A molecular dynamics study of the interprotein interactions in collagen fibrils.
A molecular dynamics study of the interprotein interactions in collagen fibrils.
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DOI：
10.1039/c0sm01192d
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发表时间：
2011-04-07
期刊：
影响因子：
3.4
通讯作者：
de Leeuw NH
中科院分区：
文献类型：
--
作者：
Streeter I;de Leeuw NH
胶原蛋白的分子动力学模拟用于在原子水平上研究胶原纤维内存在的蛋白质间相互作用的性质，这些相互作用决定了纤维的热力学稳定性。对胶原原纤维和完全溶剂化的原胶原的模拟进行比较，以研究原纤维形成过程中蛋白质之间出现的相互作用。研究的相互作用包括直接的蛋白质间氢键、水介导的蛋白质间氢键和疏水性相互作用。模拟用于量化形成的蛋白质间相互作用的数量；研究哪些功能组对相互作用贡献最大；并研究整个原纤维 D 期蛋白质间相互作用的空间分布。然后将胶原纤维生成和蛋白质折叠的过程进行比较，因为这两个物理过程在概念上有许多相似之处，并且后者已得到更广泛的研究。噬菌体 T4 溶菌酶蛋白（无论是天然状态还是未折叠状态）的分子动力学模拟被用作典型蛋白质折叠过程的说明性示例，以便与胶原蛋白模拟进行直接比较。
Molecular dynamics simulations of collagen are used to investigate at the atomistic level the nature of the interprotein interactions that are present within a collagen fibril, and which are responsible for the fibril’s thermodynamic stability. Simulations both of a collagen fibril and of a fully solvated tropcollagen are compared in order to study the interactions that arise between the proteins upon the process of fibrillogenesis. The interactions studied include direct interprotein hydrogen bonds, water-mediated interprotein hydrogen bonds, and hydrophobic interactions. The simulations are used to quantify the number of interprotein interactions that form; to study which functional groups contribute most towards the interactions; and to study the spatial distribution of interprotein interactions throughout the fibril’s D period. The processes of collagen fibrillogenesis and protein folding are then compared with each other, because these two physical processes share many similarities in concept, and the latter has been more widely studied. Molecular dynamics simulations of a bacteriophage T4 lysozyme protein, both in its native state and in and unfolded state, are used as an illustrative example of a typical protein folding process, for direct comparison with the collagen simulations.