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Alam S, Pardue S, Shen X, Glawe JD, Yagi T, Bhuiyan MAN, Patel RP, Dominic PS, Virk CS, Bhuiyan MS, Orr AW, Petit C, Kolluru GK, Kevil CG. Hypoxia increases persulfide and polysulfide formation by AMP kinase dependent cystathionine gamma lyase phosphorylation. Redox Biol 2023; 68:102949. [PMID: 37922764 PMCID: PMC10641705 DOI: 10.1016/j.redox.2023.102949] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023] Open
Abstract
Hydropersulfide and hydropolysulfide metabolites are increasingly important reactive sulfur species (RSS) regulating numerous cellular redox dependent functions. Intracellular production of these species is known to occur through RSS interactions or through translational mechanisms involving cysteinyl t-RNA synthetases. However, regulation of these species under cell stress conditions, such as hypoxia, that are known to modulate RSS remain poorly understood. Here we define an important mechanism of increased persulfide and polysulfide production involving cystathionine gamma lyase (CSE) phosphorylation at serine 346 and threonine 355 in a substrate specific manner, under acute hypoxic conditions. Hypoxic phosphorylation of CSE occurs in an AMP kinase dependent manner increasing enzyme activity involving unique inter- and intramolecular interactions within the tetramer. Importantly, both cellular hypoxia and tissue ischemia result in AMP Kinase dependent CSE phosphorylation that regulates blood flow in ischemic tissues. Our findings reveal hypoxia molecular signaling pathways regulating CSE dependent persulfide and polysulfide production impacting tissue and cellular response to stress.
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Affiliation(s)
- Shafiul Alam
- Department of Pathology, LSU Health Sciences Center, Shreveport, USA
| | - Sibile Pardue
- Department of Pathology, LSU Health Sciences Center, Shreveport, USA
| | - Xinggui Shen
- Department of Pathology, LSU Health Sciences Center, Shreveport, USA
| | - John D Glawe
- Department of Pathology, LSU Health Sciences Center, Shreveport, USA
| | - Takashi Yagi
- Department of Pathology, LSU Health Sciences Center, Shreveport, USA
| | | | - Rakesh P Patel
- Department of Pathology, University of Alabama at Birmingham, USA
| | - Paari S Dominic
- Internal Medicine-Cardiovascular Medicine, University of Iowa Healthcare, Iowa, USA
| | - Chiranjiv S Virk
- Department of Surgery, LSU Health Sciences Center, Shreveport, USA
| | | | - A Wayne Orr
- Department of Pathology, LSU Health Sciences Center, Shreveport, USA
| | - Chad Petit
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, USA
| | - Gopi K Kolluru
- Department of Pathology, LSU Health Sciences Center, Shreveport, USA
| | - Christopher G Kevil
- Department of Pathology, LSU Health Sciences Center, Shreveport, USA; Department of Cellular Biology and Anatomy, LSU Health Sciences Center, Shreveport, USA; Department of Molecular and Cellular Physiology, LSU Health Sciences Center, Shreveport, USA.
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2
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Cuesta-Hernández HN, Contreras J, Soriano-Maldonado P, Sánchez-Wandelmer J, Yeung W, Martín-Hurtado A, Muñoz IG, Kannan N, Llimargas M, Muñoz J, Plaza-Menacho I. An allosteric switch between the activation loop and a c-terminal palindromic phospho-motif controls c-Src function. Nat Commun 2023; 14:6548. [PMID: 37848415 PMCID: PMC10582172 DOI: 10.1038/s41467-023-41890-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 09/18/2023] [Indexed: 10/19/2023] Open
Abstract
Autophosphorylation controls the transition between discrete functional and conformational states in protein kinases, yet the structural and molecular determinants underlying this fundamental process remain unclear. Here we show that c-terminal Tyr 530 is a de facto c-Src autophosphorylation site with slow time-resolution kinetics and a strong intermolecular component. On the contrary, activation-loop Tyr 419 undergoes faster kinetics and a cis-to-trans phosphorylation switch that controls c-terminal Tyr 530 autophosphorylation, enzyme specificity, and strikingly, c-Src non-catalytic function as a substrate. In line with this, we visualize by X-ray crystallography a snapshot of Tyr 530 intermolecular autophosphorylation. In an asymmetric arrangement of both catalytic domains, a c-terminal palindromic phospho-motif flanking Tyr 530 on the substrate molecule engages the G-loop of the active kinase adopting a position ready for entry into the catalytic cleft. Perturbation of the phospho-motif accounts for c-Src dysfunction as indicated by viral and colorectal cancer (CRC)-associated c-terminal deleted variants. We show that c-terminal residues 531 to 536 are required for c-Src Tyr 530 autophosphorylation, and such a detrimental effect is caused by the substrate molecule inhibiting allosterically the active kinase. Our work reveals a crosstalk between the activation and c-terminal segments that control the allosteric interplay between substrate- and enzyme-acting kinases during autophosphorylation.
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Affiliation(s)
- Hipólito Nicolás Cuesta-Hernández
- Kinases, Protein Phosphorylation and Cancer Group, Structural Biology Programme, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain
| | - Julia Contreras
- Kinases, Protein Phosphorylation and Cancer Group, Structural Biology Programme, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain
| | - Pablo Soriano-Maldonado
- Kinases, Protein Phosphorylation and Cancer Group, Structural Biology Programme, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria (UFV), 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Jana Sánchez-Wandelmer
- Proteomics Unit, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain
| | - Wayland Yeung
- Institute of Bioinformatics, Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Ana Martín-Hurtado
- Kinases, Protein Phosphorylation and Cancer Group, Structural Biology Programme, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain
| | - Inés G Muñoz
- Protein Crystallography Unit, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain
| | - Natarajan Kannan
- Institute of Bioinformatics, Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Marta Llimargas
- Institute of Molecular Biology of Barcelona (IMBB) CSIC, 08028, Barcelona, Spain
| | - Javier Muñoz
- Proteomics Unit, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain
- Ikerbasque, Basque Foundation for Science, IIS Biocruces Bizkaia, Building Biocruces Bizkaia 1, 48903, Cruces, Bizkaia, Spain
| | - Iván Plaza-Menacho
- Kinases, Protein Phosphorylation and Cancer Group, Structural Biology Programme, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain.
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3
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Sad K, Jones CY, Adams M, Lustenberger S, Lee RS, Elayavalli SR, Farhi J, Lemon LD, Fasken MB, Corbett AH, Spangle JM. Histone H3 E50K mutation confers oncogenic activity and supports an EMT phenotype. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.11.561775. [PMID: 37873162 PMCID: PMC10592736 DOI: 10.1101/2023.10.11.561775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Sequencing of human patient tumors has identified recurrent missense mutations in genes encoding core histones. We report that mutations that convert histone H3 amino acid 50 from a glutamate to a lysine (H3E50K) support an oncogenic phenotype in human cells. Expression of H3E50K is sufficient to transform human cells as evidenced by a dramatic increase in cell migration and invasion, and a statistically significant increase in proliferation and clonogenicity. H3E50K also increases the invasive phenotype in the context of co-occurring BRAF mutations, which are present in patient tumors characterized by H3E50K. H3E50 lies on the globular domain surface in a region that contacts H4 within the nucleosome. We find that H3E50K perturbs proximal H3 post-translational modifications globally and dysregulates gene expression, activating the epithelial to mesenchymal transition. Functional studies using S. cerevisiae reveal that, while yeast cells that express H3E50K as the sole copy of histone H3 show sensitivity to cellular stressors, including caffeine, H3E50K cells display some genetic interactions that are distinct from the characterized H3K36M oncohistone yeast model. Taken together, these data suggest that additional histone H3 mutations have the potential to be oncogenic drivers and function through distinct mechanisms that dysregulate gene expression.
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Affiliation(s)
- K Sad
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322
| | - CY Jones
- Department of Biology; Emory College of Arts and Sciences, Atlanta GA 30322
| | - M Adams
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322
| | - S Lustenberger
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - RS Lee
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322
| | - SR Elayavalli
- Department of Biology; Emory College of Arts and Sciences, Atlanta GA 30322
| | - J Farhi
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322
| | - LD Lemon
- Department of Biology; Emory College of Arts and Sciences, Atlanta GA 30322
| | - MB Fasken
- Department of Biology; Emory College of Arts and Sciences, Atlanta GA 30322
| | - AH Corbett
- Department of Biology; Emory College of Arts and Sciences, Atlanta GA 30322
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322
| | - JM Spangle
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322
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Bradley D, Hogrebe A, Dandage R, Dubé AK, Leutert M, Dionne U, Chang A, Villén J, Landry CR. The fitness cost of spurious phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.08.561337. [PMID: 37873463 PMCID: PMC10592693 DOI: 10.1101/2023.10.08.561337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The fidelity of signal transduction requires the binding of regulatory molecules to their cognate targets. However, the crowded cell interior risks off-target interactions between proteins that are functionally unrelated. How such off-target interactions impact fitness is not generally known, but quantifying this is required to understand the constraints faced by cell systems as they evolve. Here, we use the model organism S. cerevisiae to inducibly express tyrosine kinases. Because yeast lacks bona fide tyrosine kinases, most of the resulting tyrosine phosphorylation is spurious. This provides a suitable system to measure the impact of artificial protein interactions on fitness. We engineered 44 yeast strains each expressing a tyrosine kinase, and quantitatively analysed their phosphoproteomes. This analysis resulted in ~30,000 phosphosites mapping to ~3,500 proteins. Examination of the fitness costs in each strain revealed a strong correlation between the number of spurious pY sites and decreased growth. Moreover, the analysis of pY effects on protein structure and on protein function revealed over 1000 pY events that we predict to be deleterious. However, we also find that a large number of the spurious pY sites have a negligible effect on fitness, possibly because of their low stoichiometry. This result is consistent with our evolutionary analyses demonstrating a lack of phosphotyrosine counter-selection in species with bona fide tyrosine kinases. Taken together, our results suggest that, alongside the risk for toxicity, the cell can tolerate a large degree of non-functional crosstalk as interaction networks evolve.
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Affiliation(s)
- David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexander Hogrebe
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Rohan Dandage
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Ugo Dionne
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexis Chang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
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5
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El Khoury G, Azzam W, Rebehmed J. PyProtif: a PyMol plugin to retrieve and visualize protein motifs for structural studies. Amino Acids 2023; 55:1429-1436. [PMID: 37698713 DOI: 10.1007/s00726-023-03323-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 08/24/2023] [Indexed: 09/13/2023]
Abstract
Proteins often possess several motifs and the ones with similar motifs were found to have similar biochemical properties and thus related biological functions. Thereby, multiple databases were developed to store information on such motifs in proteins. For instance, PDBsum stores the results of Promotif's generated structural motifs and Pfam stores pre-computed patterns of functional domains. In addition to the fact that all this stored information is extremely useful, we can further augment its importance if we ought to integrate these motifs into visualization software. In this work, we have developed PyProtif, a plugin for the PyMOL molecular visualization program, which automatically retrieves protein structural and functional motifs from different databases and integrates them in PyMOL for visualization and analyses. Through an expendable menu and a user-friendly interface, the plugin grants the users the ability to study simultaneously multiple proteins and to select and manipulate each motif separately. Thus, this plugin will be of great interest for structural, evolutionary and classification studies of proteins.
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Affiliation(s)
- Gilbert El Khoury
- Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon
| | - Wael Azzam
- Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon
| | - Joseph Rebehmed
- Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon.
