Biomedical Engineering Reference
In-Depth Information
Protein Modelling and Surface Folding
by Limiting the Degrees of Freedom
Meir Israelowitz, Birgit Weyand, Syed W. H. Rizvi, Christoph Gille
and Herbert P. von Schroeder
Abstract One aspect of tissue engineering represents modelling of the extracel-
lular matrix of connective tissue as the fiber network arrangement of the matrix
determines its tensile strength. In order to define the correct position of the e.g.
collagen in a structure, an optimized tertiary structure must be characterized.
Existing approaches of protein models consider random packing of rigid spheres.
We propose an alternative strategy to model protein structure by focusing on the
folding. Our model considers (a) segments of amino-acid peptides or beads,
(b) hydrogen bond distances, and (c) the distance geometry as functional compo-
nents rather than minimizing distances between the centers of atoms. We reduced
the molecular volume by using concepts from low dimensional topology, such as
braids and surfaces, via differential geometry. A braid group maintains the conti-
nuity of a sequence while the spatial minimization is performed, and guarantees the
continuity during the process. We have applied this approach to different examples
of known protein sequences using ab initio protocols of ProteoRubix Systems TM .
Sequence files of three different proteins types were tested and modeled by Pro-
teoRubix TM
and compared to models derived by other methods. ProteoRubix TM
M. Israelowitz S. W. H. Rizvi C. Gille H. P. von Schroeder (
&
)
Biomimetics Technologies Inc, Toronto, Canada
e-mail: herb.vonschroeder@uhn.ca
B. Weyand
Department of Plastic, Hand and Reconstructive Surgery, Hannover Medical School,
Hannover, Germany
C. Gille
Institute of Biochemistry, Charite Universitsaetsmedizin, Berlin, Germany
H. P. von Schroeder
University Health Network, Toronto, Canada
H. P. von Schroeder
University of Toronto, Toronto, Canada
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