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  1. Article ; Online: Analysis of Glutamine Deamidation: Products, Pathways, and Kinetics.

    Riggs, Dylan L / Silzel, Jacob W / Lyon, Yana A / Kang, Amrik S / Julian, Ryan R

    Analytical chemistry

    2019  Volume 91, Issue 20, Page(s) 13032–13038

    Abstract: Spontaneous chemical modifications play an important role in human disease and aging at the molecular level. Deamidation and isomerization are known to be among the most prevalent chemical modifications in long-lived human proteins and are implicated in ... ...

    Abstract Spontaneous chemical modifications play an important role in human disease and aging at the molecular level. Deamidation and isomerization are known to be among the most prevalent chemical modifications in long-lived human proteins and are implicated in a growing list of human pathologies, but the relatively minor chemical change associated with these processes has presented a long standing analytical challenge. Although the adoption of high-resolution mass spectrometry has greatly aided the identification of deamidation sites in proteomic studies, isomerization (and the isomeric products of deamidation) remain exceptionally challenging to characterize. Herein, we present a liquid chromatography/mass spectrometry-based approach for rapidly characterizing the isomeric products of Gln deamidation using diagnostic fragments that are abundantly produced and capable of unambiguously identifying both Glu and isoGlu. Importantly, the informative fragment ions are produced through orthogonal fragmentation pathways, thereby enabling the simultaneous detection of both isomeric forms while retaining compatibility with shotgun proteomics. Furthermore, the diagnostic fragments associated with isoGlu pinpoint the location of the modified residue. The utility of this technique is demonstrated by characterizing the isomeric products generated during
    MeSH term(s) Chromatography, Liquid ; Crystallins/analysis ; Crystallins/chemistry ; Crystallins/metabolism ; Glutamine/analogs & derivatives ; Glutamine/analysis ; Glutamine/metabolism ; Humans ; Hydrolysis ; Iodobenzoates/chemistry ; Kinetics ; Lens, Crystalline/chemistry ; Mass Spectrometry ; Time Factors
    Chemical Substances Crystallins ; Iodobenzoates ; Glutamine (0RH81L854J)
    Language English
    Publishing date 2019-09-25
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.9b03127
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4033: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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  2. Article: Dietary Intake and Pneumococcal Vaccine Response Among Children (5-7 Years) in Msambweni Division, Kwale County, Kenya.

    Migliore, Eleonora / Amaitsa, Vivian K / Mutuku, Francis M / Malhotra, Indu J / Mukoko, Dunstan / Sharma, Anika / Kalva, Prathik / Kang, Amrik S / King, Charles H / LaBeaud, A Desiree

    Frontiers in nutrition

    2022  Volume 9, Page(s) 830294

    Abstract: Background: Vaccine and sufficient food availability are key factors for reducing pneumonia outbreaks in sub-Saharan Africa.: Methods: In this study, the 10-valent pneumococcal conjugate vaccine (Synflorix® or PCV10) was administered to a child ... ...

    Abstract Background: Vaccine and sufficient food availability are key factors for reducing pneumonia outbreaks in sub-Saharan Africa.
    Methods: In this study, the 10-valent pneumococcal conjugate vaccine (Synflorix® or PCV10) was administered to a child cohort (5-7 years old,
    Findings: Chronic malnutrition was prevalent in the cohort (15% stunting, 16% underweight). Unbalanced dietary intake was observed, with mean energy intake 14% below Recommended Dietary Allowances (1,822 Kcal) for 5-7 years age range. 72% of the daily energy was derived from carbohydrates, 18% from fats and only 10% from proteins. Poor anthropometric status (stunting/underweight) was associated with low socioeconomic/educational status and younger mother/caregiver age (
    Interpretation: Overall, this study highlights ongoing food scarcity and malnutrition in Kenya and demonstrates the links between adequate socioeconomic conditions, adequate nutrient intake, and vaccine efficacy.
    Language English
    Publishing date 2022-05-23
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2776676-7
    ISSN 2296-861X
    ISSN 2296-861X
    DOI 10.3389/fnut.2022.830294
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Human ARMT1 structure and substrate specificity indicates that it is a DUF89 family damage-control phosphatase.

    Dennis, Taylor N / Kenjić, Nikola / Kang, Amrik S / Lowenson, Jonathan D / Kirkwood, Jay S / Clarke, Steven G / Perry, J Jefferson P

    Journal of structural biology

    2020  Volume 212, Issue 1, Page(s) 107576

    Abstract: Metabolite damage control is a critical but poorly defined aspect of cellular biochemistry, which likely involves many of the so far functionally uncharacterized protein domain (domains of unknown function; DUFs). We have determined the crystal structure ...