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Li L, Nguyen BA, Mullapudi V, Li Y, Saelices L, Joachimiak LA. Disease-associated patterns of acetylation stabilize tau fibril formation. Structure 2023; 31:1025-1037.e4. [PMID: 37348495 PMCID: PMC10527703 DOI: 10.1016/j.str.2023.05.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/03/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
Assembly of tau into beta-sheet-rich amyloids dictates the pathology of a diversity of diseases. Lysine acetylation has been proposed to drive tau amyloid assembly, but no direct mechanism has emerged. Using tau fragments, we identify patterns of acetylation that flank amyloidogenic motifs on the tau fragments that promote rapid fibril assembly. We determined a 3.9 Å cryo-EM amyloid fibril structure assembled from an acetylated tau fragment uncovering how lysine acetylation can mediate gain-of-function interactions. Comparison of the structure to an ex vivo tauopathy fibril reveals regions of structural similarity. Finally, we show that fibrils encoding disease-associated patterns of acetylation are active in cell-based tau aggregation assays. Our data uncover the dual role of lysine residues in limiting tau aggregation while their acetylation leads to stabilizing pro-aggregation interactions. Design of tau sequence with specific acetylation patterns may lead to controllable tau aggregation to direct folding of tau into distinct amyloid folds.
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Affiliation(s)
- Li Li
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Binh A Nguyen
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vishruth Mullapudi
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yang Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lorena Saelices
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lukasz A Joachimiak
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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7
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Pattanayak R, Petit CM, Yacoubian TA. 14-3-3 phosphorylation inhibits 14-3-3θ's ability to regulate LRRK2 kinase activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.27.542591. [PMID: 37398189 PMCID: PMC10312468 DOI: 10.1101/2023.05.27.542591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
LRRK2 mutations are among the most common genetic causes for Parkinson's disease (PD), and toxicity is associated with increased kinase activity. 14-3-3 proteins are key interactors that regulate LRRK2 kinase activity. Phosphorylation of the 14-3-3θ isoform at S232 is dramatically increased in human PD brains. Here we investigate the impact of 14-3-3θ phosphorylation on its ability to regulate LRRK2 kinase activity. Both wildtype and the non-phosphorylatable S232A 14-3-3θ mutant reduced the kinase activity of wildtype and G2019S LRRK2, whereas the phosphomimetic S232D 14-3-3θ mutant had minimal effects on LRRK2 kinase activity, as determined by measuring autophosphorylation at S1292 and T1503 and Rab10 phosphorylation. However, wildtype and both 14-3-3θ mutants similarly reduced the kinase activity of the R1441G LRRK2 mutant. 14-3-3θ phosphorylation did not promote global dissociation with LRRK2, as determined by co-immunoprecipitation and proximal ligation assays. 14-3-3s interact with LRRK2 at several phosphorylated serine/threonine sites, including T2524 in the C-terminal helix, which can fold back to regulate the kinase domain. Interaction between 14-3-3θ and phosphorylated T2524 LRRK2 was important for 14-3-3θ's ability to regulate kinase activity, as wildtype and S232A 14-3-3θ failed to reduce the kinase activity of G2019S/T2524A LRRK2. Molecular modeling showed that 14-3-3θ phosphorylation causes a partial rearrangement of its canonical binding pocket, thus affecting the interaction between 14-3-3θ and the C-terminus of LRRK2. We conclude that 14-3-3θ phosphorylation destabilizes the interaction of 14-3-3θ with LRRK2 at T2524, which consequently promotes LRRK2 kinase activity.
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Affiliation(s)
- Rudradip Pattanayak
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, 1719 Sixth Avenue South, Civitan International Research Building 510A, Birmingham, AL 35294, USA
| | - Chad M. Petit
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, 720 20 Street South, Kaul 452, Birmingham, AL 35294, USA
| | - Talene A. Yacoubian
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, 1719 Sixth Avenue South, Civitan International Research Building 510A, Birmingham, AL 35294, USA
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Lasorsa A, Bera K, Malki I, Dupré E, Cantrelle FX, Merzougui H, Sinnaeve D, Hanoulle X, Hritz J, Landrieu I. Conformation and Affinity Modulations by Multiple Phosphorylation Occurring in the BIN1 SH3 Domain Binding Site of the Tau Protein Proline-Rich Region. Biochemistry 2023. [PMID: 37167199 DOI: 10.1021/acs.biochem.2c00717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
An increase in phosphorylation of the Tau protein is associated with Alzheimer's disease (AD) progression through unclear molecular mechanisms. In general, phosphorylation modifies the interaction of intrinsically disordered proteins, such as Tau, with other proteins; however, elucidating the structural basis of this regulation mechanism remains challenging. The bridging integrator-1 gene is an AD genetic determinant whose gene product, BIN1, directly interacts with Tau. The proline-rich motif recognized within a Tau(210-240) peptide by the SH3 domain of BIN1 (BIN1 SH3) is defined as 216PTPP219, and this interaction is modulated by phosphorylation. Phosphorylation of T217 within the Tau(210-240) peptide led to a 6-fold reduction in the affinity, while single phosphorylation at either T212, T231, or S235 had no effect on the interaction. Nonetheless, combined phosphorylation of T231 and S235 led to a 3-fold reduction in the affinity, although these phosphorylations are not within the BIN1 SH3-bound region of the Tau peptide. Using nuclear magnetic resonance (NMR) spectroscopy, these phosphorylations were shown to affect the local secondary structure and dynamics of the Tau(210-240) peptide. Models of the (un)phosphorylated peptides were obtained from molecular dynamics (MD) simulation validated by experimental data and showed compaction of the phosphorylated peptide due to increased salt bridge formation. This dynamic folding might indirectly impact the BIN1 SH3 binding by a decreased accessibility of the binding site. Regulation of the binding might thus not only be due to local electrostatic or steric effects from phosphorylation but also to the modification of the conformational properties of Tau.
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Affiliation(s)
- Alessia Lasorsa
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille F-59000, France
| | - Krishnendu Bera
- CEITEC MU, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Idir Malki
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
| | - Elian Dupré
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille F-59000, France
| | - François-Xavier Cantrelle
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille F-59000, France
| | - Hamida Merzougui
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
| | - Davy Sinnaeve
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille F-59000, France
| | - Xavier Hanoulle
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille F-59000, France
| | - Jozef Hritz
- CEITEC MU, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Isabelle Landrieu
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille F-59000, France
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9
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Biojone C, C Casarotto P, Cannarozzo C, Fred SM, Herrera-Rodríguez R, Lesnikova A, Voipio M, Castrén E. nNOS-induced tyrosine nitration of TRKB impairs BDNF signaling and restrains neuronal plasticity. Prog Neurobiol 2023; 222:102413. [PMID: 36682419 DOI: 10.1016/j.pneurobio.2023.102413] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 12/01/2022] [Accepted: 01/17/2023] [Indexed: 01/21/2023]
Abstract
Nitric oxide (NO) has been long recognized as an important modulator of neural plasticity, but characterization of the molecular mechanisms involved - specially the guanylyl cyclase-independent ones - has been challenging. There is evidence that NO could modify BDNF-TRKB signaling, a key mediator of neuronal plasticity. However, the mechanism underlying the interplay of NO and TRKB remains unclear. Here we show that NO induces nitration of the tyrosine 816 in the TRKB receptor in vivo and in vitro, and that post-translational modification inhibits TRKB phosphorylation and binding of phospholipase Cγ1 (PLCγ1) to this same tyrosine residue. Additionally, nitration triggers clathrin-dependent endocytosis of TRKB through the adaptor protein AP-2 and ubiquitination, thereby increasing translocation of TRKB away from the neuronal surface and directing it towards lysosomal degradation. Accordingly, inhibition of nitric oxide increases TRKB phosphorylation and TRKB-dependent neurite branching in neuronal cultures. In vivo, chronic inhibition of neuronal nitric oxide synthase (nNOS) dramatically reduced TRKB nitration and facilitated TRKB signaling in the visual cortex, and promoted a shift in ocular dominance upon monocular deprivation - an indicator of increased plasticity. Altogether, our data describe and characterize a new molecular brake on plasticity, namely nitration of TRKB receptors.
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Affiliation(s)
- Caroline Biojone
- Neuroscience Center, HiLife, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland; Aarhus University, Department of Biomedicine, Faculty of Health, and Translational Neuropsychiatry Unit, Department of Clinical Medicine.
| | - Plinio C Casarotto
- Neuroscience Center, HiLife, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
| | - Cecilia Cannarozzo
- Neuroscience Center, HiLife, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
| | - Senem Merve Fred
- Neuroscience Center, HiLife, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
| | | | - Angelina Lesnikova
- Neuroscience Center, HiLife, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
| | - Mikko Voipio
- Neuroscience Center, HiLife, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
| | - Eero Castrén
- Neuroscience Center, HiLife, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland.
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10
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Remodeling of algal photosystem I through phosphorylation. Biosci Rep 2023; 43:232211. [PMID: 36477263 PMCID: PMC9874419 DOI: 10.1042/bsr20220369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/29/2022] [Accepted: 12/07/2022] [Indexed: 12/12/2022] Open
Abstract
Photosystem I (PSI) with its associated light-harvesting system is the most important generator of reducing power in photosynthesis. The PSI core complex is highly conserved, whereas peripheral subunits as well as light-harvesting proteins (LHCI) reveal a dynamic plasticity. Moreover, in green alga, PSI-LHCI complexes are found as monomers, dimers, and state transition complexes, where two LHCII trimers are associated. Herein, we show light-dependent phosphorylation of PSI subunits PsaG and PsaH as well as Lhca6. Potential consequences of the dynamic phosphorylation of PsaG and PsaH are structurally analyzed and discussed in regard to the formation of the monomeric, dimeric, and LHCII-associated PSI-LHCI complexes.
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11
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Hong X, Song K, Rahman MU, Wei T, Zhang Y, Da LT, Chen HF. Phosphorylation Regulation Mechanism of β2 Integrin for the Binding of Filamin Revealed by Markov State Model. J Chem Inf Model 2023; 63:605-618. [PMID: 36607244 DOI: 10.1021/acs.jcim.2c01177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Leukocyte adhesion deficiency-1 (LAD-1) disorder is a severe immunodeficiency syndrome caused by deficiency or mutation of β2 integrin. The phosphorylation on threonine 758 of β2 integrin acts as a molecular switch inhibiting the binding of filamin. However, the switch mechanism of site-specific phosphorylation at the atom level is still poorly understood. To resolve the regulation mechanism, all-atom molecular dynamics simulation and Markov state model were used to study the dynamic regulation pathway of phosphorylation. Wild type system possessed lower binding free energy and fewer number of states than the phosphorylated system. Both systems underwent local disorder-to-order conformation conversion when achieving steady states. To reach steady states, wild type adopted less number of transition paths/shortest path according to the transition path theory than the phosphorylated system. The underlying phosphorylated regulation pathway was from P1 to P0 and then P4 state, and the main driving force should be hydrogen bond and hydrophobic interaction disturbing the secondary structure of phosphorylated states. These studies will shed light on the pathogenesis of LAD-1 disease and lay a foundation for drug development.
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Affiliation(s)
- Xiaokun Hong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Kaiyuan Song
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Mueed Ur Rahman
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Ting Wei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Yan Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Lin-Tai Da
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai200240, China
- Shanghai Center for Bioinformation Technology, Shanghai200240, China
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12
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Li L, Nguyen B, Mullapudi V, Saelices L, Joachimiak LA. Disease-associated patterns of acetylation stabilize tau fibril formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.10.523459. [PMID: 36711822 PMCID: PMC9882070 DOI: 10.1101/2023.01.10.523459] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Assembly of the microtubule-associated protein into tauopathy fibril conformations dictates the pathology of a diversity of diseases. Recent cryogenic Electron Microscopy (cryo-EM) structures have uncovered distinct fibril conformations in different tauopathies but it remains unknown how these structures fold from a single protein sequence. It has been proposed that post-translational modifications may drive tau assembly but no direct mechanism for how modifications drive assembly has emerged. Leveraging established aggregation-regulating tau fragments that are normally inert, we tested the effect of chemical modification of lysines with acetyl groups on tau fragment conversion into amyloid aggregates. We identify specific patterns of acetylation that flank amyloidogenic motifs on the tau fragments that drive rapid fibril assembly. To understand how this pattern of acetylation may drive assembly, we determined a 3.9 Å cryo-EM structure of an amyloid fibril assembled from an acetylated tau fragment. The structure uncovers how lysine acetylation patterns mediate gain-of-function interactions to promote amyloid assembly. Comparison of the structure to an ex vivo tau fibril conformation from Pick's Disease reveals regions of high structural similarity. Finally, we show that our lysine- acetylated sequences exhibit fibril assembly activity in cell-based tau aggregation assays. Our data uncover the dual role of lysine residues in limiting aggregation while their acetylation leads to stabilizing pro-aggregation interactions. Design of tau sequence with specific acetylation patterns may lead to controllable tau aggregation to direct folding of tau into distinct folds.
