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Article ; Online: The Crystal Structure of L-Leucine Dehydrogenase from

Kim, Seheon / Koh, Seri / Kang, Wonchull / Yang, Jin Kuk

2022 Volume 45, Issue 7, Page(s) 495–501

Abstract: Leucine dehydrogenase (LDH, EC 1.4.1.9) catalyzes the reversible deamination of branched-chain L-amino acids to their corresponding keto acids using ... ...

Abstract	Leucine dehydrogenase (LDH, EC 1.4.1.9) catalyzes the reversible deamination of branched-chain L-amino acids to their corresponding keto acids using NAD
MeSH term(s)	Amino Acids ; Leucine Dehydrogenase/metabolism ; NAD/metabolism ; Pseudomonas aeruginosa ; Substrate Specificity
Chemical Substances	Amino Acids ; NAD (0U46U6E8UK) ; Leucine Dehydrogenase (EC 1.4.1.9)
Language	English
Publishing date	2022-06-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	1148964-9
ISSN	0219-1032 ; 1016-8478
ISSN (online)	0219-1032
ISSN	1016-8478
DOI	10.14348/molcells.2022.0012
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Article ; Online: Structural basis for recognition and methylation of p97 by METTL21D, a valosin-containing protein lysine methyltransferase.

Nguyen, Thang Quyet / Koh, Seri / Kwon, Jiin / Jang, Soyeon / Kang, Wonchull / Yang, Jin Kuk

iScience

2023 Volume 26, Issue 7, Page(s) 107222

Abstract: p97 is a human AAA+ (ATPase associated with diverse cellular activities, also known as valosin-containing protein [VCP]) ATPase, which is involved in diverse cellular processes such as membrane fusion and proteolysis. Lysine-specific methyltransferase of ...

Abstract	p97 is a human AAA+ (ATPase associated with diverse cellular activities, also known as valosin-containing protein [VCP]) ATPase, which is involved in diverse cellular processes such as membrane fusion and proteolysis. Lysine-specific methyltransferase of p97 (METTL21D) was identified as a class I methyltransferase that catalyzes the trimethylation of Lys315 of p97, a so-called VCP lysine methyltransferase (VCPKMT). Interestingly, VCPKMT disassembles a single hexamer ring consisting of p97-D1 domain and methylates Lys315 residue. Herein, the structures of S-adenosyl-L-methionine-bound VCPKMT and S-adenosyl-L-homocysteine-bound VCPKMT in complex with p97 N/D1 (N21-Q458) were reported at a resolution of 1.8 Å and 2.8 Å, respectively. The structures revealed the molecular details for the recognition and methylation of monomeric p97 by VCPKMT. Using biochemical analysis, we also investigated whether the methylation of full-length p97 could be sufficiently enhanced through cooperation between VCPKMT and the C terminus of alveolar soft part sarcoma locus (ASPL). Our study provides the groundwork for future structural and mechanistic studies of p97 and inhibitors.
Language	English
Publishing date	2023-06-26
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.107222
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Article ; Online: Structural basis for recognition and methylation of p97 by METTL21D, a valosin-containing protein lysine methyltransferase

Thang Quyet Nguyen / Seri Koh / Jiin Kwon / Soyeon Jang / Wonchull Kang / Jin Kuk Yang

iScience, Vol 26, Iss 7, Pp 107222- (2023)

2023

Abstract: Summary: p97 is a human AAA+ (ATPase associated with diverse cellular activities, also known as valosin-containing protein [VCP]) ATPase, which is involved in diverse cellular processes such as membrane fusion and proteolysis. Lysine-specific ... ...

Abstract	Summary: p97 is a human AAA+ (ATPase associated with diverse cellular activities, also known as valosin-containing protein [VCP]) ATPase, which is involved in diverse cellular processes such as membrane fusion and proteolysis. Lysine-specific methyltransferase of p97 (METTL21D) was identified as a class I methyltransferase that catalyzes the trimethylation of Lys315 of p97, a so-called VCP lysine methyltransferase (VCPKMT). Interestingly, VCPKMT disassembles a single hexamer ring consisting of p97-D1 domain and methylates Lys315 residue. Herein, the structures of S-adenosyl-L-methionine-bound VCPKMT and S-adenosyl-L-homocysteine-bound VCPKMT in complex with p97 N/D1 (N21-Q458) were reported at a resolution of 1.8 Å and 2.8 Å, respectively. The structures revealed the molecular details for the recognition and methylation of monomeric p97 by VCPKMT. Using biochemical analysis, we also investigated whether the methylation of full-length p97 could be sufficiently enhanced through cooperation between VCPKMT and the C terminus of alveolar soft part sarcoma locus (ASPL). Our study provides the groundwork for future structural and mechanistic studies of p97 and inhibitors.
Keywords	Biochemistry ; Molecular biology ; Structural biology ; Science ; Q
Subject code	570
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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Article ; Online: MEAM potential-based MD simulations of melting transition on Ni surfaces.