    Abstract Metabolite damage control is a critical but poorly defined aspect of cellular biochemistry, which likely involves many of the so far functionally uncharacterized protein domain (domains of unknown function; DUFs). We have determined the crystal structure of the human DUF89 protein product of the C6ORF211 gene to 1.85 Å. The crystal structure shows that the protein contains a core α-β-α fold with an active site-bound metal ion and α-helical bundle N-terminal cap, which are both conserved features of subfamily III DUF89 domains. The biochemical activities of the human protein are conserved with those of a previously characterized budding yeast homolog, where an in vitro phosphatase activity is supported by divalent cations that include Co
    MeSH term(s) Binding Sites/physiology ; Catalysis ; Humans ; Kinetics ; Metals/metabolism ; Phosphoric Monoester Hydrolases/metabolism ; Polysaccharides/metabolism ; Protein Conformation ; Protein O-Methyltransferase/metabolism ; Saccharomyces cerevisiae/metabolism ; Substrate Specificity/physiology
    Chemical Substances Metals ; Polysaccharides ; Armt1 protein, human (EC 2.1.1.-) ; Protein O-Methyltransferase (EC 2.1.1.-) ; Phosphoric Monoester Hydrolases (EC 3.1.3.2)
    Language English
    Publishing date 2020-07-15
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1032718-6
    ISSN 1095-8657 ; 1047-8477
    ISSN (online) 1095-8657
    ISSN 1047-8477
    DOI 10.1016/j.jsb.2020.107576
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1428: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article: Analysis of Glutamine Deamidation: Products, Pathways, and Kinetics

    Riggs, Dylan L / Silzel, Jacob W / Lyon, Yana A / Kang, Amrik S / Julian, Ryan R

    Analytical chemistry. 2019 Sept. 09, v. 91, no. 20

    2019  

    Abstract: Spontaneous chemical modifications play an important role in human disease and aging at the molecular level. Deamidation and isomerization are known to be among the most prevalent chemical modifications in long-lived human proteins and are implicated in ... ...

    Abstract Spontaneous chemical modifications play an important role in human disease and aging at the molecular level. Deamidation and isomerization are known to be among the most prevalent chemical modifications in long-lived human proteins and are implicated in a growing list of human pathologies, but the relatively minor chemical change associated with these processes has presented a long standing analytical challenge. Although the adoption of high-resolution mass spectrometry has greatly aided the identification of deamidation sites in proteomic studies, isomerization (and the isomeric products of deamidation) remain exceptionally challenging to characterize. Herein, we present a liquid chromatography/mass spectrometry-based approach for rapidly characterizing the isomeric products of Gln deamidation using diagnostic fragments that are abundantly produced and capable of unambiguously identifying both Glu and isoGlu. Importantly, the informative fragment ions are produced through orthogonal fragmentation pathways, thereby enabling the simultaneous detection of both isomeric forms while retaining compatibility with shotgun proteomics. Furthermore, the diagnostic fragments associated with isoGlu pinpoint the location of the modified residue. The utility of this technique is demonstrated by characterizing the isomeric products generated during in vitro aging of a series of glutamine-containing peptides. Sequence-dependent product profiles are obtained, and the abundance of deamidation-linked racemization is examined. Finally, comparisons are made between Gln deamidation, which is relatively poorly understood, and asparagine deamidation, which has been more thoroughly studied.
    Keywords asparagine ; deamidation ; glutamine ; human diseases ; humans ; ions ; isomerization ; liquid chromatography ; mass spectrometry ; pathogenesis ; peptides ; proteins ; proteomics
    Language English
    Dates of publication 2019-0909
    Size p. 13032-13038.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.9b03127
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

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  5. Article ; Online: A Heck-Based Strategy To Generate Anacardic Acids and Related Phenolic Lipids for Isoform-Specific Bioactivity Profiling.

    Weigel, William K / Dennis, Taylor N / Kang, Amrik S / Perry, J Jefferson P / Martin, David B C

    Organic letters

    2018  Volume 20, Issue 19, Page(s) 6234–6238

    Abstract: A synthetic strategy for phenolic lipids such as anacardic acid and ginkgolic acid derivatives using an efficient and selective redox-relay Heck reaction followed by a stereoselective olefination is reported. This approach controls both the alkene ... ...

    Abstract A synthetic strategy for phenolic lipids such as anacardic acid and ginkgolic acid derivatives using an efficient and selective redox-relay Heck reaction followed by a stereoselective olefination is reported. This approach controls both the alkene position and stereochemistry, allowing the synthesis of natural and unnatural unsaturated lipids as single isomers. By this strategy, the activities of different anacardic acid and ginkgolic acid derivatives have been examined in a matrix metalloproteinase inhibition assay.
    MeSH term(s) Alkenes/chemistry ; Anacardic Acids/chemical synthesis ; Lipids/chemical synthesis ; Matrix Metalloproteinase Inhibitors/chemical synthesis ; Molecular Structure ; Oxidation-Reduction ; Palladium/chemistry ; Phenols/chemistry ; Salicylates/chemical synthesis ; Stereoisomerism ; Structure-Activity Relationship
    Chemical Substances Alkenes ; Anacardic Acids ; Lipids ; Matrix Metalloproteinase Inhibitors ; Phenols ; Salicylates ; ginkgolic acid (22910-60-7) ; Palladium (5TWQ1V240M)
    Language English
    Publishing date 2018-09-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1523-7052
    ISSN (online) 1523-7052
    DOI 10.1021/acs.orglett.8b02705
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Targeting high-risk multiple myeloma genotypes with optimized anti-CD70 CAR-T cells.

