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윤권찬(Gwonchan Yoon),엄길호(Kilho Eom),나성수(Sungsoo Na) 대한기계학회 2010 대한기계학회 춘추학술대회 Vol.2010 No.11
The development of nano- and bio-technology enables us to observe the structural changes of single molecule proteins. Although single molecule proteins have nm scales, it can be mechanically manipulated by atomic force microscopy, optical tweezers and magnetic tweezers. Also, using molecular simulation methods, the angstrom scale’s protein dynamic and mechanical motion is visualized. The molecular dynamics simulation is one of the most well-known in silico technique, the dynamic and mechanical behavior of protein can be calculated by the Newtonian approach. From this in vitro and in silico approach of single molecule proteins, we can understand the origin of structural and functional relationship of proteins, design the proteins that what we need. In this presentation, we want to talk about the state of art in research of single molecule proteins’ structural change and introduce our efficient simulation method, coarse-grained method, of single molecule proteins’ dynamics and mechanics.
분자 동역학 기법을 이용한 아밀로이드 단백질의 구조적 특성 연구
김경우(Kyungwoo Kim),윤권찬(Gwonchan Yoon),김재인(Jae In Kim),이명상(Myeongsang Lee),엄길호(Kilho Eom),나성수(Sungsoo Na) 대한기계학회 2012 대한기계학회 춘추학술대회 Vol.2012 No.11
Amyloid fibrils are self-assembly and self-aggregated molecular structure related to the fatal diseases such as Alzheimer’s disease, Parkinson’s disease, and type ?? diabetes. The β2-microglobulin (β₂m) is one of the amyloid fibrils, which induce devastating effects of dialysis-related amyloidosis. It deposits as amyloid fibrils within joints during long-term hemodialysis treatment. The molecule structure of the β₂m is concerned with experimental research. It has 99 residues before amyloidosis. In this research, we consider the K3 segment(residue 20-41) whose pdb id is 2E8D, whose cross-section exhibits U-shape. Especially, the hydropathic peptide (²¹NFLNCYVSGFH³¹) is believed to play an important role in the amyloidosis of the β₂m. Therefore, in this research, the amyloid fibril of β₂m whose sequence is NFLNCYVSGFH is investigated. We construct the amyloid fibril of β₂m varying thickness with various number of filaments, and obtain the helical pitch of the fibrils using Molecular Dynamic Simulation technique. Moreover, the mechanical properties such as elastic modulus are calculated by using Elastic Network Model with normal mode analysis. We anticipate that this research sheds light on the understanding the structure-property-function relationship of the amyloid fibrils.