• EDISON SW 활용 경진대회 논문집
• /
• 제4회(2015년)
• /
• pp.14-23
• /
• 2015

Alzheimer's disease is one of the most common types of degenerative dementia. As a considerable cause of Alzheimer's disease, neurotoxic plaques composed of 39 to 42 residue-long amyloid beta($A{\beta}$) fibrils have been found in the patient's brain in large quantity. A previous study found that erythrosine B (ER), a red color food dye approved by FDA, inhibits the formation of amyloid beta fibril structures. Here, in an attempt to elucidate the inhibition mechanism, we performed molecular dynamics simulations to demonstrate the conformational change of $A{\beta}40$ induced by 2 ERs in atomistic detail. During the simulation, the ERs bound to the surfaces of both N-terminus and C-terminus regions of $A{\beta}40$ rapidly. The observed stacking of the ERs and the aromatic side chains near the N-terminus region suggests a possible inhibition mechanism in which disturbing the inter-chain stacking of PHEs destabilizes beta-sheet enriched in amyloid beta fibrils. The bound ERs block water molecules and thereby help stabilizing alpha helical structure at the main chain of C-terminus and interrupt the formation of the salt-bridge ASP23-LYS28 at the same time. Our findings can help better understanding of the current and upcoming treatment studies for Alzheimer's disease by suggesting inhibition mechanism of ER on the conformational transition of $A{\beta}40$ at the molecular level.

• 멤브레인
• /
• 제12권4호
• /
• pp.207-215
• /
• 2002

한정된 미세공간에서의 제한확산(hindered diffusion)은 멤브레인 기공(pore)에서 입자들의 운동에 의해 결정되는 여과 메카니즘을 매우 미세한 수준에서 이해하는데 중요한 현상이다. 구형(spherical) 콜로이드 입자에 비해 보다 복잡한 형태(conformation)인 고분자사슬 구조를 갖는 다가전해질(polyelectrolyte)의 제한확산 거동에는 다양한 인자들이 관련되어 있기 때문에, 이론 접근은 물론 실험적 접근도 한층 어려운 것이 사실이다. 본 연구에서는, 슬릿형 미세기공에 한정되어 있는 단일한 다가전해질(single polyelectrolyte)에 coarse-grained bead spring model과 먼거리(long-range) 정전상호작용(electrostatic interaction)인 Debye-Huckel potential을 적용하여 분자시뮬레이션 기법인 브라운 동력학 모사를 수행하였다. 기공과 다가전해질 사슬(Polyelectrolyte chain)의 주어진 크기에서, 용액의 전해질 이온농도가 감소함에 따른 사슬의 신장(extension)효과는 제한확산계수를 감소시켰고, 기공 벽면의 하전성은 제한확산계수를 더욱 감소시켰다. 이는, 다가전해질 사슬(polyelectrolyte chain)의 입체적 장애(steric hindrance)와 함께 정전반발력이 미세기공에서의 확산이동을 억제함을 의미한다.

• 한국자기공명학회논문지
• /
• 제19권2호
• /
• pp.67-73
• /
• 2015

The microcystin is a cyclic heptapeptide from metabolites of cyanobacteria in the genera mycrocystis, anabaeba as a result of eutrophication. It has been known that microcystin-LR is a potent inhibitor of the catalytic subunits of protein phosphatase-1 (PP-1) as well as powerful tumor promoter. The active site of microcystin actually has two metal ions $Fe^{2+}/Zn^{2+}$ close to the nucleophilic portion of PP-1-microcystin complex. We report the isolation and purification of this microcystin-LR from cyanobacteria (blue-green algae) obtained from Daechung Dam in Chung-cheong Do, Korea. Microcystin-LR was extracted from solid-phase extraction (SPE) sample preparation using a CN cartridge. The cyanobacteria extract was purified to obtain microcystin-LR by HPLC method and identified by LC/MS. The detail structural studies that can elucidate the possible role of monovalent and divalent metal ions in PP-1-microcystin complexation were carried out by utilizing molecular dynamics. Conformational changes in metal binding for ligands were monitored by molecular dynamic computation and potential of mean force (PMF) using the method of the free energy perturbation. The microcystin-metal binding PMF simulation results exhibit that microcystin can have very stable binding free energy of -10.95 kcal/mol by adopting the $Mg^{2+}$ ion at broad geometrical distribution of $0.5{\sim}4.5{\AA}$, and show that the $K^+$ ion can form a stable metal complex rather than other monovalent alkali metal ions.

