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  1. Article ; Online: Asymmetric protonation of glutamate residues drives a preferred transport pathway in EmrE.

    Li, Jianping / Sae Her, Ampon / Traaseth, Nathaniel J

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

    2021  Volume 118, Issue 41

    Abstract: ... EmrE is ... ...

    Abstract EmrE is an
    MeSH term(s) Anti-Bacterial Agents/metabolism ; Antiporters/genetics ; Antiporters/metabolism ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Glutamic Acid/chemistry ; Magnetic Resonance Spectroscopy ; Protein Domains/physiology ; Protein Transport/physiology ; Static Electricity
    Chemical Substances Anti-Bacterial Agents ; Antiporters ; Escherichia coli Proteins ; EmrE protein, E coli (147995-06-0) ; Glutamic Acid (3KX376GY7L)
    Language English
    Publishing date 2021-10-04
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2110790118
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    Zs.A 1148: Show issues Location:
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  2. Article ; Online: Gatekeeper mutations activate FGF receptor tyrosine kinases by destabilizing the autoinhibited state.

    Besch, Alida / Marsiglia, William M / Mohammadi, Moosa / Zhang, Yingkai / Traaseth, Nathaniel J

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

    2023  Volume 120, Issue 8, Page(s) e2213090120

    Abstract: Many types of human cancers are being treated with small molecule ATP-competitive inhibitors targeting the kinase domain of receptor tyrosine kinases. Despite initial successful remission, long-term treatment almost inevitably leads to the emergence of ... ...

    Abstract Many types of human cancers are being treated with small molecule ATP-competitive inhibitors targeting the kinase domain of receptor tyrosine kinases. Despite initial successful remission, long-term treatment almost inevitably leads to the emergence of drug resistance mutations at the gatekeeper residue hindering the access of the inhibitor to a hydrophobic pocket at the back of the ATP-binding cleft. In addition to reducing drug efficacy, gatekeeper mutations elevate the intrinsic activity of the tyrosine kinase domain leading to more aggressive types of cancer. However, the mechanism of gain-of-function by gatekeeper mutations is poorly understood. Here, we characterized fibroblast growth factor receptor (FGFR) tyrosine kinases harboring two distinct gatekeeper mutations using kinase activity assays, NMR spectroscopy, bioinformatic analyses, and MD simulations. Our data show that gatekeeper mutations destabilize the autoinhibitory conformation of the DFG motif locally and of the kinase globally, suggesting they impart gain-of-function by facilitating the kinase's ability to populate the active state.
    MeSH term(s) Humans ; Receptor Protein-Tyrosine Kinases ; Receptors, Fibroblast Growth Factor/genetics ; Neoplasms/drug therapy ; Mutation ; Adenosine Triphosphate/therapeutic use ; Tyrosine ; Protein Kinase Inhibitors/chemistry
    Chemical Substances Receptor Protein-Tyrosine Kinases (EC 2.7.10.1) ; Receptors, Fibroblast Growth Factor ; Adenosine Triphosphate (8L70Q75FXE) ; Tyrosine (42HK56048U) ; Protein Kinase Inhibitors
    Language English
    Publishing date 2023-02-15
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2213090120
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Site-specific resolution of anionic residues in proteins using solid-state NMR spectroscopy.

    Li, Jianping / Sae Her, Ampon / Traaseth, Nathaniel J

    Journal of biomolecular NMR

    2020  Volume 74, Issue 6-7, Page(s) 355–363

    Abstract: NMR spectroscopy is commonly used to infer site-specific acid dissociation constants ( ... ...

    Abstract NMR spectroscopy is commonly used to infer site-specific acid dissociation constants (pK
    MeSH term(s) Anions/chemistry ; Antiporters/chemistry ; Asparagine/chemistry ; Aspartic Acid/chemistry ; Crystallization ; Escherichia coli Proteins/chemistry ; Glutamic Acid/chemistry ; Glutamine/chemistry ; Lipid Bilayers/chemistry ; Membrane Proteins/chemistry ; Nuclear Magnetic Resonance, Biomolecular/methods ; Proof of Concept Study ; Proteins/chemistry ; Ubiquitin/chemistry
    Chemical Substances Anions ; Antiporters ; Escherichia coli Proteins ; Lipid Bilayers ; Membrane Proteins ; Proteins ; Ubiquitin ; Glutamine (0RH81L854J) ; EmrE protein, E coli (147995-06-0) ; Aspartic Acid (30KYC7MIAI) ; Glutamic Acid (3KX376GY7L) ; Asparagine (7006-34-0)
    Language English
    Publishing date 2020-06-08
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1081696-3
    ISSN 1573-5001 ; 0925-2738
    ISSN (online) 1573-5001
    ISSN 0925-2738
    DOI 10.1007/s10858-020-00323-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 4132: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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  4. Article ; Online: Programmed Supramolecular Assemblies Using Orthogonal Pairs of Heterodimeric Coiled Coil Peptides.

