Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8

Krieger, Elmar,Joo, Keehyoung,Lee, Jinwoo,Lee, Jooyoung,Raman, Srivatsan,Thompson, James,Tyka, Mike,Baker, David,Karplus, Kevin Wiley Subscription Services, Inc., A Wiley Company 2009 Proteins Vol.77 No.suppl9

<P>A correct alignment is an essential requirement in homology modeling. Yet in order to bridge the structural gap between template and target, which may not only involve loop rearrangements, but also shifts of secondary structure elements and repacking of core residues, high-resolution refinement methods with full atomic details are needed. Here, we describe four approaches that address this 'last mile of the protein folding problem' and have performed well during CASP8, yielding physically realistic models: YASARA, which runs molecular dynamics simulations of models in explicit solvent, using a new partly knowledge-based all atom force field derived from Amber, whose parameters have been optimized to minimize the damage done to protein crystal structures. The LEE-SERVER, which makes extensive use of conformational space annealing to create alignments, to help Modeller build physically realistic models while satisfying input restraints from templates and CHARMM stereochemistry, and to remodel the side-chains. ROSETTA, whose high resolution refinement protocol combines a physically realistic all atom force field with Monte Carlo minimization to allow the large conformational space to be sampled quickly. And finally UNDERTAKER, which creates a pool of candidate models from various templates and then optimizes them with an adaptive genetic algorithm, using a primarily empirical cost function that does not include bond angle, bond length, or other physics-like terms.</P>

Bimodal colloid gels of highly size-asymmetric particles.

Lee, Jooyoung,Lee, Seong Jae,Ahn, Kyung Hyun,Lee, Seung Jong Published by the American Physical Society through 2015 Physical review. E, Statistical, nonlinear, and so Vol.92 No.1

<P>We report a type of colloidal gel, induced by a minute incremental addition of mutually attractive small particles (size ???12 nm) to a suspension of highly charged large particles (size ???500 nm). The gel's morphological behavior does not follow the typical power-law scaling for fractal clusters. Its unique scaling behavior has two distinct power-law indices, based on particle volume fraction. We show the unique scaling behavior arises when nonfractal networks of large particles are bridged by small-particle clusters, which occurs between a lower and upper critical boundary of small particle volume fraction.</P>

한국 중세 서사시의 서사 구성 방식과 장르적 특질

이주영(Lee Jooyoung) 서강대학교 인문과학연구소 2012 서강인문논총 Vol.0 No.33

고려 중후기와 조선 초기의 서사시와 관련된 장르 논의는 아직 합의된 결론에 이르지 못했다. 특히 조선 초의 『용비어천가』는 서사시라 말해지기도 하고 악장(樂章)으로 분류되기도 한다. 서사시로의 규정 역시 에피소드식 구성으로 인해 교술시라는 주장이 있었다. 그럼에도 불구하고 본고에서 다룬 4편의 작품에 관해 논할 때 서사시적 성격을 언제나 언급하는 것도 사실이다. 따라서 이 글에서는 고려 중후기 이규보의 『동명왕편(東明王篇)』, 이승휴의 『제왕운기(帝王韻紀)』, 조선 초기의 『용비어천가(龍飛御天歌)』, 『월인천강지곡(月印千江之曲)』 4편의 작품을 서사시로 느끼게 하는 것이 무엇인지 살펴보는 데 초점을 맞추면서 동시에 서사시의 장르적 성격에 대해서도 살피려는 데 목적을 두었다. 그 결과 4편의 작품들은 모두 집단적 보편성을 가진 세계관을 갖고 있으면서도 서사 구성 방식에 있어서는 유기적인 플롯과 에피소드로 나누어짐을 확인했다. 이런 구성 방식은 차이는 주제의 보편성을 전제하는가, 보편성을 추구하는가의 차이에서 비롯된 것이었다. 보편성이 전제될 경우 유기적 플롯을 통해 주제를 집약해 강조하여 보여주는 형태를 가졌다. 반대로 보편성을 추구할 경우 그 주제를 폭넓은 사건을 통해 입증하려는 형태를 취했다. 하지만 그것은 시적 화자의 시점이 집단적 보편성 위에 기초하고 있다는 걸 말해준다. 나아가 보편적 세계관 아래 이 시적 화자의 시점은 독자의 시점, 그리고 제시된 사건인 객관적 상관물과도 동질성을 가진다. 그로 인해 시적 화자와 객관적 상관물 사이의 동질성 지향은 서정적 성격을, 시적 화자와 독자 시점의 동질성 지향은 교술적 성격을 갖게 했다. The genre discussion which relates with an epic poem of the middle and the latter period of the Goryeo and the early Joseon does not reach an agreed conclusion. Especially 『Yongbieocheon-ga(龍飛御天歌)』 of the early Joseon was called as epic poem and classified as Ak-Jang(樂章). There was assertion which is depiction poem by episode composition. Despite when discussing about Lee Gyu-Bo’s 『King Dongmyeong(東明王篇)』, Lee Sung-Hew’s 『Ghewangungi(帝王韻記)』, 『Yongbieocheon-ga(龍飛御天歌)』 and 『Wolinchonkangchikok(月印千江之曲)』 which it will treat from this dissertation to, the epic poem character is frequently referred. So, from this dissertation, it adjusts the focus the element which does to make these works feel with epic poem is what, simultaneously put a objective in even about genre character of epic poem. When it sees the result, 4 works had the view of the world which has all group universality, and the narrative composition method was coming to divide with organic composition and episode. This difference of composition method originated with difference which the universality of subject is prerequisite, or it pursues the universality of subject. The case where the universality is prerequisite had the form which emphasize a subject by integrating. In opposition, the case which pursue a universality had the form which proof the subject by various events. The fact show that a visual point of poetic speaker exists above group universality. Further from lower part of universal view of the world, this visual point of poetic speaker has homogeneity with the point of view of the reader and the objective correlatives-events which are presented. With the result, homogeneous intention of poetic speaker and objective correlatives make lyric character, homogeneous intention of poetic speaker and the point of view of the reader make character of depiction.

