• Bulletin of the Korean Chemical Society
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• 제32권9호
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• pp.3425-3428
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• 2011

Apolipoprotein A-I (Apo A-I) is a major component for high density lipoproteins (HDL). A number of mimetic peptides of Apo A-I were screened from the phase-displayed random peptide library by utilizing monoclonal antibodies (A12). Mimetic peptide for A12 epitope against Apo A-I was selected as CPFARLPVEHHDVVGL (pA1). From the BLAST search, the mimetic peptide pA1 had 40% homology with Apo A-I. As a result of the structural determination of this mimotope using homo/hetero nuclear 2D-NMR techniques and NMR-based distance geometry (DG)/molecular dynamic (MD) computations, DG structure had low penalty value of 0.3-0.7 ${\AA}^2$ and the total RMSD was 0.6-1.6 ${\AA}$. The mimotope pA1 exhibited characteristic conformation including a ${\beta}$-turn from Pro[7] to His[11].

• Bulletin of the Korean Chemical Society
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• 제32권11호
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• pp.4016-4020
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• 2011

A number of mimetic peptides of apolipoprotein A-I, a major component for high density lipoproteins (HDL), were screened from the phase-displayed random peptide library by utilizing monoclonal antibodies (A12). A mimetic peptide for A12 epitope against apolipoprotein A-I was selected as FVLVRDTFPSSVCCP(pA2) exhibiting 45% homology with Apo A-I in the BLAST search. Solution structure determination of this mimotope was made by using 2D-NMR data and NMR-based distance geometry (DG)/molecular dynamic calculations. The resulting DG structures had low penalty value of 0.4-0.6 ${\AA}^2$ and the total RMSD of 0.7-1.7 ${\AA}$. The mimotope pA2 exhibited a characteristic ${\beta}$-turn conformation from Val[2] to Phe[8] near Pro[9] residue.

• Bulletin of the Korean Chemical Society
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• 제25권12호
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• pp.1845-1849
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• 2004

Apolipoprotein B-100 (Apo-B100) is a major protein component for low density lipoproteins (LDL). A number of mimetic peptides of Apo-B100 were screened from the phase-displayed random peptide library by utilizing monoclonal antibody (B9). Mimetic peptide for B9 epitope against apo B-100 was CRNVPPIFNDVYWIAF (pB1). From the BLAST search, the mimetic peptide pB1 had 40% homology with apo B-100. As a result of the structural determination of this mimotope using homo/hetero nuclear 2D-NMR techniques and NMR-based distance geometry (DG)/molecular dynamic (MD) computations, DG structure had low penalty value of 0.3-0.6 ${\AA}^2$ and the total RMSD was 0.5-1.5 ${\AA}. Moreover, pB1 structure included a weak $3_{10}$-helix from $Ile^7$,/TEX> to $Trp^{13}$.

• 한국자기공명학회논문지
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• 제25권4호
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• pp.58-63
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• 2021

Apolipoprotein B-100 (apo B-100), the main protein component that makes up LDL (Low density lipoprotein), consists of 4,536 amino acids and serves to combine with the LDL receptor. The oxidized LDL peptides by malondialdehyde (MDA) or acetylation in vivo act as immunoglobulin (Ig) antigens and peptide groups were classified into 7 peptide groups with subsequent 20 amino acids (P1-P302). The biomimetic peptide P143 (IALDD AKINF NEKLS QLQTY) out of C-group peptides carrying the highest value of IgG antigens were selected for structural studies that may provide antigen specificity. Experimental results show that P143 has β-sheet in Ile[1]-Asn[9] and α-helice in Gln[16]-Tyr[20] structure. Homonuclear 2D-NMR (COSY, TOCSY, NOESY) experiments were carried out for NMR signal assignments and structure determination for P143. On the basis of these completely assigned NMR spectra and proton distance information, distance geometry (DG) and molecular dynamic (MD) were carried out to determine the structures of P143. 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 P143 obtained upon superposition of all atoms were in the set range. The solution state P143 has a mixed structure of pseudo α-helix and β-turn(Phe[10] to Glu[12]). These results are well consistent with calculated structure from experimental data of NOE spectra. Structural studies based on NMR may contribute to the prevent oxidation studies of atherosclerosis and observed conformational characteristics of apo B-100 in LDL using monoclonal antibodies.

