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Proteins in Motion.

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Proteins in Motion
Macromolecular crystal structures
are the unsurpassed gold-standard of
accuracy in structural analysis. Owing
to the method itself—and the repeated
criticism of X-ray crystallographic analysis—such structures imply that proteins
are rigid entities. On the contrary, proteins are inherently flexible. Indeed,
they must be in order to carry out their
specific biological functions. Classic
examples of such flexibility in proteins
include the regulatory protein calmodulin, the muscle protein myosin, and the
enzymes hexokinase and nucleoside
monophosphate kinase. The latter had
already been used in a study conducted
by George Schulz and colleagues (University of Freiburg, Germany) over
10 years ago, in which alternate substrate-induced enzyme conformations
were collected to produce an animated
sequence of images which demonstrates
the impressive flexibility of this protein.[1]
This is where the Database of Macromolecular Movements (DMM) ties
in. It collates the knowledge of unique
protein conformations from different
crystal structures, pairs them, analyzes
the movements involved, and interpolates the intermediate steps to allow
the
generation
of
movies
(or
“morphs”) by lining up images of the
intermediates. Each movie provides an
intuitive impression of the conformational flexibility of the protein in question.
The DMM homepage (Figure 1) is
friendly and clearly organized. The
informational content is color-coded:
available movies are accessible through
the green area, the established Morph
Server is in blue, and additional databases focused on individual topics are
found in the pink region.
The probability of finding your
favorite protein is not too high, as the
DMM presently contains about 250 protein conformer ensembles, less than 1 %
of the 26 000 protein structure entries of
the Protein Data Base (PDB). Perhaps
more interesting and rewarding is a
simple exploration of the movie database by using the available listings; the
colorful pictures and protein contortions
can be quite inspiring. The “motion”
link of each entry provides the user
Figure 1. By no means rigid: Database of Macromolecular Movements.
4428
$ 2005 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
DOI: 10.1002/anie.200502001
with the corresponding “motion
report”, a detailed listing of the type of
motion involved, the PDB code of the
individual protein conformers, appropriate references, plus a list of morphs,
which can occasionally be overwhelmingly long. Each morph portrays the
transition between two protein conformations, yet it is important to bear in
mind that the intermediate stages are
derived by interpolation and do not necessarily represent true physiological
states.
For more information, visit:
http://molmovdb.org/
or contact
Mark.Gerstein@yale.edu
The morph reports contain two
enticingly
multicolored
thumbnail
movies, which give the user the impression that a single mouse-click will
deliver a clear, colorful, high-resolution
morph. This is, however, where the
DMM fails to deliver in a rather disappointing manner: instead of the colorful
animation anticipated, the visitor is provided with a highly dated black-andwhite rendition—if there is even an animation at all. Not infrequently, the user
is linked to an empty white page with a
small error message tucked in the
corner. Retracing one<s steps, some
compensation may be found in a variable section titled “Custom PyMOL
MPEG movies”, which lists protein
motion movies created individually.
Clashing with the professionalism of
the welcoming page, these deficiencies
and inconsistencies unfairly deflect the
attention of the casual visitor away
from the treasure trove of information
provided by the DMM. A small
amount of effort combined with commonly accessible graphics software, an
average PC, and the simplest of macros
should be sufficient to bring the wealth
of information on this site to a modern
standard of presentation, securing its
relevance into the future.
Dirk Heinz, Wolf-Dieter Schubert
German Research Centre for
Biotechnology (GBF), Braunschweig
(Germany)
[1] C. Vonrhein, G. J. Schlauderer, G. E.
Schulz, Structure 1995, 3, 483.
Angew. Chem. Int. Ed. 2005, 44, 4428
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