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Künzel N, Helms V. How Peptides Bind to PSD-95/Discs-Large/ZO-1 Domains. J Chem Theory Comput 2022; 18:3845-3859. [PMID: 35608157 DOI: 10.1021/acs.jctc.1c01140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
PSD-95/discs-large/ZO-1 (PDZ) domains form a large family of adaptor proteins that bind to the C-terminal tails of their binding partner proteins. Via extensive molecular dynamics simulations and alchemical free energy calculations, we characterized the binding modi of phosphorylated and unphosphorylated EQVSAV peptides and of a EQVEAV phosphate mimic to the hPTP1E PDZ2 and MAGI1 PDZ1 domains. The simulations reproduced the well-known binding characteristics such as tight coordination of the peptidic carboxyl tail and pronounced hydrogen bonding between the peptide backbone and the backbone atoms of a β-sheet in PDZ. Overall, coordination by hPTP1E PDZ2 appeared tighter than by MAGI1 PDZ1. Simulations of wild-type PDZ and arginine mutants suggest that contacts with Arg79/85 in hPTP1E/MAGI1 are more important for the EQVEAV peptide than for EQVSAV. Alchemical free energy calculations and PaCS-MD simulations could well reproduce the difference in binding free energy between unphosphorylated EQVSAV and EQVEAV peptides and the absolute binding free energy of EQVSAV. However, likely due to small force field inaccuracies, the simulations erroneously favored binding of the phosphorylated peptide instead of its unphosphorylated counterpart, which is in contrast to the experiment.
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Affiliation(s)
- Nicolas Künzel
- Center for Bioinformatics, Saarland University, P.O. Box 15 11 50, D-66041 Saarbrücken, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, P.O. Box 15 11 50, D-66041 Saarbrücken, Germany
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Knapp ML, Alansary D, Poth V, Förderer K, Sommer F, Zimmer D, Schwarz Y, Künzel N, Kless A, Machaca K, Helms V, Mühlhaus T, Schroda M, Lis A, Niemeyer BA. A longer isoform of Stim1 is a negative SOCE regulator but increases cAMP-modulated NFAT signaling. EMBO Rep 2021; 23:e53135. [PMID: 34942054 PMCID: PMC8892257 DOI: 10.15252/embr.202153135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 11/23/2021] [Accepted: 12/07/2021] [Indexed: 11/23/2022] Open
Abstract
Alternative splicing is a potent modifier of protein function. Stromal interaction molecule 1 (Stim1) is the essential activator of store‐operated Ca2+ entry (SOCE) triggering activation of transcription factors. Here, we characterize Stim1A, a splice variant with an additional 31 amino acid domain inserted in frame within its cytosolic domain. Prominent expression of exon A is found in astrocytes, heart, kidney, and testes. Full‐length Stim1A functions as a dominant‐negative regulator of SOCE and ICRAC, facilitating sequence‐specific fast calcium‐dependent inactivation and destabilizing gating of Orai channels. Downregulation or absence of native Stim1A results in increased SOCE. Despite reducing SOCE, Stim1A leads to increased NFAT translocation. Differential proteomics revealed an interference of Stim1A with the cAMP‐SOCE crosstalk by altered modulation of phosphodiesterase 8 (PDE8), resulting in reduced cAMP degradation and increased PIP5K activity, facilitating NFAT activation. Our study uncovers a hitherto unknown mechanism regulating NFAT activation and indicates that cell‐type‐specific splicing of Stim1 is a potent means to regulate the NFAT signalosome and cAMP‐SOCE crosstalk.
