation time estimation would be 
measurement of (say) 13C or 15N relaxation for a nucleus with
a directly attached proton and with out extensive molecular motion,
so a backbone 15N in a protein would be suitable. An H-H noe build
up rate between say a Gly HA1-HA2 might also be suitable. In
DNA the Cyt H5-H6 vector is of fixed length and is often used 
for this purpose.

If you want a very rough method, that my experience suggests is
still within a factor of two, the try 
	MW in KDa = tauc_c in ns
of true tau_c values depend upon the temperature, solvent etc
and can in practice differ for different atom-atom vectors in the
molecule if it exhibits differential mobility.

There are also formulas based upon hydrodynamic models in the 
literature that can predict tau_c for both isotropic and anisotropic
reorientation. 

Hope this helps.

---

From: Konstantin Momot <[email-masked]>
Date: Thu, 23 Mar 1995 12:19:06 -0700 (MST)

On Wed, 22 Mar 1995 [email-masked] wrote:

> Dear netters: 
> 
> When doing NOE simulation from structure, it is needed to give the correlation time value. Yah, to my know, it is dependent on the molecular weight, the shape
> (structure) of the molecule. How to roughtly estimate the correlation time when doing this kind of calculation ???
> 
> Any suggestion will be great appreciated.
> 
> Any suggestion can mail to me directly. Thanks.
> 
> ccchuang
> 

In general, this depends on the particular model of molecular motion
you assume. The most consistent discussion of the question is given in
Abragam's book, Ch.VIII, Part E (especially pp. 298-300 of the last
English edition). 

If you only consider rotation in a liquid and assume the molecule to be a
rigid sphere (very rough estimate, but sufficient for most practical
problems !), then you have the correlation time

          4pi*R^3*mu/3kT

where mu is solvent's viscosity and R is the molecule's radius.

Cheers,

Konstantin             <[email-masked]>