Collagen is a ubiquitous extracellular matrix protein. Its biological functions, including maintenance of the structural integrity of tissues, depend on its multiscale, hierarchical structure. Three elongated, twisted peptide chains of >1000 amino acids each assemble into trimeric proteins characterized by the defining triple helical domain. The trimers associate into fibrils, which pack into fibers. We conducted a 10 ns molecular dynamics simulation of the full-length triple helical domain. The calculation included ~1.8 million atoms, including solvent, and took approximately 11 months using the CPUs of over a quarter of a million computers. Specialized analysis protocols and a relational database were developed to process the large amounts of data, which are publicly available. The simulated structures exhibit heterogeneity in the triple helical domain consistent with experimental results but at higher resolution. The results structures serve as the foundation for studies of higher order forms of the protein and for modeling the effects of disease-associated mutations.
Bodian DL, Radmer RJ, Holbert S, Klein TE. Molecular dynamics simulations of the full triple helical region of collagen type I provide an atomic scale view of the protein's regional heterogeneity. Submitted. (2010)
Provides the raw and derived data from molecular dynamics simulation of the full-length collagen type I triple helix
This project contains the supplementary materials for the cited publication on molecular dynamics simulations of collagen type I.
Jul 2, 2010
Jul 2, 2010
1. Provides the raw and derived data from the molecular dynamics simulations, stored in postgres format, and the database schema.
2. Provides the data used to create Figure 3.