Nanoengineering Department, Joint School of Nanoscience and Nanoengineering, North Carolina A&T State University, Greensboro, NC 27401.
Computational Data Science and Engineering Department, North Carolina A&T State University, Greensboro, NC 27401.
J Biomech Eng. 2021 Aug 1;143(8). doi: 10.1115/1.4050648.
Molecular dynamics modeling is used to simulate, model, and analyze mechanical deformation behavior and predictive properties of three different synthetic collagen proteins obtained from RSC-PDB, 1BKV, 3A08, and 2CUO, with varying concentrations of hydroxyproline (HYP). Hydroxyproline is credited with providing structural support for the collagen protein molecules. Hydroxyproline's influence on these three synthetic collagen proteins' mechanical deformation behavior and predictive properties is investigated in this paper. A detailed study and inference of the protein's mechanical characteristics associated with HYP content are investigated through fraying deformation behavior. A calculated Gibbs free energy value (ΔG) of each polypeptide α chain that corresponds with a complete unfolding of a single polypeptide α-chain from a triple-helical protein is obtained with umbrella sampling. The force needed for complete separation of the polypeptide α-chain from the triple-helical protein is analyzed for proteins to understand the influence of HYP concentration and is discussed in this paper. Along with a difference in ΔG, different unfolding pathways for the molecule and individual chains are observed. The correlation between the fraying deformation mechanical characteristics and the collagen proteins' hydroxyproline content is provided in this study via the three collagen proteins' resulting binding energies.
分子动力学模拟用于模拟、建模和分析三种不同的合成胶原蛋白的机械变形行为和预测特性，这些胶原蛋白是从 RSC-PDB、1BKV、3A08 和 2CUO 获得的，具有不同浓度的羟脯氨酸 (HYP)。羟脯氨酸被认为为胶原蛋白分子提供了结构支撑。本文研究了羟脯氨酸对这三种合成胶原蛋白的机械变形行为和预测特性的影响。通过磨损变形行为，对与 HYP 含量相关的蛋白质机械特性进行了详细的研究和推断。通过伞状采样获得了与单个多肽α链完全展开相对应的每个多肽α链的吉布斯自由能值 (ΔG)。分析了从三螺旋蛋白中完全分离多肽α链所需的力，以了解 HYP 浓度的影响，并在本文中进行了讨论。除了 ΔG 的差异外，还观察到了分子和各个链的不同展开途径。本研究通过三种胶原蛋白的结合能，提供了胶原蛋白的机械变形特性与羟脯氨酸含量之间的相关性。
