1
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Anderson JW, Vaisar D, Jones DN, Pegram LM, Vigers GP, Chen H, Moffat JG, Ahn NG. Conformation selection by ATP-competitive inhibitors and allosteric communication in ERK2. eLife 2024; 12:RP91507. [PMID: 38537148 PMCID: PMC10972564 DOI: 10.7554/elife.91507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Activation of the extracellular signal-regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange between two conformational states of the active kinase, named 'L' and 'R,' where R is associated with a catalytically productive ATP-binding mode. An ATP-competitive ERK1/2 inhibitor, Vertex-11e, has properties of conformation selection for the R-state, revealing movements of the activation loop that are allosterically coupled to the kinase active site. However, the features of inhibitors important for R-state selection are unknown. Here, we survey a panel of ATP-competitive ERK inhibitors using HDX-MS and NMR and identify 14 new molecules with properties of R-state selection. They reveal effects propagated to distal regions in the P+1 and helix αF segments surrounding the activation loop, as well as helix αL16. Crystal structures of inhibitor complexes with ERK2 reveal systematic shifts in the Gly loop and helix αC, mediated by a Tyr-Tyr ring stacking interaction and the conserved Lys-Glu salt bridge. The findings suggest a model for the R-state involving small movements in the N-lobe that promote compactness within the kinase active site and alter mobility surrounding the activation loop. Such properties of conformation selection might be exploited to modulate the protein docking interface used by ERK substrates and effectors.
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Affiliation(s)
- Jake W Anderson
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | - David Vaisar
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | - David N Jones
- Department of Pharmacology, University of Colorado Anschutz Medical CenterBoulderUnited States
| | - Laurel M Pegram
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | | | - Huifen Chen
- Genentech, Inc.South San FranciscoUnited States
| | | | - Natalie G Ahn
- Department of Biochemistry, University of ColoradoBoulderUnited States
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2
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Anderson JW, Vaisar D, Jones DN, Pegram LM, Vigers GP, Chen H, Moffat JG, Ahn NG. Conformation Selection by ATP-competitive Inhibitors and Allosteric Communication in ERK2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557258. [PMID: 37745518 PMCID: PMC10515847 DOI: 10.1101/2023.09.12.557258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Activation of the extracellular signal regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange between two conformational states of the active kinase, named "L" and "R", where R is associated with a catalytically productive ATP-binding mode. An ATP-competitive ERK1/2 inhibitor, Vertex-11e, has properties of conformation selection for the R-state, revealing movements of the activation loop that are allosterically coupled to the kinase active site. However, the features of inhibitors important for R-state selection are unknown. Here we survey a panel of ATP-competitive ERK inhibitors using HDX-MS and NMR and identify 14 new molecules with properties of R-state selection. They reveal effects propagated to distal regions in the P+1 and helix αF segments surrounding the activation loop, as well as helix αL16. Crystal structures of inhibitor complexes with ERK2 reveal systematic shifts in the Gly loop and helix αC, mediated by a Tyr-Tyr ring stacking interaction and the conserved Lys-Glu salt bridge. The findings suggest a model for the R-state involving small movements in the N-lobe that promote compactness within the kinase active site and alter mobility surrounding the activation loop. Such properties of conformation selection might be exploited to modulate the protein docking interface used by ERK substrates and effectors.
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Affiliation(s)
| | - David Vaisar
- Department of Biochemistry, University of Colorado, Boulder, CO
| | - David N. Jones
- Department of Pharmacology, University of Colorado Anschutz Medical Center, Aurora, CO
| | - Laurel M. Pegram
- Department of Biochemistry, University of Colorado, Boulder, CO
- Present address: Loxo Oncology, Louisville, CO 80027
| | - Guy P. Vigers
- Array BioPharma, Inc., Boulder, CO
- Present address: Allium Consulting LLC, Boulder, CO 80304
| | - Huifen Chen
- Genentech, Inc. South San Francisco, CA, USA
| | | | - Natalie G. Ahn
- Department of Biochemistry, University of Colorado, Boulder, CO
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3
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Maass T, Westermann LT, Creutznacher R, Mallagaray A, Dülfer J, Uetrecht C, Peters T. Assignment of Ala, Ile, Leu proS, Met, and Val proS methyl groups of the protruding domain of murine norovirus capsid protein VP1 using methyl-methyl NOEs, site directed mutagenesis, and pseudocontact shifts. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:97-107. [PMID: 35050443 PMCID: PMC9068638 DOI: 10.1007/s12104-022-10066-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 01/12/2022] [Indexed: 05/14/2023]
Abstract
The protruding domain (P-domain) of the murine norovirus (MNV) capsid protein VP1 is essential for infection. It mediates receptor binding and attachment of neutralizing antibodies. Protein NMR studies into interactions of the P-domain with ligands will yield insights not easily available from other biophysical techniques and will extend our understanding of MNV attachment to host cells. Such studies require at least partial NMR assignments. Here, we describe the assignment of about 70% of the Ala, Ile, LeuproS, Met, and ValproS methyl groups. An unfavorable distribution of methyl group resonance signals prevents complete assignment based exclusively on 4D HMQC-NOESY-HMQC experiments, yielding assignment of only 55 out of 100 methyl groups. Therefore, we created point mutants and measured pseudo contact shifts, extending and validating assignments based on methyl-methyl NOEs. Of note, the P-domains are present in two different forms caused by an approximate equal distribution of trans- and cis-configured proline residues in position 361.
