• Proceeding of EDISON Challenge
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• 2016.03a
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• pp.62-66
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• 2016

Tumor suppressor protein p53 loses its function upon binding with the HDM2 protein, and inhibiting the p53-HDM2 interaction is critical to suppress tumor cell growth. Recently, the cyclized helix-loop-helix peptide (cHLH) mimicking the ${\alpha}-helix$ part of the p53 protein has been designed and found to exhibit high binding affinity with HDM2. Here, we report the structural and thermodynamic characteristics of the bound complex of the cHLH peptide with the HDM2 protein. We performed molecular dynamics simulations to investigate the structural features of the cHLH peptide as well as its complex with the HDM2. The binding free energy calculation based on the integral equation theory was also executed to quantify the binding affinity for the cHLH/HDM2 complex and to understand the factors contributing to the binding affinity. We found a variety of factors for the helix stability of the cHLH peptide as well as in the complexation with the HDM2, which may provide an insight into the development of anti-cancer drug designs.

• Bulletin of the Korean Chemical Society
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• v.30 no.8
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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.

• Journal of the Korean Chemical Society
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• v.24 no.6
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• pp.444-451
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• 1980

In order to further elucidate the process of electron solvation in liquids, the medium effect, as the difference between the free energy of $H^+$ in aqueous and non-aqueous states (${\Delta}{\Delta}G_0$), of THF-water mixtures has been investigated. (${\Delta}{\Delta}G_0$) were determined by electromotive force masurements of the cell Pt$H_2Q$, Q, HCI, THF, $H_2O$|KC1 | $Hg_2Cl_2$|Hg(Pt), where $H_2Q$ and Q are hydroquinone and quinone respectively. The effect of dielectric constant on the difference of free energy and the absorption energy of solvated electrons have been studied. For the consideration of these effect the polymerization of water in THF has been studied. Near infrared spectrum of O-H stetching energy has been used to measure the extent of water aggregates. The expermental results indicate that at least in some composition of binary mixtures the electrons or other ions are solvated preferentially with one component of solvents.

• Bulletin of the Korean Chemical Society
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• v.23 no.6
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• pp.837-845
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• 2002

Based on ab initio calculations at the MP2(FULL)/6-31+G**//RHF/6-31G** level, we compare the energetic and mechanistic features of a model reaction for catalytic action of Δ?-3-ketosteroid isomerase (KSL,E.C.5.3,3.1) with those of a corresponding nonenzymatic reaction in aqueous solution. The results show that the two catalytic acid residues,Tyr14 and Asp99, can lower the free energy of activation by 8.6kcal/mol, which is in good agreement with the experimentally predicted~9 kcal/mol,contribution of electrophilic catalyses to the whole enzymatic rate enhancement. The dienolate intermediate formed by proton transfer from the substrate carbon acid to the catalytic base residue (Asp38) ins predicted to be stabilized by 12.0 kcal/mol in the enzymatic reaction, making its formation thermodynamically favorable. It has been argued that enzymes catalyzing the reactions of carbon acids should resolve the thermodynamic problem of stabilizing the enolate intermediate as well as the kinetic porblem of lowering the free energy of activation for porton abstraction. We find that KSI can successfully overcome the thermodynamic difficulty ingerent in the nonenzymatic reaction through the electrophilic catalyses of the two acid residues. Owing to the stabilization of dienolate intermediate, the reketonization step could influence the overall reaction rate more significantly in the KSI- catalyzed reaction than in the nonenzymatic reaction, further supporting the previous experimental findings. However, the electrophilic catalyses alone cannot account for the whole catalygic capability (12-13 kcal/mol), confiming the earlier experimental implications for the invement of additional catalytic components. The present computational study indicates clearly how catalytic residues of KSI resolve the fundamental problems associated with the entropic penalty for forming the rate-limiting transition state and its destabilization in the bulk solvation environment.