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Affiliation(s)
- Li Li
- Center for Alzheimer’s and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Binh Nguyen
- Center for Alzheimer’s and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Vishruth Mullapudi
- Center for Alzheimer’s and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Lorena Saelices
- Center for Alzheimer’s and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Lukasz A. Joachimiak
- Center for Alzheimer’s and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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13
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Cuervo NZ, Grandvaux N. Redox proteomics and structural analyses provide insightful implications for additional non-catalytic thiol-disulfide motifs in PDIs. Redox Biol 2022; 59:102583. [PMID: 36567215 PMCID: PMC9868663 DOI: 10.1016/j.redox.2022.102583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/12/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Protein disulfide isomerases (PDIs) catalyze redox reactions that reduce, oxidize, or isomerize disulfide bonds and act as chaperones of proteins as they fold. The characteristic features of PDIs are the presence of one or more catalytic thioredoxin (TRX)-like domains harboring typical CXXC catalytic motifs responsible for redox reactions, as well as non-catalytic TRX-like domain. As increasing attention is paid to oxidative post-translational modifications of cysteines (Cys ox-PTMs) with the recognition that they control cellular signaling, strategies to identify sites of Cys ox-PTM by redox proteomics have been optimized. Exploration of an available Cys redoxome dataset supported by modeled structure provided arguments for the existence of an additional non-catalytic thiol-disulfide motif, distinct from those contained in the TRX type patterns, typical of PDIAs. Further structural analysis of PDIA3 and 6 allows us to consider the possibility that this hypothesis could be extended to other members of PDI. These elements invite future studies to decipher the exact role of these non-catalytic thiol-disulfide motifs in the functions of PDIs. Strategies that would allow to validate this hypothesis are discussed.
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Affiliation(s)
- Natalia Zamorano Cuervo
- CRCHUM – Centre de Recherche du Centre Hospitalier de l’Université de Montréal, 900 rue Saint Denis, Montréal, H2X 0A9, Québec, Canada
| | - Nathalie Grandvaux
- CRCHUM - Centre de Recherche du Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal, H2X 0A9, Québec, Canada; Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, H3C 3J7, Québec, Canada.
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14
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Cool AM, Lindert S. Umbrella Sampling Simulations Measure Switch Peptide Binding and Hydrophobic Patch Opening Free Energies in Cardiac Troponin. J Chem Inf Model 2022; 62:5666-5674. [PMID: 36283742 PMCID: PMC9712266 DOI: 10.1021/acs.jcim.2c00508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The cardiac troponin (cTn) complex is an important regulatory protein in heart contraction. Upon binding of Ca2+, cTn undergoes a conformational shift that allows the troponin I switch peptide (cTnISP) to be released from the actin filament and bind to the troponin C hydrophobic patch (cTnCHP). Mutations and modifications to this complex can change its sensitivity to Ca2+ and alter the energetics of the transition from the Ca2+-unbound, cTnISP-unbound form to the Ca2+-bound, cTnISP-bound form. We utilized targeted molecular dynamics (TMD) to obtain a trajectory of this transition pathway, followed by umbrella sampling to estimate the free energy associated with the cTnISP-cTnCHP binding and the cTnCHP opening events for wild-type (WT) cTn. We were able to reproduce experimental values for the cTnISP-cTnCHP binding event and obtain cTnCHP opening free energies in agreement with previous computational measurements of smaller cTnC systems. This excellent agreement for WT cTn demonstrated the strength of computational methods in studying the dynamics and energetics of the cTn complex. We then introduced mutations to the cTn complex that cause cardiomyopathy or alter its Ca2+ sensitivity and observed a general decrease in the free energy of opening the cTnCHP. For these same mutations, we observed no general trend in the effect on the cTnISP-cTnCHP binding event. Our method sets the stage for future computational studies on this system that predict the consequences of yet uncharacterized mutations on cTn dynamics and energetics.
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Affiliation(s)
- Austin M Cool
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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15
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Weigle AT, Feng J, Shukla D. Thirty years of molecular dynamics simulations on posttranslational modifications of proteins. Phys Chem Chem Phys 2022; 24:26371-26397. [PMID: 36285789 PMCID: PMC9704509 DOI: 10.1039/d2cp02883b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Posttranslational modifications (PTMs) are an integral component to how cells respond to perturbation. While experimental advances have enabled improved PTM identification capabilities, the same throughput for characterizing how structural changes caused by PTMs equate to altered physiological function has not been maintained. In this Perspective, we cover the history of computational modeling and molecular dynamics simulations which have characterized the structural implications of PTMs. We distinguish results from different molecular dynamics studies based upon the timescales simulated and analysis approaches used for PTM characterization. Lastly, we offer insights into how opportunities for modern research efforts on in silico PTM characterization may proceed given current state-of-the-art computing capabilities and methodological advancements.
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Affiliation(s)
- Austin T Weigle
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jiangyan Feng
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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16
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Petzold A. The 2022 Lady Estelle Wolfson lectureship on neurofilaments. J Neurochem 2022; 163:179-219. [PMID: 35950263 PMCID: PMC9826399 DOI: 10.1111/jnc.15682] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 01/11/2023]
Abstract
Neurofilament proteins (Nf) have been validated and established as a reliable body fluid biomarker for neurodegenerative pathology. This review covers seven Nf isoforms, Nf light (NfL), two splicing variants of Nf medium (NfM), two splicing variants of Nf heavy (NfH), α -internexin (INA) and peripherin (PRPH). The genetic and epigenetic aspects of Nf are discussed as relevant for neurodegenerative diseases and oncology. The comprehensive list of mutations for all Nf isoforms covers Amyotrophic Lateral Sclerosis, Charcot-Marie Tooth disease, Spinal muscular atrophy, Parkinson Disease and Lewy Body Dementia. Next, emphasis is given to the expanding field of post-translational modifications (PTM) of the Nf amino acid residues. Protein structural aspects are reviewed alongside PTMs causing neurodegenerative pathology and human autoimmunity. Molecular visualisations of NF PTMs, assembly and stoichiometry make use of Alphafold2 modelling. The implications for Nf function on the cellular level and axonal transport are discussed. Neurofilament aggregate formation and proteolytic breakdown are reviewed as relevant for biomarker tests and disease. Likewise, Nf stoichiometry is reviewed with regard to in vitro experiments and as a compensatory mechanism in neurodegeneration. The review of Nf across a spectrum of 87 diseases from all parts of medicine is followed by a critical appraisal of 33 meta-analyses on Nf body fluid levels. The review concludes with considerations for clinical trial design and an outlook for future research.
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Affiliation(s)
- Axel Petzold
- Department of NeurodegenerationQueen Square Insitute of Neurology, UCLLondonUK
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17
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Tao S, Li J, Wang H, Ding S, Han W, He R, Ren Z, Wei G. Anti-colon Cancer Effects of Dendrobium officinale Kimura & Migo Revealed by Network Pharmacology Integrated With Molecular Docking and Metabolomics Studies. Front Med (Lausanne) 2022; 9:879986. [PMID: 35847793 PMCID: PMC9280342 DOI: 10.3389/fmed.2022.879986] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 05/23/2022] [Indexed: 11/26/2022] Open
Abstract
Objective The present study aimed to investigate the potential mechanism of Dendrobium officinale (D. officinale) on colorectal cancer and the relevant targets in the pathway using a network pharmacological approach. Methods (1) We identified the major bioactive components of D. officinale by UPLC-ESI-MS/MS and established the in-house library by using the literature mining method. (2) Target prediction was performed by SwissADME and SwissTargetPrediction. (3) A protein–protein interaction (PPI) network and component–target–pathway network (C-T-P network) were constructed. (4) The GO pathways and the KEGG pathway enrichment analysis were carried out by the Metascape database. (5) Molecular docking was performed by AutoDock software. (6) A series of experimental assays including cell proliferation, cell invasion and migration, and TUNEL staining in CRC were performed in CRC cell lines (HT-29, Lovo, SW-620, and HCT-116) to confirm the inhibitory effects of D. officinale. Results (1) In total, 396 candidate active components of D. officinale were identified by UPLC-ESI-MS/MS and selected from the database. (2) From OMIM, GeneCards, DrugBank, and TTD databases, 1,666 gene symbols related to CRC were gathered, and (3) 34 overlapping gene symbols related to CRC and drugs were obtained. (4) These results suggested that the anti-CRC components of D. officinale were mainly apigenin, naringenin, caffeic acid, γ-linolenic acid, α-linolenic acid, cis-10-heptadecenoic acid, etc., and the core targets of action were mainly ESR1, EGFR, PTGS2, MMP9, MMP2, PPARG, etc. (5) The proliferation of muscle cells, the regulation of inflammatory response, the response of cells to organic cyclic compounds, and the apoptotic signaling pathway might serve as principal pathways for CRC treatment. (6) The reliability of some important active components and targets was further validated by molecular docking. The molecular docking analysis suggested an important role of apigenin, naringenin, PTGS2, and MMP9 in delivering the pharmacological activity of D. officinale against CRC. (7) These results of the evaluation experiment in vitro suggested that D. officinale had a strong inhibitory effect on CRC cell lines, and it exerted anti-CRC activity by activating CRC cell apoptosis and inhibiting CRC cell migration and invasion. Conclusion This study may provide valuable insights into exploring the mechanism of action of D. officinale against CRC.
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Affiliation(s)
- Shengchang Tao
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Pharmacy, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China
| | - Jinyan Li
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
- The Research Centre of Chinese Herbal Resource, Shaoguan Institute of Danxia Dendrobium Officinale, Shaoguan, China
| | - Huan Wang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
- The Research Centre of Chinese Herbal Resource, Shaoguan Institute of Danxia Dendrobium Officinale, Shaoguan, China
| | - Shaobo Ding
- Department of Pharmacy, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China
| | - Weichao Han
- Department of Pharmacy, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China
| | - Ruirong He
- Department of Pharmacy, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China
| | - Zhiyao Ren
- The Research Centre of Chinese Herbal Resource, Shaoguan Institute of Danxia Dendrobium Officinale, Shaoguan, China
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, China
- NHC Key Laboratory of Male Reproduction and Genetics, Guangzhou, China
- Department of Central Laboratory, Family Planning Research Institute of Guangdong Province, Guangzhou, China
| | - Gang Wei
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Gang Wei
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18
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EZH2 engages TGFβ signaling to promote breast cancer bone metastasis via integrin β1-FAK activation. Nat Commun 2022; 13:2543. [PMID: 35538070 PMCID: PMC9091212 DOI: 10.1038/s41467-022-30105-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/19/2022] [Indexed: 02/07/2023] Open
Abstract
Bone metastases occur in 50-70% of patients with late-stage breast cancers and effective therapies are needed. The expression of enhancer of zeste homolog 2 (EZH2) is correlated with breast cancer metastasis, but its function in bone metastasis hasn't been well-explored. Here we report that EZH2 promotes osteolytic metastasis of breast cancer through regulating transforming growth factor beta (TGFβ) signaling. EZH2 induces cancer cell proliferation and osteoclast maturation, whereas EZH2 knockdown decreases bone metastasis incidence and outgrowth in vivo. Mechanistically, EZH2 transcriptionally increases ITGB1, which encodes for integrin β1. Integrin β1 activates focal adhesion kinase (FAK), which phosphorylates TGFβ receptor type I (TGFβRI) at tyrosine 182 to enhance its binding to TGFβ receptor type II (TGFβRII), thereby activating TGFβ signaling. Clinically applicable FAK inhibitors but not EZH2 methyltransferase inhibitors effectively inhibit breast cancer bone metastasis in vivo. Overall, we find that the EZH2-integrin β1-FAK axis cooperates with the TGFβ signaling pathway to promote bone metastasis of breast cancer.