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Affiliation(s)
- Thorben Maass
- Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, University of Luebeck, Ratzeburger Allee 160, 23562, Luebeck, Germany
| | - Leon Torben Westermann
- Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, University of Luebeck, Ratzeburger Allee 160, 23562, Luebeck, Germany
| | - Robert Creutznacher
- Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, University of Luebeck, Ratzeburger Allee 160, 23562, Luebeck, Germany
| | - Alvaro Mallagaray
- Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, University of Luebeck, Ratzeburger Allee 160, 23562, Luebeck, Germany
| | - Jasmin Dülfer
- Leibniz Institute for Experimental Virology (HPI), 20251, Hamburg, Germany
| | - Charlotte Uetrecht
- Leibniz Institute for Experimental Virology (HPI), 20251, Hamburg, Germany
- School of Life Sciences, University of Siegen, 57076 Siegen & Centre for Structural Systems Biology (CSSB), & Deutsches Elektronensynchrotron (DESY), 22607 Hamburg & European XFEL GmbH, 22869, Schenefeld, Germany
| | - Thomas Peters
- Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, University of Luebeck, Ratzeburger Allee 160, 23562, Luebeck, Germany.
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4
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Tong MHG, Jeeves M, Rajesh S, Ludwig C, Lenoir M, Kumar J, McClelland DM, Berditchevski F, Hubbard JA, Kenyon C, Butterworth S, Knapp S, Overduin M. Backbone resonance assignments of the catalytic and regulatory domains of Ca 2+/calmodulin-dependent protein kinase 1D. BIOMOLECULAR NMR ASSIGNMENTS 2020; 14:221-225. [PMID: 32535836 PMCID: PMC7462902 DOI: 10.1007/s12104-020-09950-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/21/2020] [Indexed: 06/11/2023]
Abstract
The CaMK subfamily of Ser/Thr kinases are regulated by calmodulin interactions with their C-terminal regions. They are exemplified by Ca2+/calmodulin dependent protein kinase 1δ which is known as CaMK1D, CaMKIδ or CKLiK. CaMK1D mediates intracellular signalling downstream of Ca2+ influx and thereby exhibits amplifications of Ca2+signals and polymorphisms that have been implicated in breast cancer and diabetes. Here we report the backbone 1H, 13C, 15N assignments of the 38 kDa human CaMK1D protein in its free state, including both the canonical bi-lobed kinase fold as well as the autoinhibitory and calmodulin binding domains.
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Affiliation(s)
- Michael H G Tong
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Sundaresan Rajesh
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Christian Ludwig
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Marc Lenoir
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Jitendra Kumar
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Darren M McClelland
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Fedor Berditchevski
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Julia A Hubbard
- Computational, Analytical and Structural Sciences, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Colin Kenyon
- Faculty of Medicine and Health Sciences, Stellenbosch University, Francie Van Zijl Dr, Parow, Cape Town, 7505, South Africa
| | - Sam Butterworth
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, M13 9PL, UK
| | - Stefan Knapp
- Structural Genomics Consortium and Buchmann Institute for Molecular Life Sciences, Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
| | - Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada.