• Bulletin of the Korean Chemical Society
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• v.35 no.9
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• pp.2655-2659
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• 2014

Dual specificity protein phosphatase 4 (DUSP4) has been considered a promising target for the development of therapeutics for various human cancers. Here, we report the first example for a successful application of the structure-based virtual screening to identify the novel small-molecule DUSP4 inhibitors. As a consequence of the virtual screening with the modified scoring function to include an effective molecular solvation free energy term, five micromolar DUSP4 inhibitors are found with the associated $IC_{50}$ values ranging from 3.5 to $10.8{\mu}M$. Because these newly identified inhibitors were also screened for having desirable physicochemical properties as a drug candidate, they may serve as a starting point of the structure-activity relationship study to optimize the medical efficacy. Structural features relevant to the stabilization of the new inhibitors in the active site of DUSP4 are discussed in detail.

• Proceeding of EDISON Challenge
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• 2017.03a
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• pp.158-164
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• 2017

암을 억제시키는 기능을 하는 단백질로 잘 알려진 p53은, 주로 종양세포에서 과도하게 발현되는 단백질인 HDM2와 복합체를 형성하여 비활성화되고 항암기능을 상실하게 됩니다. 때문에 종양세포에서의 p53-HDM2의 상호작용을 억제하기 위해 현재까지 많은 연구가 진행되어왔으며, 다양한 p53-HDM2 억제제가 개발된 바 있습니다. 최근 연구들에 따르면, HDM2와 결합친화도를 높이고 소수성 작용(hydrophobic interaction)에 기여하여 보다 안정한 구조를 만드는 탄화수소체인(staple)을 연결시킨 펩타이드 설계에 대한 관심이 높아지고 있는 추세입니다. 이에, 본 연구에서는 분자동역학 모의실험을 통해서 얻은 탄화수소체인-p53과 비탄화수소체인-p53 및 각각의 HDM2와 결합한 복합체를 기반으로 EDISON의 용매화 자유에너지(Solvation Free Energy) 프로그램을 이용하여 탄화수소체인의 특징 및 역할을 구조적인 측면과 열역학적인 측면으로 분석하여 비교하고자 합니다. 우리 연구에서 비탄화수소체인-p53의 구조는 분자동역학 시뮬레이션을 수행하는 동안 나선구조형태로 풀려 HDM2와 결합 유도 시에 주요결합 아미노산 잔기가 올바른 결합부위와 상호작용하지 못한 결과를 확인한 반면, 탄화수소체인이 형성된 구조는 시뮬레이션 동안에도 펩타이드의 나선구조를 유지시켜 HDM2와 주요 결합을 형성하는 아미노산 잔기들을 올바른 방향으로 배치시켜 HDM2와의 결합친화도를 높였습니다. 이 연구 결과는 탄화수소체인이 펩타이드의 나선성을 유지시키고, HDM2와의 상호작용을 통한 구조적인 안정성 유도 및 용매화 자유에너지에 큰 기여를 통해 p53-HDM2상호작용 억제제에서 긍정적인 역할을 할 가능성을 보여줍니다.

• Journal of the Korean Magnetic Resonance Society
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• v.22 no.4
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• pp.139-143
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• 2018

Short antimicrobial peptide, A4W, have been studied by molecular dynamics (MD) simulation in an explicit dodecylphosphocholine (DPC) micelle. Peptide was aligned with DPC micelle and transferred new peptide-micelle coordinates within the same solvent box using specific micelle topology parameters. After initial energy minimization and equilibration, the conformation and orientation of the peptide were analyzed from trajectories obtained from the RMD (restrained molecular dynamics) or the subsequent free MD. Also, the information of solvation in the backbone and the side chain of the peptide, hydrogen bonding, and the properties of the dynamics were obtained. The results showed that the backbone residues of peptide are either solvated using water or in other case, they relate to hydrogen bonding. These properties could be a critical factor against the insertion mode of interaction. Most of the peptide-micelle interactions come from the hydrophobic interaction between the side chains of peptide and the structural interior of micelle system. The interaction of peptide-micelle, electrostatic potential and hydrogen bonding, between the terminal residues of peptide and the headgroups in micelle were observed. These interactions could be effect on the structure and flexibility of the peptide terminus.

