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以分子動力學電腦模擬之方法探討溫度對膠原蛋白力學特性之影響
Other Title
Effect of Temperature on the Mechanical Properties of Collagen Molecule: A Computational Study Using Molecular Dynamics
Type
thesis
Date Issued
2018-01-04
Author(s)
吳茵茵
Advisor
陳祥和
張書瑋
Subjects
系所名稱：醫學科學研究所
Description
學位別：碩士
語文別：英文
指導教授：陳祥和
共同指導教授：張書瑋
口試委員：曾厚;黃豪銘;蕭惠心
中文關鍵字：分子動力學電腦模擬;膠原蛋白力學特性
英文關鍵字：Molecular Dynamic Simulation;collagen mechanical properties
語文別：英文
指導教授：陳祥和
共同指導教授：張書瑋
口試委員：曾厚;黃豪銘;蕭惠心
中文關鍵字：分子動力學電腦模擬;膠原蛋白力學特性
英文關鍵字：Molecular Dynamic Simulation;collagen mechanical properties
Abstract
ABSTRACT
Sports injuries of the ligament or tendon may have devastating consequences and mark the end of an athlete's career. Since collagen is a major component of ligament and tendon, we would like to know how temperature affects the mechanical properties of collagen molecules. It might help preventing athletes from these injuries while playing in very hot or cold weather and might also provide new insight into sports injury therapy. The mechanical properties of collagen using mechanical testing devices, X-ray diffraction, and Atomic Force Microscopy have been studied. To study the dynamic evolution of collagen at the molecular level, this study was done by molecular dynamics simulation.
LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulations) code was used to run simulations and VMD (Visual Molecular Dynamics) was used to visualize the results. Three models of collagen molecules were created: 1. GPO: a tropocollagen of 30 residues with a Gly-Pro-Hyp sequence. 2. Gap: a small segment at the gap region of type 1 collagen with a Gly-X-Y sequence where X and Y could be any amino acid. 3. Overlap: a small segment at the overlap region of type 1 collagen. The real sequences of type 1 α1 and type 1 α2 chains of mus musculus (+/+ mouse) were adopted from NCBI protein database and were built into a triple helical collagen by the software THeBuScr. The three models were first equilibrated under various temperatures with three random initial velocities, then the collagen was pulled at a constant velocity (steered molecular dynamics) to test its stiffness.
The three models of collagen molecules were equilibrated for 20 nanoseconds with three random seed velocities under temperatures 305K, 310K, and 315K. Average end-to-end distance and the average number of hydrogen bonds were calculated. GPO collagen has a relatively constant end-to-end distance while those of the gap collagen and the overlap collagen change with temperature. However, no significant correlation between collagen end-to-end distance and temperature was observed from the results. The major findings in our study are (1) The mechanical property of the three collagen models response differently to temperature change, indicating that thermal stability of the Gap and Overlap collagens are different from that of the GPO collagen. (2) The number and location of hydrogen bonds affect the collagen conformation, and therefore determines its stiffness.
Sports injuries of the ligament or tendon may have devastating consequences and mark the end of an athlete's career. Since collagen is a major component of ligament and tendon, we would like to know how temperature affects the mechanical properties of collagen molecules. It might help preventing athletes from these injuries while playing in very hot or cold weather and might also provide new insight into sports injury therapy. The mechanical properties of collagen using mechanical testing devices, X-ray diffraction, and Atomic Force Microscopy have been studied. To study the dynamic evolution of collagen at the molecular level, this study was done by molecular dynamics simulation.
LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulations) code was used to run simulations and VMD (Visual Molecular Dynamics) was used to visualize the results. Three models of collagen molecules were created: 1. GPO: a tropocollagen of 30 residues with a Gly-Pro-Hyp sequence. 2. Gap: a small segment at the gap region of type 1 collagen with a Gly-X-Y sequence where X and Y could be any amino acid. 3. Overlap: a small segment at the overlap region of type 1 collagen. The real sequences of type 1 α1 and type 1 α2 chains of mus musculus (+/+ mouse) were adopted from NCBI protein database and were built into a triple helical collagen by the software THeBuScr. The three models were first equilibrated under various temperatures with three random initial velocities, then the collagen was pulled at a constant velocity (steered molecular dynamics) to test its stiffness.
The three models of collagen molecules were equilibrated for 20 nanoseconds with three random seed velocities under temperatures 305K, 310K, and 315K. Average end-to-end distance and the average number of hydrogen bonds were calculated. GPO collagen has a relatively constant end-to-end distance while those of the gap collagen and the overlap collagen change with temperature. However, no significant correlation between collagen end-to-end distance and temperature was observed from the results. The major findings in our study are (1) The mechanical property of the three collagen models response differently to temperature change, indicating that thermal stability of the Gap and Overlap collagens are different from that of the GPO collagen. (2) The number and location of hydrogen bonds affect the collagen conformation, and therefore determines its stiffness.