Enzyme free cell detachment using pH-responsive poly(amino ester) for tissue regeneration

Tae-Jin Lee,Tepeng Wu,Jung Hwan Park,Jihun Song,Gun-Jae Jeong,Jiyu Hyun,Jooyoung Lee,Soo-Hong Lee,Doo Sung Lee,Suk Ho Bhang 한국공업화학회 2020 Journal of Industrial and Engineering Chemistry Vol.88 No.-

Despite the advantages of stem cell injection to the skin wound site, this technique is limited in terms ofthe delivery of therapeutically functional stem cells to the wound site. Considering the abnormalmicroenvironment of a wound site, even a small damage or loss of cell function induced by severe trypsintreatment might lead to decrement of the therapeutic efficacy of stem cells. In this study, we havesynthesized pH-responsive polymer mixed poly(amino ester) (mPAE), which can provide the appropriatecell culture condition for cell growth without cytotoxicity along with the maintenance of extracellularmatrix after detachment using low pH (6.0) PBS. Human adipose derive stem cells (hADSCs) cultured onand detached from mPAE-coated tissue culture plates (TCPs) showed similar cell adhesion andangiogenic paracrine factor secretion, compared to hADSCs cultured on and detached from TCPs withtrypsin. As a result, hADSCs detached with pH 6.0 PBS from mPAE-coated TCPs showed similartherapeutic angiogenesis and wound regeneration, compared to the hADSCs detached with trypsin fromTCPs. In conclusion, our pH-responsive polymer, mPAE, might be utilized as an enzyme-free celldetachment system for future tissue engineering.

Rice WRKY11 Plays a Role in Pathogen Defense and Drought Tolerance

Lee, Heyoung,Cha, Jooyoung,Choi, Changhyun,Choi, Naeyoung,Ji, Hyun-So,Park, Sang Ryeol,Lee, Seungbum,Hwang, Duk-Ju Springer US 2018 Rice Vol.11 No.-

<P><B>Background</B></P><P>Plants are frequently subjected to abiotic and biotic stresses, and WRKY proteins play a pivotal role in the response to such stress. <I>Os</I>WRKY11 is induced by pathogens, drought, and heat, suggesting a function in biotic and abiotic stress responses.</P><P><B>Results</B></P><P>This study identified <I>Os</I>WRKY11, a member of WRKY group IIc. It is a transcriptional activator that localized to the nucleus. Ectopic expression of <I>OsWRKY11</I> resulted in enhanced resistance to a bacterial pathogen, <I>Xanthomonas oryzae</I> pv. <I>oryzae</I>; resistance was compromised in transgenic lines under-expressing <I>OsWRKY11</I>. Ectopic expression of <I>OsWRKY11</I> resulted in constitutive expression of defense-associated genes, whereas knock-down (kd) of <I>OsWRKY11</I> reduced expression of defense-associated genes during pathogen attack, suggesting that <I>OsWRKY11</I> activates defense responses. <I>Os</I>WRKY11 bound directly to the promoter of <I>CHITINASE 2</I>, a gene associated with defense, and activated its transcription. In addition, ectopic expression of <I>OsWRKY11</I> enhanced tolerance to drought stress and induced constitutive expression of drought-responsive genes. Induction of drought-responsive genes was compromised in <I>OsWRKY11-</I>kd plants. <I>Os</I>WRKY11 also bound directly to the promoter of a drought-responsive gene, <I>RAB21</I>, activating its transcription. In addition, <I>Os</I>WRKY11 protein levels were controlled by the ubiquitin-proteasome system.</P><P><B>Conclusion</B></P><P><I>Os</I>WRKY11 integrates plant responses to pathogens and abiotic stresses by positively modulating the expression of biotic and abiotic stress-related genes.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (10.1186/s12284-018-0199-0) contains supplementary material, which is available to authorized users.</P>

