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Kim M, Oh Y, Lee D, Casey V, Kim J. PCN81 The Role of Different Specialties in the Management of NON-SMALL CELL LUNG Cancer: Insights from a Real-World Study. Value Health Reg Issues 2020. [DOI: 10.1016/j.vhri.2020.07.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Kwon B, Mandal T, Elkins MR, Oh Y, Cui Q, Hong M. Cholesterol Interaction with the Trimeric HIV Fusion Protein gp41 in Lipid Bilayers Investigated by Solid-State NMR Spectroscopy and Molecular Dynamics Simulations. J Mol Biol 2020; 432:4705-4721. [PMID: 32592698 PMCID: PMC7781112 DOI: 10.1016/j.jmb.2020.06.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/07/2020] [Accepted: 06/18/2020] [Indexed: 12/13/2022]
Abstract
HIV-1 entry into cells is mediated by the fusion protein gp41. Cholesterol plays an important role in this virus-cell fusion, but molecular structural information about cholesterol-gp41 interaction is so far absent. Here, we present experimental and computational data about cholesterol complexation with gp41 in lipid bilayers. We focus on the C-terminal region of the protein, which comprises a membrane-proximal external region (MPER) and the transmembrane domain (TMD). We measured peptide-cholesterol contacts in virus-mimetic lipid bilayers using solid-state NMR spectroscopy, and augmented these experimental data with all-atom molecular dynamics simulations. 2D 19F NMR spectra show correlation peaks between MPER residues and the cholesterol isooctyl tail, indicating that cholesterol is in molecular contact with the MPER-TMD trimer. 19F-13C distance measurements between the peptide and 13C-labeled cholesterol show that C17 on the D ring and C9 at the intersection of B and C rings are ~7.0 Å from the F673 side-chain 4-19F. At high peptide concentrations in the membrane, the 19F-13C distance data indicate three cholesterol molecules bound near F673 in each trimer. Mutation of a cholesterol recognition amino acid consensus motif did not change these distances, indicating that cholesterol binding does not require this sequence motif. Molecular dynamics simulations further identify two hotspots for cholesterol interactions. Taken together, these experimental data and simulations indicate that the helix-turn-helix conformation of the MPER-TMD is responsible for sequestering cholesterol. We propose that this gp41-cholesterol interaction mediates virus-cell fusion by recruiting gp41 to the boundary of the liquid-disordered and liquid-ordered phases to incur membrane curvature.
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Feng Z, Wang H, Wang F, Oh Y, Berciu C, Cui Q, Egelman EH, Xu B. Artificial Intracellular Filaments. CELL REPORTS. PHYSICAL SCIENCE 2020; 1:100085. [PMID: 32776017 PMCID: PMC7413147 DOI: 10.1016/j.xcrp.2020.100085] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Intracellular protein filaments are ubiquitous for cellular functions, but forming bona fide biomimetic intracellular filaments of small molecules in living cells remains elusive. Here, we report the in situ formation of self-limiting intracellular filaments of a small peptide via enzymatic morphological transition of a phosphorylated and trimethylated heterochiral tetrapeptide. Enzymatic dephosphorylation reduces repulsive intermolecular electrostatic interactions and converts the peptidic nanoparticles into filaments, which exhibit distinct types of cross-β structures with either C7 or C2 symmetries, with the hydrophilic C-terminal residues at the periphery of the helix. Macromolecular crowding promotes the peptide filaments to form bundles, which extend from the plasma membrane to nuclear membrane and hardly interact with endogenous components, including cytoskeletons. Stereochemistry and post-translational modification (PTM) of peptides are critical for generating the intracellular bundles. This work may offer a way to gain lost functions or to provide molecular insights for understanding normal and aberrant intracellular filaments.
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Jo KI, Oh Y, Sung BJ, Kim TH, Um MS, Choi WJ, Bang J, Yuan G, Satija SK, Koo J. Enhanced Dynamics of Confined Polymers near the Immiscible Polymer-Polymer Interface: Neutron Reflectivity Studies. ACS Macro Lett 2020; 9:210-215. [PMID: 35638684 DOI: 10.1021/acsmacrolett.9b01011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
For polymer-blend films, local dynamics in confined polymer domains tend to differ from the bulk because of significant contributions from the polymer-polymer interface. Herein, we investigated the diffusion dynamics of entangled polymer thin films confined between different polymers in a direction perpendicular to the surface using neutron reflectivity. We found that a bilayer of poly(methyl methacrylate) (PMMA) and deuterated PMMA (dPMMA) sandwiched between polystyrene (PS) layers exhibited significant increase in mobility near the polymer-polymer interface with decreasing PMMA thickness. This indicates that the contribution of repulsive interactions at the immiscible polymer-polymer interface becomes more significant as the film thickness decreases. We also found that the interfacial roughness between PMMA and PS (28 Å at equilibrium) and soft confinement of PS layers did not significantly affect the change in the diffusion dynamics of the adjacent PMMA. This was evidenced by comparison with the diffusion results of multilayers with a flat interface (8 Å at equilibrium) between PMMA and hard PS by UV cross-linking.
