> I note on overlaying backbones from the different models of my protein that
> some parts form a tight bundle of backbones, while others form a
> fairyly ill defined region. The ends of the protein are also "fuzzy"
> in this manner. Does this mean that there was too little information
> in the data set to define the backbone precisely, and if so does this simply
> reflect a problem with NMR or does this actually identify
> flexible regions of the protein?
>
> My instincts are the former, but I am wondering about the
> latter.
I think, your are right with both suggestions. NMR structures are derived
from proteins in solution, so its much more likely that the structures
you get are in some extend more flexible than those solved by X-RAY
analysis. Nevertheless, there is a high accordance between the results
obtained so far by both methods for the same protein.
The rigid dispay of a structure is a little bit irritating and maybe
not the ultimate picture of a protein in nature. All models displayed
in the NMR data file are likely to represtent the native structure.
So the term "ill-defined" gives the impression the something is
not right with the structure there, or with the data substracted
from NMR measurement. The case is not, that there is a "lack" of data
- in contrary - it looks like there is a huge amount of data
pointing out that more than one rigid position for the backbone
is most likely.
These are my thougts about structure display, and must not be right.
Any comments are very wellcome,
Markus (Phe-Group)
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Markus Jaritz
Center for Applied Molecular Engineering
University of Salzburg
Jakob Haringer Str. 1
5020 Salzburg
Austria
e-mail: markus@olga.came.sbg.ac.at