A new paradigm of materials processing—heterogeneity control

Lee, Jooyoung,Sung, Sanghoon,Kim, Youngseok,Park, Jun Dong,Ahn, Kyung Hyun Elsevier Science B.V.Amsterdam 2017 Current opinion in chemical engineering Vol.16 No.-

<P>In most emerging industries including batteries, solar cells, electronic components, printed electronics, the material processing can be understood based on a single platform – ‘transport phenomena of complex fluids’ – which has rarely been in the subject of academic research. This paper covers the complexity in these applications, which is strengthened by the use of nanoparticles. The key concept hidden underneath of this platform is heterogeneity which keeps on changing during processing, leading to a broad spectrum of microstructure and composition. Thus, we have to control heterogeneity for better design of materials and processing. Conventional approach is not enough, and we need a new paradigm in materials processing, which is the control of heterogeneity.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Heterogeneity always appears in materials processing. </LI> <LI> Microstructure constantly changes during the whole process. </LI> <LI> Same recipe never guarantees same product. </LI> <LI> Compositional distribution to the thickness direction during drying. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>

A study on the factors of successful Korean government R&D program

JooYoung Lee(이주영),Nagyeong An(안나경) 한국신재생에너지학회 2017 한국신재생에너지학회 학술대회논문집 Vol.2017 No.9

An efficient molecular docking using conformational space annealing

Lee, Kyoungrim,Czaplewski, Cezary,Kim, Seung-Yeon,Lee, Jooyoung John Wiley Sons, Inc. 2005 Journal of computational chemistry Vol.26 No.1

<P>Molecular docking falls into the general category of global optimization problems because its main purpose is to find the most stable complex consisting of a receptor and its ligand. Conformational space annealing (CSA), a powerful global optimization method, is incorporated with the Tinker molecular modeling package to perform molecular docking simulations of six receptor–ligand complexes (3PTB, 1ULB, 2CPP, 1STP, 3CPA, and 1PPH) from the Protein Data Bank. In parallel, Monte Carlo with the minimization (MCM) method is also incorporated into the Tinker package for comparison. The energy function, consisting of electrostatic interactions, van der Waals interactions, and torsional energy terms, is calculated using the AMBER94 all-atom empirical force field. Rigid docking simulations for all six complexes and flexible docking simulations for three complexes (1STP, 3CPA, and 1PPH) are carried out using the CSA and the MCM methods. The simulation results show that the docking procedures using the CSA method generally find the most stable complexes as well as the native-like complexes more efficiently and accurately than those using the MCM, demonstrating that CSA is a promising search method for molecular docking problems. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 78–87, 2005</P> <B>Graphic Abstract</B> <img src='wiley_img/01928651-2005-26-1-JCC20147-gra001.gif' alt='wiley_img/01928651-2005-26-1-JCC20147-gra001'>

Nanostructuring of metal surfaces by corrosion for efficient water splitting

Lee, Jooyoung,Lim, Guh-Hwan,Lim, Byungkwon Elsevier 2016 Chemical physics letters Vol.644 No.-

<P>We show that simply by corroding Ni foam in an aqueous solution, it is possible to produce nanostructured surfaces. When Ni foam was corroded in water or an aqueous solution containing NaCl, a dense array of Ni(OH)(2) nanosheets was produced on the surface of the foam. When corroded in the presence of RuCl3, the nanostructured surface composed of Ni(OH)(2) nanosheets decorated with ultrasmall RuO2 nanoparticles was obtained. At an applied voltage of 1.7 V, the combination of these two nanostructured surfaces yielded a water-splitting current density more than three times that obtained on the commercial Pt wire electrodes. (C) 2015 Elsevier B.V. All rights reserved.</P>

Folding Models of Mini-Protein FSD-1

Lee, In-Ho,Kim, Seung-Yeon,Lee, Jooyoung American Chemical Society 2012 The Journal of physical chemistry B Vol.116 No.23

<P>We have carried out all-atom action-derived molecular dynamics (ADMD) folding simulations of the full-size FSD-1. FSD-1 is a designed mini-protein of 28 residues containing both α and β secondary structure elements. Multiple folding pathways are found for FSD-1, which is consistent with existing computational studies. Hydrophobic collapse is observed first, and then subsequent folding events proceeds by forming either α-helix or β-hairpin. Concurrent formation of the full tertiary structure and the secondary structure elements of α-helix and β-hairpin is observed. The folding pathway of FSD-1 elucidated by ADMD simulations does not follow the scenario of the framework model. ADMD simulations provide significant insights for the general mechanisms of protein folding and conformational changes.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jpcbfk/2012/jpcbfk.2012.116.issue-23/jp300074f/production/images/medium/jp-2012-00074f_0010.gif'></P>