• Bulletin of the Korean Chemical Society
• /
• 제30권5호
• /
• pp.1043-1046
• /
• 2009

Human protein tyrosine kinase-6 (PTK6) is a member of the non-receptor protein tyrosine kinase family and it is found in two-thirds of all breast tumors. Very recently, we proposed that the SH3 domain of PTK6 interacts with the linker region (Linker) between the SH2 and kinase domains, proving that the interaction between SH3 domain and Linker plays an important role in auto-inhibition mechanism. Residues from 1 to 191 corresponding region of SH3-SH2-Linker (SH32L) of PTK6 was cloned into the pET32a expression vector with Tobbaco etch virus (TEV) protease enzyme site by sequence homology and 3D structural model. The purified PTK6-SH32L was determined as a monomer conformation in solution. The amide proton resonances in the $^{15}N-^{1}H$ 2D-HSQC spectrum suggest that PTK6-SH32L possesses disordered structural region of the flexible/unstructured linker region. In addition, the backbone amide proton chemical shifts of the SH3 domain in the PTK6-SH32L differ from that of the independent domain, indicating that intra-molecular interaction between SH3 and Linker in the PTK6-SH32L is present.

• Biomolecules & Therapeutics
• /
• 제32권4호
• /
• pp.474-480
• /
• 2024

Streptomyces avermitilis genome includes 33 genes encoding monooxygenation-catalyzing cytochrome P450 enzymes. We investigated the structure of CYP107P2 and its interactions with terpenoid compounds. The recombinant CYP107P2 protein was expressed in Escherichia coli and the purified enzyme exhibited a typical P450 spectrum upon CO-binding in its reduced state. Type-I substrate-binding spectral titrations were observed with various terpenoid compounds, including α-pinene, β-pinene, α-terpinyl acetate, and (+)-3-carene. The calculated binding affinities (Kd) ranged from 15.9 to 50.8 µM. The X-ray crystal structure of CYP107P2 was determined at 1.99 Å resolution, with a well-conserved overall P450 folding conformation. The terpenoid compound docking models illustrated that the structural interaction between monoterpenes and CYP107P2, with the distance between heme and terpenes ranging from 3.4 to 5.4 Å, indicates potential substrate binding for P450 enzyme. This study suggests that CYP107P2 is a Streptomyces P450 enzyme capable of catalyzing terpenes as substrates, signifying noteworthy advancements in comprehending a novel P450 enzyme's involvement in terpene reactions.

• 한국잠사곤충학회지
• /
• 제41권1호
• /
• pp.54-60
• /
• 1999

염산 또는 수산화나트륨 수용액의 농도, 온도, 시간 등 처리조건에 따른 작잠견사의 가수분해율을 측정하였으며 산처리 작잠분말과 알칼리처리 작잠분말의 형태 및 구조특성을 주사전자현미경, 적외선 분광분석, X-선 회절분석 등의 방법으로 분석한 결과 다음과 같은 결과를 얻었다. 1. 작잠견사에 대한 염산 및 수산화나트륨의 처리농도와 온도가 높을수록 또한 처리시간이 길어질수록 작잠견사의 가수분해율은 증가하는 경향을 나타내었으나 고온, 고농도의 조건하에서 수산화나트륨을 작잠견사에 처리하는 경우 작잠견사의 가수분해율이 오히려 떨어지는 경향을 보였다. 2. 산 및 알칼리 처리에 의하여 제조된 작잠분말의 형태는 용해도가 30 wt% 부근에서는 섬유상의 형태를 유지하였으며 산처리 분말의 경우 용해도가 증가함에 따라 섬유축 방향으로 조각난 미세한 입자형태를 나타내었으나 알칼리처리 분말의 경우에는 부정형의 입자형태를 나타내었다. 3. 적외선 분광분석 결과 작잠분말은 처리조건과 무관하게 ${\beta}$-sheet 구조의 특성을 반영하는 1635, 1532, 1226, 960, 700 cm$^{-1}$ 흡수대와 ${\alpha}$-helix 구조의 특성을 반영하는 616 cm$^{-1}$ 흡수대가 뚜렷하게 나타나 작잠분말의 주요 conformation은 ${\beta}$-sheet 구조와 ${\alpha}$-helix 구조임을 확인하였다. 4. X-선 회절분석 결과 가수분해율이 낮을 경우 (35 wt%)에는 ${\beta}$-sheet 구조와 ${\alpha}$-helix 구조에 기인하는 회절 피크가 뚜렷하게 나타났으나 가수분해율이 80 wt% 이상으로 증가하면 2${\theta}$=17.1$^{\circ}$ 및 20.0$^{\circ}$의 회절피크만 강하게 나타났다.

