• Bulletin of the Korean Chemical Society
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• 제22권2호
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• pp.145-148
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• 2001

The interaction between tetradecyl trimethyl ammonium bromide (TTAB) with bovine ${\alpha}-lactalbumin$ has been investigated at pH = 9 and at $37^{\circ}C$ by isothermal titration calorimetry, equilibrium dialysis and UV-Vis spectrophotometry methods. The binding data from unusual Scatchard plot have been analyzed in terms of the Hill equation for three sets of binding sites. The calorimetric data show that TTAB interacts endothermically with ${\alpha}-lactalbumin$ and causes protein unfolding below 2 mM concentration of TTAB, which is confirmed by spectrophotometric data. The unfolding of the protein would be mainly due to occupation of the second set of binding sites.

• BMB Reports
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• 제29권1호
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• pp.1-10
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• 1996

The binding interaction of ethidium to a series of synthetic deoxyoligonucleotides containing a B-Z junction between left-handed Z-DNA and right-handed B-DNA, was studied. The series of deoxyoligonucleotides was designed so as to vary a dinucleotide step immediately adjacent to a B-Z junction region. Ethidium binds to the right-handed DNA forms and hybrid B-Z forms which contain a B-Z junction, in a highly cooperative manner. In a series of deoxyoligonucleotides, the binding affinity of ethidium with DNA forms which were initially hybrid B-Z forms shows over an order of magnitude higher than that with any other DNA forms, which were entirely in B-form DNA The cooperativity of binding isotherms were described by an allosteric binding model and by a neighbor exclusion model. The binding data were statistically compared for two models. The conformation of allosterically converted DNA forms under binding with ethidium is found to be different from that of the initial B-form DNA as examined by CD spectra. The ratio of the binding constant was interestingly correlated to the free energy of base unstacking and the conformational conversion of the dinucleotide. The more the base stacking of the dinucleotide is unstable, or the harder the conversion of B to A conformation, the higher the ratio of the binding constant of ethidium with the allosterically converted DNA forms and with the initial B-Z hybrid forms. DNA sequence around a B-Z junction region affects the binding affinity of ethidium. The results in this study demonstrate that ethidium could preferentially interact with unusual DNA structures.

• Archives of Pharmacal Research
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• 제19권4호
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• pp.269-274
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• 1996

The binding interactions between human serum albumin (HSA) and the edible food dyes amaranth, tartrazine and sunset yellow have been studied. Intrinsic association constants and the free energy changes associated with dye-protein binding at physiological pH for amaranth and tartrazine, and at two different pH values for sunset yellow have been calculated from ultrafiltration data. The temperature dependence $(20-40^{\circ}C)$ of the intrinsic association constants at pH 7.4 for amaranth-HSA and tartrazine-HSA mixtures have been measured, from which a plot of the van't Hoff isochore exhibits a marked change in slope around $30^{\circ}C$ indicating a possible change in protein conformation. The number of dye binding sites on HSA is reported for all the above conditions. HSA-ligand binding enthalpies have been used in conjunction with the N-B transitional binding enthalpy for HSA, to calculate the enthalpy for the N-B transition when ligands are bound with the protein.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.35-40
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• 2005

Interaction of twelve erythromycin A analogues with 50S ribosomal subunit were studied employing AutoDock 3.0.5. Results showed that all active macrolides bound at the same binding site with erythromycin A in contrast to the inactive analogues which bound at location slightly different than erythromycin A. The binding site showed consistency with the X-ray data from the perspectives of hydrogen bonding and hydrophobic interactions formed by erythromycins, roxithromycin, azithromycin, cethromycin and telithromycin with the ribosome. The inactive derivatives of erythromycin A anhydride showed higher binding free energy, while 5-desosaminyl erythronolides A and B even though having quiet similar values of binding free energy with the active analogues, docked at binding sites which are quiet different than the active analogues. These results suggest the molecular docking technique can be used in predicting the binding of erythromycin A analogues to their ribosomal target.

• 정보처리학회논문지:소프트웨어 및 데이터공학
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• 제10권6호
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• pp.243-250
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• 2021

최근 VR/AR/MR 기술과 3D 주변 장치의 발전에 의해 3D 가상현실 응용 서비스 개발이 증가하고 있으며 이에 따라 3D 데이터의 호환성과 이식성에 대한 요구가 증가하고 있다. 여러 장치의 응용 프로그램의 데이터를 공동으로 사용할 수 있도록 하기 위해서는 3D 표준 데이터 형식의 파일 처리가 요구된다. 이 때 가상환경 장면 처리에 필요한 공통의 파일 형식과 함께 함수와 변수 클래스들을 표준화된 라이브러리와 데이터구조를 제공한다면 응용 별로 서로 다른 파일 형식과 데이터구조의 사용으로 인해 발생하는 불필요한 처리 과정을 생략할 수 있어서 보다 효율적인 시스템 구성이 가능할 것이다. 본 연구에서는 이러한 공통의 데이터 파일과 데이터구조 사용 기능을 위해서 특정의 프로그래밍 언어를 이용하여 공용의 3D 표준 파일에 접근하여 다양한 서비스를 개발할 수 있도록 표준화된 데이터를 생성하고 저장할 수 있는 프로그래밍 바인딩 도구를 제공하는 것이 목적이다. 이를 위해 본 논문에서는 Python 프로그래밍 언어를 이용하여 X3D 파일을 표준화된 방식으로 접근할 수 있도록 클래스와 함수를 포함하는 공통의 데이터구조를 정의하며 이 언어 바인딩 인터페이스를 기반으로 X3D 장면 데이터 파일을 렌더링 하는 X3D VR 뷰어인 Python 언어 바인딩 뷰어 구현에 대해 기술한다. 이 뷰어는 X3D 오브젝트의 생성, 변경, 교환 및 전송을 위한 Python 기반의 3D 장면 라이브러리들과 데이터구조를 포함한다. 그리고 이를 이용하여 X3D 오브젝트를 디스플레이하고 이벤트들을 처리한다.

