• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.36-36
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• 2017

Out of twenty common protein amino acids, there are many kinds of non protein amino acids (NPAAs) that exist as secondary metabolites and exert ecological functions in plants. Mimosine (Mim), one of those NPAAs derived from L. leucocephala acts as an iron chelator and reversely block mammalian cell cycle at G1/S phases. Cysteine (Cys) is decisive for protein and glutathione that acts as an indispensable sulfur grantor for methionine and many other sulfur-containing secondary products. Cys biosynthesis includes consecutive two steps using two enzymes-serine acetyl transferase (SAT) and O-acetylserine (thiol)lyase (OASTL) and appeared in plant cytosol, chloroplast, and mitochondria. In the first step, the acetylation of the ${\beta}$-hydroxyl of L-serine by acetyl-CoA in the existence of SAT and finally, OASTL triggers ${\alpha}$, ${\beta}$-elimination of acetate from OAS and bind $H_2S$ to catalyze the synthesis of Cys. Mimosine synthase, one of the isozymes of the OASTLs, is able to synthesize Mim with 3-hydroxy-4-pyridone (3H4P) instead of $H_2S$ for Cys in the last step. Thus, the aim of this study was to clone and characterize the cytosolic (Cy) OASTL gene from L. leucocephala, express the recombinant OASTL in Escherichia coli, purify it, do enzyme kinetic analysis, perform docking dynamics simulation analysis between the receptor and the ligands and compare its performance between Cys and Mim synthesis. Cy-OASTL was obtained through both directional degenerate primers corresponding to conserved amino acid region among plant Cys synthase family and the purified protein was 34.3KDa. After cleaving the GST-tag, Cy-OASTL was observed to form mimosine with 3H4P and OAS. The optimum Cys and Mim reaction pH and temperature were 7.5 and $40^{\circ}C$, and 8.0 and $35^{\circ}C$ respectively. Michaelis constant (Km) values of OAS from Cys were higher than the OAS from Mim. Inter fragment interaction energy (IFIE) of substrate OAS-Cy-OASTL complex model showed that Lys, Thr81, Thr77 and Gln150 demonstrated higher attraction force for Cys but 3H4P-mimosine synthase-OAS intermediate complex showed that Gly230, Tyr227, Ala231, Gly228 and Gly232 might provide higher attraction energy for the Mim. It may be concluded that Cy-OASTL demonstrates a dual role in biosynthesis both Cys and Mim and extending the knowledge on the biochemical regulatory mechanism of mimosine and cysteine.

• Archives of Pharmacal Research
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• 제24권5호
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• pp.455-465
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• 2001

The highly potent cytotoxic DNA-DNA cross-linker consists of two cyclopropa[c]pyrrolo[3,4-3]indol-4(5H)-ones insoles [(+)-CPI-I] joined by a bisamido pyrrole (abbreviated to "Pyrrole"). The Pyrrole is a synthetic analog of Bizelesin, which is currently in phase II clinical trials due to its excellent in vivo antitumor activity. The Pyrrole has 10 times more potent cytotoxicity than Bizelesin and mostly form DNA-DNA interstrand cross-links through the N3 of adenines spaced 7 bp apart. The Pyrrole requires a centrally positioned GC base pair for high cross-linking reactivity (i.e., $5^1$-T$AT_2$A*-$3^1$), while Bizelesin prefers purely AT-rich sequences (i.e., $5^1$-T$AT_4$A*-$3^1$, where /(equation omitted) represents the cross-strand adenine alkylation and A* represents an adenine alkylation) (Park et al., 1996). In this study, the high-field $^1$H-NMR and rMD studies are conducted on the 1 1-mer DNA duplex adduct of the Pyrrole where the 5′(equation omitted)TAGTTA*-3′sequence is cross-linked by the drug. A severe structural perturbation is observed in the intervening sequences of cross-linking site, while a normal B-DNA structure is maintained in the region next to the drug-modified adenines. Based upon these observations, we propose that the interplay between the bisamido pyrrole unit of the drug and central C/C base pair (hydrogen-bonding interactions) is involved in the process of cross-linking reaction, and sequence specificity is the outcome of those interactions. This study suggests a mechanism for the sequence specific cross-linking reaction of the Pyrrole, and provides a further insight to develop new DNA sequence selective and distortive cross-linking agents.