Jin, Hak-Son / Jong, Gwang-Byol / Ri, Kyong-Ho / Kim, Dong-Kuk / Yang, He

Journal of molecular modeling

2022 Volume 28, Issue 11, Page(s) 368

Abstract: Based on the modified embedded atom method (MEAM) potential suggested by Jin et al. (Appl. Phys ...

Abstract	Based on the modified embedded atom method (MEAM) potential suggested by Jin et al. (Appl. Phys. A120: 189, 2015), the molecular dynamics (MD) simulations were adopted to investigate the melting transition of the FCC transition metal Ni, and in the MD simulations, the forces acting on atoms were calculated by using the newly derived formulas. We first studied the melting points of Ni samples with low-index surfaces including Ni(100), Ni(110), and Ni(111). Then, we investigated the structural properties on the surface layers with increasing temperature up to the melting points. The simulation results exhibit that with the temperature increasing, the (110) surface firstly disorders, followed by the (100) surface, while the stability of the (111) surface is maintained until near the melting point. The disorder of surface layer atoms diffuses from the surface to the inside of the crystal lattice. With the density of atoms decreasing on the surface, the premelting effect also increases, being most pronounced on Ni(110) which corresponds to the lowest surface density. This conclusion is linked with the behavior found for the BCC transition metal Fe in our previous simulation study.
Language	English
Publishing date	2022-10-28
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-022-05357-8
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Article ; Online: MEAM potential–based MD simulations of melting transition on Ni surfaces

Jin, Hak-Son / Jong, Gwang-Byol / Ri, Kyong-Ho / Kim, Dong-Kuk / Yang, He

J Mol Model. 2022 Nov., v. 28, no. 11, p. 368

2022 , Page(s) 368

Abstract: Based on the modified embedded atom method (MEAM) potential suggested by Jin et al. (Appl. Phys ...

Abstract	Based on the modified embedded atom method (MEAM) potential suggested by Jin et al. (Appl. Phys. A120: 189, 2015), the molecular dynamics (MD) simulations were adopted to investigate the melting transition of the FCC transition metal Ni, and in the MD simulations, the forces acting on atoms were calculated by using the newly derived formulas. We first studied the melting points of Ni samples with low-index surfaces including Ni(100), Ni(110), and Ni(111). Then, we investigated the structural properties on the surface layers with increasing temperature up to the melting points. The simulation results exhibit that with the temperature increasing, the (110) surface firstly disorders, followed by the (100) surface, while the stability of the (111) surface is maintained until near the melting point. The disorder of surface layer atoms diffuses from the surface to the inside of the crystal lattice. With the density of atoms decreasing on the surface, the premelting effect also increases, being most pronounced on Ni(110) which corresponds to the lowest surface density. This conclusion is linked with the behavior found for the BCC transition metal Fe in our previous simulation study.
Keywords	models ; molecular dynamics ; temperature
Language	English
Dates of publication	2022-11
Size	p. 368
Publishing place	Springer Berlin Heidelberg
Document type	Article ; Online
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-022-05357-8
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Death effecter domain for the assembly of death-inducing signaling complex.

Yang, Jin Kuk

Apoptosis : an international journal on programmed cell death

2015 Volume 20, Issue 2, Page(s) 235–239

Abstract: Death-inducing signaling complex (DISC) is a platform for the activation of initiator caspase in extrinsic apoptosis. Assembly of DISC is accomplished by two different types of homotypic interaction: one is between death domains (DDs) of a death receptor ...

