• Bulletin of the Korean Chemical Society
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• 제30권8호
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• pp.1845-1850
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• 2009

We have performed replica-exchange molecular dynamics (REMD) simulations on the dimer formation of fibrilforming segments of $\alpha$-Synuclein (residues 71 - 82) using implicit solvation models with two kinds of force fields- AMBER parm99SB and parm96. We observed spontaneous formation of dimers from the extensive simulations, demonstrating the self-aggregating and fibril forming properties of the peptides. Secondary structure profile and clustering analysis showed that dimers with antiparallel $\beta$-sheet conformations, stabilized by well-defined hydrogen boding, are major species corresponding to global free energy minimum. Parallel dimers with partial $\beta$-sheets are found to be off-pathway intermediates. The relative instability of the parallel arrangements is due to the repulsive interactions between bulky and polar side chains as well as weaker backbone hydrogen bonds.

• Bulletin of the Korean Chemical Society
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• 제33권3호
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• pp.848-854
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• 2012

We have studied the oligomerization of a fibril-forming segment of ${\alpha}$-Synulcein using a replica exchange molecular dynamics (REMD) simulation. The simulation was performed with trimers and tetramers of a 12 amino acid residue stretch (residues 71-82) of ${\alpha}$-Synulcein. From extensive REMD simulations, we observed the spontaneous formation of both trimer and tetramer, demonstrating the self-aggregating and fibril-forming properties of the peptides. Secondary structure profile and clustering analysis illustrated that antiparallel ${\beta}$-sheet structures are major species corresponding to the global free energy minimum. As the size of the oligomer increases from a dimer to a tetramer, conformational stability is increased. We examined the evolution of simple order parameters and their free energy profiles to identify the process of aggregation. It was found that the degree of aggregation increased as time passed. Tetramer formation was slower than trimer formation and a transition in order parameters was observed, indicating the full development of tetramer conformation which is more stable than that of the trimer. The shape of free energy surface and change of order parameter distributions indicate that the oligomer formation follows a dock-and-lock process.

• Bulletin of the Korean Chemical Society
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• 제31권8호
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• pp.2386-2388
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• 2010

• Bulletin of the Korean Chemical Society
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• 제33권3호
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• pp.828-832
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• 2012

We performed replica exchange molecular dynamics (REMD) simulations of the tripzip2 peptide (betahairpin) using the GB implicit and TI3P explicit solvation models. By comparing the resulting free energy surfaces of these two solvation model, we found that the GB solvation model produced a distorted free energy map, but the explicit solvation model yielded a reasonable free energy landscape with a precise location of the native structure in its global free energy minimum state. Our result showed that in particular, the GB solvation model failed to describe the tryptophan packing of trpzip2, leading to a distorted free energy landscape. When the GB solvation model is replaced with the explicit solvation model, the distortion of free energy shape disappears with the native-like structure in the lowest free energy minimum state and the experimentally observed tryptophan packing is precisely recovered. This finding indicates that the main source of this problem is due to artifact of the GB solvation model. Therefore, further efforts to refine this model are needed for better predictions of various aromatic side chain packing forms in proteins.

• EDISON SW 활용 경진대회 논문집
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• 제5회(2016년)
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• pp.32-36
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• 2016

단일금속 나노입자에 비해 나노합금입자는 발광이나 촉매력과 같은 여러 특징들이 더 뛰어나게 나타난다고 잘 알려져 있다. 이에 따라 실험적인 연구뿐 아니라 이론적으로도 나노합금입자의 특성과 구조를 밝히려는 노력이 이루어지고 있다. 그러나 대부분의 연구는 자유공간을 상정하여 진행되고 있어, 갇힌 공간 속의 입자에 대한 연구는 부족한 실정이다. 이러한 배경으로 본 연구에서는 Sutton-Chen (SC) 포텐셜을 주요 이론으로 하여, 복제교환분자동력학(replica exchange molecular dynamics, REMD) 모의실험을 통해 가두는 공간의 크기에 따라 금-팔라듐 나노합금입자(Au17Pd17)의 구조와 특성이 어떻게 달라지는지 EDISON에 등록된 metal_alloy 프로그램(molecular dynamics simulation of metal alloy nano-cluster)을 사용해 살펴보았다. 결과적으로 입자가 상전이 이전의 낮은 온도에서 존재하면, 둘러싼 공간의 크기와 무관하게 안정한 구조의 중심에 항상 팔라듐 원자가 위치한다는 것이 확인되었다. 또, 가두는 공간의 크기마다 상전이가 일어나는 온도 구간의 차이가 나타났으며, 작은 공간에 갇힌 입자일수록 입자의 최대 직경이 작아지면서 상대적으로 높은 에너지를 가지는 구조를 형성하였다. 이는 입자가 존재하는 공간이 좁을수록 에너지의 증가를 통하면서 최대한 공간을 활용할 수 있는 구조를 선택하는 것으로 보인다.