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19
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Kannan S, Krishnankutty R, Souchelnytskyi S. Novel Post-translational Modifications in Human Serum Albumin. Protein Pept Lett 2022; 29:473-484. [DOI: 10.2174/0929866529666220318152509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/11/2022] [Accepted: 01/25/2022] [Indexed: 11/22/2022]
Abstract
Aim:
This study aims to identify novel post-translational modifications in human serum
albumin by mass spectrometry.
Background:
Serum albumin is the most abundant protein in plasma, has many physiological
functions, and is in contact with most of the cells and tissues of the human body. Post-translational
modifications (PTMs) may affect functions, stability, and localization of albumin.
Objective:
Identify novel PTMs in human serum albumin by mass spectrometry.
Methods:
Human serum albumin (HSA) was used for tryptic digestion in-solution or in-gel. Mass
spectrometry was applied to identify PTMs in HSA. 3-dimensional modeling was applied to explore
the potential impact of PTMs on known functions of albumin.
Results:
Here, we report the identification of 61 novel PTMs of human serum albumin.
Phosphorylation, glycosylation, nitrosylation, deamidation, methylation, acetylation, palmitoylation,
geranylation, and farnesylation are some examples of the identified PTMs. Mass spectrometry was
used for the identification of PTMs in a purified HSA and HSA from the human plasma. Threedimensional
modeling of albumin with selected PTMs showed the location of these PTMs in the
regions involved in albumin interactions with drugs, metals, and fatty acids. The location of PTMs
in these regions may modify the binding capacity of albumin.
Conclusion:
This report adds 61 novel PTMs to the catalog of human albumin.
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Affiliation(s)
- Surya Kannan
- College of Medicine, QU Health, Qatar University, Doha, Qatar
| | | | - Serhiy Souchelnytskyi
- College of Medicine, QU Health, Qatar University, Doha, Qatar
- Oranta Cancer Diagnostics AB, Uppsala, 75263, Sweden
- Lviv National
University, Lviv, 79010, Ukraine
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20
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Karapetnyan L, Sharoyan S, Mardanyan S, Lupidi G, Cuccioloni M, Angeletti M, Markarian S, Shilajyan H, Antonyan A. Citrullination of adenosine deaminase impairs its binding to dipeptidyl peptidase IV. Biophys Chem 2022; 286:106820. [DOI: 10.1016/j.bpc.2022.106820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 11/29/2022]
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21
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Sirtuin-1 sensitive lysine-136 acetylation drives phase separation and pathological aggregation of TDP-43. Nat Commun 2022; 13:1223. [PMID: 35264561 PMCID: PMC8907366 DOI: 10.1038/s41467-022-28822-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
Trans-activation response DNA-binding protein of 43 kDa (TDP-43) regulates RNA processing and forms neuropathological aggregates in patients with amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Investigating TDP-43 post-translational modifications, we discovered that K84 acetylation reduced nuclear import whereas K136 acetylation impaired RNA binding and splicing capabilities of TDP-43. Such failure of RNA interaction triggered TDP-43 phase separation mediated by the C-terminal low complexity domain, leading to the formation of insoluble aggregates with pathologically phosphorylated and ubiquitinated TDP-43. Introduction of acetyl-lysine at the identified sites via amber suppression confirmed the results from site-directed mutagenesis. K84-acetylated TDP-43 showed cytoplasmic mislocalization, and the aggregation propensity of K136-acetylated TDP-43 was confirmed. We generated antibodies selective for TDP-43 acetylated at these lysines, and found that sirtuin-1 can potently deacetylate K136-acetylated TDP-43 and reduce its aggregation propensity. Thus, distinct lysine acetylations modulate nuclear import, RNA binding and phase separation of TDP-43, suggesting regulatory mechanisms for TDP-43 pathogenesis.
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22
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Ikedife J, He J, Wei Y. PEA-15 engages in allosteric interactions using a common scaffold in a phosphorylation-dependent manner. Sci Rep 2022; 12:116. [PMID: 34997083 PMCID: PMC8742051 DOI: 10.1038/s41598-021-04099-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/15/2021] [Indexed: 11/10/2022] Open
Abstract
Phosphoprotein enriched in astrocytes, 15 kDa (PEA-15) is a death-effector domain (DED) containing protein involved in regulating mitogen-activated protein kinase and apoptosis pathways. In this molecular dynamics study, we examined how phosphorylation of the PEA-15 C-terminal tail residues, Ser-104 and Ser-116, allosterically mediates conformational changes of the DED and alters the binding specificity from extracellular-regulated kinase (ERK) to Fas-associated death domain (FADD) protein. We delineated that the binding interfaces between the unphosphorylated PEA-15 and ERK2 and between the doubly phosphorylated PEA-15 and FADD are similarly composed of a scaffold that includes both the DED and the C-terminal tail residues of PEA-15. While the unphosphorylated serine residues do not directly interact with ERK2, the phosphorylated Ser-116 engages in strong electrostatic interactions with arginine residues on FADD DED. Upon PEA-15 binding, FADD repositions its death domain (DD) relative to the DED, an essential conformational change to allow the death-inducing signaling complex (DISC) assembly.
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Affiliation(s)
- Joyce Ikedife
- Department of Chemistry, New Jersey City University, Jersey City, NJ, 07305, USA
| | - Jianlin He
- Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005, Fujian, China
| | - Yufeng Wei
- Department of Chemistry, New Jersey City University, Jersey City, NJ, 07305, USA.
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23
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Martin IM, Aponte-Santamaría C, Schmidt L, Hedtfeld M, Iusupov A, Musacchio A, Gräter F. Phosphorylation tunes elongation propensity and cohesiveness of INCENP's intrinsically disordered region. J Mol Biol 2021; 434:167387. [PMID: 34883116 DOI: 10.1016/j.jmb.2021.167387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022]
Abstract
The inner centromere protein, INCENP, is crucial for correct chromosome segregation during mitosis. It connects the kinase Aurora B to the inner centromere allowing this kinase to dynamically access its kinetochore targets. However, the function of its central, 440-residue long intrinsically disordered region (IDR) and its multiple phosphorylation sites is unclear. Here, we determined the conformational ensemble of INCENP's IDR, systematically varying the level of phosphorylation, using all-atom and coarse-grain molecular dynamics simulations. Our simulations show that phosphorylation expands INCENP's IDR, both locally and globally, mainly by increasing its overall net charge. The disordered region undergoes critical globule-to-coil conformational transitions and the transition temperature non-monotonically depends on the degree of phosphorylation, with a mildly phosphorylated case of neutral net charge featuring the highest collapse propensity. The IDR transitions from a multitude of globular states, accompanied by several specific internal contacts that reduce INCENP length by loop formation, to weakly interacting and highly extended coiled conformations. Phosphorylation critically shifts the population between these two regimes. It thereby influences cohesiveness and phase behavior of INCENP IDR assemblies, a feature presumably relevant for INCENP's function in the chromosomal passenger complex. Overall, we propose the disordered region of INCENP to act as a phosphorylation-regulated and length-variable component, within the previously defined "dog-leash" model, that thereby regulates how Aurora B reaches its targets for proper chromosome segregation.
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Affiliation(s)
- Isabel M Martin
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany. https://twitter.com/@IsabelMMartin
| | - Camilo Aponte-Santamaría
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany; Max Planck Tandem Group in Computational Biophysics, University of Los Andes, Cra. 1 #18a-12, 111711 Bogotá, Colombia. https://twitter.com/@camiloapontelab
| | - Lisa Schmidt
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Marius Hedtfeld
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany; International Max Planck Research School for Living Matter, Otto-Hahn-Straße 11, 44227 Dortmund, Germany; Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Adel Iusupov
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany; University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany; Max Planck School Matter to Life, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany; Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany. https://twitter.com/@AndreaMusacchi1
| | - Frauke Gräter
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany; Max Planck School Matter to Life, Jahnstrasse 29, 69120 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing, Heidelberg University, INF 205, 69120 Heidelberg, Germany.
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24
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De Rossi P, Lewis AJ, Furrer J, De Vos L, Demeter T, Zbinden A, Zhong W, Wiersma VI, Scialo C, Weber J, Guo Z, Scaramuzza S, Di Fabrizio M, Böing C, Castaño‐Díez D, Al‐Amoudi A, Pérez‐Berlanga M, Lashley T, Stahlberg H, Polymenidou M. FTLD-TDP assemblies seed neoaggregates with subtype-specific features via a prion-like cascade. EMBO Rep 2021; 22:e53877. [PMID: 34806807 PMCID: PMC8647015 DOI: 10.15252/embr.202153877] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 11/21/2022] Open
Abstract
Morphologically distinct TDP-43 aggregates occur in clinically different FTLD-TDP subtypes, yet the mechanism of their emergence and contribution to clinical heterogeneity are poorly understood. Several lines of evidence suggest that pathological TDP-43 follows a prion-like cascade, but the molecular determinants of this process remain unknown. We use advanced microscopy techniques to compare the seeding properties of pathological FTLD-TDP-A and FTLD-TDP-C aggregates. Upon inoculation of patient-derived aggregates in cells, FTLD-TDP-A seeds amplify in a template-dependent fashion, triggering neoaggregation more efficiently than those extracted from FTLD-TDP-C patients, correlating with the respective disease progression rates. Neoaggregates are sequentially phosphorylated with N-to-C directionality and with subtype-specific timelines. The resulting FTLD-TDP-A neoaggregates are large and contain densely packed fibrils, reminiscent of the pure compacted fibrils present within cytoplasmic inclusions in postmortem brains. In contrast, FTLD-TDP-C dystrophic neurites show less dense fibrils mixed with cellular components, and their respective neoaggregates are small, amorphous protein accumulations. These cellular seeding models replicate aspects of the patient pathological diversity and will be a useful tool in the quest for subtype-specific therapeutics.
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Affiliation(s)
- Pierre De Rossi
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Amanda J Lewis
- Laboratory of Biological Electron MicroscopyInstitute of Physics, SB, EPFLDepartment of Fundamental MicrobiologyFaculty of Biology and MedicineUNILLausanneSwitzerland
| | - Johanna Furrer
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Laura De Vos
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Tomas Demeter
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Aurélie Zbinden
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Weijia Zhong
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Vera I Wiersma
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Carlo Scialo
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Julien Weber
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Zhongning Guo
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Stefano Scaramuzza
- C‐CINABiozentrumUniversity of BaselBaselSwitzerland
- BioEM LabBiozentrumUniversity of BaselBaselSwitzerland
| | - Marta Di Fabrizio
- Laboratory of Biological Electron MicroscopyInstitute of Physics, SB, EPFLDepartment of Fundamental MicrobiologyFaculty of Biology and MedicineUNILLausanneSwitzerland
| | | | | | | | | | - Tammaryn Lashley
- Queen Square Brain Bank for Neurological diseasesDepartment of Movement DisordersUCL Institute of NeurologyLondonUK
- Department of Neurodegenerative DiseaseUCL Institute of NeurologyLondonUK
| | - Henning Stahlberg
- Laboratory of Biological Electron MicroscopyInstitute of Physics, SB, EPFLDepartment of Fundamental MicrobiologyFaculty of Biology and MedicineUNILLausanneSwitzerland
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25
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Bittner ZA, Liu X, Mateo Tortola M, Tapia-Abellán A, Shankar S, Andreeva L, Mangan M, Spalinger M, Kalbacher H, Düwell P, Lovotti M, Bosch K, Dickhöfer S, Marcu A, Stevanović S, Herster F, Cardona Gloria Y, Chang TH, Bork F, Greve CL, Löffler MW, Wolz OO, Schilling NA, Kümmerle-Deschner JB, Wagner S, Delor A, Grimbacher B, Hantschel O, Scharl M, Wu H, Latz E, Weber ANR. BTK operates a phospho-tyrosine switch to regulate NLRP3 inflammasome activity. J Exp Med 2021; 218:212658. [PMID: 34554188 PMCID: PMC8480672 DOI: 10.1084/jem.20201656] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 03/18/2021] [Accepted: 08/05/2021] [Indexed: 12/18/2022] Open
Abstract
Activity of the NLRP3 inflammasome, a critical mediator of inflammation, is controlled by accessory proteins, posttranslational modifications, cellular localization, and oligomerization. How these factors relate is unclear. We show that a well-established drug target, Bruton’s tyrosine kinase (BTK), affects several levels of NLRP3 regulation. BTK directly interacts with NLRP3 in immune cells and phosphorylates four conserved tyrosine residues upon inflammasome activation, in vitro and in vivo. Furthermore, BTK promotes NLRP3 relocalization, oligomerization, ASC polymerization, and full inflammasome assembly, probably by charge neutralization, upon modification of a polybasic linker known to direct NLRP3 Golgi association and inflammasome nucleation. As NLRP3 tyrosine modification by BTK also positively regulates IL-1β release, we propose BTK as a multifunctional positive regulator of NLRP3 regulation and BTK phosphorylation of NLRP3 as a novel and therapeutically tractable step in the control of inflammation.