Abstract	Death-inducing signaling complex (DISC) is a platform for the activation of initiator caspase in extrinsic apoptosis. Assembly of DISC is accomplished by two different types of homotypic interaction: one is between death domains (DDs) of a death receptor and FADD, and the other is between death effecter domains (DEDs) of FADD, procaspase-8/-10 and cFLIP. Recent biochemical investigations on the stoichiometry of DISC have revealed that single-DED-containing FADD exists in DISC in a substantially lower abundance than the sum of tandem-DEDs-containing components that are procaspase-8 and cFLIP. In addition, the homology models of the tandem DEDs in procaspase-8 and cFLIP show that two different interaction faces, H1-H4 face and H2-H5 face, are exposed for possible inter-molecular DED-DED interactions. These recent findings led to a proposal of the DED chain model for the interactions between FADD, procaspase-8 and cFLIP in DISC. This emerging view provides new insights on the topology of DED-DED network in DISC and furthermore on how procaspase-8 and cFLIP cluster for dimerization and proteolytic activation.
MeSH term(s)	Animals ; Apoptosis ; Death Domain Receptor Signaling Adaptor Proteins/physiology ; Humans ; Inflammation/metabolism ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Signal Transduction
Chemical Substances	Death Domain Receptor Signaling Adaptor Proteins
Language	English
Publishing date	2015-02
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1452360-7
ISSN	1573-675X ; 1360-8185
ISSN (online)	1573-675X
ISSN	1360-8185
DOI	10.1007/s10495-014-1060-6
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Zs.A 5178: Show issues

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Article ; Online: Spatiotemporal informer: A new approach based on spatiotemporal embedding and attention for air quality forecasting.

Feng, Yang / Kim, Ju-Song / Yu, Jin-Won / Ri, Kuk-Chol / Yun, Song-Jun / Han, Il-Nam / Qi, Zhanfeng / Wang, Xiaoli

Environmental pollution (Barking, Essex : 1987)

2023 Volume 336, Page(s) 122402

Abstract: Accurate prediction of air pollution is essential for public health protection. Air quality, however, is difficult to predict due to the complex dynamics, and its accurate forecast still remains a challenge. This study suggests a spatiotemporal Informer ... ...

Abstract	Accurate prediction of air pollution is essential for public health protection. Air quality, however, is difficult to predict due to the complex dynamics, and its accurate forecast still remains a challenge. This study suggests a spatiotemporal Informer model, which uses a new spatiotemporal embedding and spatiotemporal attention, to improve AQI forecast accuracy. In the first phase of the proposed forecast mechanism, the input data is transformed by the spatiotemporal embedding. Next, the spatiotemporal attention is applied to extract spatiotemporal features from the embedded data. The final forecast is obtained based on the attention tensors. In the proposed forecast model, the input is a 3-dimensional data that consists of air quality data (AQI, PM
Language	English
Publishing date	2023-08-17
Publishing country	England
Document type	Journal Article
ZDB-ID	280652-6
ISSN	1873-6424 ; 0013-9327 ; 0269-7491
ISSN (online)	1873-6424
ISSN	0013-9327 ; 0269-7491
DOI	10.1016/j.envpol.2023.122402
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Article ; Online: RNA outperforms DNA-based metabarcoding in assessing the diversity and response of microeukaryotes to environmental variables in the Arctic Ocean.

Kong, Hejun / Yang, Eun-Jin / Jiao, Nianzhi / Lee, Youngju / Jung, Jinyoung / Cho, Kyoung-Ho / Moon, Jong-Kuk / Kim, Jee-Hoon / Xu, Dapeng

The Science of the total environment

2023 Volume 876, Page(s) 162608

Abstract: The Arctic Ocean (AO) has a harsh environment characterized by low temperatures, extensive ice coverage, and periodic freezing and melting of sea ice, which has provided diverse habitats for microorganisms. Prior studies primarily focused on ... ...

Abstract	The Arctic Ocean (AO) has a harsh environment characterized by low temperatures, extensive ice coverage, and periodic freezing and melting of sea ice, which has provided diverse habitats for microorganisms. Prior studies primarily focused on microeukaryote communities in the upper water or sea ice based on environmental DNA, leaving the composition of active microeukaryotes in the diverse AO environments largely unknown. This study provided a vertical assessment of microeukaryote communities in the AO from snow and ice to sea water at a depth of 1670 m using high-throughput sequencing of co-extracted DNA and RNA. RNA extracts depicted microeukaryote community structure and intergroup correlations more accurately and responded more sensitively to environmental conditions than those derived from DNA. Using RNA:DNA ratios as a proxy for relative activity of major taxonomic groups, the metabolic activities of major microeukaryote groups were determined along depth. Analysis of co-occurrence networks showed that parasitism between Syndiniales and dinoflagellates/ciliates in the deep ocean may be significant. This study increased our knowledge of the diversity of active microeukaryote communities and highlighted the importance of using RNA-based sequencing over DNA-based sequencing to examine the relationship between microeukaryote assemblages and the responses of microeukaryotes to environmental variables in the AO.
MeSH term(s)	RNA ; Ecosystem ; Seawater/chemistry ; DNA ; Dinoflagellida ; Oceans and Seas
Chemical Substances	RNA (63231-63-0) ; DNA (9007-49-2)
Language	English
Publishing date	2023-03-04
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2023.162608
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Article ; Online: Clinical and molecular predictors of mortality in patients with carbapenem-resistant Acinetobacter baumannii bacteremia: A retrospective cohort study.

