• Molecules and Cells
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• 제45권1호
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• pp.33-40
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• 2022

The various DNA-protein interactions associated with the expression of genetic information involve double-stranded DNA (dsDNA) bending. Due to the importance of the formation of the dsDNA bending structure, dsDNA bending properties have long been investigated in the biophysics field. Conventionally, DNA bendability is characterized by innate averaging data from bulk experiments. The advent of single-molecule methods, such as atomic force microscopy, optical and magnetic tweezers, tethered particle motion, and single-molecule fluorescence resonance energy transfer measurement, has provided valuable tools to investigate not only the static structures but also the dynamic properties of bent dsDNA. Here, we reviewed the single-molecule methods that have been used for investigating dsDNA bendability and new findings related to dsDNA bending. Single-molecule approaches are promising tools for revealing the unknown properties of dsDNA related to its bending, particularly in cells.

• 터널과지하공간
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• 제10권1호
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• pp.70-79
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• 2000

입자수, 압력, 온도일정의 앙상블(NPT-ensemble) 분자동력학(MD) 시뮬레이션을 이용하여 300$^{\circ}$K에서 $\alpha$-quartz의 결정축에 따른 일축압축강도를 계산하고, 자연산 $\alpha$-quartz 단결정 코아를 제작하여 일축압축강도시험을 실시하였다. $\alpha$-quartz 단결정 코아에 대한 일축압축시험에서 측정된 결과에 의하면 재하 방향이 c축에 평행한 경우가 수직인 경우보다 높은 강도를 나타내지만, MD 시뮬레이션에서 계산된 완전무결함 $\alpha$-quartz의 경우 이와 반대의 결과를 보이고 있다. 두 경우 모두 재하방향에 따른 강도 이방성을 보이고 있으나, 그 이유는 서로 다르다. MD 시뮬레이션에 의해 계산된 무결함 $\alpha$-quartz의 강도 이방성은 결정구조의 차이에 기인하는 것으로 사료된다. 이에 반해 일축압축시험을 통해 측정된 $\alpha$-quartz의 강도 이방성은 결정성장과정에서 생기는 주상 미세결함에 의해 영향을 받는다.

• Bulletin of the Korean Chemical Society
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• 제32권8호
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• pp.2537-2543
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• 2011

A self-assembled Al-bridged diiminopyridine-based ligand (3) was synthesized and characterized by FT-IR, ESI-MS and NMR spectroscopy. Electron spectral titrations were performed to confirm the formation of a novel trinuclear bis(imino)pyridyl iron(II) complex (4) upon addition of $FeCl_2$ into Al-bridged ligand 3 in methanol solution. Simultaneously, a typical bis(imino)pyridine-iron(II) complex (2) was synthesized and fully characterized. The X-ray crystal study of the iron(II) complex 2 disclosed a five-coordinate, distorted square-pyramidal structure with the tridentate N^N^N ligand and chlorides. The optimal molecular structure of 4 was obtained by means of molecular mechanics, which showed that each iron atom in the complex 4 is surrounded by two chlorides, a tridentate N^N^N ligand and one oxygen atom, supporting considerations about the possibility of six-coordinate geometry from MMAO or the ethylene access. A comparison of 4 with the reference 2 revealed a remarkable decrease of the catalytic activity and MMAO consumption (activity up to $0.41{\times}10^3\;kg\;{mol_{Fe}}^{-1}h^{-1}bar^{-1}$, Al/Fe = 650 for 4 and $7.02{\times}10^3\;kg\;{mol_{Fe}}^{-1}h^{-1}bar^{-1}$, Al/Fe = 1600 for 2).

• BMB Reports
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• 제31권5호
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• pp.459-467
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• 1998

