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.

Dynamic folding pathway models of the villin headpiece subdomain (HP-36) structure

Lee, In-Ho,Kim, Seung-Yeon,Lee, Jooyoung Wiley Subscription Services, Inc., A Wiley Company 2010 Journal of computational chemistry Vol.31 No.1

<P>We have investigated the folding pathway of the 36-residue villin headpiece subdomain (HP-36) by action-derived molecular dynamics simulations. The folding is initiated by hydrophobic collapse, after which the concurrent formation of full tertiary structure and α-helical secondary structure is observed. The collapse is observed to be associated with a couple of specific native contacts contrary to the conventional nonspecific hydrophobic collapse model. Stable secondary structure formation after the collapse suggests that the folding of HP-36 follows neither the framework model nor the diffusion-collision model. The C-terminal helix forms first, followed by the N-terminal helix positioned in its native orientation. The short middle helix is shown to form last. Signs for multiple folding pathways are also observed. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010</P> <B>Graphic Abstract</B> <P> <img src='wiley_img/01928651-2010-31-1-JCC21288-gra001.gif' alt='wiley_img/01928651-2010-31-1-JCC21288-gra001'> </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>

The Atomistic Mechanism of Conformational Transition of Adenylate Kinase Investigated by Lorentzian Structure-Based Potential

Lee, Juyong,Joo, Keehyoung,Brooks, Bernard R.,Lee, Jooyoung American Chemical Society 2015 Journal of chemical theory and computation Vol.11 No.7

<P>We present a new all-atom structure-based method to study protein conformational transitions using Lorentzian attractive interactions based on native structures. The variability of each native contact is estimated based on evolutionary information using a machine learning method. To test the validity of this approach, we have investigated the conformational transition of adenylate kinase (ADK). The intrinsic boundedness of the Lorentzian attractive interactions facilitated frequent conformational transitions, and consequently we were able to observe more than 1000 structural interconversions between the open and closed states of ADK out of a total of 6 μs MD simulations. ADK has three domains: the nucleoside monophosphate (NMP) binding domain, the LID-domain, and the CORE domain, which catalyze the interconversion between ATP and ADP. We identified two transition states: a more frequent LID-closed-NMP-open (TS1) state and a less frequent LID-open-NMP-closed (TS2) state. The transition was found to be symmetric in both directions via TS1. We also obtained an off-pathway metastable state that was previously observed with physics-based all-atom simulations but not with coarse-grained models. In the metastable state, the LID domain was slightly twisted and formed contacts with the NMP domain. Our model correctly identified a total of 14 out of the top 16 residues with highest fluctuation by NMR experiment, thus showing excellent agreement with experimental NMR relaxation data and overwhelmingly better results than existing models.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jctcce/2015/jctcce.2015.11.issue-7/acs.jctc.5b00268/production/images/medium/ct-2015-002683_0011.gif'></P>

Security of permutation-based compression function

Lee, Jooyoung,Kwon, Daesung Elsevier 2014 Information processing letters Vol.114 No.7

Collision Resistance of the JH Hash Function

Jooyoung Lee,Deukjo Hong IEEE 2012 IEEE transactions on information theory Vol.58 No.3

<P>In this paper, we analyze collision resistance of the JH hash function in the ideal primitive model. The JH hash function is one of the five SHA-3 candidates accepted for the final round of evaluation. The JH hash function uses a mode of operation based on a permutation, while its security has been elusive even in the random permutation model. One can find a collision for the JH compression function only with two backward queries to the basing primitive. However, the security is significantly enhanced in iteration. For c≤ n/2, we prove that the JH hash function using an ideal -bit permutation and producing -bit outputs by truncation is collision resistant up to O(2<SUP>c/2</SUP>)queries. This bound implies the optimal collision resistance of the JH hash function in the random permutation model.</P>

Balloon Expulsion Test Does Not Seem to Be Useful for Screening or Exclusion of Dyssynergic Defecation as a Single Test

( Jooyoung Lee ),( Kyoung Sup Hong ),( Joo Sung Kim ),( Hyun Chae Jung ) 대한소화기기능성질환·운동학회(구 대한소화관운동학회) 2017 Journal of Neurogastroenterology and Motility (JNM Vol.23 No.3

Background/Aims Balloon expulsion test (BET) is regarded as a screening tool of dyssynergic defecation (DD). However, some patients with normal BET results may be treated effectively by biofeedback training. This study aims to validate BET as a single screening test. Methods Two hundred and thirty-two patients who were diagnosed with functional constipation or irritable bowel syndrome with constipation who underwent anorectal manometry (ARM) and BET at Seoul National University Hospital were enrolled. We evaluated the validity of BET based on ARM and electromyography (EMG) during biofeedback training. Results If BET ≤ 1 minute was defined as normal, sensitivity and negative predictive value (NPV) of BET in predicting paradoxical contraction based on ARM findings were 71.4% and 13.9%. If BET ≤ 3 minutes was defined as normal, sensitivity and NPV were 35.2% and 6.6%. Specificity and positive predictive value (PPV) of BET ≤ 3 minutes criteria were 84.8% and 93.3%. Same analysis was conducted in 107 patients who underwent EMG during biofeedback training. With 1-minute criteria, sensitivity and NPV of BET were 70.3% and 14.3%. With 3 minutes criteria, sensitivity and NPV of BET was 38.6% and 8.8%. Specificity and positive predictive values were both 100.0%. Conclusions Based on either ARM or EMG during biofeedback training, sensitivity was at most 71.4% and NPV was less than 15.0% irrespective of whether BET was within 1minute or within 3 minutes. BET seems to have a limitation as both a screening test for dyssynergic defecation and a simple assessment to rule out the necessity of biofeedback training. (J Neurogastroenterol Motil 2017;23:446-452)