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5
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Iverson DB, Xiao Y, Jones DN, Eisenmesser EZ, Ahn NG. Activation Loop Dynamics Are Coupled to Core Motions in Extracellular Signal-Regulated Kinase-2. Biochemistry 2020; 59:2698-2706. [PMID: 32643366 DOI: 10.1021/acs.biochem.0c00485] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The activation loop segment in protein kinases is a common site for regulatory phosphorylation. In extracellular signal-regulated kinase 2 (ERK2), dual phosphorylation and conformational rearrangement of the activation loop accompany enzyme activation. X-ray structures show the active conformation to be stabilized by multiple ion pair interactions between phosphorylated threonine and tyrosine residues in the loop and six arginine residues in the kinase core. Despite the extensive salt bridge network, nuclear magnetic resonance Carr-Purcell-Meiboom-Gill relaxation dispersion experiments show that the phosphorylated activation loop is conformationally mobile on a microsecond to millisecond time scale. The dynamics of the loop match those of previously reported global exchange within the kinase core region and surrounding the catalytic site that have been found to facilitate productive nucleotide binding. Mutations in the core region that alter these global motions also alter the dynamics of the activation loop. Conversely, mutations in the activation loop perturb the global exchange within the kinase core. Together, these findings provide evidence for coupling between motions in the activation loop and those surrounding the catalytic site in the active state of the kinase. Thus, the activation loop segment in dual-phosphorylated ERK2 is not held statically in the active X-ray conformation but instead undergoes exchange between conformers separated by a small energetic barrier, serving as part of a dynamic allosteric network controlling nucleotide binding and catalytic function.
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Affiliation(s)
- Dylan B Iverson
- Department of Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Yao Xiao
- Department of Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | | | | | - Natalie G Ahn
- Department of Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, United States
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6
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Pritišanac I, Alderson TR, Güntert P. Automated assignment of methyl NMR spectra from large proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 118-119:54-73. [PMID: 32883449 DOI: 10.1016/j.pnmrs.2020.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 05/05/2023]
Abstract
As structural biology trends towards larger and more complex biomolecular targets, a detailed understanding of their interactions and underlying structures and dynamics is required. The development of methyl-TROSY has enabled NMR spectroscopy to provide atomic-resolution insight into the mechanisms of large molecular assemblies in solution. However, the applicability of methyl-TROSY has been hindered by the laborious and time-consuming resonance assignment process, typically performed with domain fragmentation, site-directed mutagenesis, and analysis of NOE data in the context of a crystal structure. In response, several structure-based automatic methyl assignment strategies have been developed over the past decade. Here, we present a comprehensive analysis of all available methods and compare their input data requirements, algorithmic strategies, and reported performance. In general, the methods fall into two categories: those that primarily rely on inter-methyl NOEs, and those that utilize methyl PRE- and PCS-based restraints. We discuss their advantages and limitations, and highlight the potential benefits from standardizing and combining different methods.
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Affiliation(s)
- Iva Pritišanac
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - T Reid Alderson
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Güntert
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany; Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland; Department of Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan.
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7
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Müller-Hermes C, Creutznacher R, Mallagaray A. Complete assignment of Ala, Ile, Leu ProS, Met and Val ProS methyl groups of the protruding domain from human norovirus GII.4 Saga. BIOMOLECULAR NMR ASSIGNMENTS 2020; 14:123-130. [PMID: 31993958 PMCID: PMC7069894 DOI: 10.1007/s12104-020-09932-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/16/2020] [Indexed: 05/05/2023]
Abstract
Attachment of human noroviruses to histo blood group antigens (HBGAs) is thought to be essential for infection, although how this binding event promotes infection is unknown. Recent studies have shown that 60% of all GII.4 epidemic strains may undergo a spontaneous post-translational modification (PTM) in an amino acid located adjacent to the binding pocket for HBGAs. This transformation proceeds with an estimated half-life of 1-2 days under physiological conditions, dramatically affecting HBGA recognition. The surface-exposed position of this PTM and its sequence conservation suggests a relevant role in immune escape and host-cell recognition. As a first step towards the understanding of the biological implications of this PTM at atomic resolution, we report the complete assignment of methyl resonances of a MILProSVProSA methyl-labeled sample of a 72 kDa protruding domain from a GII.4 Saga human norovirus strain. Assignments were obtained from methyl-methyl NOESY experiments combined with site-directed mutagenesis and automated assignment. This data provides the basis for a detailed characterization of the PTM-driven modulation of immune recognition in human norovirus on a molecular level.
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Affiliation(s)
- Christoph Müller-Hermes
- Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Robert Creutznacher
- Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Alvaro Mallagaray
- Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.
