Computational Studies on the Effect of the Transmembrane Alky1 Chains on the Structure and Dynamics of Membrane

Jung, Seunho 건국대학교 산업기술연구원 1995 건국기술연구논문지 Vol.20 No.-

최근에 발견된 막 횡단(ω-1 위치에서 연결된 탄소사슬구조) 지방질의 분자 운동적 효과를 조사하기 위해서, 긴 사슬 지방산과 지방질로 세포막의 분자 모델을 구축하고, 분자 역학과 분자동력학적인 방법을 이용하였다. 분자 운동을 기술하기 위한 변수로 분자들간의 평균거리 요동 값과 평균각도 요동 값을 사용하였다. 전형적인 이중막 모델의 경우와 막횡단 지방질의 경우는 10피코 초의 동력학적 모의 실험을 통해 조사하였다. 전형적인 이중 막이 양극성인 막 횡단 단일 막화되었을 때, 분자운동의 자유도에 있어서 극적인 감소 효과가 관찰되었다. 특히 단일막화 되면서 지방질 상호간의 겹침(Interdigitation)이 심화되어, 긴 사슬 상호간의 반데 왈스(van der Waals) 결합이 강화되어 전체 세포막의 안전성이 부여되는 사실을 관찰할 수가 있었다. 막 횡단 지방질을 포함하고 있는 세포막의 형태상의 변화를 조사해 보기 위해 컴퓨터 모의실험(Simulated annealing method)을 한 결과, 세포막의 강한 응집이 지방질내(Intra-)에서와 지방질 상호간의 겹침(Interdigitation)으로 기인됨을 발견할 수 있었다. 이와 같은 연구는 최근에 발견된 자극유도성 막 횡단 단일 세포막에 관한 일련의 발견들 및 응용성과 연관하여 특별한 중요성을 보인다고 할 수 있다. The effect of transmembrance (ω-1 linked hydrocarbon chains) on the molecular motions of model systems from the free hydrocarbon chains to whole membrane model (64 lipids) were studied using molecular mechanics and molecular dynamics simulation methods. RMS (Root Mean Square) distance fluctation and angle parmeters were used for the indices for the description and characterization of the molecular motions. The molecular motional parameters of the lipid in the typical bilayer form and monolayer form (ω-1 linked) were compared during a 10ps dynamic simulation. A dramatic decrease in the degree of the motional freedom was observed on going from the bilayer to the bipolar monolayer form. this change of the motional dynamics appears to induce the favorable interdigitation of the tails of the chains thus enhancing van der Waals attraction. Simulated annealing method was used for the general prediction of the membrane structures before and after the transition from the bilayer to monolayer systems. After the transition to the monolayer form, the interdigitation of the acyl chains of the membrane resulted in compaction of the membrane structure. These findings have special significance in light of recent discovery of the structural transition from the bilayer to bipolar monolayer in a strict anaerobic facultative eubacteria, Sarcina ventriculi and a strict anaerobic thermophile, Thermoanaerobacter ethanolicus. Computer simulation/Transmembrane fatty acids/Membrane/Simulated Annealing.

Mutant Recombinant Hemoglobin (α96Val→Tyr) Exhibits Low Oxygen Affinity and High Cooperativity

Kim, Hyun-Won,Choi, Jong-Whan,Yeh, Byung-Il,Han, Dong-Pyou,Lee, Hyean-Woo,Sohn, Joon Hyung,Jung, Seunho The Korea Science and Technology Center 1998 BMB Reports Vol.31 No.6

To investigate conformational information of a low oxygen affinity recombinant hemoglobin (rHb) containing 96Val->Trp mutation at the α96 position, we have produced rHb (α96vAL->Phe) and rHb (α96vAL->Tyr), using the Escherichia coli expression system and site-directed mutagenesis. The oxygen affinity of rHb (α96Val->Phe) is similar to that of human normal adult hemoglobin (Hb A). However, the oxygen affinity of rHb (α96Val->Tyr) showed much lower oxygen affinity than Hb A which is similar to that of rHb (α96Val->Trp), providing an opportunity as a potential candidate for a hemoglobin-based blood substitute. Both rHb (α96Val->Phe) and rHb (α96Val->Tyr) showed high cooperativity in oxygen binding. ¹H-NMR spectroscopy shows that both rHb (α96Val->Phe) and rHb (α96Val->Tyr) have very similar tertiary structure around the heme pockets and quaternary structure in the α₁β₁subunit interface compared to Hb A. The low oxygen affinity of rHb (α96Val->Tyr) has been suggested to be due to a hydrogen bond caused by an extra hydroxyl group and not present in rHb (α96Val->Phe). However, investigation of the carbonmonoxy form of rHb (α96Val->Phe) and (α96Val->Tyr) in the presence of inositol hexaphosphate at low temperature suggests that low oxygen affinity of (α96Val->Tyr) may arise from a mechanism different to that of rHb (α96Val->Trp).