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Jung J, Kwon T, Oh Y, Lee YR, Sung BJ. Spatial Dependence of Non-Gaussian Diffusion of Nanoparticles in Free-Standing Thin Polymer Films. J Phys Chem B 2019; 123:9250-9259. [PMID: 31589036 DOI: 10.1021/acs.jpcb.9b07236] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The addition of nanoparticles (NPs) to a free-standing polymer film affects the properties of the film such as viscosity and glass transition temperature. Recent experiments, for example, showed that the glass transition temperature of thin polymer films was dependent on how NPs were distributed within the polymer films. However, the spatial arrangement of NPs in free-standing polymer films and its effect on the diffusion of NPs and polymers remain elusive at a molecular level. In this study, we employ generic coarse-grained models for polymers and NPs and perform extensive molecular dynamics simulations to investigate the diffusion of polymers and NPs in free-standing thin polymer films. We find that small NPs are likely to stay at the interfacial region of the polymer film, while large NPs tend to stay at the center of the film. On the other hand, as the interaction between a NP and a monomer becomes more attractive, the NP is more likely to be placed at the film center. The diffusion of monomers slows down slightly as more NPs are added to the film. Interestingly, the NP diffusion is dependent strongly on the spatial arrangement of the NPs: NPs at the interfacial region diffuse faster and undergo more non-Gaussian diffusion than NPs at the film center, which implies that the interfacial region would be more mobile and dynamically heterogeneous than the film center. We also find that the mechanism for non-Gaussian diffusion of NPs at the film center differs from that at the interfacial region and that the NP diffusion would reflect the local viscosity of the polymer films.
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Heo J, Oh Y, Noh O, Chun M, Cho O. PO-0711 Second Primary Cancer in Salivary gland cancer in South Korea: A Nationwide Population-based Study. Radiother Oncol 2019. [DOI: 10.1016/s0167-8140(19)31131-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Cho O, Oh Y, Chun M, Noh O, Heo J. PV-0042 Radiation related lymphopenia as a predictor of locoregional recurrence in early breast cancer. Radiother Oncol 2019. [DOI: 10.1016/s0167-8140(19)30462-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Heo J, Oh Y, Noh O, Chun M, Kim C, Shin Y. PO-139 Second Primary Cancer in Salivary gland cancer: A Nationwide Population-based Study. Radiother Oncol 2019. [DOI: 10.1016/s0167-8140(19)30305-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Oh Y, Sung BJ. Facilitated and Non-Gaussian Diffusion of Cholesterol in Liquid Ordered Phase Bilayers Depends on the Flip-Flop and Spatial Arrangement of Cholesterol. J Phys Chem Lett 2018; 9:6529-6535. [PMID: 30346769 DOI: 10.1021/acs.jpclett.8b02982] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The diffusion of cholesterol in biological membranes is critical to cellular processes such as the formation of cholesterol-enriched domains. The cholesterol diffusion may be complicated especially when cholesterol flip-flops and/or stays at the membrane center. Understanding the diffusion mechanism of cholesterol at a molecular level should be, therefore, a topic of interest. We perform molecular dynamics simulations up to 100 μs for lipid bilayers with various concentrations of cholesterol. We find that cholesterol diffusion in the liquid ordered phase depends on whether it is within leaflets or at the bilayer center, is non-Gaussian for several microseconds, and is enhanced significantly compared to that of lipids. Cholesterol at the bilayer center diffuses fast, while cholesterol in the hydrocarbon region with upright orientation diffuses relatively slowly. Such position-dependent dynamics of cholesterol leads to facilitated and non-Gaussian diffusion.