    Jiang, Linhai / Zuo, Xiaobing / Li, Jianping / Traaseth, Nathaniel J / Kirshenbaum, Kent

    Angewandte Chemie (International ed. in English)

    2022  Volume 61, Issue 27, Page(s) e202201895

    Abstract: Despite recent progress, it remains challenging to program biomacromolecules to assemble into discrete nanostructures with pre-determined sizes and topologies. We report here a novel strategy to address this challenge. By using two orthogonal pairs of ... ...

    Abstract Despite recent progress, it remains challenging to program biomacromolecules to assemble into discrete nanostructures with pre-determined sizes and topologies. We report here a novel strategy to address this challenge. By using two orthogonal pairs of heterodimeric coiled coils as the building blocks, we constructed six discrete supramolecular assemblies, each composed of a prescribed number of coiled coil components. Within these assemblies, different coiled coils were connected via end-to-side covalent linkages strategically pre-installed between the non-complementary pairs. The overall topological features of two highly complex assemblies, a "barbell" and a "quadrilateral" form, were characterized experimentally and were in good agreement to the designs. This work expands the design paradigms for peptide-based discrete supramolecular assemblies and will provide a route for de novo fabrication of functional protein materials.
    MeSH term(s) Biophysical Phenomena ; Nanostructures/chemistry ; Peptides/chemistry ; Protein Domains ; Proteins/chemistry
    Chemical Substances Peptides ; Proteins
    Language English
    Publishing date 2022-05-05
    Publishing country Germany
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; 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.202201895
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  5. Article ; Online: Afterglow Solid-State NMR Spectroscopy.

    Abramov, Gili / Traaseth, Nathaniel J

    Methods in molecular biology (Clifton, N.J.)

    2017  Volume 1688, Page(s) 55–66

    Abstract: Biomolecular solid-state NMR experiments have traditionally been collected through detection ... ...

    Abstract Biomolecular solid-state NMR experiments have traditionally been collected through detection of
    MeSH term(s) Antiporters/chemistry ; Antiporters/metabolism ; Bacteria/metabolism ; Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Nuclear Magnetic Resonance, Biomolecular/methods ; Protein Conformation
    Chemical Substances Antiporters ; Bacterial Proteins
    Language English
    Publishing date 2017-11-18
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-7386-6_3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: NMR Spectroscopy Approach to Study the Structure, Orientation, and Mechanism of the Multidrug Exporter EmrE.

    Leninger, Maureen / Traaseth, Nathaniel J

    Methods in molecular biology (Clifton, N.J.)

    2017  Volume 1700, Page(s) 83–96

    Abstract: Multidrug exporters are a class of membrane proteins that remove antibiotics from the cytoplasm of bacteria and in the process confer multidrug resistance to the organism. This chapter outlines the sample preparation and optimization of oriented solid- ... ...

    Abstract Multidrug exporters are a class of membrane proteins that remove antibiotics from the cytoplasm of bacteria and in the process confer multidrug resistance to the organism. This chapter outlines the sample preparation and optimization of oriented solid-state NMR experiments applied to the study of structure and dynamics for the model transporter EmrE from the small multidrug resistance (SMR) family.
    MeSH term(s) Antiporters/chemistry ; Antiporters/isolation & purification ; Drug Resistance, Multiple, Bacterial ; Escherichia coli/chemistry ; Escherichia coli/metabolism ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/isolation & purification ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Protein Conformation
    Chemical Substances Antiporters ; Escherichia coli Proteins ; EmrE protein, E coli (147995-06-0)
    Language English
    Publishing date 2017-11-22
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-7454-2_6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Inducing conformational preference of the membrane protein transporter EmrE through conservative mutations.

    Leninger, Maureen / Sae Her, Ampon / Traaseth, Nathaniel J

    eLife

    2019  Volume 8

    Abstract: Transporters from bacteria to humans contain inverted repeat domains thought to arise evolutionarily from the fusion of smaller membrane protein genes. Association between these domains forms the functional unit that enables transporters to adopt ... ...

    Abstract Transporters from bacteria to humans contain inverted repeat domains thought to arise evolutionarily from the fusion of smaller membrane protein genes. Association between these domains forms the functional unit that enables transporters to adopt distinct conformations necessary for function. The small multidrug resistance (SMR) family provides an ideal system to explore the role of mutations in altering conformational preference since transporters from this family consist of antiparallel dimers that resemble the inverted repeats present in larger transporters. Here, we show using NMR spectroscopy how a single conservative mutation introduced into an SMR dimer is sufficient to change the resting conformation and function in bacteria. These results underscore the dynamic energy landscape for transporters and demonstrate how conservative mutations can influence structure and function.
    MeSH term(s) Amino Acid Sequence ; Antiporters/chemistry ; Antiporters/genetics ; Antiporters/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Gene Expression Regulation, Bacterial ; Magnetic Resonance Spectroscopy ; Membrane Transport Proteins/genetics ; Membrane Transport Proteins/metabolism ; Models, Molecular ; Models, Theoretical ; Mutagenesis ; Mutation ; Protein Conformation
    Chemical Substances Antiporters ; Escherichia coli Proteins ; Membrane Transport Proteins ; EmrE protein, E coli (147995-06-0)
    Language English
    Publishing date 2019-10-22
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.48909
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  8. Article: A CURE Biochemistry Laboratory Module to Study Protein-Protein Interactions by NMR Spectroscopy.