Functional Defects of Hb Kempsey (β99Asp→Asn) Can be Compensated by Insertion of a New Intersubunit Hydrogen Bond at the α₁β₂Subunit Interface

Kim, Hyun-Won,Yeh, Byung-Il,Choi, Jong-Whan,Sohn, Joon Hyung,Lee, Hyean-Woo,Han, Dong-Pyou,Jung, Seunho The Korea Science and Technology Center 1998 BMB Reports Vol.31 No.6

X-ray crystallograhic studies of the deoxy form of human adult hemoglobin (Hb A) have shown that β99Asp is hydrogen bonded to both α42Tyr and α97Asn in the α₁β₂subunit interface, suggesting that the essential role of β99Asp is to stabilize the deoxy-Hb by creating the intersubunit hydrogen bond. In particular, for Hb Kempsy (β99Asp->Asn), molecular dynamics simulation indicated that a new hydrogen bond involving β99Asn can be induced by replacing α42Tyr with a strong hydrogen-bond acceptor such as Asp. Designed mutant recombinant (r) Hb (β99Asp->Asn, α42Tyr->Asp) have been produced in the Escherichia coli expression system and have shown that functional defects of Hb Kempsey could be compensated by the α42Tyr-> Asp substitution. However, as the α42Tyr->Asp mutation has never been reported before, it is still possible that the functional properties of r Hb (β99Asp->Asn, α42Tyr->Asp) may be due to the mutation itself. Thus, it s required to produce r Hb (α42Tyr->Asp) and r Hb Kempsey(β99Asp->Asn) as controls, and to compare their properties with those of r Hb (β99Asp->Asn, α42Tyr->Asp). r Hb (α42Tyr->Asp) could not be purified because it is an unstable hemoglobin which forms Heinz bodies. r Hb KempseyZ(β99Asp->Asn) exhibits very high oxygen affinity and greatly reduced cooperativity. Thus, r Hb (β99Asp->Asn) and r Hb (α42Tyr-> Asp) compensate each other.

Binding Geometry of Inclusion Complex as a Determinant Factor for Aqueous Solubility of the Flavonoid/β-Cyclodextrin Complexes Based on Molecular Dynamics Simulations

Seunho Jung,Jonghyun Lee,Kum Won Cho,Suntae Hwang,Karpjoo Jeong,Youngjin Choi 대한화학회 2005 Bulletin of the Korean Chemical Society Vol.26 No.8

A computational study based on molecular dynamics (MD) simulations was performed in order to explain the difference in aqueous solubilities of two flavonoid/-cyclodextrin (-CD) complexes, hesperetin/-CD and naringenin/-CD. The aqueous solubility of each flavonoid/-CD complex could be characterized by complex-water interaction not by flavonoid-CD interaction. The radial distribution of water around each inclusion complex elucidated the difference of an experimentally observed solubility of each flavonoid/-CD complex. The analyzed results suggested that a bulky hydrophobic moiety (-OCH3) of B-ring of hesperetin nearby primary rim of -CD was responsible for lower aqueous solubility of the hesperetin/-CD complex.