• Bulletin of the Korean Chemical Society
• /
• 제33권11호
• /
• pp.3601-3606
• /
• 2012

Structural properties of a small hexapeptide molecule modeled after metal-binding siderochrome immersed in a room-temperature ionic liquid (RTIL) are studied via molecular dynamics simulations. We consider two different RTILs, each of which is made up of the same cationic species, 1-butyl-3-methylimidazolium ($BMI^+$), but different anions, hexafluorophosphate ($PF_6{^-}$) and chloride ($Cl^-$). We investigate how anionic properties such as hydrophobicity/hydrophilicity or hydrogen bonding capability affect the stabilization of the peptide in RTILs. To examine the effect of peptide-RTIL electrostatic interactions on solvation, we also consider a hypothetical solvent $BMI^0Cl^0$, a non-ionic counter-part of $BMI^+Cl^-$. For reference, we investigate solvation structures in common polar solvents, water and dimethylsulfoxide (DMSO). Comparison of $BMI^+Cl^-$ and $BMI^0Cl^0$ shows that electrostatic interactions of the peptide and RTIL play a significant role in the conformational fluctuation of the peptide. For example, strong electrostatic interactions between the two favor an extended conformation of the peptide by reducing its structural fluctuations. The hydrophobicity/hydrophilicity of RTIL anions also exerts a notable influence; specifically, structural fluctuations of the peptide become reduced in more hydrophilic $BMI^+Cl^-$, compared with those in more hydrophobic $BMI^+PF_6{^-}$. This is ascribed to the good hydrogen-bond accepting power of chloride anions, which enables them to bind strongly to hydroxyl groups of the peptide and to stabilize its structure. Transport properties of the peptide are examined briefly. Translations of the peptide significantly slow down in highly viscous RTILs.

• Bulletin of the Korean Chemical Society
• /
• 제25권6호
• /
• pp.838-842
• /
• 2004

Amyloid peptide (A${\beta}$) is the major component of senile plaques found in the brain of patient of Alzheimer's disease. ${\beta}$-amyloid peptide (25-35) (A${\beta}$25-35) is biologically active fragment of A${\beta}$. The three-dimensional structure of A${\beta}$25-35 in aqueous solution with 50% (vol/vol) TFE determined by NMR spectroscopy previously adopts an ${\alpha}$-helical conformation from $Ala^{30}$ to $Met^{35}$. It has been proposed that A${\beta}$(25-35) exhibits pH- and concentration-dependent ${\alpha}-helix{\leftrightarrow}{\beta}$sheet transition. This conformational transition with concomitant peptide aggregation is a possible mechanism of plaque formation. Here, in order to gain more insight into the mechanism of ${\alpha}$-helix formation of A${\beta}$25-35 peptide by TFE, which particularly stabilizes ${\alpha}$-helical conformation, we studied the secondary-structural elements of A${\beta}$25-35 peptide by molecular dynamics simulations. Secondary structural elements determined from NMR spectroscopy in aqueous TFE solution are preserved during the MD simulation. TFE/water mixed solvent has reduced capacity for forming hydrogen bond to the peptide compared to pure water solvent. TFE allows A${\beta}$25-35 to form bifurcated hydrogen bonds to TFE as well as to residues in peptide itself. MD simulation in this study supports the notion that TFE can act as an ${\alpha}$-helical structure forming solvent.

• 한국자기공명학회논문지
• /
• 제14권1호
• /
• pp.45-54
• /
• 2010

HP1423 (Y1423_HELPY) is a conserved hypothetical protein from H. pylori strain 26695. However, Sequence Blast result indicates that HP1423 belongs to S4 (PF01479) superfamily. According to Pfam database, the S4 domain is a small domain consisting of 60-65 amino acid residues, that probably mediates binding to RNA. In this study, we report the sequence-specific backbone resonance assignment of HP1423, which has 84 amino acid residues. We could assign unambiguously about 88% of all $^{1}H_{N}$, $^{15}N$, $^{13}C_{\alpha}$, $^{13}C_{\beta}$ and $^{13}C=O$ resonances. We could not detect the resonances from residues 15-20, and disappearance of these peaks seems to be related with the intermediate-conformational exchange. These assigned NMR peaks of HP1423 can be used for studying the role of protein dynamics in millisecond timescale, and Protein-RNA binding.

