Computational modeling of type I collagen fibers to determine the extracellular matrix structure of connective tissues
Computational modeling of type I collagen fibers to determine the extracellular matrix structure of connective tissues
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DOI：
10.1093/protein/gzi037
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发表时间：
2005-07-01
影响因子：
2.4
通讯作者：
von Schroeder, HP
中科院分区：
文献类型：
--
作者：
Israelowitz, M;Rizvi, SWH;von Schroeder, HP
提出了一种用于生成生物组织的计算机模型的方法。该方法利用细胞外基质蛋白的特性来预测组成组织的元素的结构和物理化学。该方法从蛋白质数据库中氨基酸的坐标位置开始，作为TissueLab软件的输入。根据氨基酸序列，通过计算构建I型胶原样三螺旋骨架，并基于氨基酸的已知化学和物理性质添加边界球。边界球确定的胶原蛋白分子和分子间的相互作用的接触表面的特性，然后确定通过考虑接触表面的关系，并通过解决能量最小状态，使用可行的序列二次规划。由此，软件创建了与已知胶原蛋白参数完全对应的原纤维，并通过有限元建模进一步确认。然后使用计算衍生的原纤维来创建胶原纤维和三维胶原基质。通过解析能量最小状态，可以确定细胞外空间的大的复杂组分以及其他结构，以提供分子、分子相互作用和它们形成的组织的三维结构。
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.