• Bulletin of the Korean Chemical Society
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• 제33권3호
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• pp.770-774
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• 2012

Protein loops are often involved in diverse biological functions, and some functional loops show conformational changes upon ligand binding. Since this conformational change is directly related to ligand binding pose and protein function, there have been numerous attempts to predict this change accurately. In this study, we show that it is plausible to obtain meaningful ensembles of loop conformations for flexible, ligand-binding protein loops efficiently by applying a loop modeling method. The loop modeling method employs triaxial loop closure algorithm for trial conformation generation and conformational space annealing for global energy optimization. When loop modeling was performed on the framework of ligand-free structure, loop structures within $3\AA$ RMSD from the crystal loop structure for the ligand-bound state were sampled in 4 out of 6 cases. This result is encouraging considering that no information on the ligand-bound state was used during the loop modeling process. We therefore expect that the present loop modeling method will be useful for future developments of flexible protein-ligand docking methods.

• Journal of Microbiology and Biotechnology
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• 제31권10호
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• pp.1393-1400
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• 2021

Acetone-butanol-ethanol (ABE) fermentation by the anaerobic bacterium Clostridium acetobutylicum has been considered a promising process of industrial biofuel production. Phosphotransbutyrylase (phosphate butyryltransferase, PTB) plays a crucial role in butyrate metabolism by catalyzing the reversible conversion of butyryl-CoA into butyryl phosphate. Here, we report the crystal structure of PTB from the Clostridial host for ABE fermentation, C. acetobutylicum, (CaPTB) at a 2.9 Å resolution. The overall structure of the CaPTB monomer is quite similar to those of other acyltransferases, with some regional structural differences. The monomeric structure of CaPTB consists of two distinct domains, the N- and C-terminal domains. The active site cleft was formed at the interface between the two domains. Interestingly, the crystal structure of CaPTB contained eight molecules per asymmetric unit, forming an octamer, and the size-exclusion chromatography experiment also suggested that the enzyme exists as an octamer in solution. The structural analysis of CaPTB identifies the substrate binding mode of the enzyme and comparisons with other acyltransferase structures lead us to speculate that the enzyme undergoes a conformational change upon binding of its substrate.

• 한국결정학회:학술대회논문집
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• 한국결정학회 2002년도 정기총회 및 추계학술연구발표회
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• pp.24-24
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• 2002

HtrA (high temperature requirement A), a periplasmic heat shock protein, is known to have molecular chaperone function at low temperatures and proteolytic activity at elevated temperatures. To investigate the mechanism of functional switch to pretense, we have determined the crystal structure of the N-terminal protease domain (PD) of HtrA from Thermotoga maritima. HtrA PD shares the same fold with chymotrypsin-like serine professes. However, crystal structure suggests that HtrA PD is not an active pretense at current state since its active site is not formed properly and blocked by an additional helical lid. On the surface of the lid, HtrA PD has hydrophobic patches that could be potential substrate binding sites for molecular chaperone activity. Present structure suggests that the activation of the proteolytic function of HtrA PD at elevated temperatures might occur by the conformational change.

• Molecules and Cells
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• 제38권2호
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• pp.105-111
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• 2015

The beta2-adrenergic receptor (${\beta}2AR$) belongs to the G protein coupled receptor (GPCR) family, which is the largest family of cell surface receptors in humans. Extra attention has been focused on the human GPCRs because they have been studied as important protein targets for pharmaceutical drug development. In fact, approximately 40% of marketed drugs directly work on GPCRs. GPCRs respond to various extracellular stimuli, such as sensory signals, neurotransmitters, chemokines, and hormones, to induce structural changes at the cytoplasmic surface, activating downstream signaling pathways, primarily through interactions with heterotrimeric G proteins or through G-protein independent pathways, such as arrestin. Most GPCRs, except for rhodhopsin, which contains covalently linked 11 cis-retinal, bind to diffusible ligands, having various conformational states between inactive and active structures. The first human GPCR structure was determined using an inverse agonist bound ${\beta}2AR$ in 2007 and since then, more than 20 distinct GPCR structures have been solved. However, most GPCR structures were solved as inactive forms, and an agonist bound fully active structure is still hard to obtain. In a structural point of view, ${\beta}2AR$ is relatively well studied since its fully active structure as a complex with G protein as well as several inactive structures are available. The structural comparison of inactive and active states gives an important clue in understanding the activation mechanism of ${\beta}2AR$. In this review, structural features of inactive and active states of ${\beta}2AR$, the interaction of ${\beta}2AR$ with heterotrimeric G protein, and the comparison with ${\beta}1AR$ will be discussed.

• 생명과학회지
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• 제18권4호
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• pp.585-589
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• 2008

Actin cytoskeleton rearrangement를 조절하는 cofilin은 인산기가 제거되면서 활성화되는데 이를 담당하는 효소가 chronophin이다. 이 효소는 비타민 $B_6$의 활성형태인 pyridoxal 5'-phosphate (PLP)의 세포 내 농도를 조절하는 PLP phosphatase로도 알려져 있다. Chronophin은 cap 도메인과 core 도메인을 갖는 HAD family에 속하는 phosphatase이며 다른 HAD phosphatase와 같이 기질결합을 위해 cap 도메인과 core 도메인 사이의 활성부위가 노출되는 열린 형태로의 전환이 있을 것으로 추정되었다. 이전의 밝혀진 chronophin/PLPP의 결정구조에서는 단백질의 결정화과정이 산화된 상태에 이루어졌기에 cap 도메인의 C91과 core 도메인의 C221 사이에 disulfide bond가 있었으며 이것이 cap 도메인과 core 도메인사이의 움직임을 막고 있었다. 본 연구에서는 환원된 상태의 chronophin의 결정체를 얻어 chronophin의 구조를 규명하였다. 환원된 상태의 chronophin의 구조에는 C91과 C221간의 disulfide 결합은 없었으나 산화된 상태와 동일한 닫힌 형태이었으며 국부적인 core 도메인의 움직임이외에는 core 도메인과 cap 도메인의 구조에는 변화가 없었다. 이는 chronophin이 기질이 없는 상태에서 닫힌 형태로 유지되는 것이 disulfide bond에 의한 것이 아님을 의미하며 세포 내의 환원된 상태에서도 닫힌 구조를 유지함으로서 높은 기질 특이성을 보여줄 것임을 암시한다.