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Lee S, Oh Y, Nam K, Oh B, Roh M, Chung K. Mohs micrographic surgery for dermatofibrosarcoma protuberans: comparison of frozen and paraffin techniques. J Eur Acad Dermatol Venereol 2018; 32:2171-2177. [DOI: 10.1111/jdv.15201] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/12/2018] [Indexed: 11/28/2022]
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Lee S, Oh Y, Nam K, Oh B, Roh M, Chung K. 575 Comparative single-institute analysis of slow Mohs micrographic surgery and frozen section Mohs micrographic surgery for dermatofibrosarcoma protuberans. J Invest Dermatol 2018. [DOI: 10.1016/j.jid.2018.03.583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Oh Y, June Sung B. Lateral Diffusivity of Cholesterol Depends on its Spatial Arrangement in Lipid Membranes. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Baskaran R, Lee CJ, Kang SM, Oh Y, Jin SE, Lee DH, Yang SG. Poly(lactic-co-glycolic acid) Microspheres Containing a Recombinant Parathyroid Hormone (1-34) for Sustained Release in a Rat Model. Indian J Pharm Sci 2018. [DOI: 10.4172/pharmaceutical-sciences.1000429] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Cho O, Oh Y, Chun M, Noh O, Heo J. P1.15-015 Prognostic Implication of the FEV1/FVC Ratio in Limited-Stage Small Cell Lung Cancer. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.1051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Oh Y, Schreiter JH, Okada H, Wloka C, Okada S, Yan D, Duan X, Bi E. Hof1 and Chs4 Interact via F-BAR Domain and Sel1-like Repeats to Control Extracellular Matrix Deposition during Cytokinesis. Curr Biol 2017; 27:2878-2886.e5. [PMID: 28918945 PMCID: PMC5658023 DOI: 10.1016/j.cub.2017.08.032] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 07/07/2017] [Accepted: 08/15/2017] [Indexed: 11/24/2022]
Abstract
Localized extracellular matrix (ECM) remodeling is thought to stabilize the cleavage furrow and maintain cell shape during cytokinesis [1-14]. This remodeling is spatiotemporally coordinated with a cytoskeletal structure pertaining to a kingdom of life, for example the FtsZ ring in bacteria [15], the phragmoplast in plants [16], and the actomyosin ring in fungi and animals [17, 18]. Although the cytoskeletal structures have been analyzed extensively, the mechanisms of ECM remodeling remain poorly understood. In the budding yeast Saccharomyces cerevisiae, ECM remodeling refers to sequential formations of the primary and secondary septa that are catalyzed by chitin synthase-II (Chs2) and chitin synthase-III (the catalytic subunit Chs3 and its activator Chs4), respectively [18, 19]. Surprisingly, both Chs2 and Chs3 are delivered to the division site at the onset of cytokinesis [6, 20]. What keeps Chs3 inactive until secondary septum formation remains unknown. Here, we show that Hof1 binds to the Sel1-like repeats (SLRs) of Chs4 via its F-BAR domain and inhibits Chs3-mediated chitin synthesis during cytokinesis. In addition, Hof1 is required for rapid accumulation as well as efficient removal of Chs4 at the division site. This study uncovers a mechanism by which Hof1 controls timely activation of Chs3 during cytokinesis and defines a novel interaction and function for the conserved F-BAR domain and SLR that are otherwise known for their abilities to bind membrane lipids [21, 22] and scaffold protein complex formation [23].
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Im H, Oh Y, Cho HW, Kim J, Paeng K, Sung BJ. The spatial arrangement of a single nanoparticle in a thin polymer film and its effect on the nanoparticle diffusion. SOFT MATTER 2017; 13:5897-5904. [PMID: 28766660 DOI: 10.1039/c7sm01115f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The spatial arrangement of nanoparticles (NPs) within thin polymer films may influence their properties such as the glass transition temperature. Questions regarding what may affect the spatial arrangement of NPs, however, still remain unanswered at a molecular level. In this work, we perform molecular dynamics simulations for a free-standing thin polymer film with a single NP. We find from simulations that depending on the NP size and the inter-particle interaction between the NP and polymers, one may control the spatial arrangement of the NP. When the interaction between the NP and polymers is sufficiently attractive (repulsive), the NP is likely to be placed at the center (at the surface) of the thin film in equilibrium. Interestingly, for a moderate interaction between the NP and polymers, the first-order transition occurs in the spatial arrangement of the NP as one increases the NP size: a small NP prefers the surface of the polymer film whereas a large NP prefers the center. Such a first-order transition is corroborated by calculating the free energy of the NP as a function of the position and can be understood in terms of a sixth-order Landau free energy. More interestingly, the diffusion of the NP also changes drastically due to the first-order transition in the spatial arrangement. The NP diffusion is enhanced drastically (more than expected in bulk polymer melts) as the NP is shifted to the polymer film surface.