메리필드(Merrifield RB.)와 파우너(Powner M.)의 펩타이드 화학합성연구에 대한 현대 과학적 발견들이 시사하는 펩타이드 및 단백질의 비생물속생설 비판

정선호(Seunho Jung) 한국창조과학회 2021 Origin Research Journal Vol.1 No.1

1861년 루이 파스퇴르 (Louis Pasteur)의 백조목 플라스크 실험은 생물의 기원에 대한 자연발생 이론을 반박하고 생물은 생물에서만 그 기원을 설명 할 수 있다는 생물속생설 (biogenesis)을 제안했다. 그후 러시아 생화학자인 오파린 (Alexander Ivanovich Oparin)은 1924년에 원시 지구 생명체의 기원에 대한 화학진화가설을 제안하게 되었다. 이 제안은 1952년에 유레이와 밀러(Urey & Miller)의 실험결과에 기반한 프리바이오틱 화학(prebiotic chemistry)연구를 통해서 보다 다양한 생물의 기원에 대한 실험결과들을 이끌어 낼 수 있었다. 본 소고에서는 최근에 메리필드(Merrifield B.)와 파우너(Powner M.)가 Science 지와 Nature 지등에 각각 발표한 펩타이드의 화학합성 메커니즘과 관련된 연구결과와 과학적 발견들을 고찰하고 해석하였다. 그들의 연구결과들은 펩타이드와 단백질의 기원이 생물의 비생물속생설(abiogenesis)에 근거한 비생체내발생을 의미하는 자연발생이론으로는 설명이 불가능하여, 아직까지도 펩타이드와 단백질의 기원은 파스퇴르의 생물속생설(biogenesis) 이론에 따른 생체내발생을 통해서만 설명이 유효함을 시사하고 있음을 나타낸다. In 1861, Louis Pasteur"s swan-neck flask experiment refuted the spontaneous theory of the origin of life and proposed the theory of biogenesis, which states that living things (life) can only explain their origins. Then, in 1924, Russian biochemist Alexander Ivanovich Oparin proposed the chemical evolutionary hypothesis on the origin of life under the primitive Earth. This proposal could lead to more diverse research results on prebiotic chemistry through the experiments of Urey and Miller in 1952. Here, we provide insight and interpretation of research results and scientific findings related to the chemical synthetic mechanism of peptides recently published by Merrifield RB. and Powner M. in Science and Nature journals. Their research results suggested that the origin of peptides and proteins cannot be explained by abiogenesis, the theory of spontaneous generation of organisms, and that the validity of the Pasteur"s theory of biogenesis still holds true.

다윈학설 vs 설계추론

정선호(Seunho Jung) 한국창조과학회 2024 Origin Research Journal Vol.4 No.1

진화론은 1859년 11월 다윈이 생물의 형태, 질서, 다양성이 자연선택이라는 목적 없는 무작위 과정의 우연한 산물이라는 이론을 담은 책인 ‘종의 기원’을 출판하면서 확립되었다. 이후 다윈의 진화론은 목적론적 세계관의 종말을 가져왔고, 유물론적 세계관을 통한 다윈주의 자연관은 모든 과학계의 주류가 되었다. 그러나 1953년 4월에 발표된 900단어 네이처 논문인 ‘DNA의 분자 구조’에 대한 연구 결과1), DNA는 생명체의 유전정보의 저장소이며 화학적 염기서열을 통해 디지털 정보로 변환된다는 사실이 보고되었다. 1980년대 이후 분자생물학 연구를 통해 세포는 DNA를 유전정보로 담고 있을 뿐만 아니라, 세포 내에는 복잡하고 정교한 유전정보 처리시스템을 갖고 있다는 사실이 밝혀졌다. 다윈의 진화론과 설계 추론에 대한 역사과학적 고찰을 통해 생명정보의 기원은 물질우선(matter-first) 철학의 유물론적 세계관이 아닌 설계지성에 기초한 정신우선(mind-first) 철학적 세계관을 지지하는 것으로 나타났다. The theory of evolution was established in November 1859 when Darwin published ‘The Origin of Species’, a book containing the theory that the form, order, and diversity of living things are the accidental products of a purposeless random process called natural selection. Afterwards, Darwin’s theory of evolution brought about the end of the teleological worldview, and Darwin’s view of nature through a materialistic worldview became the mainstream of all scientific circles. However, as a result of research on ‘Molecular Structure of DNA’, a 900-word Nature paper published in April 1953, it was reported that DNA is a repository of genetic information of living things and is converted into digital information through chemical base sequences. Since the 1980s, molecular biology research has revealed that cells not only contain DNA as genetic information, but also have a complex and sophisticated genetic information processing system within the cell. Through historical and scientific examination of Darwin’s theory of evolution and design reasoning, the origin of life information was found to support a mind-first philosophical worldview based on design intelligence rather than a materialistic worldview of material-first philosophy.

