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  1. Article ; Online: A Membrane-Permeable and Immobilized Metal Affinity Chromatography (IMAC) Enrichable Cross-Linking Reagent to Advance In Vivo Cross-Linking Mass Spectrometry.

    Jiang, Pin-Lian / Wang, Cong / Diehl, Anne / Viner, Rosa / Etienne, Chris / Nandhikonda, Premchendar / Foster, Leigh / Bomgarden, Ryan D / Liu, Fan

    Angewandte Chemie (International ed. in English)

    2022  Volume 61, Issue 12, Page(s) e202113937

    Abstract: Cross-linking mass spectrometry (XL-MS) is an attractive method for the proteome-wide characterization of protein structures and interactions. Currently, the depth of in vivo XL-MS studies is lagging behind the established applications to cell lysates, ... ...

    Abstract Cross-linking mass spectrometry (XL-MS) is an attractive method for the proteome-wide characterization of protein structures and interactions. Currently, the depth of in vivo XL-MS studies is lagging behind the established applications to cell lysates, because cross-linking reagents that can penetrate intact cells and strategies to enrich cross-linked peptides lack efficiency. To tackle these limitations, we have developed a phosphonate-containing cross-linker, tBu-PhoX, that efficiently permeates various biological membranes and can be robustly enriched using routine immobilized metal ion affinity chromatography. We have established a tBu-PhoX-based in vivo XL-MS approach that enables cross-links in intact human cells to be identified in high numbers with substantially reduced analysis time. Collectively, the developed cross-linker and XL-MS approach pave the way for the comprehensive XL-MS characterization of living systems.
    MeSH term(s) Chromatography, Affinity ; Cross-Linking Reagents/chemistry ; Humans ; Imidazoles ; Mass Spectrometry/methods ; Proteome
    Chemical Substances Cross-Linking Reagents ; Imidazoles ; Proteome ; imidazoleacetic acid (IGZ30Z24EJ)
    Language English
    Publishing date 2022-01-27
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2011836-3
    ISSN 1521-3773 ; 1433-7851
    ISSN (online) 1521-3773
    ISSN 1433-7851
    DOI 10.1002/anie.202113937
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  2. Article ; Online: An abiotic fluorescent probe for cardiac troponin I.

    Nandhikonda, Premchendar / Heagy, Michael D

    Journal of the American Chemical Society

    2011  Volume 133, Issue 38, Page(s) 14972–14974

    Abstract: The first ratiometric fluorescent reporter was designed for the detection of cardiac troponin I (cTnI), a key protein elicited during cardiac muscle cell death. In designing this abiotic fluorescent probe, docking simulation studies were performed to ... ...

    Abstract The first ratiometric fluorescent reporter was designed for the detection of cardiac troponin I (cTnI), a key protein elicited during cardiac muscle cell death. In designing this abiotic fluorescent probe, docking simulation studies were performed to predict the probe/protein interactions along the solvent exposed regions of cTnI. Simple cuvette titration experiments in aqueous buffered solution indicate remarkable selectivity for cardiac troponin in the clinically relevant nM region versus skeletal troponin.
    MeSH term(s) Biomarkers/blood ; Biomarkers/chemistry ; Fluorescent Dyes/chemical synthesis ; Fluorescent Dyes/chemistry ; Humans ; Models, Molecular ; Molecular Structure ; Myocytes, Smooth Muscle/chemistry ; Myocytes, Smooth Muscle/metabolism ; Troponin I/blood ; Troponin I/chemistry
    Chemical Substances Biomarkers ; Fluorescent Dyes ; Troponin I
    Language English
    Publishing date 2011-09-28
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/ja205211a
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: An organic white light-emitting dye: very small molecular architecture displays panchromatic emission.

    Nandhikonda, Premchendar / Heagy, Michael D

    Chemical communications (Cambridge, England)

    2010  Volume 46, Issue 42, Page(s) 8002–8004

    Abstract: The synthesis and photophysical characterization of a new white-light fluorophore is described. The optimization of excitation wavelengths allows the naphthalimide (NI) dyes to display blue, green or white light emission depending on the excitation ... ...

    Abstract The synthesis and photophysical characterization of a new white-light fluorophore is described. The optimization of excitation wavelengths allows the naphthalimide (NI) dyes to display blue, green or white light emission depending on the excitation wavelength.
    Language English
    Publishing date 2010-11-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/c0cc02598d
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  4. Article ; Online: Dual fluorescent N-aryl-2,3- naphthalimides: applications in ratiometric DNA detection and white organic light-emitting devices.

    Nandhikonda, Premchendar / Heagy, Michael D

    Organic letters

    2010  Volume 12, Issue 21, Page(s) 4796–4799

    Abstract: A ten element matrix of 5- and 6-substituted-(2,3)-naphthalimides was prepared for the appropriate placement of substituents necessary to promote dual fluorescence (DF). As prescribed by our balanced seesaw photophysical model this matrix yielded nine ... ...

