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Effects of Deformation Rate on the Unbinding Pathway of the MMP8-Aggrecan_IGD Complex in Cartilage

Deng Li1, Shuwei Chang1,*
Department of Civil Engineering, National Taiwan University, Taipei 10617, Taiwan.
*Corresponding Author: Shuwei Chang. Email: .
(This article belongs to this Special Issue: Nano/Micro Structures in Application of Computational Mechanics)

Computer Modeling in Engineering & Sciences 2019, 120(2), 305-318. https://doi.org/10.32604/cmes.2019.06475

Abstract

Mechanical force plays a critical role in the remodeling and degradation of cartilage tissues. The cartilage tissue generates, absorbs, and transmits mechanical force, enabling specific biological processes in our body. A moderate intensity mechanical force is necessary for cartilage tissue remodeling and the adaptation of biomechanical properties, but a high intensity mechanical force can lead to pathological degradation of cartilage tissue. However, the molecular mechanism of cartilage degradation is still unclear. We use full atomistic simulations with SMD simulations to investigate whether the magnitude of mechanical force affects the unbinding pathway of the MMP8-Aggrecan_IGD complex. We find that when the pulling velocity is slow, the mechanical force required to unbind the Aggrecan_IGD from MMP8 is higher, and a three-step unbinding pathway is observed. On the other hand, when the pulling velocity is fast, the mechanical force required to unbind the Aggrecan_IGD from MMP8 is lower, and a two-step unbinding pathway is observed. Our results help us to understand how the magnitude of the mechanical force affects the unbinding pathway of the enzyme-ligand complex in cartilage tissue at the molecular level.

Keywords

Mechanical force, steered molecular dynamics (SMD), unbinding pathway, potential of mean force (PMF)

Cite This Article

Li, D., Chang, S. (2019). Effects of Deformation Rate on the Unbinding Pathway of the MMP8-Aggrecan_IGD Complex in Cartilage. CMES-Computer Modeling in Engineering & Sciences, 120(2), 305–318.



This work is licensed under a Creative Commons Attribution 4.0 International License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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