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Affiliation(s)
- Zsófia Agnes Bittner
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Xiao Liu
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Maria Mateo Tortola
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Ana Tapia-Abellán
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Sangeetha Shankar
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Liudmila Andreeva
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
| | - Matthew Mangan
- Institute of Innate Immunity, University Hospital Bonn, Bonn, Germany.,German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Marianne Spalinger
- Department for Gastroenterology and Hepatology, University Hospital Zürich and University of Zürich, Zürich, Switzerland
| | - Hubert Kalbacher
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Peter Düwell
- Institute of Innate Immunity, University Hospital Bonn, Bonn, Germany
| | - Marta Lovotti
- Institute of Innate Immunity, University Hospital Bonn, Bonn, Germany
| | - Karlotta Bosch
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Sabine Dickhöfer
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Ana Marcu
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Franziska Herster
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Yamel Cardona Gloria
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Tzu-Hsuan Chang
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Francesca Bork
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Carsten L Greve
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Markus W Löffler
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Tübingen, Germany.,Department of Clinical Pharmacology, University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence 2180, Image-Guided and Functionally Instructed Tumor Therapies, University of Tübingen, Tübingen, Germany
| | - Olaf-Oliver Wolz
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Nadine A Schilling
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Jasmin B Kümmerle-Deschner
- Division of Pediatric Rheumatology and Autoinflammation Reference Center Tübingen, Department of Pediatrics, University Hospital Tübingen, Tübingen, Germany
| | - Samuel Wagner
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.,Cluster of Excellence 2124, Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany
| | - Anita Delor
- Centre of Chronic Immunodeficiency, University Hospital Freiburg, Freiburg, Germany
| | - Bodo Grimbacher
- Centre of Chronic Immunodeficiency, University Hospital Freiburg, Freiburg, Germany.,Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs University, Freiburg, Germany.,German Center for Infection Research, Freiburg, Germany.,Center for Integrative Biological Signaling Studies, Albert-Ludwigs University, Freiburg, Germany.,Cluster of Excellence 2155, Resolving Infection Susceptibility, Hanover Medical School, Freiburg, Germany
| | - Oliver Hantschel
- Institute of Physiological Chemistry, Faculty of Medicine, Philipps University of Marburg, Marburg, Germany
| | - Michael Scharl
- Department for Gastroenterology and Hepatology, University Hospital Zürich and University of Zürich, Zürich, Switzerland
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
| | - Eicke Latz
- Institute of Innate Immunity, University Hospital Bonn, Bonn, Germany.,Division of Infectious Diseases and Immunology, University of Massachusetts, Worcester, MA
| | - Alexander N R Weber
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence 2180, Image-Guided and Functionally Instructed Tumor Therapies, University of Tübingen, Tübingen, Germany.,Cluster of Excellence 2124, Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany.,German Cancer Consortium, Tübingen, Germany
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26
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Lee S. Development of High Affinity Calcitonin Analog Fragments Targeting Extracellular Domains of Calcitonin Family Receptors. Biomolecules 2021; 11:biom11091364. [PMID: 34572577 PMCID: PMC8466238 DOI: 10.3390/biom11091364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/08/2021] [Accepted: 09/11/2021] [Indexed: 01/18/2023] Open
Abstract
The calcitonin and amylin receptors (CTR and AMY receptors) are the drug targets for osteoporosis and diabetes treatment, respectively. Salmon calcitonin (sCT) and pramlintide were developed as peptide drugs that activate these receptors. However, next-generation drugs with improved receptor binding profiles are desirable for more effective pharmacotherapy. The extracellular domain (ECD) of CTR was reported as the critical binding site for the C-terminal half of sCT. For the screening of high-affinity sCT analog fragments, purified CTR ECD was used for fluorescence polarization/anisotropy peptide binding assay. When three mutations (N26D, S29P, and P32HYP) were introduced to the sCT(22–32) fragment, sCT(22–32) affinity for the CTR ECD was increased by 21-fold. CTR was reported to form a complex with receptor activity-modifying protein (RAMP), and the CTR:RAMP complexes function as amylin receptors with increased binding for the peptide hormone amylin. All three types of functional AMY receptor ECDs were prepared and tested for the binding of the mutated sCT(22–32). Interestingly, the mutated sCT(22–32) also retained its high affinity for all three types of the AMY receptor ECDs. In summary, the mutated sCT(22–32) showing high affinity for CTR and AMY receptor ECDs could be considered for developing the next-generation peptide agonists.
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Affiliation(s)
- Sangmin Lee
- Department of Basic Pharmaceutical Sciences, Fred Wilson School of Pharmacy, High Point University, High Point, NC 27268, USA
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27
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Daly LA, Brownridge PJ, Batie M, Rocha S, Sée V, Eyers CE. Oxygen-dependent changes in binding partners and post-translational modifications regulate the abundance and activity of HIF-1α/2α. Sci Signal 2021; 14:eabf6685. [PMID: 34285132 DOI: 10.1126/scisignal.abf6685] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cellular adaptation to low-oxygen environments is mediated in part by the hypoxia-inducible factors (HIFs). Like other transcription factors, the stability and transcriptional activity of HIFs-and consequently, the hypoxic response-are regulated by post-translational modifications (PTMs) and changes in protein-protein interactions. Our current understanding of PTM-mediated regulation of HIFs is primarily based on in vitro protein fragment-based studies typically validated in fragment-expressing cells treated with hypoxia-mimicking compounds. Here, we used immunoprecipitation-based mass spectrometry to characterize the PTMs and binding partners for full-length HIF-1α and HIF-2α under normoxic (21% oxygen) and hypoxic (1% oxygen) conditions. Hypoxia substantially altered the complexity and composition of the HIFα protein interaction networks, particularly for HIF-2α, with the hypoxic networks of both isoforms being enriched for mitochondrial proteins. Moreover, both HIFα isoforms were heavily covalently modified. We identified ~40 PTM sites composed of 13 different types of modification on both HIFα isoforms, including multiple cysteine modifications and an unusual phosphocysteine. More than 80% of the PTMs identified were not previously known and about half exhibited oxygen dependency. We further characterized an evolutionarily conserved phosphorylation of Ser31 in HIF-1α as a regulator of its transcriptional function, and we propose functional roles for Thr406, Thr528, and Ser581 in HIF-2α. These data will help to delineate the different physiological roles of these closely related isoforms in fine-tuning the hypoxic response.
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Affiliation(s)
- Leonard A Daly
- Department of Biochemistry and System Biology, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
- Centre for Proteome Research, University of Liverpool, Liverpool L69 7ZB, UK
| | - Philip J Brownridge
- Centre for Proteome Research, University of Liverpool, Liverpool L69 7ZB, UK
| | - Michael Batie
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Sonia Rocha
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Violaine Sée
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
- Centre for Cell Imaging, University of Liverpool, Liverpool L69 7ZB, UK
| | - Claire E Eyers
- Department of Biochemistry and System Biology, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
- Centre for Proteome Research, University of Liverpool, Liverpool L69 7ZB, UK
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28
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Das R, Eniyan K, Bajpai U. Computational identification and characterization of antigenic properties of Rv3899c of Mycobacterium tuberculosis and its interaction with human leukocyte antigen (HLA). Immunogenetics 2021; 73:357-368. [PMID: 34228167 DOI: 10.1007/s00251-021-01220-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/26/2021] [Indexed: 10/20/2022]
Abstract
A rise in drug-resistant tuberculosis (TB) cases demands continued efforts towards the discovery and development of drugs and vaccines. Secretory proteins of Mycobacterium tuberculosis (H37Rv) are frequently studied for their antigenicity and their scope as protein subunit vaccines requires further analysis. In this study, Rv3899c of H37Rv emerges as a potential vaccine candidate on its evaluation by several bioinformatics tools. It is a non-toxic, secretory protein with an 'immunoglobulin-like' fold which does not show similarity with a human protein. Through BlastP and MEME suite analysis, we found Rv3899c homologs in several mycobacterial species and its antigenic score (0.54) to compare well with the known immunogens such as ESAT-6 (0.56) and Rv1860 (0.52). Structural examination of Rv3899c predicted ten antigenic peptides, an accessibility profile of the antigenic determinants constituting B cell epitope-rich regions and a low abundance of antigenic regions (AAR) value. Significantly, STRING analysis showed ESX-2 secretion system proteins and antigenic PE/PPE proteins of H37Rv as the interacting partners of Rv3899c. Further, molecular docking predicted Rv3899c to interact with human leukocyte antigen HLA-DRB1*04:01 through its antigenically conserved motif (RAAEQQRLQRIVDAVARQEPRISWAAGLRDDGTT). Interestingly, the binding affinity was observed to increase on citrullination of its Arg1 residue. Taken together, the computational characterization and predictive information suggest Rv3899c to be a promising TB vaccine candidate, which should be validated experimentally.
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Affiliation(s)
- Ritam Das
- Department of Life Science, Acharya Narendra Dev College (University of Delhi), Govindpuri, New Delhi, 110019, India
| | - Kandasamy Eniyan
- Department of Biomedical Science, Acharya Narendra Dev College (University of Delhi), 110019, Govindpuri, New Delhi, India.,Antibiotic Resistance and Phage Therapy Laboratory, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Urmi Bajpai
- Department of Biomedical Science, Acharya Narendra Dev College (University of Delhi), 110019, Govindpuri, New Delhi, India.
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29
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Cool AM, Lindert S. Computational Methods Elucidate Consequences of Mutations and Post-translational Modifications on Troponin I Effective Concentration to Troponin C. J Phys Chem B 2021; 125:7388-7396. [PMID: 34213339 DOI: 10.1021/acs.jpcb.1c03844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ca2+ binding to cardiac troponin C (cTnC) causes a conformational shift that exposes a hydrophobic patch (cTnCHP) for binding of the cTnI switch peptide (cTnISP), ultimately resulting in contraction of the heart. The inhibitory peptide (cTnIIP), attached at the N-terminal end of the cTnISP, serves as a tether for the cTnISP to the rest of the troponin complex. Due to this tethered nature, the cTnISP remains within proximity of the hydrophobic patch region, resulting in the cTnCHP experiencing an elevated "effective concentration" of the cTnISP. Mutations to the cTnIIP region have been hypothesized to cause disease by affecting the ability of the cTnISP to "find" the hydrophobic patch, resulting in alterations to the heart's ability to contract normally. We tested this hypothesis using molecular dynamics (MD) simulations of the troponin complex using a model that contained all three subunits of troponin: C, I, and T. We developed methods that allowed us to quantitatively measure the effective concentration of the cTnISP from the simulations. A significant reduction in the cTnISP effective concentration was observed when the cTnIIP was removed from the system, showcasing the importance of a tethered cTnISP. Through accelerated MD methods, we proposed the minimum effective concentration of a tethered cTnISP to be approximately 21 mM. Modification of the cTnIIP via PKC-mediated phosphorylation of T143 was shown to significantly increase the estimated effective concentration of cTnISP, help the cTnISP find the cTnCHP more effectively, and maintain the relative shape of the cTnIIP when compared to the native model. All of these data indicate that pT143 may be able to help promote binding of cTnISP to the cTnCHP. We then tested six mutations within the cTnIIP region that are known cTnC Ca2+-sensitizing mutations and have been linked with cardiomyopathy. We did not observe a significant reduction in the effective concentration upon the introduction of these mutations; however, we did observe increased variability in the flexibility and dynamics of the cTnIIP region when compared to native. Our observations led us to hypothesize that the mechanism by which these cardiomyopathic mutations affect Ca2+ sensitivity is by altering the off rate of cTnISP from the hydrophobic patch.