• 한국자기공명학회논문지
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• 제20권3호
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• pp.95-101
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• 2016

Apolipoprotein B-100 (Apo-B100) is a major component of low density lipoprotein (LDL). Apo B-100 protein has 4,536 amino acid sequence and these amino acids are classified into peptide groups A to G with subsequent 20 amino acids (P1-P302). The peptide groups were act as immunoglobulin (Ig) antigens which oxidized via malondialdehyde (MDA). The mimetic peptide P1 (EEEMLENVSLVCPKDAT RFK) out of D-group peptides carrying the highest value of IgG antigens were selected for structural studies that may provide antigen specificity. Circular Dichroism (CD) spectra were measured for peptide secondary structure in the range of 190-250 nm. Experimental results show that P1 exhibit partial of ${\beta}-sheet$ and random coil structure. Homonuclear (COSY, TOCSY, NOESY) 2D-NMR experiments were carried out for NMR signal assignments and structure determination for P1. On the basis of these completely assigned NMR spectra and distance data, distance geometry (DG) and Molecular dynamics (MD) were carried out to determine the structures of P1. The proposed structure was selected by comparisons between experimental NOE spectra and back calculated 2D NOE results from determined structure showing acceptable agreement. The total Root-Mean-Square-Deviation (RMSD) value of P1 obtained upon superposition of all atoms was in the range $0.33{\AA}$. The solution state P1 has mixed structure of ${\beta}-sheet$ (Glu[1] to Cys[12]) and random coil (Pro[13] to Lys[20]). These NMR results are well consistent with secondary structure from experimental results of circular dichroism. Structural studies based on NMR may contribute to the studies of atherosclerosis and observed conformational characteristics of apo B-100 in LDL using monoclonal antibodies.

• 멤브레인
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• 제29권1호
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• pp.11-17
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• 2019

수처리 분리막 분야에서 고분자는 세라믹과 함께 가장 중요한 소재로 이용되고 있다. 본 총설에서는 이러한 고분자 분리막 소재의 기술동향을 상용화 제품을 중심으로 분석하고자 하였으며, 이를 위하여 수처리 분리막의 종류에 따라 MF (Microfiltration), UF (Ultrafiltration), NF (Nanofiltration)/RO (Reverse Osmosis) 분리막으로 구분하여, 국가별, 소재별, 회사별 고분자 분리막 제품 동향을 살펴보았다. 이를 통하여, 각 분리막 종류별로 주로 사용되고 있는 소재의 종류를 파악할 수 있었으며, 동시에 시장 지배적인 위치에 있는 업체들을 파악하고 이들 업체들이 어떤 소재들로 제품 포트폴리오를 구성하고 있는지 분석할 수 있었다. 이러한 결과들을 바탕으로 각각의 분리막 종류에 따른 소재 시장의 특징을 제시하였으며, 이런 특징을 바탕으로 각 시장에 신규로 진입하기 위한 기술 개발 전략을 제안하였다.

• 멤브레인
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• 제30권1호
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• pp.57-65
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• 2020

본 연구에서는 고분자 전해질막을 구성하고 있는 고분자 주쇄의 반복단위 개수를 변경해 가며 수화채널 모폴로지와 이온전도도의 변화를 비교하였고, 최종적으로 분자동역학 전산모사 수행 시에 적정한 고분자 모델을 선정하기 위한 기준을 제시하고자 하였다. 고분자 주쇄의 길이가 가장 짧은 모델에서 주쇄 및 술폰산기의 움직임이 커지는 것을 관찰할 수 있었지만, 수화채널 모폴로지는 특별한 상관관계를 발견할 수 없었다. 또한, 수화채널 모폴로지에 가장 큰 영향을 받는 수소이온 전달 능력의 특성 상, 수소이온 전도도에서도 고분자 주쇄의 길이와 큰 상관관계를 보이지는 않았다. 이러한 결과는 특히 바인더용 이오노머 제조에 대한 중요한 정보를 제공한다. 일반적으로 바인더용 이오노머의 경우 고분자 전해질막 소재를 저분자량으로 합성하여 사용하게 되는데, 이때 주쇄/술폰산기의 움직임이 향상되므로 촉매층을 잘 둘러싸는 역할을 할 수 있는 반면에, 수소이온 전달 능력 자체에 있어서는 특별한 변화가 없을 것을 예상할 수 있다. 결론적으로, 바인더용 이오노머 제조시에는 수소이온 전달 성능보다는 물성에 좀 더 초점을 맞추어 분자량 및 구조 설계가 필요할 것이다.