    Kasap, Corynn / Izgutdina, Adila / Patiño-Escobar, Bonell / Kang, Amrik / Chilakapati, Nikhil / Akagi, Naomi / Johnson, Haley / Rashid, Tasfia / Werner, Juwita / Barpanda, Abhilash / Geng, Huimin / Lin, Yu-Hsiu T / Rampersaud, Sham / Gil-Alós, Daniel / Sobh, Amin / Dupéré-Richer, Daphné / Wicaksono, Gianina / Kawehi Kelii, K M / Dalal, Radhika /
    Ramos, Emilio / Vijayanarayanan, Anjanaa / Salangsang, Fernando / Phojanakong, Paul / Serrano, Juan Antonio Camara / Zakraoui, Ons / Tariq, Isa / Steri, Veronica / Shanmugam, Mala / Boise, Lawrence H / Kortemme, Tanja / Stieglitz, Elliot / Licht, Jonathan D / Karlon, William J / Barwick, Benjamin G / Wiita, Arun P

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Despite the success of BCMA-targeting CAR-Ts in multiple myeloma, patients with high-risk cytogenetic features still relapse most quickly and are in urgent need of additional therapeutic options. Here, we identify CD70, widely recognized as a favorable ... ...

    Abstract Despite the success of BCMA-targeting CAR-Ts in multiple myeloma, patients with high-risk cytogenetic features still relapse most quickly and are in urgent need of additional therapeutic options. Here, we identify CD70, widely recognized as a favorable immunotherapy target in other cancers, as a specifically upregulated cell surface antigen in high risk myeloma tumors. We use a structure-guided design to define a CD27-based anti-CD70 CAR-T design that outperforms all tested scFv-based CARs, leading to >80-fold improved CAR-T expansion in vivo. Epigenetic analysis via machine learning predicts key transcription factors and transcriptional networks driving CD70 upregulation in high risk myeloma. Dual-targeting CAR-Ts against either CD70 or BCMA demonstrate a potential strategy to avoid antigen escape-mediated resistance. Together, these findings support the promise of targeting CD70 with optimized CAR-Ts in myeloma as well as future clinical translation of this approach.
    Language English
    Publishing date 2024-02-28
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.02.24.581875
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Spontaneous Isomerization of Long-Lived Proteins Provides a Molecular Mechanism for the Lysosomal Failure Observed in Alzheimer's Disease.

    Lambeth, Tyler R / Riggs, Dylan L / Talbert, Lance E / Tang, Jin / Coburn, Emily / Kang, Amrik S / Noll, Jessica / Augello, Catherine / Ford, Byron D / Julian, Ryan R

    ACS central science

    2019  Volume 5, Issue 8, Page(s) 1387–1395

    Abstract: Proteinaceous aggregation is a well-known observable in Alzheimer's disease (AD), but failure and storage of lysosomal bodies within neurons is equally ubiquitous and actually precedes bulk accumulation of extracellular amyloid plaque. In fact, AD shares ...

    Abstract Proteinaceous aggregation is a well-known observable in Alzheimer's disease (AD), but failure and storage of lysosomal bodies within neurons is equally ubiquitous and actually precedes bulk accumulation of extracellular amyloid plaque. In fact, AD shares many similarities with certain lysosomal storage disorders though establishing a biochemical connection has proven difficult. Herein, we demonstrate that isomerization and epimerization, which are spontaneous chemical modifications that occur in long-lived proteins, prevent digestion by the proteases in the lysosome (namely, the cathepsins). For example, isomerization of aspartic acid into l-isoAsp prevents digestion of the N-terminal portion of Aβ by cathepsin L, one of the most aggressive lysosomal proteases. Similar results were obtained after examination of various target peptides with a full series of cathepsins, including endo-, amino-, and carboxy-peptidases. In all cases peptide fragments too long for transporter recognition or release from the lysosome persisted after treatment, providing a mechanism for eventual lysosomal storage and bridging the gap between AD and lysosomal storage disorders. Additional experiments with microglial cells confirmed that isomerization disrupts proteolysis in active lysosomes. These results are easily rationalized in terms of protease active sites, which are engineered to precisely orient the peptide backbone and cannot accommodate the backbone shift caused by isoaspartic acid or side chain dislocation resulting from epimerization. Although Aβ is known to be isomerized and epimerized in plaques present in AD brains, we further establish that the rates of modification for aspartic acid in positions 1 and 7 are fast and could accrue prior to plaque formation. Spontaneous chemistry can therefore provide modified substrates capable of inducing gradual lysosomal failure, which may play an important role in the cascade of events leading to the disrupted proteostasis, amyloid formation, and tauopathies associated with AD.
    Language English
    Publishing date 2019-08-07
    Publishing country United States
    Document type Journal Article
    ISSN 2374-7943
    ISSN 2374-7943
    DOI 10.1021/acscentsci.9b00369
    Database MEDical Literature Analysis and Retrieval System OnLINE

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