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Affiliation(s)
- Austin M Cool
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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30
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Serrano-López EM, López-Martínez D, Gómez-Fernández JC, Egea-Jiménez AL, Corbalán-García S. PKCε controls the fusion of secretory vesicles in mast cells in a phosphatidic acid-dependent mode. Int J Biol Macromol 2021; 185:377-389. [PMID: 34147527 DOI: 10.1016/j.ijbiomac.2021.06.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 11/28/2022]
Abstract
PKCε is highly expressed in mast cells and plays a fundamental role in the antigen-triggered activation of the allergic reaction. Although its regulation by diacylglycerols has been described, its regulation by acidic phospholipids and how this regulation leads to the control of downstream vesicle secretion is barely known. Here, we used structural and evolutionary studies to find the molecular mechanism that explains the selectivity of the C1B domain of PKCε by Phosphatidic Acid (PA). This resided in a collection of Arg residues that form a specific rim on the outer surface of the C1B domain, around the diacylglycerol binding cleft. In RBL-2H3 cells, this basic rim allowed the kinase to respond specifically to phosphatidic acid signals that induced its translocation to the plasma membrane and subsequent activation. Further experiments in cells that overexpress PKCε and a mutant of the PA binding site, showed that PA-dependent PKCε activation increased vesicle degranulation in RBL-2H3 cells, and this correlated with increased SNAP23 phosphorylation. Over-expression of PKCε in these cells also induced an increase in the number of docked vesicles containing SNAP23, when stimulated with PA. This accumulation could be attributed to the stabilizing effect of phosphorylation on the formation of the SNARE complex, which ultimately led to increased release of content in the presence of Ca2+ during the fusion process. Therefore, these findings reinforce the importance of PA signaling in the activation of PKCε, which could be an important target to inhibit the exacerbated responses of these cells in the allergic reaction.
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Affiliation(s)
- Emilio M Serrano-López
- Department of Biochemistry and Molecular Biology A, Veterinary School, Universidad de Murcia, IMIB, CEIR Campus Mare Nostrum (CMN), Campus Espinardo, 30100 Murcia, Spain
| | - David López-Martínez
- Department of Biochemistry and Molecular Biology A, Veterinary School, Universidad de Murcia, IMIB, CEIR Campus Mare Nostrum (CMN), Campus Espinardo, 30100 Murcia, Spain
| | - Juan C Gómez-Fernández
- Department of Biochemistry and Molecular Biology A, Veterinary School, Universidad de Murcia, IMIB, CEIR Campus Mare Nostrum (CMN), Campus Espinardo, 30100 Murcia, Spain.
| | - Antonio Luis Egea-Jiménez
- Centre de Recherche en Cancérologie de Marseille (CRCM), Equipe labellisée LIGUE 2018, Aix-Marseille Université, Marseille F-13284, France; Inserm U1068, Institut Paoli-Calmettes, and CNRS UMR7258, Marseille F-13009, France.
| | - Senena Corbalán-García
- Department of Biochemistry and Molecular Biology A, Veterinary School, Universidad de Murcia, IMIB, CEIR Campus Mare Nostrum (CMN), Campus Espinardo, 30100 Murcia, Spain.
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31
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Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV. Nature 2021; 594:246-252. [PMID: 33845483 DOI: 10.1038/s41586-021-03493-4] [Citation(s) in RCA: 371] [Impact Index Per Article: 123.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 03/25/2021] [Indexed: 02/06/2023]
Abstract
The emergence and global spread of SARS-CoV-2 has resulted in the urgent need for an in-depth understanding of molecular functions of viral proteins and their interactions with the host proteome. Several individual omics studies have extended our knowledge of COVID-19 pathophysiology1-10. Integration of such datasets to obtain a holistic view of virus-host interactions and to define the pathogenic properties of SARS-CoV-2 is limited by the heterogeneity of the experimental systems. Here we report a concurrent multi-omics study of SARS-CoV-2 and SARS-CoV. Using state-of-the-art proteomics, we profiled the interactomes of both viruses, as well as their influence on the transcriptome, proteome, ubiquitinome and phosphoproteome of a lung-derived human cell line. Projecting these data onto the global network of cellular interactions revealed crosstalk between the perturbations taking place upon infection with SARS-CoV-2 and SARS-CoV at different levels and enabled identification of distinct and common molecular mechanisms of these closely related coronaviruses. The TGF-β pathway, known for its involvement in tissue fibrosis, was specifically dysregulated by SARS-CoV-2 ORF8 and autophagy was specifically dysregulated by SARS-CoV-2 ORF3. The extensive dataset (available at https://covinet.innatelab.org ) highlights many hotspots that could be targeted by existing drugs and may be used to guide rational design of virus- and host-directed therapies, which we exemplify by identifying inhibitors of kinases and matrix metalloproteases with potent antiviral effects against SARS-CoV-2.
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Ao D, Liu X, Xia P, Wang H, Jiang S, Zheng W, Chen N, Meurens F, Zhu J. Identification of imidazoquinoline derivative (IQD) interacting sites of porcine TLR8 and the underlying species specificity. Mol Immunol 2021; 136:45-54. [PMID: 34082258 DOI: 10.1016/j.molimm.2021.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/24/2021] [Accepted: 05/17/2021] [Indexed: 02/08/2023]
Abstract
Toll-like receptor 8 (TLR8), as an important innate immune receptor, can recognize specific ligands, activate intracellular signaling and produce an inflammatory response to kill and eliminate pathogenic microorganisms. Recent studies have resolved the crystal structure of human TLR8 (hTLR8) and two types of ligand binding sites were identified. Among the conserved binding site 1 of hTLR8, the residues interacting with imidazoquinoline derivatives (IQDs) were determined. We previously showed that porcine TLR8 (pTLR8) exhibited species specificity for recognition of the hTLR7 agonist imiquimod (R837). Given the species specificity, the pTLR8 residues interacting with IQDs may be different from hTLR8 counterparts. The present study was aimed to identify the pTLR8 residues interacting with small molecular IQDs. Via molecular docking, the pTLR8 residues interacting with R837 and R848 were predicted. The corresponding mutants were tested for pTLR8 signaling in response to IQDs R837, R848 and CL075, and the results showed that five of nine predicted residues (Y336, K341, K342, F395 and G562) are critical for pTLR8 signaling and these residues are partially different from those reported in hTLR8. Further, we found that the pTLR8 GQKNG motif corresponding to hTLR8 RQSYA exhibited disparity to CL075 stimulation. Our study thus reveals fine TLR8 species specificity which deepens the understanding of TLR8 activation mechanism.
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Affiliation(s)
- Da Ao
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, China; College Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Xueliang Liu
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, China; College Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Pengpeng Xia
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, China; College Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Hui Wang
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, China; College Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Sen Jiang
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, China; College Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Wanglong Zheng
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, China; College Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Nanhua Chen
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, China; College Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - François Meurens
- BIOEPAR, INRAE, Oniris, 44307, Nantes, France; Department of Veterinary Microbiology and Immunology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, S7N 5E2, Canada
| | - Jianzhong Zhu
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, China; College Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
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Šoštarić N, van Noort V. Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions. PLoS Comput Biol 2021; 17:e1008988. [PMID: 33979327 PMCID: PMC8143416 DOI: 10.1371/journal.pcbi.1008988] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 05/24/2021] [Accepted: 04/21/2021] [Indexed: 12/13/2022] Open
Abstract
Post-translational modifications (PTMs) play a vital, yet often overlooked role in the living cells through modulation of protein properties, such as localization and affinity towards their interactors, thereby enabling quick adaptation to changing environmental conditions. We have previously benchmarked a computational framework for the prediction of PTMs’ effects on the stability of protein-protein interactions, which has molecular dynamics simulations followed by free energy calculations at its core. In the present work, we apply this framework to publicly available data on Saccharomyces cerevisiae protein structures and PTM sites, identified in both normal and stress conditions. We predict proteome-wide effects of acetylations and phosphorylations on protein-protein interactions and find that acetylations more frequently have locally stabilizing roles in protein interactions, while the opposite is true for phosphorylations. However, the overall impact of PTMs on protein-protein interactions is more complex than a simple sum of local changes caused by the introduction of PTMs and adds to our understanding of PTM cross-talk. We further use the obtained data to calculate the conformational changes brought about by PTMs. Finally, conservation of the analyzed PTM residues in orthologues shows that some predictions for yeast proteins will be mirrored to other organisms, including human. This work, therefore, contributes to our overall understanding of the modulation of the cellular protein interaction networks in yeast and beyond. Proteins are a diverse set of biological molecules responsible for numerous functions within cells, such as obtaining energy from food or transport of small molecules, and many processes rely on interactions of specific proteins. Moreover, a single protein may acquire different roles depending on cellular requirements and as a response to changes in the environment. A commonly used way to quickly change protein’s function or activity is by introducing small chemical modifications on specific locations within the protein. These modifications can cause the protein to interact in a more or less stable way with other proteins. We have previously developed a computational pipeline for predicting the effect of modifications on interactions of proteins, and in this work we apply it to all yeast proteins with known structures. We find differences in effects on the binding for different types of modifications. Importantly, we demonstrate that the modifications far from the interaction interface also significantly contribute to binding due to their impact on protein’s shape, which is often neglected by other methods. This work contributes to our understanding of the modulation of protein interactions in yeast due to modifications, while our widely applicable method will allow similar investigations in other organisms.
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Affiliation(s)
| | - Vera van Noort
- KU Leuven, Centre of Microbial and Plant Genetics, Leuven, Belgium
- Leiden University, Institute of Biology Leiden, Leiden, The Netherlands
- * E-mail:
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How multisite phosphorylation impacts the conformations of intrinsically disordered proteins. PLoS Comput Biol 2021; 17:e1008939. [PMID: 33945530 PMCID: PMC8148376 DOI: 10.1371/journal.pcbi.1008939] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 05/25/2021] [Accepted: 04/06/2021] [Indexed: 12/15/2022] Open
Abstract
Phosphorylation of intrinsically disordered proteins (IDPs) can produce changes in structural and dynamical properties and thereby mediate critical biological functions. How phosphorylation effects intrinsically disordered proteins has been studied for an increasing number of IDPs, but a systematic understanding is still lacking. Here, we compare the collapse propensity of four disordered proteins, Ash1, the C-terminal domain of RNA polymerase (CTD2’), the cytosolic domain of E-Cadherin, and a fragment of the p130Cas, in unphosphorylated and phosphorylated forms using extensive all-atom molecular dynamics (MD) simulations. We find all proteins to show V-shape changes in their collapse propensity upon multi-site phosphorylation according to their initial net charge: phosphorylation expands neutral or overall negatively charged IDPs and shrinks positively charged IDPs. However, force fields including those tailored towards and commonly used for IDPs overestimate these changes. We find quantitative agreement of MD results with SAXS and NMR data for Ash1 and CTD2’ only when attenuating protein electrostatic interactions by using a higher salt concentration (e.g. 350 mM), highlighting the overstabilization of salt bridges in current force fields. We show that phosphorylation of IDPs also has a strong impact on the solvation of the protein, a factor that in addition to the actual collapse or expansion of the IDP should be considered when analyzing SAXS data. Compared to the overall mild change in global IDP dimension, the exposure of active sites can change significantly upon phosphorylation, underlining the large susceptibility of IDP ensembles to regulation through post-translational modifications. Intrinsically disordered proteins (IDPs) are a class of proteins that lack secondary and tertiary structures and instead explore a broad conformational ensemble. Their functions, from transcriptional regulation to signal transmission, are tightly regulated. IDPs are subject of extensive reversible post-translational modifications (PTMs), such as phosphorylation, methylation and glycosylation. Among these PTMs, phosphorylation is one of the most common and important PTMs. However, the mechanism of how phosphorylation affects the conformations and functions of IDPs remains unclear. To answer this question, we have performed extensive all-atom molecular dynamics simulations for four representative IDPs: Ash1, E-Cadherin, CTD2’ and p130Cas in their unphosphorylated and phosphorylated forms. Our results showed that all IDPs undergo a mild change upon multi-site phosphorylation, which is V-shaped: phosphorylation moderately expands neutral or overall negatively charged IDPs and shrinks positively charged IDPs. More importantly, in two of these IDPs, only two biologically relevant phosphorylation sites suffice to render the adjacent negatively charged active site significantly more exposed to the environment, which implies a higher probability to interact with other binding partners.