The Putative Guanine Nucleotide Exchange Factor RicA Mediates Upstream Signaling for Growth and Development in Aspergillus

Kwon, Nak-Jung,Park, Hee-Soo,Jung, Seunho,Kim, Sun Chang,Yu, Jae-Hyuk American Society for Microbiology 2012 EUKARYOTIC CELL Vol.11 No.11

<B>ABSTRACT</B><P> Heterotrimeric G proteins (G proteins) govern growth, development, and secondary metabolism in various fungi. Here, we characterized <I>ricA</I> , which encodes a putative GDP/GTP exchange factor for G proteins in the model fungus Aspergillus nidulans and the opportunistic human pathogen Aspergillus fumigatus . In both species, <I>ricA</I> mRNA accumulates during vegetative growth and early developmental phases, but it is not present in spores. The deletion of <I>ricA</I> results in severely impaired colony growth and the total (for A. nidulans ) or near (for A. fumigatus ) absence of asexual sporulation (conidiation). The overexpression (OE) of the <I>A. fumigatus ricA</I> gene (Af <I>ricA</I> ) restores growth and conidiation in the ΔAn <I>ricA</I> mutant to some extent, indicating partial conservation of RicA function in Aspergillus . A series of double mutant analyses revealed that the removal of RgsA (an RGS protein of the GanB Gα subunit), but not <I>sfgA</I> , <I>flbA</I> , <I>rgsB</I> , or <I>rgsC</I> , restored vegetative growth and conidiation in ΔAn <I>ricA</I> . Furthermore, we found that RicA can physically interact with GanB in yeast and <I>in vitro</I> . Moreover, the presence of two copies or OE of <I>pkaA</I> suppresses the profound defects caused by ΔAn <I>ricA</I> , indicating that RicA-mediated growth and developmental signaling is primarily through GanB and PkaA in A. nidulans . Despite the lack of conidiation, <I>brlA</I> and <I>vosA</I> mRNAs accumulated to normal levels in the Δ <I>ricA</I> mutant. In addition, mutants overexpressing <I>fluG</I> or <I>brlA</I> (OE <I>fluG</I> or OE <I>brlA</I> ) failed to restore development in the ΔAn <I>ricA</I> mutant. These findings suggest that the commencement of asexual development requires unknown RicA-mediated signaling input in A. nidulans . </P>

Dye-sensitized solar cells with silica-coated quantum dot-embedded nanoparticles used as a light-harvesting layer

Rho, Won-Yeop,Choi, Jung-Woo,Lee, Hea-Yeon,Kyeong, San,Lee, Sang Hun,Jung, Heung Su,Jung, Seunho,Sung, Yung-Eun,Lee, Yoon-Sik,Jun, Bong-Hyun The Royal Society of Chemistry 2014 NEW JOURNAL OF CHEMISTRY Vol.38 No.3

<P>A dye-sensitized solar cell (DSSC) was fabricated using silica-coated quantum dot-embedded silica nanoparticles (SiO<SUB>2</SUB>/QD/SiO<SUB>2</SUB> NPs) as a light-harvesting layer. Compared to an unmodified DSSC, the power conversion efficiency of a DSSC with SiO<SUB>2</SUB>/QD/SiO<SUB>2</SUB> NPs (SiO<SUB>2</SUB>/QD/SiO<SUB>2</SUB> DSSC) increased from 3.92% to 4.82%, an enhancement of approximately 23.0%.</P> <P>Graphic Abstract</P><P>A dye-sensitized solar cell (DSSC) was fabricated using silica-coated quantum dot-embedded silica nanoparticles as a light-harvesting layer. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c3nj01345f'> </P>

Preparation of Amino-cyclosophoraoses from the Neutral Cyclosophoraoses Isolated fromRhizobium leguminosarum bv. trifolii

박혜린,Seunho Jung* 대한화학회 2006 Bulletin of the Korean Chemical Society Vol.27 No.9

Study of Rhizobial Succinoglycan/poly(N-isopropylacrylamide)-based Hydrogel for Temperature/pH-responsive Drug Delivery System

Yiluo HU,Seunho JUNG 한국생물공학회 2022 한국생물공학회 학술대회 Vol.2022 No.9