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 1996년도 정기총회 및 학술발표회
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• pp.4-4
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• 1996

$\alpha$$_1$-arantitrypsin, a member of the serpin (serine protease inhibitor) family, undergoes a large structural rearrangement upon the cleavage and insertion of the reactive site loop. This conformational change is driven by the metastability of the native serpin structures and has an important role in the regulation of the inhibitory-serpin function. (omitted)

• Molecules and Cells
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• 제43권9호
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• pp.784-792
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• 2020

Arginine kinase (AK), a bioenergy-related enzyme, is distributed widely in invertebrates. The role of highly conserved histidines in AKs is still unascertained. In this study, the highly conserved histidine 284 (H284) in AK of Daphnia magna (DmAK) was replaced with alanine to elucidate the role of H284. We examined the alteration of catalytic activity and structural changes of H284A in DmAK. The catalytic activity of H284A was reduced dramatically compared to that in wild type (WT). Thus the crystal structure of H284A displayed several structural changes, including the alteration of D324, a hydrogen-bonding network around H284, and the disruption of π-stacking between the imidazole group of the H284 residue and the adenine ring of ATP. These findings suggest that such alterations might affect a conformational change of the specific loop consisting of G310-V322 at the antiparallel β-sheet region. Thus, we speculated that the H284 residue might play an important role in the conformational change of the specific loop when ATP binds to the substrate-binding site of DmAK.

• 한국결정성장학회지
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• 제15권2호
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• pp.86-91
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• 2005

층상 구조의 유기-무기 페로브스카이트 복합 소재 $(C_nH_{2n+1}NH_3)_2CuC1_4$ (n=6, 8, 10, 12)을 합성하였다. $(C_nH_{2n+1}NH_3)_2CuC1_4$ 화합물에서 긴 사슬의 양성자화된 알킬 암모늄 이온은 기울어진 이중층의 구조로 $CuCl_6$ 팔면체의 구석을 공유하고 있는 페로브스카이트형의 층들 사이에의 삽입되었다. 페로브스카이트 층상 화합물에서의 3개의 고체상을 HT-XRD와 DSC를 사용하여 조사하였다. $(C_nH_{2n+1}NH_3)_2CuC1_4$ 화합물은 단계적인 층간거리의 증가와 함께 고체-고체 상전이 현상을 보여준다 3개의 다른 구조는 긴 사슬의 양성자화된 알킬 암모늄 이온의 형태 변화로 설명하였다.

• 대한화학회지
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• 제38권4호
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• pp.283-287
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• 1994

비치오놀 설폭사이드, $C_{12}H_6Cl_4O_3S$의 결정구조를 흑연으로 단색화된 $Mo-K\alpha방사선을$ 이용하는 CAD-4 회절기를 사용하여 수집한 2295개의 독립된 회절반점을 이용하여 해석하였다. 결정계는 단사정계이며, 공간군은 P2$_1$/n이고, 격자상수는 a = 12.448(4), b = 9.740(1), c = $11.815(2)\AA$, $\beta$ = $100.06^{\circ}$, $\mu$ = 9.02 $cm^{-1}$, Dm = 1.76 g/$cm^3$, Dc = 1.75 g/$cm^3$, F(000) = 744, and Z = 4이다. 구조는 직접법으로 해석하였으며, 최소자승법으로 정밀화하여 최종 신뢰도 R=0.037인 모형을 구하였다. 분자의 전체적인 형태는 비치오놀의 경우와 비교하여 2개의 페닐링 중 한 개와 설폭사이드기를 축으로 삼아 대략 $180^{\circ}$ 정도로 회전하였음을 알 수 있었으며, 이와 같은 구조적인 변화는 S-O(3)---H-O(1)형의 분자내 수소결합의 존재와 설폭사이드기와 다른 페닐링간의 입체장에 현상 때문이다. 두 개의 페닐링은 평면구조를 나타내며, 두 평면간의 이면각은 $99.22^{\circ}$이다. 결정구조는 O(3)---H-O(2)형 분자간 수소결합에 의해 결합되어 있다.

• Journal of Photoscience
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• 제12권3호
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• pp.175-183
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• 2005

Plants dissipate excess excitation energy from their photosynthetic apparatus by a process called non-photochemical quenching (NPQ). The major part of NPQ is energy dependent quenching (qE) which is dependent on the thylakoid pH and regulated by xanthophyll cycle carotenoids associated with photosystem (PS) II of higher plants. The acidification of the lumen leads to protonation and thus conformational change of light harvesting complex (LHC) proteins as well as PsbS protein of PSII, which results in the induction of qE. Although physiological importance of qE has been well established, the mechanistic understanding is rather insufficient. However, recent finding of crystal structure of LHCII trimer and identification of qE mutants in higher plants and algae enrich and sharpen our understanding of this process. This review summarizes our current knowledge on the qE mechanism. The nature of quenching sites and components involved in this process, and their contribution and interaction for the generation of qE appeared in the proposed models for the qE mechanism are discussed.