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Zamorano Cuervo N, Fortin A, Caron E, Chartier S, Grandvaux N. Pinpointing cysteine oxidation sites by high-resolution proteomics reveals a mechanism of redox-dependent inhibition of human STING. Sci Signal 2021; 14:14/680/eaaw4673. [PMID: 33906974 DOI: 10.1126/scisignal.aaw4673] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein function is regulated by posttranslational modifications (PTMs), among which reversible oxidation of cysteine residues has emerged as a key regulatory mechanism of cellular responses. Given the redox regulation of virus-host interactions, the identification of oxidized cysteine sites in cells is essential to understand the underlying mechanisms involved. Here, we present a proteome-wide identification of reversibly oxidized cysteine sites in oxidant-treated cells using a maleimide-based bioswitch method coupled to mass spectrometry analysis. We identified 2720 unique oxidized cysteine sites within 1473 proteins with distinct abundances, locations, and functions. Oxidized cysteine sites were found in numerous signaling pathways, many relevant to virus-host interactions. We focused on the oxidation of STING, the central adaptor of the innate immune type I interferon pathway, which is stimulated in response to the detection of cytosolic DNA by cGAS. We demonstrated the reversible oxidation of Cys148 and Cys206 of STING in cells. Molecular analyses led us to establish a model in which Cys148 oxidation is constitutive, whereas Cys206 oxidation is inducible by oxidative stress or by the natural ligand of STING, 2'3'-cGAMP. Our data suggest that the oxidation of Cys206 prevented hyperactivation of STING by causing a conformational change associated with the formation of inactive polymers containing intermolecular disulfide bonds. This finding should aid the design of therapies targeting STING that are relevant to autoinflammatory disorders, immunotherapies, and vaccines.
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Affiliation(s)
- Natalia Zamorano Cuervo
- CRCHUM-Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal, H2X 0A9 Québec, Canada
| | - Audray Fortin
- CRCHUM-Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal, H2X 0A9 Québec, Canada
| | - Elise Caron
- CRCHUM-Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal, H2X 0A9 Québec, Canada
| | - Stéfany Chartier
- CRCHUM-Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal, H2X 0A9 Québec, Canada
| | - Nathalie Grandvaux
- CRCHUM-Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal, H2X 0A9 Québec, Canada. .,Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, H3C 3J7 Québec, Canada
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Rajala RVS, McCauley A, Rajala R, Teel K, Rajala A. Regulation of Phosphoinositide Levels in the Retina by Protein Tyrosine Phosphatase 1B and Growth Factor Receptor-Bound Protein 14. Biomolecules 2021; 11:biom11040602. [PMID: 33921658 PMCID: PMC8073254 DOI: 10.3390/biom11040602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 11/16/2022] Open
Abstract
Protein tyrosine kinases and protein phosphatases play a critical role in cellular regulation. The length of a cellular response depends on the interplay between activating protein kinases and deactivating protein phosphatases. Protein tyrosine phosphatase 1B (PTP1B) and growth factor receptor-bound protein 14 (Grb14) are negative regulators of receptor tyrosine kinases. However, in the retina, we have previously shown that PTP1B inactivates insulin receptor signaling, whereas phosphorylated Grb14 inhibits PTP1B activity. In silico docking of phosphorylated Grb14 and PTP1B indicate critical residues in PTP1B that may mediate the interaction. Phosphoinositides (PIPs) are acidic lipids and minor constituents in the cell that play an important role in cellular processes. Their levels are regulated by growth factor signaling. Using phosphoinositide binding protein probes, we observed increased levels of PI(3)P, PI(4)P, PI(3,4)P2, PI(4,5)P2, and PI(3,4,5)P3 in PTP1B knockout mouse retina and decreased levels of these PIPs in Grb14 knockout mouse retina. These observations suggest that the interplay between PTP1B and Grb14 can regulate PIP metabolism.
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Affiliation(s)
- Raju V. S. Rajala
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (A.M.); (K.T.); (A.R.)
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- Dean McGee Eye Institute, Oklahoma City, OK 73104, USA
- Correspondence: ; Tel.: +1-405-271-8255; Fax: +1-405-271-8128
| | - Austin McCauley
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (A.M.); (K.T.); (A.R.)
- Dean McGee Eye Institute, Oklahoma City, OK 73104, USA
| | - Rahul Rajala
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- Cardiovascular Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Kenneth Teel
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (A.M.); (K.T.); (A.R.)
- Dean McGee Eye Institute, Oklahoma City, OK 73104, USA
| | - Ammaji Rajala
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (A.M.); (K.T.); (A.R.)
- Dean McGee Eye Institute, Oklahoma City, OK 73104, USA
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Garnish SE, Meng Y, Koide A, Sandow JJ, Denbaum E, Jacobsen AV, Yeung W, Samson AL, Horne CR, Fitzgibbon C, Young SN, Smith PPC, Webb AI, Petrie EJ, Hildebrand JM, Kannan N, Czabotar PE, Koide S, Murphy JM. Conformational interconversion of MLKL and disengagement from RIPK3 precede cell death by necroptosis. Nat Commun 2021; 12:2211. [PMID: 33850121 PMCID: PMC8044208 DOI: 10.1038/s41467-021-22400-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
Phosphorylation of the MLKL pseudokinase by the RIPK3 kinase leads to MLKL oligomerization, translocation to, and permeabilization of, the plasma membrane to induce necroptotic cell death. The precise choreography of MLKL activation remains incompletely understood. Here, we report Monobodies, synthetic binding proteins, that bind the pseudokinase domain of MLKL within human cells and their crystal structures in complex with the human MLKL pseudokinase domain. While Monobody-32 constitutively binds the MLKL hinge region, Monobody-27 binds MLKL via an epitope that overlaps the RIPK3 binding site and is only exposed after phosphorylated MLKL disengages from RIPK3 following necroptotic stimulation. The crystal structures identified two distinct conformations of the MLKL pseudokinase domain, supporting the idea that a conformational transition accompanies MLKL disengagement from RIPK3. These studies provide further evidence that MLKL undergoes a large conformational change upon activation, and identify MLKL disengagement from RIPK3 as a key regulatory step in the necroptosis pathway.
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Affiliation(s)
- Sarah E Garnish
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Yanxiang Meng
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Akiko Koide
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Jarrod J Sandow
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Eric Denbaum
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Annette V Jacobsen
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Andre L Samson
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Christopher R Horne
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Cheree Fitzgibbon
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Samuel N Young
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Phoebe P C Smith
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Andrew I Webb
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Emma J Petrie
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Joanne M Hildebrand
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Peter E Czabotar
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA.
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
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Leonard C, Phillips C, McCarty J. Insight Into Seeded Tau Fibril Growth From Molecular Dynamics Simulation of the Alzheimer's Disease Protofibril Core. Front Mol Biosci 2021; 8:624302. [PMID: 33816551 PMCID: PMC8017153 DOI: 10.3389/fmolb.2021.624302] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/09/2021] [Indexed: 12/15/2022] Open
Abstract
Aggregates of the microtubule associated tau protein are a major constituent of neurofibrillary lesions that define Alzheimer’s disease (AD) pathology. Increasing experimental evidence suggests that the spread of tau neurofibrillary tangles results from a prion-like seeding mechanism in which small oligomeric tau fibrils template the conversion of native, intrinsically disordered, tau proteins into their pathological form. By using atomistic molecular dynamics (MD) simulations, we investigate the stability and dissociation thermodynamics of high-resolution cryo-electron microscopy (cryo-EM) structures of both the AD paired-helical filament (PHF) and straight filament (SF). Non-equilibrium steered MD (SMD) center-of-mass pulling simulations are used to probe the stability of the protofibril structure and identify intermolecular contacts that must be broken before a single tau peptide can dissociate from the protofibril end. Using a combination of exploratory metadynamics and umbrella sampling, we investigate the complete dissociation pathway and compute a free energy profile for the dissociation of a single tau peptide from the fibril end. Different features of the free energy surface between the PHF and SF protofibril result from a different mechanism of tau unfolding. Comparison of wild-type tau PHF and post-translationally modified pSer356 tau shows that phosphorylation at this site changes the dissociation free energy surface of the terminal peptide. These results demonstrate how different protofibril morphologies template the folding of endogenous tau in distinct ways, and how post-translational modification can perturb the folding mechanism.
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Affiliation(s)
- Cass Leonard
- Department of Chemistry, Western Washington University, Bellingham, WA, United States
| | - Christian Phillips
- Department of Chemistry, Western Washington University, Bellingham, WA, United States
| | - James McCarty
- Department of Chemistry, Western Washington University, Bellingham, WA, United States
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Rosenberger FA, Atanassov I, Moore D, Calvo-Garrido J, Moedas MF, Wedell A, Freyer C, Wredenberg A. Stable Isotope Labeling of Amino Acids in Flies (SILAF) Reveals Differential Phosphorylation of Mitochondrial Proteins Upon Loss of OXPHOS Subunits. Mol Cell Proteomics 2021; 20:100065. [PMID: 33640490 PMCID: PMC8050774 DOI: 10.1016/j.mcpro.2021.100065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/01/2021] [Accepted: 02/08/2021] [Indexed: 02/01/2023] Open
Abstract
Drosophila melanogaster has been a workhorse of genetics and cell biology for more than a century. However, proteomic-based methods have been limited due to the complexity and dynamic range of the fly proteome and the lack of efficient labeling methods. Here, we advanced a chemically defined food source into direct stable-isotope labeling of amino acids in flies (SILAF). It allows for the rapid and cost-efficient generation of a large number of larvae or flies, with full incorporation of lysine-[13C6] after six labeling days. SILAF followed by fractionation and enrichment gave proteomic insights at a depth of 7196 proteins and 8451 phosphorylation sites, which substantiated metabolic regulation on enzymatic level. We applied SILAF to quantify the mitochondrial phosphoproteome of an early-stage leucine-rich PPR motif-containing protein (LRPPRC)-knockdown fly model of mitochondrial disease that almost exclusively affects protein levels of the oxidative phosphorylation (OXPHOS) system. While the mitochondrial compartment was hypo-phosphorylated, two conserved phosphosites on OXPHOS subunits NDUFB10 and NDUFA4 were significantly upregulated upon impaired OXPHOS function. The ease and versatility of the method actuate the fruit fly as an appealing model in proteomic and posttranslational modification studies, and it enlarges potential metabolic applications based on heavy amino acid diets.
