• 대한화학회지
• /
• 제55권5호
• /
• pp.746-750
• /
• 2011

Fluorescence correlation spectroscopy (FCS) is an emerging fluorescence technique used to study the dynamics of proteins on a millisecond to microsecond time scale at the single-molecule level. Solution pH-modulated protein conformational changes can be manifested by binding rate, fluorescence lifetime, and binding specificity of a probe molecule. The fluorescence lifetime of Nile red (NR) bound to apomyoglobin (apoMb) was measured to be $6{\pm}0.3$ ns, much longer than that in water solution ($2.9{\pm}0.2$ ns). As the unfolding population of apoMb increased by lowering pH of solution, the fraction for the longer lifetime of NR decreased with an increasing fraction for the shorter lifetime of NR in water. Unlike 1-anilino-8-naphthalene sulfonic acid, which has many lifetimes due to nonspecific binding to the unfolded apoMb, NR bound to apoMb possesses only a single lifetime. These results suggest that NR binds specifically to native apoMb and thus can be utilized to probe the folding/unfolding dynamics of apoMb using FCS.

• International Journal of Control, Automation, and Systems
• /
• 제4권3호
• /
• pp.382-393
• /
• 2006

Mechanical system dynamics plays an important role in the area of computational structural biology. Elastic network models (ENMs) for macromolecules (e.g., polymers, proteins, and nucleic acids such as DNA and RNA) have been developed to understand the relationship between their structure and biological function. For example. a protein, which is basically a folded polypeptide chain, can be simply modeled as a mass-spring system from the mechanical viewpoint. Since the conformational flexibility of a protein is dominantly subject to its chemical bond interactions (e.g., covalent bonds, salt bridges, and hydrogen bonds), these constraints can be modeled as linear spring connections between spatially proximal representatives in a variety of coarse-grained ENMs. Coarse-graining approaches enable one to simulate harmonic and anharmonic motions of large macromolecules in a PC, while all-atom based molecular dynamics (MD) simulation has been conventionally performed with an aid of supercomputer. A harmonic analysis of a macroscopic mechanical system, called normal mode analysis, has been adopted to analyze thermal fluctuations of a microscopic biological system around its equilibrium state. Furthermore, a structure-based system optimization, called elastic network interpolation, has been developed to predict nonlinear transition (or folding) pathways between two different functional states of a same macromolecule. The good agreement of simulation and experiment allows the employment of coarse-grained ENMs as a versatile tool for the study of macromolecular dynamics.

• Animal cells and systems
• /
• 제7권3호
• /
• pp.207-211
• /
• 2003

Caveolin-1 is a principal protein in the plasma membrane microdomains called caveolae. Caveolae play an important role in the transcytosis and pinocytosis. Therefore, caveolin-1 is most likely to work for the membrane dynamic events. In addition, caveolin-1 interacts with various signaling molecules. Although caveolin-1 possesses a variety of physiological functions, its structural properties were little construed. Here we analyzed the structural dynamics of the N-terminal caveolin-1 (residues 1-101), in order to better understand the structural properties in terms of its versatile functionality. We first analyzed its oligomeric form using GST-fused N-terminal domain, revealing that it equilibrates between a dimer and monomers in av concentration-dependent manner. The N-terminal domain of caveolin-1 was previously found to form a heptamer, so that our data suggest the dimeric form as an intermediate structure for the heptamer formation. Then, we obtained the folding profile, which indicated that $\DeltaG_{H2O}\;is\;about\;0.5\;\pm0.03$ kcal/mol. The stability of N-terminal domain is relatively low, indicating that N-terminal domain may not be crystalline. Conclusively, the dynamic and flexible structure of N-terminal domain appears more favorable to maintain the versatile functions of caveolin-1.

• 정보처리학회논문지D
• /
• 제12D권6호
• /
• pp.921-930
• /
• 2005

본 논문에서는 개발된 범용 분자 시뮬레이션 시스템에 대해 기술하고자 한다. 본 연구에서 개발된 분자 시뮬레이션 시스템의 가장 큰 장점은 다른 무엇보다도 Langevin dynamics simulation이나 dissipative particle dynamics simulation 기법을 도입하여 all-atom 모델뿐만 아니라coarse-grain 모델까지도 다룰 수 있도록 설계하였고 따라서 미시영역은 물론 중간영역에서 일어나는 현상까지도 시뮬레이션 할 수 있도록 설계하였다는 점이다. 이를 통해 하나의 통합된 분자 시뮬레이션 시스템으로 생체막 내에서 마취제의 분포, 단백질 접힘 현상, 마이크로 채널 내에서 생체고분자의 구조와 유동 특성 등과 같이 미시영역에서부터 중간영역에 이르는 다양한 현상을 연구할 수 있게 되었다 개발된 시스템을 이용하면 molecular dynamics simulation에 기반한 분자 시뮬레이션 시스템으로는 불가능한 여러 중요한 바이오/나노 시스템을 시뮬레이션 할 수 있을 것으로 기대한다 마지막으로 벤치마크 결과를 통해 개발된 분자 시뮬레이션 시스템의 성능을 측정하였고 성능 최적화를 위한 병목지점을 조사하였다.