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Affiliation(s)
- Mona L Knapp
- Molecular Biophysics, Saarland University, Homburg, Germany
| | - Dalia Alansary
- Molecular Biophysics, Saarland University, Homburg, Germany
| | - Vanessa Poth
- Molecular Biophysics, Saarland University, Homburg, Germany
| | | | - Frederik Sommer
- Molecular Biotechnology and Systems Biology, TU Kaiserslautern, Kaiserslautern, Germany
| | - David Zimmer
- Computational Systems Biology, TU Kaiserslautern, Kaiserslautern, Germany
| | - Yvonne Schwarz
- Molecular Neurophysiology, Center for Integrative Physiology and Molecular Medicine (CIPMM), Saarland University, Homburg, Germany
| | - Nicolas Künzel
- Center for Bioinformatics, Saarland University, Saarbruecken, Germany
| | - Achim Kless
- Grünenthal Innovation, Drug Discovery Technologies, Grünenthal GmbH, Aachen, Germany
| | | | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbruecken, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, TU Kaiserslautern, Kaiserslautern, Germany
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, TU Kaiserslautern, Kaiserslautern, Germany
| | - Annette Lis
- Biophysics, Saarland University, Homburg, Germany
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Cappello S, Sung HM, Ickes C, Gibhardt CS, Vultur A, Bhat H, Hu Z, Brafford P, Denger A, Stejerean-Todoran I, Köhn RM, Lorenz V, Künzel N, Salinas G, Stanisz H, Legler T, Rehling P, Schön MP, Lang KS, Helms V, Herlyn M, Hoth M, Kummerow C, Bogeski I. Protein Signatures of NK Cell-Mediated Melanoma Killing Predict Response to Immunotherapies. Cancer Res 2021; 81:5540-5554. [PMID: 34518212 DOI: 10.1158/0008-5472.can-21-0164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 07/07/2021] [Accepted: 09/10/2021] [Indexed: 11/16/2022]
Abstract
Despite impressive advances in melanoma-directed immunotherapies, resistance is common and many patients still succumb to metastatic disease. In this context, harnessing natural killer (NK) cells, which have thus far been sidelined in the development of melanoma immunotherapy, could provide therapeutic benefits for cancer treatment. To identify molecular determinants of NK cell-mediated melanoma killing (NKmK), we quantified NK-cell cytotoxicity against a panel of genetically diverse melanoma cell lines and observed highly heterogeneous susceptibility. Melanoma protein microarrays revealed a correlation between NKmK and the abundance and activity of a subset of proteins, including several metabolic factors. Oxidative phoshorylation, measured by oxygen consumption rate, negatively correlated with melanoma cell sensitivity toward NKmK, and proteins involved in mitochondrial metabolism and epithelial-mesenchymal transition were confirmed to regulate NKmK. Two- and three-dimensional killing assays and melanoma xenografts established that the PI3K/AKT/mTOR signaling axis controls NKmK via regulation of NK cell-relevant surface proteins. A "protein-killing-signature" based on the protein analysis predicted NKmK of additional melanoma cell lines and the response of patients with melanoma to anti-PD-1 checkpoint therapy. Collectively, these findings identify novel NK cell-related prognostic biomarkers and may contribute to improved and personalized melanoma-directed immunotherapies. SIGNIFICANCE: NK-cell cytotoxicity assays and protein microarrays reveal novel biomarkers of NK cell-mediated melanoma killing and enable development of signatures to predict melanoma patient responsiveness to immunotherapies.
