Coarse-Grained Model of Collagen Molecules Using an Extended MARTINI Force Field
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- 作者：Alfonso Gautieri ; Antonio Russo ; Simone Vesentini ; Alberto Redaelli ; Markus J. Buehler
- 刊名：Journal of Chemical Theory and Computation
- 出版年：2010
- 出版时间：April 13, 2010
- 年：2010
- 卷：6
- 期：4
- 页码：1210-1218
- 全文大小：219K
- 年卷期：v.6,no.4(April 13, 2010)
- ISSN：1549-9626
文摘
Collagen is the most abundant protein in the human body, providing mechanical stability, elasticity, and strength to connective tissues such as tendons, ligaments, and bone. Here, we report an extension of the MARTINI coarse-grained force field, originally developed for lipids, proteins, and carbohydrates, used to describe the structural and mechanical properties of collagen molecules. We identify MARTINI force field parameters to describe hydroxyproline amino acid residues and for the triple helical conformational structure found in collagen. We validate the extended MARTINI model through direct molecular dynamics simulations of Young’s modulus of a short 8-nm-long collagen-like molecule, resulting in a value of approximately 4 GPa, in good agreement with earlier full atomistic simulations in explicit solvent as well as experimental results. We also apply the extended MARTINI model to simulate a 300-nm-long human type I collagen molecule with the actual amino acid sequence and calculate its persistence length from molecular dynamics trajectories. We obtain a value of 51.5 ± 6.7 nm for the persistence length, which is within the range of earlier experimental results. Our work extends the applicability of molecular models of collagenous tissues by providing a modeling tool to study collagen molecules and fibrils at much larger scales than accessible to existing full atomistic models, while incorporating key chemical and mechanical features and thereby presenting a powerful approach to computational materiomics.