• 대한기계학회논문집B
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• 제38권7호
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• pp.595-600
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• 2014

충돌시 부서져 사라지는 승화성 나노 탄환입자로 표면 위에 붙어있는 고체 나노입자를 가격하는 과정에서 탄환입자로부터 목표입자로의 운동에너지 전달특성을 분자동역학 전산모사 방법을 이용하여 해석하였다. 탄환입자는 이산화탄소로 이루어져있으며 탄환의 크기, 온도 및 발사속도를 바꿔가며 전산모사를 수행하였다. 탄환입자로부터 목표입자에 전달되는 운동에너지 전달비율은 탄환 속도와 크기에 관계없이 일정하였지만 탄환의 온도에 따라 민감하게 변하였는데, 이는 온도에 따른 탄환입자의 결합력의 변화에서 기인하는 것이었다. 동일조건의 아르곤 탄환에 비하여 이산화탄소 탄환의 에너지 전달효율은 약 2 배 정도이며, 여기에서 이산화탄소 탄환의 높은 세정성능이 비롯됨을 최초로 확인하였다.

• Journal of Applied Biological Chemistry
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• 제63권4호
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• pp.429-437
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• 2020

This study aimed to investigate the change in physicochemical properties and lactic acid bacterial communities during kimchi fermentation at different temperatures (8, 15, and 25 ℃) using two molecular genetics approaches, multiplex polymerase chain reaction and 16S rRNA gene sequencing. The pH during fermentation at 8, 15, and 25 ℃ decreased from 6.17 on the initial fermentation day to 3.92, 3.79, and 3.48 after 54, 30, and 24 days of fermentation, respectively, while the acidity increased from 0.24% to 1.12, 1.35, and 1.54%, respectively. In particular, the levels of lactic acid increased from 3.74 g/L on the initial day (day 0) to 14.43, 20.60, and 27.69 g/L during the fermentation after 24, 18, and 12 days at 8, 15, and 25 ℃, respectively, after that the lactic acid concentrations decreased slowly. The predominance of lactic acid bacteria (LAB) in the fermented kimchi was dependent on fermentation stage and temperature: Lactobacillus sakei appeared during the initial stage and Leuconsotoc mesenteroides was observed during the optimum-ripening stage at 8, 15, and 25 ℃. Lac. sakei and Lactobacillus plantarum grew rapidly in kimchi produced at 8, 15, and 25 ℃. In addition, Weissella koreensis first appeared at days 12, 9, and 6 at 8, 15, and 25 ℃ of fermentation, respectively. This result suggests that LAB population dynamics are rather sensitive to environmental conditions, such as pH, acidity, salinity, temperature, and chemical factors including free sugar and organic acids.

• 한국전산구조공학회논문집
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• 제25권4호
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• pp.315-321
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• 2012

본 연구에서는 분자동역학 전산모사와 유한요소해석 기반의 균질화 기법을 통해 나노복합재의 열전도 특성을 정확하고 효율적으로 예측할 수 있는 순차적 멀티스케일 균질화 해석기법을 제안하였다. 나노입자의 크기효과가 나노복합재의 유효 열전도 특성에 미치는 영향을 조사하기 위해 크기가 다른 구형 나노입자가 첨가된 나노복합재의 열전도 계수를 분자동역학 전산모사를 통해 예측했고, 그 결과 나노입자의 크기가 작아질수록 계면에서의 Kapitza열저항에 의해 나노복합재의 열전도 계수가 점차 감소하는 것으로 나타났다. 이러한 나노입자의 크기효과를 균질화 해석모델을 통해 정확하게 묘사하기 위해 Kapitza 열저항에 의한 계면에서의 온도 불연속 구간과 고분자 기지가 높은 밀도를 가지며 흡착되는 유효계면을 추가적인 상으로 도입하여 나노복합재를 입자, Kapitza 계면, 유효계면, 기지로 구성된 4상의 연속체 구조로 모델링하였다. 이후 순차적 멀티스케일 균질화 해석기법을 통해 유효계면의 열전도 계수를 나노복합재의 열전도 계수로부터 역으로 예측했으며, 이를 입자의 반경에 대한 함수로 근사하였다. 근사 함수를 토대로 다양한 입자 체적분율과 반경에 대한 나노복합재의 유효 열전도 특성을 예측하였으며, 유효계면에 대한 매개변수 연구를 수행하였다.