A new set of functional group interaction energy descriptors relevant to the ACE (Angiotensin-Converting Enzyme) inhibitory peptide, QSAR (Quantitative Structure Activity Relationships), is presented. The functional group interaction energies approximate the charged interactions and distances between functional groups in molecules. The effective energies of the computationally derived geometries are useful parameters for deriving 3D-QSAR models, especially in the absence of experimentally known active site conformation. ACE is a regulatory zinc protease in the renin-angiotensin system. Therapeutic inhibition of this enzyme has proven to be a very effective treatment for the management of hypertension. The non bond interaction energy values among functional groups of six-feature of ACE inhibitory peptides were used as descriptor terms and analyzed for multivariate correlation with ACE inhibition activity. The functional group interaction energy descriptors used in the regression analysis were obtained by a series of inhibitor structures derived from molecular mechanics and semi-empirical calculations. The descriptors calculated using electrostatic and steric fields from the precisely defined functional group were sufficient to explain the biological activity of inhibitor. Application of the descriptors to the inhibition of ACE indicates that the derived QSAR has good predicting ability and provides insight into the mechanism of enzyme inhibition. The method, functional group interaction energy analysis, is expected to be applicable to predict enzyme inhibitory activity of the rationally designed inhibitors.

• Bulletin of the Korean Chemical Society
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• 제35권8호
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• pp.2494-2504
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• 2014

P38 mitogen activated protein (MAP) kinase is an important anti-inflammatory drug target, which can be activated by responding to various stimuli such as stress and immune response. Based on the conformation of the conserved DFG loop (in or out), binding inhibitors are termed as type-I and II. Type-I inhibitors are ATP competitive, whereas type-II inhibitors bind in DFG-out conformation of allosteric pocket. It remains unclear that how these allosteric inhibitors stabilize the DFG-out conformation and interact. Organosilicon compounds provide unusual opportunity to enhance potency and diversity of drug molecules due to their low toxicity. However, very few examples have been reported to utilize this property. In this regard, we performed docking of an inhibitor (BIRB) and its silicon analog (Si-BIRB) in an allosteric binding pocket of p38. Further, molecular dynamics (MD) simulations were performed to study the dynamic behavior of the simulated complexes. The difference in the biological activity and mechanism of action of the simulated inhibitors could be explained based on the molecular mechanics/generalized Born surface area (MM/GBSA) binding free energy per residue decomposition. MM/GBSA showed that biological activities were related with calculated binding free energy of inhibitors. Analyses of the per-residue decomposed energy indicated that van der Waals and non-polar interactions were predominant in the ligand-protein interactions. Further, crucial residues identified for hydrogen bond, salt bridge and hydrophobic interactions were Tyr35, Lys53, Glu71, Leu74, Leu75, Ile84, Met109, Leu167, Asp168 and Phe169. Our results indicate that stronger hydrophobic interaction of Si-BIRB with the binding site residues could be responsible for its greater binding affinity compared with BIRB.

• 한국수학사학회지
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• 제21권3호
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• pp.1-30
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• 2008

뉴턴의 중력이론의 성공은 수학물리학을 태동시키는 바, 최초로 19세기 초의 분자력의 모델성립에 중요한 요소로 등장하였다. 라플라스는 여기서 회전타원체의 작용이라는 모델을 이용하였고 회전타원체의 작용은 이계편미분방정식으로 표현이 되었다. 이것을 풀어서 유체를 담은 용기의 기하학적 모습과 와 유체와 고체의 접촉각에 대응시켰다. 알 수 없는 분자간거리는 추상적이고 미지의 힘 함수 $\varphi(f)$를 써서 표현하여, 분자 작용반경이라는 개념을 도입하여 이론적인 포텐셜 함수의 이론적인 토대를 구축하였다. 뉴턴의 중력이론은 라플라스이론에서 완성을 이루었고, 이후 분자력의 모델로서 작용을 하였다. 라플라스-영의 모세관이론은 수학적으로는 극소 곡면론에서 물리학적으로는 표면장력현상으로 설명이 된다.

• 대한화학회지
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• 제37권10호
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• pp.903-909
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• 1993

팔라듐(0, II)-포스핀계 착물을 촉매로 하여 crotonic acid, methacrylic acid 및 3-butenoic acid 같은 불포화가크복실산의 카르보닐화 고리반응에서 생성가능한 물질의 구조를 확인하고, 그 반응메카니즘을 MM2 와 EHMO 계산에 의해서 추정하였다. 이 반응은 ${\pi}$ -착물을 거쳐 금속 함유 고리화합물을 만든 다음 산화성 첨가반응과 환원성 제거반응이 일어나 진행된다. ${\pi}$ -착물을 안정화시키는 crotonic acid, methacrylic acid 등은 카르보닐화 고리반응이 진행되지 않고, 3-butenoic acid는 무수카르복실산 유도체로서 glutaric anhydride와 3-methylsuccinic anhydride 및 이중결합이 자리옮김된 crotonic acid가 얻어졌다.