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8
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Siemons L, Mackenzie HW, Shukla VK, Hansen DF. Intra-residue methyl-methyl correlations for valine and leucine residues in large proteins from a 3D-HMBC-HMQC experiment. JOURNAL OF BIOMOLECULAR NMR 2019; 73:749-757. [PMID: 31720925 PMCID: PMC6875545 DOI: 10.1007/s10858-019-00287-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 11/03/2019] [Indexed: 05/21/2023]
Abstract
Methyl-TROSY based NMR experiments have over the last two decades become one of the most important means to characterise dynamics and functional mechanisms of large proteins and macromolecular machines in solution. The chemical shift assignment of methyl groups in large proteins is, however, still not trivial and it is typically performed using backbone-dependent experiments in a 'divide and conquer' approach, mutations, structure-based assignments or a combination of these. Structure-based assignment of methyl groups is an emerging strategy, which reduces the time and cost required as well as providing a method that is independent of a backbone assignment. One crucial step in available structure-based assignment protocols is linking the two prochiral methyl groups of leucine and valine residues. This has previously been achieved by recording NOESY spectra with short mixing times or by comparing NOESY spectra. Herein, we present a method based on through-bond scalar coupling transfers, a 3D-HMBC-HMQC experiment, to link the intra-residue methyl groups of leucine and valine. It is shown that the HMBC-HMQC method has several advantages over solely using NOESY spectra since a unique intra-residue cross-peak is observed. Moreover, overlap in the methyl-TROSY HMQC spectrum can easily be identified with the HMBC-HMQC experiment, thereby removing possible ambiguities in the assignment.
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Affiliation(s)
- Lucas Siemons
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Harold W Mackenzie
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Vaibhav Kumar Shukla
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK.
| | - D Flemming Hansen
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK.
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9
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Kaoud TS, Johnson WH, Ebelt ND, Piserchio A, Zamora-Olivares D, Van Ravenstein SX, Pridgen JR, Edupuganti R, Sammons R, Cano M, Warthaka M, Harger M, Tavares CDJ, Park J, Radwan MF, Ren P, Anslyn EV, Tsai KY, Ghose R, Dalby KN. Modulating multi-functional ERK complexes by covalent targeting of a recruitment site in vivo. Nat Commun 2019; 10:5232. [PMID: 31745079 PMCID: PMC6863825 DOI: 10.1038/s41467-019-12996-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 10/10/2019] [Indexed: 12/31/2022] Open
Abstract
Recently, the targeting of ERK with ATP-competitive inhibitors has emerged as a potential clinical strategy to overcome acquired resistance to BRAF and MEK inhibitor combination therapies. In this study, we investigate an alternative strategy of targeting the D-recruitment site (DRS) of ERK. The DRS is a conserved region that lies distal to the active site and mediates ERK-protein interactions. We demonstrate that the small molecule BI-78D3 binds to the DRS of ERK2 and forms a covalent adduct with a conserved cysteine residue (C159) within the pocket and disrupts signaling in vivo. BI-78D3 does not covalently modify p38MAPK, JNK or ERK5. BI-78D3 promotes apoptosis in BRAF inhibitor-naive and resistant melanoma cells containing a BRAF V600E mutation. These studies provide the basis for designing modulators of protein-protein interactions involving ERK, with the potential to impact ERK signaling dynamics and to induce cell cycle arrest and apoptosis in ERK-dependent cancers.
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Affiliation(s)
- Tamer S Kaoud
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA.,Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt
| | - William H Johnson
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Nancy D Ebelt
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Andrea Piserchio
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY, USA
| | | | - Sabrina X Van Ravenstein
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Jacey R Pridgen
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Ramakrishna Edupuganti
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Rachel Sammons
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Micael Cano
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Mangalika Warthaka
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Matthew Harger
- Biomedical Engineering Department, The University of Texas at Austin, Austin, TX, USA
| | - Clint D J Tavares
- Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jihyun Park
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mohamed F Radwan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Pengyu Ren
- Biomedical Engineering Department, The University of Texas at Austin, Austin, TX, USA
| | - Eric V Anslyn
- Department of Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | | | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY, USA.,Graduate Programs in Biochemistry, Chemistry and Physics, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA.
