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PEDS Advance Access published online on June 24, 2005
Protein Engineering Design and Selection, doi:10.1093/protein/gzi037
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oupjournals.org
Received December 23, 2004
Revised May 14, 2005
Accepted May 17, 2005

Article

Computational modeling of type I collagen fibers to determine the extracellular matrix structure of connective tissues

Meir Israelowitz 1, Syed W. H. Rizvi 1, James Kramer 2, and Herbert P. von Schroeder 3*

1 Biomimetics Technologies, Unit 101, 6 Fernwood Gardens, Toronto, Ontario M4K 2J9, Canada
2 Pittsburgh Safety and Health, Technology Center, Cochrans Mill Road, Pittsburgh, PA 15236, USA
3 Biomimetics Technologies, Unit 101, 6 Fernwood Gardens, Toronto, Ontario M4K 2J9, Canada; University of Toronto, Toronto Western Hospital, 399 Bathurst Street, Toronto, Ontario M5T 2S8, Canada

* To whom correspondence should be addressed.
Herbert P. von Schroeder, E-mail: herb.vonschroeder{at}uhn.on.ca


  Abstract

A method is presented for generating computer models of biological tissues. The method uses properties of extracellular matrix proteins to predict the structure and physical chemistry of the elements that make up the tissue. The method begins with Protein Data Bank coordinate positions of amino acids as input into TissueLab software. From the amino acid sequence, a type I collagen-like triple helix backbone was computationally constructed and boundary spheres were added based on known chemical and physical properties of the amino acids. Boundary spheres determined the contact surface characteristics of the collagen molecules and intermolecular interactions were then determined by considering the relationships of the contact surfaces and by resolving the energy-minimum state using feasible sequential quadratic programming. From this, the software created fibrils that corresponded exactly to known collagen parameters and were further confirmed by finite element modeling. Computationally derived fibrils were then used to create collagen fibers and three-dimensional collagen matrices. By resolving the energy-minimum state, large complex components of the extracellular space as well as other structures can be determined to provide three-dimensional structure of molecules, molecular interactions and the tissues that they form.

Keywords: collagen; computation; extracellular matrix; modeling; tertiary structure.
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