    Marsiglia, William M / Qamra, Rohini / Jackson, Kimberly M / Traaseth, Nathaniel J

    Journal of chemical education

    2020  Volume 97, Issue 2, Page(s) 437–442

    Abstract: Design of undergraduate laboratory courses that provide meaningful research-based experiences enhance undergraduate curricula and prepare future graduate students for research careers. In this article, a Course-based Undergraduate Research Experience ( ... ...

    Abstract Design of undergraduate laboratory courses that provide meaningful research-based experiences enhance undergraduate curricula and prepare future graduate students for research careers. In this article, a Course-based Undergraduate Research Experience (CURE) laboratory module was designed for upper-division undergraduate biochemistry and chemistry students. The laboratory module enabled students to build upon recently published data in the literature to decipher atomistic insight for an essential protein-protein interaction in human biology through the use of biomolecular NMR spectroscopy. Students compared their results with published data with the goal of identifying specific regions of the protein-protein interaction responsible for triggering an allosteric conformational change. The laboratory module introduced students to basic and advance laboratory techniques, including protein purification, NMR spectroscopy, and analysis of protein structure using molecular visualization software.
    Language English
    Publishing date 2020-01-06
    Publishing country United States
    Document type Journal Article
    ZDB-ID 218164-2
    ISSN 1938-1328 ; 0021-9584
    ISSN (online) 1938-1328
    ISSN 0021-9584
    DOI 10.1021/acs.jchemed.9b00364
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    Zs.B 1902: Show issues Location:
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  9. Article ; Online: Inducing conformational preference of the membrane protein transporter EmrE through conservative mutations

    Maureen Leninger / Ampon Sae Her / Nathaniel J Traaseth

    eLife, Vol

    2019  Volume 8

    Abstract: Transporters from bacteria to humans contain inverted repeat domains thought to arise evolutionarily from the fusion of smaller membrane protein genes. Association between these domains forms the functional unit that enables transporters to adopt ... ...

    Abstract Transporters from bacteria to humans contain inverted repeat domains thought to arise evolutionarily from the fusion of smaller membrane protein genes. Association between these domains forms the functional unit that enables transporters to adopt distinct conformations necessary for function. The small multidrug resistance (SMR) family provides an ideal system to explore the role of mutations in altering conformational preference since transporters from this family consist of antiparallel dimers that resemble the inverted repeats present in larger transporters. Here, we show using NMR spectroscopy how a single conservative mutation introduced into an SMR dimer is sufficient to change the resting conformation and function in bacteria. These results underscore the dynamic energy landscape for transporters and demonstrate how conservative mutations can influence structure and function.
    Keywords transporters ; EmrE ; membrane protein evolution ; multidrug resistance ; NMR spectroscopy ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2019-10-01T00:00:00Z
    Publisher eLife Sciences Publications Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article: Site-specific resolution of anionic residues in proteins using solid-state NMR spectroscopy

    Li, Jianping / Sae Her, Ampon / Traaseth, Nathaniel J.

    Journal of biomolecular NMR. 2020 July, v. 74, no. 6-7

    2020  

    Abstract: NMR spectroscopy is commonly used to infer site-specific acid dissociation constants (pKₐ) since the chemical shift is sensitive to the protonation state. Methods that probe atoms nearest to the functional groups involved in acid/base chemistry are the ... ...

    Abstract NMR spectroscopy is commonly used to infer site-specific acid dissociation constants (pKₐ) since the chemical shift is sensitive to the protonation state. Methods that probe atoms nearest to the functional groups involved in acid/base chemistry are the most sensitive for determining the protonation state. In this work, we describe a magic-angle-spinning (MAS) solid-state NMR approach to measure chemical shifts on the side chain of the anionic residues aspartate and glutamate. This method involves a combination of double quantum spectroscopy in the indirect dimension and REDOR dephasing to provide a sensitive and resolved view of these amino acid residues that are commonly involved in enzyme catalysis and membrane protein transport. To demonstrate the applicability of the approach, we carried out measurements using a microcrystalline soluble protein (ubiquitin) and a membrane protein embedded in lipid bilayers (EmrE). Overall, the resolution available from the double quantum dimension and confidence in identification of aspartate and glutamate residues from the REDOR filter make this method the most convenient for characterizing protonation states and deriving pKₐ values using MAS solid-state NMR.
    Keywords aspartic acid ; catalytic activity ; dissociation ; enzymes ; glutamic acid ; lipid bilayers ; membrane proteins ; nuclear magnetic resonance spectroscopy ; protein transport ; protonation ; ubiquitin
    Language English
    Dates of publication 2020-07
    Size p. 355-363.
    Publishing place Springer Netherlands
    Document type Article
    ZDB-ID 1081696-3
    ISSN 0925-2738
    ISSN 0925-2738
    DOI 10.1007/s10858-020-00323-z
    Database NAL-Catalogue (AGRICOLA)

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