Department of Inorganic chemistry, Comenius
University in Bratislava, Faculty of Natural Sciemces, 842 15 Bratislava,
Slovak Republic
Abstract
Electron density
is easily interpreted if well-phased structure factor data are available to
atomic resolution. If the data are below this resolution or the phasing is poor
then "bones" skeletonization and chicken wire representation of the
electron density are calculated. It is necessary to use computer graphics to
interpret the electron density Map interpretation is a time limiting step in
the protein structure determination an is quite subjective for low-resolution
maps. Its automation is an important step in the overall automation of the
protein structure determination and is essential for success of structure genomic
projects.
A
concept of flexible fragments has been developed for automatic building of
crystal structures [1]. Six monopeptides (AlphaP0, Beta1P0, Beta2P0, GammaP0,
BridgeP0, CisPro0) were designed as search fragments in a phased rotation and
translation function for main chain building. Electron density in a crystal and
in molecular fragments is expanded in spherical harmonics and normalized Bessel
functions [2, 3]. A fast rotation function, which is calculated at each grid
point of the asymmetric unit, is used to find the fragment orientation.
Position, orientation and internal torsion angles are refined by a phased
flexible refinement. Individual fragments are connected into chains. An
algorithm for chain building is simplified using generalized atoms and virtual
bonds. The structure is build from flexible groups rather than from individual
atoms. A sequence is aligned by a combined marker and rotamer method. The side
chains are built either by a combined marker & full conformation search or
by the rotamer method. Side chains are independent structure units. The protein
model is built with an accuracy of about 0.2Å at resolutions
1.2-2.1Å. A library of bioinorganic HET groups is currently under
development. It is designed to build structures like ferredoxin and hemoglobin
[4].
[1] F. Pavelcik. Acta Cryst., A59 (2003)
487-494.
[2] J. Friedman. Comput. Chem., 23
(1999) 9-23.
[3] F. Pavelcik, J. Zelinka, and Z. Otwinowski.
Acta Cryst. D58, (2002) 275-283.
[4] F. Pavelcik, J. Molnar. Work in progress.