• 한국자기공명학회논문지
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• 제24권4호
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• pp.136-142
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• 2020

Apolipoprotein B-100 (apo B-100), the main protein component that makes up LDL (Low density lipoprotein), consists of 4,536 amino acids and serves to combine with the LDL receptor. The oxidized LDL peptides by malondialdehyde (MDA) or acetylation in vivo were act as immunoglobulin (Ig) antigens and peptide groups were classified into 7 peptide groups with subsequent 20 amino acids (P1-P302). The biomimetic peptide P99 (KGTYG LSCQR DPNTG RLNGE) out of B-group peptides carrying the highest value of IgM 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 190-260 nm. Experimental results show that P99 has pseudo α-helice and random coil structure. Homonuclear (COSY, TOCSY, NOESY) 2D-NMR experiments were carried out for NMR signal assignments and structure determination for P99. On the basis of these completely assigned NMR spectra and proton distance information, distance geometry (DG) and molecular dynamic (MD) were carried out to determine the structures of P99. 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 P99 obtained upon superposition of all atoms were in the set range. The solution state P99 has mixed structure of pseudo α-helix and β-turn(Gln[9] to Thr[13]). These NMR results are well consistent with secondary structure from experimental results of circular dichroism. Structural studies based on NMR may contribute to the prevent oxidation studies of atherosclerosis and observed conformational characteristics of apo B-100 in LDL using monoclonal antibodies.

• Asian-Australasian Journal of Animal Sciences
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• 제25권6호
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• pp.772-784
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• 2012

Marker-assisted gene pyramiding aims to produce individuals with superior economic traits according to the optimal breeding scheme which involves selecting a series of favorite target alleles after cross of base populations and pyramiding them into a single genotype. Inspired by the science of evolutionary computation, we used the metaphor of hill-climbing to model the dynamic behavior of gene pyramiding. In consideration of the traditional cross program of animals along with the features of animal segregating populations, four types of cross programs and two types of selection strategies for gene pyramiding are performed from a practical perspective. Two population cross for pyramiding two genes (denoted II), three population cascading cross for pyramiding three genes(denoted III), four population symmetry (denoted IIII-S) and cascading cross for pyramiding four genes (denoted IIII-C), and various schemes (denoted cross program-A-E) are designed for each cross program given different levels of initial favorite allele frequencies, base population sizes and trait heritabilities. The process of gene pyramiding breeding for various schemes are simulated and compared based on the population hamming distance, average superior genotype frequencies and average phenotypic values. By simulation, the results show that the larger base population size and the higher the initial favorite allele frequency the higher the efficiency of gene pyramiding. Parents cross order is shown to be the most important factor in a cascading cross, but has no significant influence on the symmetric cross. The results also show that genotypic selection strategy is superior to phenotypic selection in accelerating gene pyramiding. Moreover, the method and corresponding software was used to compare different cross schemes and selection strategies.

• Composites Research
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• 제32권3호
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• pp.163-169
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• 2019

본 연구에서 우리는 자유 라디칼 중합에 기반한 열가소성 고분자의 동적 분자동역학 중합 알고리즘을 이용하여 95%의 변환률을 갖는 PMMA의 고분자 모델을 구성하였다. 본 알고리즘에서는 계산 수행에 필요한 시간을 줄이기 위해 PCFF 포텐셜 함수의 결합 항들 TraPPE-UA 포텐셜 함수의 비결합 항을 조합한 united-atom level의 coarse-grained 포텐셜 함수를 도입하였다. 자유 라디칼 중합 시뮬레이션을 통해 생성된 각 사슬을 분석하여 고분자의 분자량 분포와 평균 분자량을 계산하였고, 고분자의 분자량은 초기 상태에 존재하는 개시제 라디칼의 수를 이용하여 조절하였으며, 유리전이온도, 기계적 물성에 미치는 분자량의 효과에 대해 연구되었다.