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10
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Pritišanac I, Würz JM, Alderson TR, Güntert P. Automatic structure-based NMR methyl resonance assignment in large proteins. Nat Commun 2019; 10:4922. [PMID: 31664028 PMCID: PMC6820720 DOI: 10.1038/s41467-019-12837-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 10/02/2019] [Indexed: 11/10/2022] Open
Abstract
Isotopically labeled methyl groups provide NMR probes in large, otherwise deuterated proteins. However, the resonance assignment constitutes a bottleneck for broader applicability of methyl-based NMR. Here, we present the automated MethylFLYA method for the assignment of methyl groups that is based on methyl-methyl nuclear Overhauser effect spectroscopy (NOESY) peak lists. MethylFLYA is applied to five proteins (28–358 kDa) comprising a total of 708 isotope-labeled methyl groups, of which 612 contribute NOESY cross peaks. MethylFLYA confidently assigns 488 methyl groups, i.e. 80% of those with NOESY data. Of these, 459 agree with the reference, 6 were different, and 23 were without reference assignment. MethylFLYA assigns significantly more methyl groups than alternative algorithms, has an average error rate of 1%, modest runtimes of 0.4–1.2 h, and can handle arbitrary isotope labeling patterns and data from other types of NMR spectra. The structures and dynamics of large proteins can be studied with methyl-based NMR but peak assignment is still challenging. Here the authors present MethylFLYA that allows automated assignment of methyl groups and apply it to five proteins with molecular weights in the range from 28 to 358 kDa.
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Affiliation(s)
- Iva Pritišanac
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Julia M Würz
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - T Reid Alderson
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Peter Güntert
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany. .,Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland. .,Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan.
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11
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Flügge F, Peters T. Complete assignment of Ala, Ile, Leu, Met and Val methyl groups of human blood group A and B glycosyltransferases using lanthanide-induced pseudocontact shifts and methyl-methyl NOESY. JOURNAL OF BIOMOLECULAR NMR 2018; 70:245-259. [PMID: 29700756 DOI: 10.1007/s10858-018-0183-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/21/2018] [Indexed: 05/05/2023]
Abstract
Human blood group A and B glycosyltransferases (GTA, GTB) are highly homologous glycosyltransferases. A number of high-resolution crystal structures is available showing that these enzymes convert from an open conformation into a catalytically active closed conformation upon substrate binding. However, the mechanism of glycosyltransfer is still under debate, and the precise nature as well as the time scales of conformational transitions are unknown. NMR offers a variety of experiments to shine more light on these unresolved questions. Therefore, in a first step we have assigned all methyl resonance signals in MILVA labeled samples of GTA and GTB, still a challenging task for 70 kDa homodimeric proteins. Assignments were obtained from methyl-methyl NOESY experiments, and from measurements of lanthanide-induced pseudocontact shifts (PCS) using high resolution crystal structures as templates. PCSs and chemical shift perturbations, induced by substrate analogue binding, suggest that the fully closed state is not adopted in the presence of lanthanide ions.
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Affiliation(s)
- Friedemann Flügge
- Institute for Chemistry and Metabolomics, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Thomas Peters
- Institute for Chemistry and Metabolomics, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.
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12
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Simonelli L, Pedotti M, Bardelli M, Jurt S, Zerbe O, Varani L. Mapping Antibody Epitopes by Solution NMR Spectroscopy: Practical Considerations. Methods Mol Biol 2018; 1785:29-51. [PMID: 29714010 DOI: 10.1007/978-1-4939-7841-0_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Identifying an epitope, the region of the antigen in contact with an antibody, is useful in both basic and pharmaceutical research, as well as in vaccine design. Solution NMR spectroscopy is particularly well suited to the residue level characterization of intermolecular interfaces, including antibody-antigen interactions, and thus to epitope identification. Here, we describe the use of NMR for residue level characterization of protein epitopes, focusing on experimental protocols and practical considerations, highlighting advantages and drawbacks of the approach.
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Affiliation(s)
- Luca Simonelli
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Marco Bardelli
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Simon Jurt
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Oliver Zerbe
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Luca Varani
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland.