    Abstract A ten element matrix of 5- and 6-substituted-(2,3)-naphthalimides was prepared for the appropriate placement of substituents necessary to promote dual fluorescence (DF). As prescribed by our balanced seesaw photophysical model this matrix yielded nine new DF dyes out of a possible ten compounds. From this set of nine DF dyes, 4-fluoronaphthalic amide (37) was selected as a probe for ratiometric detection of DNA and demonstration of panchromatic emission.
    MeSH term(s) DNA/analysis ; DNA/chemistry ; Fluorescent Dyes/chemistry ; Light ; Naphthalimides/chemistry
    Chemical Substances Fluorescent Dyes ; Naphthalimides ; DNA (9007-49-2)
    Language English
    Publishing date 2010-11-05
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1523-7052
    ISSN (online) 1523-7052
    DOI 10.1021/ol101760m
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  5. Article: An organic white light-emitting dye: very small molecular architecture displays panchromatic emission

    Nandhikonda, Premchendar / Heagy, Michael D

    Chemical communications. 2010 Oct. 19, v. 46, no. 42

    2010  

    Abstract: The synthesis and photophysical characterization of a new white-light fluorophore is described. The optimization of excitation wavelengths allows the naphthalimide (NI) dyes to display blue, green or white light emission depending on the excitation ... ...

    Abstract The synthesis and photophysical characterization of a new white-light fluorophore is described. The optimization of excitation wavelengths allows the naphthalimide (NI) dyes to display blue, green or white light emission depending on the excitation wavelength.
    Keywords chemical reactions ; fluorescent dyes ; imides ; wavelengths ; white light
    Language English
    Dates of publication 2010-1019
    Size p. 8002-8004.
    Publishing place The Royal Society of Chemistry
    Document type Article
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/c0cc02598d
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  6. Article: Advancing understanding of microbial bioenergy conversion processes by activity-based protein profiling.

    Liu, Yun / Fredrickson, James K / Sadler, Natalie C / Nandhikonda, Premchendar / Smith, Richard D / Wright, Aaron T

    Biotechnology for biofuels

    2015  Volume 8, Page(s) 156

    Abstract: The development of renewable biofuels is a global priority, but success will require novel technologies that greatly improve our understanding of microbial systems biology. An approach with great promise in enabling functional characterization of ... ...

    Abstract The development of renewable biofuels is a global priority, but success will require novel technologies that greatly improve our understanding of microbial systems biology. An approach with great promise in enabling functional characterization of microbes is activity-based protein profiling (ABPP), which employs chemical probes to directly measure enzyme function in discrete enzyme classes in vivo and/or in vitro, thereby facilitating the rapid discovery of new biocatalysts and enabling much improved biofuel production platforms. We review general design strategies in ABPP, and highlight recent advances that are or could be pivotal to biofuels processes including applications of ABPP to cellulosic bioethanol, biodiesel, and phototrophic production of hydrocarbons. We also examine the key challenges and opportunities of ABPP in renewable biofuels research. The integration of ABPP with molecular and systems biology approaches will shed new insight on the catalytic and regulatory mechanisms of functional enzymes and their synergistic effects in the field of biofuels production.
    Language English
    Publishing date 2015-09-25
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2421351-2
    ISSN 1754-6834
    ISSN 1754-6834
    DOI 10.1186/s13068-015-0343-7
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  7. Article ; Online: TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples.

    Li, Jiaming / Van Vranken, Jonathan G / Pontano Vaites, Laura / Schweppe, Devin K / Huttlin, Edward L / Etienne, Chris / Nandhikonda, Premchendar / Viner, Rosa / Robitaille, Aaron M / Thompson, Andrew H / Kuhn, Karsten / Pike, Ian / Bomgarden, Ryan D / Rogers, John C / Gygi, Steven P / Paulo, Joao A

    Nature methods

    2020  Volume 17, Issue 4, Page(s) 399–404

    Abstract: Isobaric labeling empowers proteome-wide expression measurements simultaneously across multiple samples. Here an expanded set of 16 isobaric reagents based on an isobutyl-proline immonium ion reporter structure (TMTpro) is presented. These reagents have ... ...

    Abstract Isobaric labeling empowers proteome-wide expression measurements simultaneously across multiple samples. Here an expanded set of 16 isobaric reagents based on an isobutyl-proline immonium ion reporter structure (TMTpro) is presented. These reagents have similar characteristics to existing tandem mass tag reagents but with increased fragmentation efficiency and signal. In a proteome-scale example dataset, we compared eight common cell lines with and without Torin1 treatment with three replicates, quantifying more than 8,800 proteins (mean of 7.5 peptides per protein) per replicate with an analysis time of only 1.1 h per proteome. Finally, we modified the thermal stability assay to examine proteome-wide melting shifts after treatment with DMSO, 1 or 20 µM staurosporine with five replicates. This assay identified and dose-stratified staurosporine binding to 228 cellular kinases in just one, 18-h experiment. TMTpro reagents allow complex experimental designs-all with essentially no missing values across the 16 samples and no loss in quantitative integrity.
    MeSH term(s) Cell Line ; Humans ; Isotope Labeling ; Peptides/chemistry ; Proteome/chemistry ; Proteomics/methods ; Tandem Mass Spectrometry/methods
    Chemical Substances Peptides ; Proteome
    Language English
    Publishing date 2020-03-16
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/s41592-020-0781-4
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6022: Show issues Location:
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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
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  8. Article ; Online: Elucidation of roles for vitamin B