• BMB Reports
• /
• 제33권3호
• /
• pp.268-275
• /
• 2000

In contrast to the pyrimidine (6-4)pyrimidone photoproduct [(6-4) adduct], its Dewar valence isomer (Dewar product) is low mutagenic and produces a broad range of mutations with a 42 % replicating error frequency. In order to determine the origin of the mutagenic property of the Dewar product, we used experimental NMR restraints and molecular dynamics to determine the solution structure of a Dewar·lesion DNA decamer duplex, which contains a mismatched base pair between the 3'-T residue and an opposed G residue. The 3'-T of the Dewar lesion forms stable hydrogen bonds with the opposite G residue. The helical bending and unwinding angles of the DW/GA duplex, however, are much higher than those of the DW/AA duplex. The stable hydrogen bonding of the G 15 residue does not increase the thermal stability of the overall helix. It also does not restore the distorted backbone conformation of the DNA helix that is caused by the forming of a Dewar lesion. These structural features implicate that no thermal stability, or conformational benefits of G over A opposite the 3'-T of the Dewar lesion, facilitate the preferential incorporation of an A. This is in accordance with the A rule during translesion replication and leads to the low frequent $3'-T{\rightarrow}C$ mutation at this site.

• EDISON SW 활용 경진대회 논문집
• /
• 제4회(2015년)
• /
• pp.48-52
• /
• 2015

Control of polymer conformations in heterogeneous confinement plays an important role in natural and engineering processes. We present a simulation study on the conformational structure and dynamics of a single, flexible polymer in a dense array of nanoposts with different sizes and separations, especially, when the volume of the interstitial space formed between four nanoposts is less than the size of the polymer chain. When a polymer is placed in the array of nanoposts, the size of polymer increases compared with that in the absence of nanoposts due to the confinement effect. It is shown that when a polymer is confined in the array of nanoposts the chain is elongated in the direction parallel to the nanoposts. As the interstitial volume between four nanoposts decreases either by increasing the nanopost diameter or by decreasing the separation between nanoposts, the chain elongation becomes more pronounced. On the contrary, the polymer size varies in a non-monotonic fashion, with an initial elongation followed by a chain contraction, as the interstitial volume is reduced both by increasing the nanopost diameter and decreasing the separation at the same time while keeping constant the width of the passageway between two nanoposts. The simulation analysis shows that the non-monotonic dependence of polymer size is determined by interplay between the chain alignment along the nanoposts in each interstitial volume and the chain spreading through passageways over several interstitial volume.

• Smart Structures and Systems
• /
• 제2권3호
• /
• pp.225-235
• /
• 2006

With the discovery in plants of the proteinaceous forisome crystalloid (Knoblauch, et al. 2003), a novel, non-living, ATP-independent biological material became available to the designer of smart materials for advanced actuating and sensing. The in vitro studies of Knoblauch, et al. show that forisomes (2-4 micron wide and 10-40 micron long) can be repeatedly stimulated to contract and expand anisotropically by shifting either the ambient pH or the ambient calcium ion concentration. Because of their unique abilities to develop and reverse strains greater than 20% in time periods less than one second, forisomes have the potential to outperform current smart materials as advanced, biomimetic, multi-functional, smart sensors or actuators. Probing forisome material properties is an immediate need to lay the foundation for synthesizing forisomebased smart materials for health monitoring of structural integrity in civil infrastructure and for aerospace hardware. Microfluidics is a growing, vibrant technology with increasingly diverse applications. Here, we use microfluidics to study the surface interaction between forisome and substrate and the conformational dynamics of forisomes within a confined geometry to lay the foundation for forisome-based smart materials synthesis in controlled and repeatable environment.

• 통합자연과학논문집
• /
• 제2권2호
• /
• pp.55-58
• /
• 2009

A ligand-receptor docking program is an indispensible tool in modern pharmaceutical design. An accurate prediction of small molecular docking pose to a receptor is essential in drug design as well as molecular recognition. An effective docking program requires the ability to locate a correct binding pose in a surprisingly complex conformational space. However, there is an inherent difficulty to predict correct binding pose. The odds are more demanding than finding a needle in a haystack. This mainly comes from the flexibility of both ligand and receptor. Because the searching space to consider is so vast, receptor rigidity has been often applied in docking programs. Even nowadays the receptor may not be considered to be fully flexible although there have been some progress in search algorithm. Improving the efficiency of searching algorithm is still in great demand to explore other applications areas with inherently flexible ligand and/or receptor. In addition to classical search algorithms such as molecular dynamics, Monte Carlo, genetic algorithm and simulated annealing, rather recent algorithms such as tabu search, stochastic tunneling, particle swarm optimizations were also found to be effective. A good search algorithm would require a good balance between exploration and exploitation. It would be a good strategy to combine algorithms already developed. This composite algorithms can be more effective than an individual search algorithms.