• 한국자기공명학회논문지
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• 제10권2호
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• pp.175-187
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• 2006

Binding interactions between a positively charged porphyrin derivative TMAP(meso-tetra(p-trimethylanilinium-4-yl)porphyrin) and triple helical $(dT)_{12}{\cdot}(dA)_{12}{\cdot}(dT)_{12}$, as well as double helical $(dA)_{12}{\cdot}(dT)_{12}$ have been studied with NMR, UV and CD spectroscopy to obtain the detailed information about the binding mode and binding site. UV melting studies showed both DNA duplex and triple helix represented very similar UV absorption patterns upon binding TMAP, but the presence of third strand of triple helical $(dT)_{12}{\cdot}(dA)_{12}{\cdot}(dT)_{12}$, inhibited improvement in thermal stability in terms of melting temperature, $T_m$. In addition, the TMAP molecule is thought to bind to the major groove, according to CD and NMR data. But absence of the clear isosbestic point in UV absorption spectra represented that binding of TMAP to DNA duplex as well as DNA triplex did not show a single binding mode, rather complex binding modes.

• 한국언어정보학회:학술대회논문집
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• 한국언어정보학회 2002년도 Language, Information, and Computation Proceedings of The 16th Pacific Asia Conference
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• pp.281-289
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• 2002

This paper aims to account for the backward anaphora that seem to be against the c-command requirements in the anaphor-antecedent relations. It was claimed that the binding conditions should apply at LF fur the backward binding cases involving phych-verbs and causatives. Under the recent development of minimalism where the concept of levels disappears to adopt a cyclic derivation, the data that show the backward binding phenomena have not been discussed in the area of the binding theory. In this paper, I argue that the backward binding cases can be incorporated into the core binding phenomena with the general assumptions on the thematic prominence. It is discussed how the dependency between NPs involving backward anaphora is determined by the thematic prominency. The Agree operation takes place between the probe T and the goal with the uninterpretable u[a] and [prominent] feature, by which an anaphor is valued, producing a proper interpretation.

• 한국자기공명학회논문지
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• 제22권1호
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• pp.18-25
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• 2018

Replication protein A (RPA) is an essential single-stranded DNA binding protein in DNA processing. It is known that N terminal domain of RPA70 (RPA70N) recruits various protein partners including damage-response proteins such as p53, ATRIP, Rad9, and MRE11. Although the common binding residues of RPA70N were revealed, dynamic properties of the protein are not studied yet. In this study, we measured $^{15}N$ relaxation parameters ($T_1,\;T_2$ and heteronuclear NOE) of human RPA70N and analyzed them using model-free analysis. Our data showed that the two loops near the binding site experience fast time scale motion while the binding site does not. It suggests that the protein binding surface of RPA70N is mostly rigid for minimizing entropy cost of binding and the loops can experience conformational changes.

• Journal of Photoscience
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• 제12권1호
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• pp.25-32
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• 2005

Binding of N-Alkyl phenothiazines (NAP) to bovine serum albumin (BSA) was studied by spectroscopic methods.It was found that the phenothiazine ring common to all drugs makes major contribution to interaction. However, the nature of alkylamino group at position 10 influences the protein binding significantly. Stern-Volmer plots indicated the presence of static component in the quenching mechanism. The high magnitude of rate constant of quenching indicated that the process of energy transfer occurs by intermolecular interaction and thus the drug-binding site is in close proximity to tryptophan residues of BSA. Binding studies in presence of hydrophobic probe, 8-anilino-1-naphthalein-sulphonic acid showed that there is hydrophobic interaction between drug and the probe and they do not share common sites in BSA. Thermodynamic parameters obtained from data at different temperatures showed that the binding of NAP to BSA predominantly involve hydrophobic forces. The effects of some cations and anions common ions were investigated on NAP-BSA interactions. The CD spectrum of BSA in presence of drug showedthat binding of drug leads to change in the helicity of the protein.

• Archives of Pharmacal Research
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• 제23권6호
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• pp.633-636
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• 2000

Translationally controlled tumor protein (TCTP), also known as IgE-dependent histamine-releasing factor, is a growth-related tumor protein. Although the primary sequence of rat TCTP does not reveal any recognizable $Ca^{2+}$ -binding motif, previous studies have demonstrated that rat TCTP consisting of 172 amino acids is a $Ca^{2+}$ -binding protein. However. the region of TCTP required for $Ca^{2+}$ interaction has not been mapped to the molecule. Here, we reported that the $Ca^{2+}$ binding region of TCTP which was mapped by using a combination of deletion constructs of rat TCTP and $^{45}Ca^{2+}$-overlay assay. was confined to amino acid residues 81-112. This binding domain did not show any peculiar loop of calcium- binding motif such as CaLB domain and EF hand motif and it seems to be constituted of random coil regions neighboring the a helix. Thus, our data confirm that TCTP is a novel family of $Ca^{2+}$ -binding protein.