• Bulletin of the Korean Chemical Society
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• 제24권6호
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• pp.817-823
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• 2003

We have performed ab initio calculation on the active site of HIV-1 protease. The FEP method was used to determine the binding free energy of four different of protonated states of HIV-1 protease with inhibitor. The structure of the active site and hole structure was taken from the X-ray crystallographic coordinates of the C₂ symmetric inhibitor A74704 protease bound. The active site was modeled with the fragment molecules of binding pocket, acetic acid/ acetate anion (Asp25, Asp125), formamide (amide bond of Thr26/Gly27, Thr126/ Gly127), and methanol as inhibitor fragment. All possibly protonated states of the active site were considered, which were diprotonated state (0, 0), monoprotonated (-1, 0),(0, -1) and diunprotonated state (-1, -1). Once the binding energy Debind, of each model was calculated, more probabilistic protonated states can be proposed from binding energy. From ab-initio results, the FEP simulations were performed for the three following mutations: Ⅰ) Asp25 … Asp125 → AspH25 … Asp125, ⅱ) Asp25 … Asp125 → Asp25 … AspH125, ⅲ) AspH25 … Asp125 → AspH25 … AspH125. The free energy difference between the four states gives the information of the more realistic protonated state of active site aspartic acid. These results provide a theoretical prediction of the protonation state of the catalytic aspartic residues for A74707 complex, and may be useful for the evaluation of potential therapeutic targets.

• Bulletin of the Korean Chemical Society
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• 제35권3호
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• pp.770-774
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• 2014

The bond dissociation energy (BDE) of the chemical bond between the carbon and oxygen atoms of a simple TEMPO-derivative is calculated by employing the density functional theory, the $2^{nd}$ order M${\phi}$ller-Plesset (MP2) perturbation theory, and complete basis set (CBS) methods. We find that BDE of the positive ion of the TEMPO-derivative is larger at least by 7 kcal/mol than that of the negative ion, which implies that the dissociation reaction rate of the positive ion should be slower than that of the negative ion. Such theoretical predictions are contrary to the results of our previous experiments (Anal. Chem. 2013, 85, 7044), in which the larger energy was required for negative o-TEMPO-Bz-C(O)-peptides to undergo the dissociation reactions than for the positive ones. By comparing our theoretical results to those of the experiments, we conclude that the dissociation reaction of o-TEMPO-Bz-C(O)-peptide should occur in a complicated fashion with a charge, either positive or negative, probably being located on the amino acid residues of the peptide.

• 한국자기공명학회논문지
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• 제19권2호
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• pp.67-73
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• 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.

• 한국항해항만학회:학술대회논문집
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• 한국항해항만학회 2006년도 Asia Navigation Conference
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• pp.134-143
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• 2006

Out of all types of motions the critical motions leading to capsize is roll. The dynamic amplification in case of roll motion may be large for ships as roll natural frequency generally falls within the frequency range of wave energy spectrum typical used for estimation of motion spectrum. Roll motion is highly non-linear in nature. Den are various representations of non-linear damping and restoring available in literature. In this paper an uncoupled non-linear roll equations with three representation of damping and cubic restoring term is solved using a perturbation technique. Damping moment representations are linear plus quadratic velocity damping, angle dependant damping and linear plus cubic velocity dependant damping. Numerical value of linear damping coefficient is almost same for all types but non-linear damping is different. Linear and non-linear damping coefficients are obtained form free roll decay tests. External rolling moment is assumed as deterministic with sinusoidal form. Maximum roll amplitude of non-linear roll equation with various representations of damping is calculated using analytical procedure and compared with experimental results, which are obtained form forced tests in regular waves by varying frequency with three wave heights. Experiments indicate influence of non-linearity at resonance frequency. Both experiment and analytical results indicates increase in maximum roll amplitude with wave slope at resonance. Analytical results are compared with experiment results which indicate maximum roll amplitude analytically obtained with angle dependent and cubic velocity damping are equal and difference from experiments with these damping are less compared to non-linear equation with quadratic velocity damping.

• 대한기계학회논문집A
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• 제41권2호
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• pp.95-101
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• 2017

본 연구에서는 철도차량의 사고의 유형 중 가장 많이 발생되는 지그재깅 현상에 대해 이론 모델을 정립하여 선두차량의 지그재깅 거동에 대한 운동방정식을 도출하였다. 운동방정식을 풀기 위하여 미분방정식 수치해석법 중 가장 대표적인 Runge-Kutta 4차식을 사용하였고, 휠-레일 인터페이스에 의한 휠의 횡 변위는 운동에너지를 이용하여 추정하였다. 그리고 이론식을 검증하기 위하여 재그재깅 현상에서 가장 변위가 큰 연결기 위치에서의 횡 변위에 대해 시뮬레이션과 이론식을 비교한 결과 비 탈선 충돌조건에서 최대 편차율은 0.8 [%] ~ 4.7 [%] 발생하고, 탈선 충돌조건에서는 탈선이 일어나는 시점에서 차량의 횡 변위를 비교한 결과 최대 편차율이 0.6 [%] ~ 5.1 [%]로 잘 일치하는 것을 확인하였다. 이론식을 사용하여 사고나 현상을 시뮬레이션으로 재현할 때 필요한, 전체적인 거동에 부합하는 차량 간 연결의 초기 off-set량을 예측할 수 있다.