• Bulletin of the Korean Chemical Society
• /
• 제31권5호
• /
• pp.1326-1330
• /
• 2010

Evidences have proved the versatile role of sulfur atom in supramolecular chemistry. $^1$Presence of S atom in the molecule usually results in the specific structural properties of molecules. In the present study, $S{\cdots}arene$, $N{\cdots}arene$, $CH{\cdots}{\pi}$, $CH{\cdots}S$ and $CH{\cdots}N$ type of weak interactions stabilize the conformation and self assembly of symmetrical as well as dissymmetrical molecules.

• 한국자기공명학회논문지
• /
• 제7권2호
• /
• pp.89-97
• /
• 2003

Foot-and-mouth disease virus (FMDV) belongs to the aphthovirus genus within the picornavirus which has a single copy of a positive sense RNA. The translation initiation process of FMDV occurs by a cap-independent mechanism directed by a highly structured element (∼435 nt) termed an internal ribosome entry site (IRES). We have designed and prepared FMDV 4-2 RNA (28nt) by in vitro transcription. The 2D NMR data revealed that FMDV 4-2 IRES domain RNA has a flexible loop and bulge conformation. In further study, we need to make an isotope labeled RNA sample and conduct 3D NMR experiments to completely determine the 3D structure. This study may establish a new drug design strategy to treat foot-and mouth disease.

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

• 대한화학회지
• /
• 제21권4호
• /
• pp.235-245
• /
• 1977

교감신경 흥분성 amine류의 분자구조와 약리효과 간의 관계를 설명하기 위하여 phenethylamine에서 benzene 고리와 ethylamine의 ${\alpha},{\beta}$ 위치와 amine의 질소에 hydroxy기와 methyl기 등을 도입한 23종의 약품에 대한 분자 특성을 EHT법으로 계산하여 검토하였다.

• Bulletin of the Korean Chemical Society
• /
• 제32권12호
• /
• pp.4195-4198
• /
• 2011

Intramolecular ${\pi}-{\pi}$ and ${\sigma}-{\pi}$ interactions are omnipresent for numerous energetic and structural phenomena in nature, and the exact description of these nonbonding interactions plays an important role in the accurate prediction of the three-dimensional structures for numerous interesting molecular systems such as protein folding and polymer shaping. We have selected two prototype molecular systems for benchmarking calculations of intramolecular ${\pi}-{\pi}$ and ${\sigma}-{\pi}$ interactions. Accurately describing conformational energy of such systems requires highly elaborate but very expensive ab initio methods such as coupled cluster singles, doubles, and (triples) (CCSD(T)). Our calculations reveal a double hybrid density functional incorporating dispersion correction (B2PLYP-D) that agrees excellently with the CCSD(T) results, indicating that B2PLYP-D can serve as a practical method of choice.

• Biomolecules & Therapeutics
• /
• 제2권1호
• /
• pp.28-33
• /
• 1994

In order to obtain insight into the repair mechanism of DNA containing thymine photo-dimer, the conformation of the duplex d(GCGGTTGGCG).d(CGCCAACCGC) with a thymine dimer incorporated has been studied by proton NMR. NOE data show that, although the local environment around the thymine dimer is altered, the gross structural changes are relatively small. T$_4$endonuclease V exhibited a conformational change on complex formation with DNA. This conformational change occurred around histidine 16 which was close to tyrosine 129 located in the aromatic segment (WYKYY) near the C-terminus. It is likely that the interaction between T$_4$endonuclease V and DNA is strong since the complex was not dissociated up to 1.6 M NaCl.

• 한국응용과학기술학회지
• /
• 제24권4호
• /
• pp.362-368
• /
• 2007

To study the relationship between elementary biochemical states and structural states of the actomyosin crossbridges in muscle, the effects of binding of MgADP to myosin heads in the rigor muscle were examined by X-ray diffraction using synchrotron radiation. X-ray diffraction studies have been made to investigate the effects of binding of ADP on the structure of glycerinated rabbit skeletal muscle in the rigor state. The intensity increase was accompanied by a slight but distinct decrease in the 5.9 am layer-line intensity close to the meridian. These results strongly suggest that myosin heads altered their attached conformation in the proximal end toward the plane perpendicular to the fiber axis when MgADP was bound to them. We found that the intensity of the 14.5 nm-based meridional reflections increase by 20-50% when MgADP was added to the rigor muscle in the presence of hexokinase and myokinase inhibitor.