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Affiliation(s)
- Sabrina Cappello
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg August University, Göttingen, Germany.,Biophysics, Centre for Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
| | - Hsu-Min Sung
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg August University, Göttingen, Germany
| | - Christian Ickes
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg August University, Göttingen, Germany
| | - Christine S Gibhardt
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg August University, Göttingen, Germany
| | - Adina Vultur
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg August University, Göttingen, Germany.,The Wistar Institute, Melanoma Research Center, Philadelphia, Pennsylvania
| | - Hilal Bhat
- Institute of Immunology, Medical Faculty, University Duisburg-Essen, Essen, Germany
| | - Zhongwen Hu
- Institute of Immunology, Medical Faculty, University Duisburg-Essen, Essen, Germany
| | - Patricia Brafford
- The Wistar Institute, Melanoma Research Center, Philadelphia, Pennsylvania
| | - Andreas Denger
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Ioana Stejerean-Todoran
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg August University, Göttingen, Germany
| | - Rixa-Mareike Köhn
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg August University, Göttingen, Germany
| | - Verena Lorenz
- Department of Dermatology, Venereology and Allergology, University Medical Center, Georg August University, Göttingen, Germany
| | - Nicolas Künzel
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Gabriela Salinas
- NGS- Core Unit for Integrative Genomics, Institute for Human Genetics, University Medical Center, Göttingen, Germany
| | - Hedwig Stanisz
- Department of Dermatology, Venereology and Allergology, University Medical Center, Georg August University, Göttingen, Germany
| | - Tobias Legler
- Department of Transfusion Medicine, University Medical Center Göttingen, Göttingen, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center, Georg-August-University, Göttingen, Germany.,Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
| | - Michael P Schön
- Department of Dermatology, Venereology and Allergology, University Medical Center, Georg August University, Göttingen, Germany
| | - Karl S Lang
- Institute of Immunology, Medical Faculty, University Duisburg-Essen, Essen, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Meenhard Herlyn
- The Wistar Institute, Melanoma Research Center, Philadelphia, Pennsylvania
| | - Markus Hoth
- Biophysics, Centre for Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
| | - Carsten Kummerow
- Biophysics, Centre for Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
| | - Ivan Bogeski
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg August University, Göttingen, Germany. .,Biophysics, Centre for Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
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Vlachou E, Kümmel S, Künzel N, Breit E, Schindowski D, Pankert K, Hentsch S, Hanf V, Weber D, Graßhoff ST, Müller C, Lucke W, Deuschle P, Engellandt K, Rüland A, Dall P, Harrach H, Bruzas S, Chiari O, Reinisch M. 201TiP Evaluation of the feasibility of ultrasound-guided clipping of suspicious intramammary lesions in primary breast cancer patients receiving neoadjuvant therapy (Ultra3Detect). Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Künzel N, Helms V. How phosphorylation of peptides affects their interaction with 14-3-3η domains. Proteins 2021; 90:351-362. [PMID: 34462973 DOI: 10.1002/prot.26224] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 05/22/2021] [Accepted: 08/18/2021] [Indexed: 01/04/2023]
Abstract
Members of the 14-3-3 domain family have important functions as adapter domains. Via an amphipathic groove on their protein surface they typically bind to disordered C-terminals of other proteins. Importantly, binding partners of 14-3-3 domains usually contain a phosphorylated serine or threonine residue at their binding interface and possess one of three different sequence motifs. Binding of the respective unphosphorylated versions of the peptides is typically strongly disfavored. There is a wealth of structural and thermodynamic data available for the phosphorylated forms but not for the unphosphorylated forms as the binding affinities seem to be too weak to be measurable experimentally. Here, we characterized the mechanistic details that govern the preference for the binding of phosphorylated peptides to 14-3-3η domains by means of molecular dynamics (MD) simulations. We found that the phosphate group is ideally coordinated in the binding pocket whereas the respective unphosphorylated side-chain counterpart is not. Thus, the binding preference results from the tight coordination of the phosphorylated residue at the center of the binding interface. Furthermore, MD simulations of 14-3-3η dimers showed a preference for the simultaneous binding of two phosphorylated peptides in agreement with their experimentally observed cooperativity.
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Affiliation(s)
- Nicolas Künzel
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany.,Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Postfach 15 11 50, 66041, Saarbrücken, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany.,Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Postfach 15 11 50, 66041, Saarbrücken, Germany
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Sprott H, Hein G, Domke D, Künzel N, Uhlemann C, Wollina U, Stein G. [Enthesopathies--diagnosis and therapy]. Z Arztl Fortbild (Jena) 1997; 90:711-8. [PMID: 9133111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Problems are frequently encountered regarding the terminology, diagnosis, differential diagnosis, and therapy of diseases of thes tendons insertion point (enthesis): Terms such as tendinosis, tenopathy, tendinitis, tendovaginitis, tendoperiostitis, insertions tenopathy, tendomyosis, etc. often are used interchangeably even through they describe anatomically and pathophysiologically different conditions. The term enthesiopathy is used as a generic term in this overview article irrespective of the causality.
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Affiliation(s)
- H Sprott
- Klinik für Innere Medizin IV, Friedrich-Schiller-Universität Jena, Bad Kissingen
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