Subject: Re: CCL:coupling constant restrain of D-Amino Acid for structural refine.

From: Mark D Shenderovich <[email-masked]>
Date: Thu, 14 Mar 1996 10:46:52 -0700 (MST)

On Tue, 12 Mar 1996, Chyh-chong Chuang wrote:

> 
> Dear Netters:
> 
> 	Does any one could point me some references about how to use the 
> measured 3J-na coupling constant of a D-form amino acid as an additional 
> restrain in nmr structural refinement.
> 	Any suggest/comment will be great appreciated.
> 
> Thanks all

Dear Chuang,

If you know how to use these coupling constants for L-amino acids, there 
is no problem with D-amino acids. The only difference is that for D-AA the
angle H-N-Ca-H which is used in Karplus equation, is calculated as
|phi+60|, and for L-AA it is |phi-60|, where phi is conventional torsional
angle around N-Ca bond. Depending on available software, you may calculate
expected phi angles and use them as constrains, or you may use exptl. 
coupling constants as direct constraints in MD simulations. The latter is 
preferable. See: 

Mierke & Kessler, Biopolymers, 1993, 33, 1003;
Mierke et al., Biopolymers, 1994, 34, 559.

Best regards,

Mark Shenderovich.