• 한국전산구조공학회논문집
• /
• 제36권4호
• /
• pp.213-220
• /
• 2023

본 논문에서는 한국전통게임에 사용되는 접이식 종이구조물(이하 딱지)의 접이과정을 모델링하고 게임의 승리조건을 만족시키는 충돌조건을 유전알고리즘을 이용하여 산정하는 과정을 서술하였다. 딱지는 A4용지 2장으로 구성되는 것을 가정하였다. 접이과정은 강제경계조건을 부여하여 날개부분을 꼬임의 위치로 변형시키고 강체판의 강제경계조건을 이용하여 딱지를 압착하였다. 이후 복원력에 의한 완화해석을 수행하여 게임에 사용된 딱지의 형상과 응력상태를 구성하였다. 얻어진 동일한 2개의 딱지 중 타격딱지를 주어진 충돌위치로 강제변위에 의해서 이동시키고 주어진 충돌속력에 대한 충돌해석으로 게임의 진행과정을 해석하였다. 이 때 승리조건인 피격딱지의 반전을 일으키는 충돌조건을 산정하기 위하여 유전알고리즘을 이용한 최적화해석을 수행하였다. 이 과정에서 효율적인 해석을 위하여 충돌해석을 2단계로 나누고 1단계의 해석결과 피격딱지에 반전이 발생할 가능성이 있는 경우에만 2단계해석을 진행하였다. 1단계 해석에서 유전알고리즘의 적합함수는 피격딱지의 방향코사인이었고 2단계해석에서는 속도의 역수로 하여 전체적으로는 가장 낮은 충돌속력을 가지는 충돌조건을 찾아내고자 하였다. 해석수행결과 다양한 압착두께에 따른 최적의 충돌조건을 찾아 낼 수 있었다.

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

• 한국가시화정보학회지
• /
• 제11권3호
• /
• pp.5-11
• /
• 2013

It is of great importance to obtain the uniform layer thickness in the multi-layer co-extrusion processes. In the present study, the three-dimensional numerical simulation was carried out using the open source code named OpenFOAM(R) to understand the flow characteristics in the multi-layer die. In this numerical study, Multi-thin-layers were successfully computed depending on the number of repeating units. The generation mechanism for the multi-layer was numerically verified by the flow simulation and visualization in the co-extrusion die using OpenFOAM(R). The results suggested that the multi-layer has a divided and folded mechanism similar to the stretching and folding in the chaotic flow.

• 한국시뮬레이션학회논문지
• /
• 제27권4호
• /
• pp.19-26
• /
• 2018

공중투하형 무인비행체는 비행성능의 극대화 및 모기체 탑재시의 소요공간 최소화를 위하여 접이식 직렬날개를 주로 사용한다. 이러한 접이식 직렬날개는 전방날개의 후류에 의한 후방날개 간섭문제, 날개 전개시 전후방 날개에 걸리는 피봇 모멘트의 불균형 등 일반적인 형태의 고정익 비행체와 다른 독특한 공기역학적 문제를 가지고 있다. 이에 본 논문에서는 유한체적법 기반의 전산유체역학을 통하여 여러 경우에 대하여 모델링 및 시뮬레이션을 수행하였으며 접이식 직렬날개 방식 비행체의 여러 공기역학적 현상에 대해 분석하였다. 그 결과 받음각 변화에 따른 전방날개에 의한 후류영향을 최소화하기 위하여 전방 날개를 후방날개보다 수직방향으로 높게 설치할 필요가 있었다. 또한 공력에 의한 피봇모멘트를 고려시 전방날개에 비하여 후방날개가 훨씬 빠른 속도로 펼쳐질 수 있으므로 날개 펼침 기구 개발 시 이에 대한 고려가 필요함을 확인하였다.

• 한국우주과학회:학술대회논문집(한국우주과학회보)
• /
• 한국우주과학회 2006년도 한국우주과학회보 제15권2호
• /
• pp.52-52
• /
• 2006

Many spacecraft failures and anomalies have been attributed to energetic electrons in the Earth's magnetosphere. While the dynamics of these electrons have been studied extensively for several decades, the fundamental question of how they are accelerated is not fully resolved. Proposed theories have not been successful in explaining fast high energy increase such as REE (Relativistic electron enhancement). In this presentation, we show observations of energetic electron precipitation measured by the Korean satellite, STSAT-1 which simultaneously detect (100ev - 20 keV) and (170 - 360 keV) energy electrons at the 680 km orbit, when the RES event observed at the geosynchronous orbit on October 13, 2004. STSAT-1 observed intense electron precipitation in both energy ranges occurred in the midnight sector clearly demonstrating that electrons having wide energy band are injected from the plasma sheet. To make the balance between loss and injection, the injected electron flux should be also large. In this situation, the injected electrons can be trapped into the magnetosphere and produce REE, though they have low e-folding energies. We propose this plasma sheet injection might be the primary source of relativistic electron (1 MeV) flux increases.

• Journal of Microbiology and Biotechnology
• /
• 제26권7호
• /
• pp.1163-1172
• /
• 2016

The Ω-loop is a nonregular and flexible structure that plays an important role in molecular recognition, protein folding, and thermostability. In the present study, molecular dynamics simulation was carried out to assess the molecular stability and flexibility profile of the porcine trypsin structures. Two Ω-Loops (fragment 57-67 and fragment 78-91) were confirmed to represent the flexible region. Subsequently, glycosylation site-directed mutations (A73S, N84S, and R104S) were introduced within the Ω-loop region and its wing chain based on its potential N-glycosylation sites (Asn-Xaa-Ser/Thr consensus sequences) and structure information to improve the thermostability of trypsin. The result demonstrated that the half-life of the N84S mutant at 50℃ increased by 177.89 min when compared with that of the wild-type enzyme. Furthermore, the significant increase in the thermal stability of the N84S mutant has also been proven by an increase in the T_m values determined by circular dichroism. Additionally, the optimum temperatures of the wild-type enzyme and the N84S mutant were 75℃ and 80℃, respectively. In conclusion, we obtained the thermostability-improved enzyme N84S mutant, and the strategy used to design this mutant based on its structural information and N-linked glycosylation modification could be applied to engineer other enzymes to meet the needs of the biotechnological industry.