• 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.

• 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.

• Nuclear Medicine and Molecular Imaging
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• 제41권4호
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• pp.317-325
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• 2007

동적 PET 데이터는 구획모델과 Nonlinear Least Squares(NLS)방법을 사용하여 분석함으로서 각종 생화학적 물질의 생체 대사율 등을 정량화 할 수 있다. 하지만 NLS방법은 변수의 초기 값이 적절하지 않을 경우 지역적인 최소점에 빠지거나 계산시간이 길어 동역학 변수들을 각 화소마다 구해야 하는 파라메터 영상(parametric image) 구성에는 효과적이지 않다. Patlak 도표분석법(PGA)은 비선형 방정식을 선형화하여 값을 추정함으로서 간단하면서 적은 계산량으로 인해 파라메터 영상을 구성하는데 많이 사용되고 있으나 잡음성분과 선형구간 선정에 따라 값이 영향을 받는 단점이 있다. 따라서 이 연구에서는 3구획 비가역 모델에 적합한 다중선형분석법(MLAIR)을 고안하였으며 3구획 비가역 모델의 대표적 예인 $[^{18}F]Fluoride$ PET을 이용하여 미니돼지에서의 뼈 섭취률을 계산하여 PGA방법과 비교 분석해 보았다. 대상 및 방법: 3마리의 미니돼지를 대상으로 100MBq의 $[^{18}F]Fluoride$를 대퇴부 정맥에 주사하면서 ECAT EXAET 47 PET 스캐너를 이용하여 60분간 PET 영상을 얻었다. 케타민과 자일라진을 이용하여 30분 간격으로 마취하였으며 실험동물을 진공 쿠션을 이용하여 반드시 누운 자세로 위치하도록 고정 시켰다. 입력함수인 혈장 내 농도곡선은 대퇴동맥으로부터 스캔 시작과 함께 혈액 채취를 통해 얻었다. ROI분석을 위해 대퇴골두, 척추 뼈, 근육에 ROI를 그려 조직 내 시간-방사능 곡선을 얻었다. $k_4$가 0인 3구획 비가역 모델로부터 MLAIR와 PGA방법을 사용하여 관심영역에서의 뼈 섭취률 $K_i$와 파라메터 영상을 구성하였다. PGA방법은 선형구간의 시작점인 $t^*$선택에 따른 영향을 보기 위해 분석구간을 변화시켜가며 분석하였다. 결과: ROI 분석결과 추정된 $K_i$값은 NLS방법에 비하여 MLAIR방법과 PGA방법 모두에서 과대 추정되었으나 두 분석방법 끼리는 비슷한결과를 보였다. Patlak 기울기는 $t^*$선택에 따라 값이 변하였으며 Patlak 상수는 Fluoride 섭취가 높은 대퇴골두나 척추뼈에서 30분이 지나서야 일정한 값으로 나타났고 섭취가 낮은 근육에서는 10분만에 일정해졌다. 파라메터 영상에서는 제안한 MLAIR방법이 PGA방법에 비해 영상의 질을 향상시킴을 알 수 있었다. 또한 PGA방법을 이용하여 구성한 파라메터 영상은 $t^*$값이 커질수록 급격히 영상의 질이 저하됨을 볼 수 있다. 특히 Fluoride 섭취가 높은 영역에서 Patlak 상수가 일정해지는 시간인 $t^*$값이 30분일 때 파라메터 영상은 MLAIR와 크게 차이가 났다. 결론 결론적으로 제안한 MLAIR방법은 선형구간을 정할 필요 없이 모든 데이터를 사용하는 이점이 있으며 선형적인 방법을 통해 $K_i$값을 얻을 수 있어 계산시간을 단축 시켜 줄 뿐 아니라 잡음성분에 강해 파라메터 영상의 질을 크게 향상 시켜 줌으로 비가역 3구획모델에서의 PGA방법을 대체할 새로운 파라메터 영상구성방법으로 적합할 것이다.