Suh, Jin Woong / Park, Seung Min / Ju, Yong Kuk / Yang, Kyung Sook / Kim, Jeong Yeon / Kim, Sun Bean / Sohn, Jang Wook / Yoon, Young Kyung

Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi

2023 Volume 57, Issue 1, Page(s) 148–155

Abstract: Background/purpose: To investigate the virulence profiles and identify clinical and microbiological predictors of mortality in patients with carbapenem-resistant Acinetobacter baumannii (A. baumannii) bacteremia.: Methods: This retrospective cohort ... ...

Abstract	Background/purpose: To investigate the virulence profiles and identify clinical and microbiological predictors of mortality in patients with carbapenem-resistant Acinetobacter baumannii (A. baumannii) bacteremia. Methods: This retrospective cohort study enrolled adult patients with carbapenem-resistant A. baumannii (CRAB). Multivariate logistic regression was used to identify the predictors of 30-day mortality. All isolates were subjected to real-time polymerase chain reaction for virulence factors and genotyped using multilocus sequence typing. Results: Among the 153 patients with CRAB bacteremia, 66 % received appropriate definitive antibiotic therapy. The in-hospital and 30-day mortality rates were 58.3 and 23.5 %, respectively. Ultimately, we enrolled 125 patients with CRAB bacteremia in the analysis, excluding early mortality cases. All CRAB isolates carried bla Conclusions: Clinical factors such as hemodialysis due to acute renal injury and moderate to severe thrombocytopenia have a greater influence on mortality in CRAB bacteremia compared with microbiological factors.
MeSH term(s)	Adult ; Humans ; Carbapenems/pharmacology ; Carbapenems/therapeutic use ; Acinetobacter baumannii ; Retrospective Studies ; beta-Lactamases/genetics ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Bacteremia/microbiology ; Virulence Factors ; Thrombocytopenia
Chemical Substances	Carbapenems ; beta-Lactamases (EC 3.5.2.6) ; Anti-Bacterial Agents ; Virulence Factors
Language	English
Publishing date	2023-11-28
Publishing country	England
Document type	Journal Article
ZDB-ID	1497590-7
ISSN	1995-9133 ; 1684-1182 ; 0253-2662
ISSN (online)	1995-9133
ISSN	1684-1182 ; 0253-2662
DOI	10.1016/j.jmii.2023.11.001
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Article ; Online: Light-induced protein structural dynamics in bacteriophytochrome revealed by time-resolved x-ray solution scattering.

Lee, Sang Jin / Kim, Tae Wu / Kim, Jong Goo / Yang, Cheolhee / Yun, So Ri / Kim, Changin / Ren, Zhong / Kumarapperuma, Indika / Kuk, Jane / Moffat, Keith / Yang, Xiaojing / Ihee, Hyotcherl

Science advances

2022 Volume 8, Issue 21, Page(s) eabm6278

Abstract: Bacteriophytochromes (BphPs) are photoreceptors that regulate a wide range of biological mechanisms via red light-absorbing (Pr)-to-far-red light-absorbing (Pfr) reversible photoconversion. The structural dynamics underlying Pfr-to-Pr photoconversion in ... ...

Abstract	Bacteriophytochromes (BphPs) are photoreceptors that regulate a wide range of biological mechanisms via red light-absorbing (Pr)-to-far-red light-absorbing (Pfr) reversible photoconversion. The structural dynamics underlying Pfr-to-Pr photoconversion in a liquid solution phase are not well understood. We used time-resolved x-ray solution scattering (TRXSS) to capture light-induced structural transitions in the bathy BphP photosensory module of
Language	English
Publishing date	2022-05-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.abm6278
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