• Bulletin of the Korean Chemical Society
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• 제7권5호
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• pp.367-371
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• 1986

Dynamic and equilibrium properties of n-alkane chains immersed in solvent molecules have been investigated by a molecular dynamics method. The n-alkane chain is assumed to be a chain of elements (CH$_2$) interconnected by bonds having a fixed bond length and bond angle, but each bond of the chain is allowed to execute hindered internal rotation. We studied the effect of the number of the chain elements (N$_c$ = 10, 15 and 20) on the equilibrium properties of the system, e.g., the pair correlation functions between a chain element and solvent molecules, g$_{cs}$(r), and between the chain elements, g$_{cc}$(r), and the configurational properties such as the mean-square end-to-end distance < R$^2$ >, the mean-square radius of gyration < S$^2$ >, and the eigenvalues of the moment-of-inertia tensor < S$_i^2$ > / < S$^2$ > (i = 1, 2 and 3). We also studied the dynamic properties of the system, e.g., the autocorrelation function C(A;t) where A = R$^2$(t), = S$^2$(t), or = ${\vec{V}}(t)({\vec{V}}$ = velocity of the center of mass), and the diffusion coefficient D. The g$_{cs}$(r)'s are almost equal irrespective of the change of Nc while g$_{cc}$(r) becomes larger as N$_c$ increases; The MD computed configurational properties < R$^2$2 > and < S$^2$ > were found to be a little different from the values calculated from the statistical equations of < R$^2$ > and < S$^2$ >, it may be due to the fact that our model for the MD simulations includes a long-range volume effect. From the < S$_i^2$ > / < S$^2$ >, it is found that the chain molecule has a nearly spherical shape irrespective of the variation of N$_c$. For the dynamic properties we found that the C(R$^2$;t) and C(S$^2$;t) of lower N$_c$ decay faster than those of higher N$_c$, while the C($\vec V$;t) of the center of mass in the chain is weakly dependent on the N$_c$. The center of mass diffusion coefficient D$_c$ decreases as N$_c$ increases while the end point diffusion coefficient D$_e$ is nearly equal irrespective of the change of N$_c$.

• BMB Reports
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• 제40권3호
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• pp.315-324
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• 2007

The novel $\alpha$-amylase purified from locally isolated strain, Bacillus sp. KR-8104, (KRA) (Enzyme Microb Technol; 2005; 36: 666-671) is active in a wide range of pH. The enzyme maximum activity is at pH 4.0 and it retains 90% of activity at pH 3.5. The irreversible thermoinactivation patterns of KRA and the enzyme activity are not changed in the presence and absence of $Ca^{2+}$ and EDTA. Therefore, KRA acts as a $Ca^{2+}$-independent enzyme. Based on circular dichroism (CD) data from thermal unfolding of the enzyme recorded at 222 nm, addition of $Ca^{2+}$ and EDTA similar to its irreversible thermoinactivation, does not influence the thermal denaturation of the enzyme and its Tm. The amino acid sequence of KRA was obtained from the nucleotide sequencing of PCR products of encoding gene. The deduced amino acid sequence of the enzyme revealed a very high sequence homology to Bacillus amyloliquefaciens (BAA) (85% identity, 90% similarity) and Bacillus licheniformis $\alpha$-amylases (BLA) (81% identity, 88% similarity). To elucidate and understand these characteristics of the $\alpha$-amylase, a model of 3D structure of KRA was constructed using the crystal structure of the mutant of BLA as the platform and refined with a molecular dynamics (MD) simulation program. Interestingly enough, there is only one amino acid substitution for KRA in comparison with BLA and BAA in the region involved in the calcium-binding sites. On the other hand, there are many amino acid differences between BLA and KRA at the interface of A and B domains and around the metal triad and active site area. These alterations could have a role in stabilizing the native structure of the loop in the active site cleft and maintenance and stabilization of the putative metal triad-binding site. The amino acid differences at the active site cleft and around the catalytic residues might affect their pKa values and consequently shift its pH profile. In addition, the intrinsic fluorescence intensity of the enzyme at 350 nm does not show considerable change at pH 3.5-7.0.