Molecular dynamics simulations of the full triple helical region of collagen type I provide an atomic scale view of the protein's regional heterogeneity.

摘要: Collagen is a ubiquitous extracellular matrix protein. Its biological functions, including maintenance of the structural integrity tissues, depend on its multiscale, hierarchical structure. Three elongated, twisted peptide chains > 1000 amino acids each assemble into trimeric proteins characterized by defining triple helical domain. The trimers associate fibrils, which pack fibers. We conducted 10 ns molecular dynamics simulation full-length domain, was made computationally feasible segmenting protein overlapping fragments. calculation included ~1.8 million atoms, solvent, and took approximately 11 months using CPUs over quarter computers. Specialized analysis protocols relational database were developed to process large amounts data, are publicly available. simulated structures exhibit heterogeneity in domain consistent with experimental results but at higher resolution. serve as foundation for studies order forms modeling effects disease-associated mutations.