Protein conformations

Per Kraulis pjk19 at
Wed Mar 3 05:11:57 EST 1993

Jim Cassatt writes:

> If you pull up structures from the Protein DAta Bank that were
> determined by nmr, you will find that each file contains
> multiple structures.  If you put these on your favorite
> graphics workstation, you will find several areas where the
> structures overlap almost completely.  Other areas will show
> little agreement.  There are areas of disorder, ie, multiple
> conformations.

No. The multiple coordinate sets usually given for NMR structures in the PDB
do *not* reflect actual, physical multiple conformation, disorder or mobility.
They rather indicate which parts of the structure are well determined by the
available NMR data. The reason NMR spectroscopists generate several coordinate
sets from one single set of NMR data is to obtain an estimate of the precision
of the structure determination.  A badly defined region in an NMR structure *does
not* mean that it is physically mobile. It simply means that the NMR data for
this region could not be sorted out for whatever reason.

However, there may be cases where the lack of NMR data is a consequence of
actual physical mobility. But this statement has to be supported by additional
experimental observations, such as observation of sharper linewidths than
expected, or relaxation measurements.

> The native state of a protein can best be described as a
> collection of conformations of similar free energy.

Yes. There are several well-refined X-ray structures which show the presence
of multiple conformations of certain side-chains. I seem to remember that one
of the myoglobin structures in the PDB contains such well-defined multiple
conformations. Also, there is some evidence from the NMR data for tendamistat
that a tyrosine side chains alternates between two rotamer states (ref: Torda et
al, J Mol Biol, 1990, vol 214, pp 223-235).

Per Kraulis                         pjk19 at
Dept Biochemistry                   phone +44 223 333 596
University of Cambridge             fax   +44 223 333 345
Tennis Court Road
Cambridge CB2 1QW

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