• 대한화학회지
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• 제37권4호
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• pp.431-441
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• 1993

Acrylic acid, methacrylic acid, crotonic acid(A 그룹), 또는 3-butenoic acid 4-pentenoic acid(B group) 등이 배위된 bis(trimethylphosphine) 팔라듐(O) 착물에서 ${\pi}$-및 metallacycle의 안정한 구조와 반응성을 분자역학법과 확장분자궤도함수법으로 조사하였다. 올레핀의 HOMO 및 LUMO 계수가 큰 A 그룹 리간드는 ${\pi}$-착물이 안정화되고, LUMO 계수가 상대적으로 적은 B 그룹 리간드는 금속함유고리화합물이 안정하였으며, 특히, 3-butenoic acid에서는 6원고리 화합물보다 메틸기를 갖는 5원고리 화합물이 더 안정함을 알 수 있었다.

• Bulletin of the Korean Chemical Society
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• 제27권1호
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• pp.77-81
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• 2006

The commercially available Amberlite XAD-2 and XAD-4 resins were modified with macrocyclic protoporphyrin IX (PPIX) or tetrakis(p-carboxyphenyl) porphyrin (TCPP) to enhance the adsorption capacity for phenol and chlorophenols. The chemically modified polymeric adsorbents (XAD-2+PPIX, XAD-2+TCPP, XAD-4+PPIX, and XAD-4+TCPP) were applied to the solid phase extraction as an adsorbent material for the preconcentration of phenol and chlorophenols in environmental waters. Generally, the synthesized adsorbents showed higher recoveries than underivatized adsorbents, XAD-2 and XAD-4, without matrix interferences. Especially, XAD-4+PPIX showed more than 90% recoveries for all compounds used in this study including hydrophilic phenol. The major factor for the increase of the adsorption capacity was the increase of $\pi$-$\pi$ interaction between adsorbents and samples due to the introduction of the porphyrin molecule. However, the breakthrough volumes and recovery values of the XADs+TCPP columns were slightly decreased for the bulky chlorophenols such as TCP and PCP. Using molecular mechanics methods, the structures of TCPP and PPIX were compared with that of porphine, the parent molecule of porphyrin. Four bulky p-carboxyphenyl groups of TCPP were torsional each other, thus the molecular plane of TCPP were not on the same level. In conclusion, the decrease of breakthrough volumes and recovery values of XADs+TCPP columns for bulky phenols can be explained by the steric hindrance of the $\pi$-$\pi$ interaction between porphyrin plane and the phenols.

• Molecules and Cells
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• 제40권2호
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• pp.117-122
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• 2017

Despite the fact that porcine embryonic stem cells (ESCs) are a practical study tool, in vitro long-term maintenance of these cells is difficult in a two-dimensional (2D) microenvironment using cellular niche or extracellular matrix proteins. However, a three-dimensional (3D) microenvironment, similar to that enclosing the inner cell mass of the blastocyst, may improve in vitro maintenance of self-renewal. Accordingly, as a first step toward constructing a 3D microenvironment optimized to maintain porcine ESC self-renewal, we investigated different culture dimensions for porcine ICM-derived cells to enhance the maintenance of self-renewal. Porcine ICM-derived cells were cultured in agarose-based 3D hydrogel with self-renewal-friendly mechanics and in 2D culture plates with or without feeder cells. Subsequently, the effects of the 3D microenvironment on maintenance of self-renewal were identified by analyzing colony formation and morphology, alkaline phosphatase (AP) activity, and transcriptional and translational regulation of self-renewal-related genes. The 3D microenvironment using a 1.5% (w/v) agarose-based 3D hydrogel resulted in significantly more colonies with stereoscopic morphology, significantly improved AP activity, and increased protein expression of self-renewal-related genes compared to those in the 2D microenvironment. These results demonstrate that self-renewal of porcine ICM-derived cells can be maintained more effectively in a 3D microenvironment than in a 2D microenvironment. These results will help develop novel culture systems for ICM-derived cells derived from diverse species, which will contribute to stimulating basic and applicable studies related to ESCs.