• Journal of the Korean Chemical Society
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• v.18 no.5
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• pp.320-328
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• 1974

It is unable to derive the standard emf ($E^{\circ}$) of the cell at high pressure from the conventional method. However, when the concept of the complete equilibrium constant($K{\circ})$) is available to the conventional Nernst equation, it is possible to get the standard emf of the cell at high pressure(complete Nernst equation). Moreover, the other thermodynamic properties, such as the net change of solvation number(k), the compressibility of solvent(${\beta}$), ionization constant(K), the standard free energy change(${\Delta}G^{\circ}$), the standard enthalpy change(${\Delta}H^{\circ}$) and the standard entropy change (${\Delta}S^{\circ}$) of the cell reaction at equilibrium state have been also obtained. In this experiment, the emf of the cell; 12.5 % Cd(Hg)│$CdSO_4(3.105{\times}10^{-3}M),\;Hg_2SO_4│Hg$ have bee measured at temperature from 20 to $35^{\circ}C$ and at pressures from 1 to 2500 atms. The emf of the cell increased with increasing pressure at constant temperature, and did with increasing temperature at constant pressure. The net change of solvation number(k) of the cell reaction was 41.96 at $25^{\circ}C$, and kept constant value with pressure, while, K and ${\Delta}S^{\circ}$ increased with pressure, but whereas ${\Delta}G^{\circ}$ and ${\Delta}H^{\circ}$ decreased. Since the standard emf of the cell at high pressure can be calculated from the complete Nernst equation, the theory of chemical equilibrium could be developed with at high pressure as well as at the atmosphere.

• Journal of the Korean Chemical Society
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• v.34 no.2
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• pp.123-129
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• 1990

The rate constants for the solvolysis of $trans-[Cr(en)_2Br_2]^+$ ion were determined by the spectrophotometric method in methanol-, ethanol-, acetone-, and acetonitrile-water mixtures, at 20, 25, 30, and 35$^{\circ}C$, respectively. The rate constants increased with increasing co-solvent compositions. The rate constant did not show any relation with the reciprocal of dielectric constant of the solvent-mixtures. The m values of Grunwald-Winstein equation for methanol-, ethanol-, acetonitrile-, and acetone-water mixtures are 0.109, 0.103, 0.101, and 0.095, respectively. A free energy cycle for the process from the initial state to the transition state in water and water + co-solvent mixtures shows that the change in solvation at the transition state has a dominant effect on the rate. From the above results, it is believed that the mechanism for the aquation of this complex is the Id mechanism.

• Journal of the Korean Chemical Society
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• v.29 no.5
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• pp.472-477
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• 1985

The rates for the aquation of $cis-[Co(en)(NH_3)_2Cl_2]Cl in acetone-water mixtures have been measured at various pressures and temperatures by the electric conductivity method. The rate constant measured at 25$^{\circ}$C in pure water solvent is 3.47 ${\times}10^{-4}$/sec. Rate constants are increased with increasing temperature, and decreased with increasing pressure and mole fraction of acetone. Activation volumes and other activation parameters are calculated from these rate constants. The activation volumes are all positive and lie in the limited range +2.82~+$8.2cm^3$/mole. The rate constants in aqueous acetone solution are analyzed with the solvent compositions. Plots of log $k_{obs}$ vs. Grunwald-Winstein Y values show that log $k_{obs}$ varies linearly and the gradients are about 0.25. The applications of a free energy cycle relating the process initial state ${\to}$ transition state in water to that in acetone-water mixture show that the changes in solvation of the transition state have a dominant effect on the rate. From these results the aquation of this complex would be discussed in terms of dissociative mechanism ($I_d$).