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Lim SH, Lee T, Oh Y, Narayanan T, Sung BJ, Choi SM. Hierarchically self-assembled hexagonal honeycomb and kagome superlattices of binary 1D colloids. Nat Commun 2017; 8:360. [PMID: 28842555 PMCID: PMC5572454 DOI: 10.1038/s41467-017-00512-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 06/30/2017] [Indexed: 01/10/2023] Open
Abstract
Synthesis of binary nanoparticle superlattices has attracted attention for a broad spectrum of potential applications. However, this has remained challenging for one-dimensional nanoparticle systems. In this study, we investigate the packing behavior of one-dimensional nanoparticles of different diameters into a hexagonally packed cylindrical micellar system and demonstrate that binary one-dimensional nanoparticle superlattices of two different symmetries can be obtained by tuning particle diameter and mixing ratios. The hexagonal arrays of one-dimensional nanoparticles are embedded in the honeycomb lattices (for AB2 type) or kagome lattices (for AB3 type) of micellar cylinders. The maximization of free volume entropy is considered as the main driving force for the formation of superlattices, which is well supported by our theoretical free energy calculations. Our approach provides a route for fabricating binary one-dimensional nanoparticle superlattices and may be applicable for inorganic one-dimensional nanoparticle systems. Binary mixtures of 1D particles are rarely observed to cooperatively self-assemble into binary superlattices, as the particle types separate into phases. Here, the authors design a system that avoids phase separation, obtaining binary superlattices with different symmetries by simply tuning the particle diameter and mixture composition.
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Kim Y, Lee H, Oh Y, Kang E. RELIABILITY AND VALIDITY OF THE DEMENTIA HEALTH LITERACY SCALE: A PILOT STUDY. Innov Aging 2017. [DOI: 10.1093/geroni/igx004.4486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Aw S, Oh Y, Koh G, Vrijhoef H, Harding S, Hildon Z. MAPPING TYPOLOGIES OF SOCIAL PARTICIPATION TO PROGRAMMING FOR ELDERS IN THE CHANGING ASIAN CONTEXTS. Innov Aging 2017. [DOI: 10.1093/geroni/igx004.3168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Seo J, Roh MR, Oh Y, Nam KA, Chung KY. Palmar melanoma: a tertiary centre experience. J Eur Acad Dermatol Venereol 2017; 31:e493-e496. [PMID: 28502087 DOI: 10.1111/jdv.14338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Park H, Bae Y, Park J, Kim M, Oh Y, Chun M, Noh O, Cho O, Lee J. EP-1444: Reliable error detection in radiochromic film dosimetry with optimal density curves and corrections. Radiother Oncol 2017. [DOI: 10.1016/s0167-8140(17)31879-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Lee E, Park N, Oh Y, Yoo S, Lee H, Lee J, Kim Y. 728 3D Multi-photon imaging for evaluating the anti-aging efficacy of Paeonia Albiflora extract on UV-irradiated fibroblasts in a collagen matrix. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.02.752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Lee HJ, Ha JH, Kim SG, Choi HK, Kim ZH, Han YJ, Kim JI, Oh Y, Fragoso V, Shin K, Hyeon T, Choi HG, Oh KH, Baldwin IT, Park CM. Stem-piped light activates phytochrome B to trigger light responses in Arabidopsis thaliana roots. Sci Signal 2016; 9:ra106. [DOI: 10.1126/scisignal.aaf6530] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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49
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Parker J, Oh Y, Moazami Y, Pierce JG, Loziuk PL, Dean RA, Muddiman DC. Examining ubiquitinated peptide enrichment efficiency through an epitope labeled protein. Anal Biochem 2016; 512:114-119. [PMID: 27562526 DOI: 10.1016/j.ab.2016.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 07/02/2016] [Accepted: 08/19/2016] [Indexed: 10/21/2022]
Abstract
Ubiquitination is a dynamic process that is responsible for regulation of cellular responses to stimuli in a number of biological systems. Previous efforts to study this post-translational modification have focused on protein enrichment; however, recent research utilizes the presence of the di-glycine (Gly-Gly) remnants following trypsin digestion to immuno-enrich ubiquitinated peptides. Monoclonal antibodies developed to the cleaved ubiquitin modification epitope, (tert-butoxycarbonyl) glycylglycine (Boc-Gly-Gly-NHS)(1), are used to identify the Gly-Gly signature. Here, we have successfully generated the Boc-Gly-Gly-NHS modification and showed that when conjugated to a lysine containing protein, such as lysozyme, it can be applied as a standard protein to examine ubiquitinated peptide enrichment within a complex background.
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Hamada K, Uedo N, Hanaoka N, Ishihara R, Oh Y. Gastrointestinal: Endoscopic mucosal resection for diagnosis of infiltrating gastric cancer: A case report. J Gastroenterol Hepatol 2016; 31:1670. [PMID: 27060249 DOI: 10.1111/jgh.13404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 03/30/2016] [Indexed: 12/09/2022]
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