    Romine, Margaret F / Rodionov, Dmitry A / Maezato, Yukari / Anderson, Lindsey N / Nandhikonda, Premchendar / Rodionova, Irina A / Carre, Alexandre / Li, Xiaoqing / Xu, Chengdong / Clauss, Therese R W / Kim, Young-Mo / Metz, Thomas O / Wright, Aaron T

    Proceedings of the National Academy of Sciences of the United States of America

    2017  Volume 114, Issue 7, Page(s) E1205–E1214

    Abstract: Only a small fraction of vitamin ... ...

    Abstract Only a small fraction of vitamin B
    Language English
    Publishing date 2017-02-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1612360114
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1148: Show issues Location:
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  9. Article ; Online: Highly water-soluble monoboronic acid probes that show optical sensitivity to glucose based on 4-sulfo-1,8-naphthalic anhydride.

    Cao, Zhi / Nandhikonda, Premchendar / Heagy, Michael D

    The Journal of organic chemistry

    2009  Volume 74, Issue 9, Page(s) 3544–3546

    Abstract: Two highly water-soluble monoboronic acid probes that display the more desirable off-on fluorescence response were synthesized based on 4-sulfo-1,8-naphthalic anhydride and a remarkable sensitivity for glucose rather than fructose and galactose was also ... ...

    Abstract Two highly water-soluble monoboronic acid probes that display the more desirable off-on fluorescence response were synthesized based on 4-sulfo-1,8-naphthalic anhydride and a remarkable sensitivity for glucose rather than fructose and galactose was also observed.
    MeSH term(s) Boronic Acids/chemical synthesis ; Boronic Acids/chemistry ; Glucose/analysis ; Naphthalenes/analysis ; Naphthalimides/chemistry ; Sensitivity and Specificity ; Solubility ; Water/chemistry
    Chemical Substances 4-sulfo-1,8-naphthalic anhydride ; Boronic Acids ; Naphthalenes ; Naphthalimides ; Water (059QF0KO0R) ; Glucose (IY9XDZ35W2)
    Language English
    Publishing date 2009-04-07
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 123490-0
    ISSN 1520-6904 ; 0022-3263
    ISSN (online) 1520-6904
    ISSN 0022-3263
    DOI 10.1021/jo9002008
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4473: Show issues Location:
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  10. Article ; Online: Hepatic Cytochrome P450 Activity, Abundance, and Expression Throughout Human Development.

    Sadler, Natalie C / Nandhikonda, Premchendar / Webb-Robertson, Bobbie-Jo / Ansong, Charles / Anderson, Lindsey N / Smith, Jordan N / Corley, Richard A / Wright, Aaron T

    Drug metabolism and disposition: the biological fate of chemicals

    2016  Volume 44, Issue 7, Page(s) 984–991

    Abstract: Cytochrome P450s are oxidative metabolic enzymes that play critical roles in the biotransformation of endogenous compounds and xenobiotics. The expression and activity of P450 enzymes varies considerably throughout human development; the deficit in our ... ...

    Abstract Cytochrome P450s are oxidative metabolic enzymes that play critical roles in the biotransformation of endogenous compounds and xenobiotics. The expression and activity of P450 enzymes varies considerably throughout human development; the deficit in our understanding of these dynamics limits our ability to predict environmental and pharmaceutical exposure effects. In an effort to develop a more comprehensive understanding of the ontogeny of P450 enzymes, we employed a multi-omic characterization of P450 transcript expression, protein abundance, and functional activity. Modified mechanism-based inhibitors of P450s were used as chemical probes for isolating active P450 proteoforms in human hepatic microsomes with developmental stages ranging from early gestation to late adult. High-resolution liquid chromatography-mass spectrometry was used to identify and quantify probe-labeled P450s, allowing for a functional profile of P450 ontogeny. Total protein abundance profiles and P450 rRNA was also measured, and our results reveal life-stage-dependent variability in P450 expression, abundance, and activity throughout human development and frequent discordant relationships between expression and activity. We have significantly expanded the knowledge of P450 ontogeny, particularly at the level of individual P450 activity. We anticipate that these results will be useful for enabling predictive therapeutic dosing, and for avoiding potentially adverse and harmful reactions during maturation from both therapeutic drugs and environmental xenobiotics.
    Language English
    Publishing date 2016-07
    Publishing country United States
    Document type Journal Article
    ZDB-ID 186795-7
    ISSN 1521-009X ; 0090-9556
    ISSN (online) 1521-009X
    ISSN 0090-9556
    DOI 10.1124/dmd.115.068593
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    Zs.A 1014: Show issues Location:
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