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Ying J, Delaglio F, Torchia DA, Bax A. Sparse multidimensional iterative lineshape-enhanced (SMILE) reconstruction of both non-uniformly sampled and conventional NMR data. JOURNAL OF BIOMOLECULAR NMR 2017; 68:101-118. [PMID: 27866371 PMCID: PMC5438302 DOI: 10.1007/s10858-016-0072-7] [Citation(s) in RCA: 197] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/25/2016] [Indexed: 05/03/2023]
Abstract
Implementation of a new algorithm, SMILE, is described for reconstruction of non-uniformly sampled two-, three- and four-dimensional NMR data, which takes advantage of the known phases of the NMR spectrum and the exponential decay of underlying time domain signals. The method is very robust with respect to the chosen sampling protocol and, in its default mode, also extends the truncated time domain signals by a modest amount of non-sampled zeros. SMILE can likewise be used to extend conventional uniformly sampled data, as an effective multidimensional alternative to linear prediction. The program is provided as a plug-in to the widely used NMRPipe software suite, and can be used with default parameters for mainstream application, or with user control over the iterative process to possibly further improve reconstruction quality and to lower the demand on computational resources. For large data sets, the method is robust and demonstrated for sparsities down to ca 1%, and final all-real spectral sizes as large as 300 Gb. Comparison between fully sampled, conventionally processed spectra and randomly selected NUS subsets of this data shows that the reconstruction quality approaches the theoretical limit in terms of peak position fidelity and intensity. SMILE essentially removes the noise-like appearance associated with the point-spread function of signals that are a default of five-fold above the noise level, but impacts the actual thermal noise in the NMR spectra only minimally. Therefore, the appearance and interpretation of SMILE-reconstructed spectra is very similar to that of fully sampled spectra generated by Fourier transformation.
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Affiliation(s)
- Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Digestive and Diabetic and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Frank Delaglio
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD, 20850, USA
| | - Dennis A Torchia
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Digestive and Diabetic and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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14
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Gao Q, Chalmers GR, Moremen KW, Prestegard JH. NMR assignments of sparsely labeled proteins using a genetic algorithm. JOURNAL OF BIOMOLECULAR NMR 2017; 67:283-294. [PMID: 28289927 PMCID: PMC5434516 DOI: 10.1007/s10858-017-0101-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/22/2017] [Indexed: 05/16/2023]
Abstract
Sparse isotopic labeling of proteins for NMR studies using single types of amino acid (15N or 13C enriched) has several advantages. Resolution is enhanced by reducing numbers of resonances for large proteins, and isotopic labeling becomes economically feasible for glycoproteins that must be expressed in mammalian cells. However, without access to the traditional triple resonance strategies that require uniform isotopic labeling, NMR assignment of crosspeaks in heteronuclear single quantum coherence (HSQC) spectra is challenging. We present an alternative strategy which combines readily accessible NMR data with known protein domain structures. Based on the structures, chemical shifts are predicted, NOE cross-peak lists are generated, and residual dipolar couplings (RDCs) are calculated for each labeled site. Simulated data are then compared to measured values for a trial set of assignments and scored. A genetic algorithm uses the scores to search for an optimal pairing of HSQC crosspeaks with labeled sites. While none of the individual data types can give a definitive assignment for a particular site, their combination can in most cases. Four test proteins previously assigned using triple resonance methods and a sparsely labeled glycosylated protein, Robo1, previously assigned by manual analysis, are used to validate the method and develop a criterion for identifying sites assigned with high confidence.
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Affiliation(s)
- Qi Gao
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Gordon R Chalmers
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
- Department of Computer Science and Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.
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Rosenzweig R, Kay LE. Solution NMR Spectroscopy Provides an Avenue for the Study of Functionally Dynamic Molecular Machines: The Example of Protein Disaggregation. J Am Chem Soc 2015; 138:1466-77. [PMID: 26651836 DOI: 10.1021/jacs.5b11346] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Solution-based NMR spectroscopy has been an important tool for studying the structure and dynamics of relatively small proteins and protein complexes with aggregate molecular masses under approximately 50 kDa. The development of new experiments and labeling schemes, coupled with continued improvements in hardware, has significantly reduced this size limitation, enabling atomic-resolution studies of molecular machines in the 1 MDa range. In this Perspective, some of the important advances are highlighted in the context of studies of molecular chaperones involved in protein disaggregation. New insights into the structural biology of disaggregation obtained from NMR studies are described, focusing on the unique capabilities of the methodology for obtaining atomic-resolution descriptions of dynamic systems.
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Affiliation(s)
- Rina Rosenzweig
- Departments of Molecular Genetics, Biochemistry, and Chemistry, The University of Toronto , Toronto, Ontario, Canada M5S 1A8
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry, and Chemistry, The University of Toronto , Toronto, Ontario, Canada M5S 1A8.,Program in Molecular Structure and Function, Hospital for Sick Children , 555 University Avenue, Toronto, Ontario, Canada M5G 1X8
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