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Affiliation(s)
- Florian A Rosenberger
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ilian Atanassov
- Proteomics Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany.
| | - David Moore
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Javier Calvo-Garrido
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Marco F Moedas
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Anna Wedell
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Christoph Freyer
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden; Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden.
| | - Anna Wredenberg
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden; Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden.
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Jurásek M, Kumar J, Paclíková P, Kumari A, Tripsianes K, Bryja V, Vácha R. Phosphorylation-induced changes in the PDZ domain of Dishevelled 3. Sci Rep 2021; 11:1484. [PMID: 33452274 PMCID: PMC7810883 DOI: 10.1038/s41598-020-79398-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/04/2020] [Indexed: 01/29/2023] Open
Abstract
The PDZ domain of Dishevelled 3 protein belongs to a highly abundant protein recognition motif which typically binds short C-terminal peptides. The affinity of the PDZ towards the peptides could be fine-tuned by a variety of post-translation modifications including phosphorylation. However, how phosphorylations affect the PDZ structure and its interactions with ligands remains elusive. Combining molecular dynamics simulations, NMR titration, and biological experiments, we explored the role of previously reported phosphorylation sites and their mimetics in the Dishevelled PDZ domain. Our observations suggest three major roles for phosphorylations: (1) acting as an on/off PDZ binding switch, (2) allosterically affecting the binding groove, and (3) influencing the secondary binding site. Our simulations indicated that mimetics had similar but weaker effects, and the effects of distinct sites were non-additive. This study provides insight into the Dishevelled regulation by PDZ phosphorylation. Furthermore, the observed effects could be used to elucidate the regulation mechanisms in other PDZ domains.
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Affiliation(s)
- Miroslav Jurásek
- grid.10267.320000 0001 2194 0956National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Jitender Kumar
- grid.10267.320000 0001 2194 0956CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Petra Paclíková
- grid.10267.320000 0001 2194 0956Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500 Czech Republic
| | - Alka Kumari
- grid.10267.320000 0001 2194 0956Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500 Czech Republic
| | - Konstantinos Tripsianes
- grid.10267.320000 0001 2194 0956CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Vítězslav Bryja
- grid.10267.320000 0001 2194 0956Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500 Czech Republic ,grid.418095.10000 0001 1015 3316Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno, 612 65 Czech Republic
| | - Robert Vácha
- grid.10267.320000 0001 2194 0956National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic ,grid.10267.320000 0001 2194 0956CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
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Molecular dynamics simulations and biochemical characterization of Pf14-3-3 and PfCDPK1 interaction towards its role in growth of human malaria parasite. Biochem J 2020; 477:2153-2177. [PMID: 32484216 DOI: 10.1042/bcj20200145] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 11/17/2022]
Abstract
Scaffold proteins play pivotal role as modulators of cellular processes by operating as multipurpose conformation clamps. 14-3-3 proteins are gold-standard scaffold modules that recognize phosphoSer/Thr (pS/pT) containing conserved motifs, and confer conformational changes leading to modulation of functional parameters of their target proteins. Modulation in functional activity of kinases has been attributed to their interaction with 14-3-3 proteins. Herein, we have annotated and characterized PF3D7_0818200 as 14-3-3 isoform I in Plasmodium falciparum 3D7, and its interaction with one of the key kinases of the parasite, Calcium-Dependent Protein Kinase 1 (CDPK1) by performing various analytical biochemistry and biophysical assays. Molecular dynamics simulation studies indicated that CDPK1 polypeptide sequence (61KLGpS64) behaves as canonical Mode I-type (RXXpS/pT) consensus 14-3-3 binding motif, mediating the interaction. The 14-3-3I/CDPK1 interaction was validated in vitro with ELISA and SPR, which confirmed that the interaction is phosphorylation dependent, with binding affinity constant of 670 ± 3.6 nM. The interaction of 14-3-3I with CDPK1 was validated with well characterized optimal 14-3-3 recognition motifs: Mode I-type ARSHpSYPA and Mode II-type RLYHpSLPA, by simulation studies and ITC. This interaction was found to marginally enhance CDPK1 functional activity. Furthermore, interaction antagonizing peptidomimetics showed growth inhibitory impact on the parasite indicating crucial physiological role of 14-3-3/CDPK1 interaction. Overall, this study characterizes 14-3-3I as a scaffold protein in the malaria parasite and unveils CDPK1 as its previously unidentified target. This sets a precedent for the rational design of 14-3-3 based PPI inhibitors by utilizing 14-3-3 recognition motif peptides, as a potential antimalarial strategy.
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Effect of lysine acetylation on the regulation of Trypanosoma brucei glycosomal aldolase activity. Biochem J 2020; 477:1733-1744. [PMID: 32329788 DOI: 10.1042/bcj20200142] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/21/2020] [Accepted: 04/23/2020] [Indexed: 12/29/2022]
Abstract
Post-translational modifications provide suitable mechanisms for cellular adaptation to environmental changes. Lysine acetylation is one of these modifications and occurs with the addition of an acetyl group to Nε-amino chain of this residue, eliminating its positive charge. Recently, we found distinct acetylation profiles of procyclic and bloodstream forms of Trypanosoma brucei, the agent of African Trypanosomiasis. Interestingly, glycolytic enzymes were more acetylated in the procyclic, which develops in insects and uses oxidative phosphorylation to obtain energy, compared with the bloodstream form, whose main source of energy is glycolysis. Here, we investigated whether acetylation regulates the T. brucei fructose 1,6-bisphosphate aldolase. We found that aldolase activity was reduced in procyclic parasites cultivated in the absence of glucose and partial recovered by in vitro deacetylation. Similarly, acetylation of protein extracts from procyclics cultivated in glucose-rich medium, caused a reduction in the aldolase activity. In addition, aldolase acetylation levels were higher in procyclics cultivated in the absence of glucose compared with those cultivated in the presence of glucose. To further confirm the role of acetylation, lysine residues near the catalytic site were substituted by glutamine in recombinant T. brucei aldolase. These replacements, especially K157, inhibited enzymatic activity, changed the electrostatic surface potential, decrease substrate binding and modify the catalytic pocket structure of the enzyme, as predicted by in silico analysis. Taken together, these data confirm the role of acetylation in regulating the activity of an enzyme from the glycolytic pathway of T. brucei, expanding the factors responsible for regulating important pathways in this parasite.
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PyVibMS: a PyMOL plugin for visualizing vibrations in molecules and solids. J Mol Model 2020; 26:290. [PMID: 32986131 DOI: 10.1007/s00894-020-04508-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/04/2020] [Indexed: 02/05/2023]
Abstract
Visualizing vibrational motions calculated with different ab initio packages requires dedicated post-processing tools. Here, we present a PyMOL plugin called PyVibMS for visualizing the vibrational motions for both molecular and solid systems calculated by mainstream quantum chemical computer programs including Gaussian, Q-Chem, VASP, and CRYSTAL. Benefiting from the continuing development of the PyMOL platform, PyVibMS provides powerful functionalities and user-friendly interface. PyVibMS was written in Python and its open-source nature makes it flexible and sustainable. As an example, the motions of the Konkoli-Cremer local vibrational modes are shown in this work for the first time. PyVibMS is freely available at https://github.com/smutao/PyVibMS . Graphical abstract In this work, a PyMOL plugin named PyVibMS is developed to visualize molecular and lattice vibrations.
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Li Y, Yang Q, Yu Y. A Network Pharmacological Approach to Investigate the Mechanism of Action of Active Ingredients of Epimedii Herba and Their Potential Targets in Treatment of Alzheimer's Disease. Med Sci Monit 2020; 26:e926295. [PMID: 32980851 PMCID: PMC7528617 DOI: 10.12659/msm.926295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Epimedii Herba is a traditional Chinese herbal medicine used to treat central nervous system diseases such as Alzheimer’s disease in China. However, the pharmacological mechanism is unclear. To investigate the mechanisms of Epimedii Herba in the treatment of Alzheimer’s disease, we assessed effective compounds, corresponding targets, and related pathways of Epimedii Herba in the treatment of Alzheimer’s disease based on network pharmacology. Material/Methods The active components and targets of Epimedii Herba were obtained through the TCMSP database and the DrugBank database. The DisGeNET database and GeneCards database were used to search for Alzheimer’s disease targets. The common targets of components and disease were obtained by Wayne diagram. Gene ontology (GO) analysis and enrichment analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed using the DAVID database. The component-target-pathway interaction network model was constructed using Cytoscape software. Auto Duck Vina software was used for molecular docking to analyze the affinity of the key ingredients and the main targets. Results We screened 17 active ingredients and 27 key targets of Epimedii Herba in the treatment of Alzheimer’s disease, which were related to the HIF-1 signaling pathway, TNF signaling pathway, PI3K-Akt signaling pathway, NF-κB signaling pathway, VEGF signaling pathway, and sphingolipid signaling pathway. Conclusions Based on network pharmacology, the multi-component, multi-target, and multi-pathway characteristics of Epimedii Herba in the treatment of Alzheimer’s disease were explored. Our results provide new ideas for future pharmacological and experimental research on Epimedii Herba in the treatment of Alzheimer’s disease.
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Affiliation(s)
- Yajuan Li
- Department of Histology and Embryology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, China (mainland)
| | - Qin Yang
- Department of Histology and Embryology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, China (mainland)
| | - Yang Yu
- Department of Histology and Embryology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, China (mainland)
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Filipek K, Michalec-Wawiórka B, Boguszewska A, Kmiecik S, Tchórzewski M. Phosphorylation of the N-terminal domain of ribosomal P-stalk protein uL10 governs its association with the ribosome. FEBS Lett 2020; 594:3002-3019. [PMID: 32668052 DOI: 10.1002/1873-3468.13885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 12/25/2022]
Abstract
The uL10 protein is the main constituent of the ribosomal P-stalk, anchoring the whole stalk to the ribosome through interactions with rRNA. The P-stalk is the core of the GTPase-associated center (GAC), a critical element for ribosome biogenesis and ribosome translational activity. All P-stalk proteins (uL10, P1, and P2) undergo phosphorylation within their C termini. Here, we show that uL10 has multiple phosphorylation sites, mapped also within the N-terminal rRNA-binding domain. Our results reveal that the introduction of a negative charge within the N terminus of uL10 impairs its association with the ribosome. These findings demonstrate that uL10 N-terminal phosphorylation has regulatory potential governing the uL10 interaction with the ribosome and may control the activity of GAC.
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Affiliation(s)
- Kamil Filipek
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Barbara Michalec-Wawiórka
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Aleksandra Boguszewska
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Sebastian Kmiecik
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Marek Tchórzewski
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
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Savage SR, Zhang B. Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources. Clin Proteomics 2020; 17:27. [PMID: 32676006 PMCID: PMC7353784 DOI: 10.1186/s12014-020-09290-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 07/04/2020] [Indexed: 12/19/2022] Open
Abstract
Mass spectrometry-based phosphoproteomics is becoming an essential methodology for the study of global cellular signaling. Numerous bioinformatics resources are available to facilitate the translation of phosphopeptide identification and quantification results into novel biological and clinical insights, a critical step in phosphoproteomics data analysis. These resources include knowledge bases of kinases and phosphatases, phosphorylation sites, kinase inhibitors, and sequence variants affecting kinase function, and bioinformatics tools that can predict phosphorylation sites in addition to the kinase that phosphorylates them, infer kinase activity, and predict the effect of mutations on kinase signaling. However, these resources exist in silos and it is challenging to select among multiple resources with similar functions. Therefore, we put together a comprehensive collection of resources related to phosphoproteomics data interpretation, compared the use of tools with similar functions, and assessed the usability from the standpoint of typical biologists or clinicians. Overall, tools could be improved by standardization of enzyme names, flexibility of data input and output format, consistent maintenance, and detailed manuals.
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Affiliation(s)
- Sara R. Savage
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
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47
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Davies KA, Fitzgibbon C, Young SN, Garnish SE, Yeung W, Coursier D, Birkinshaw RW, Sandow JJ, Lehmann WIL, Liang LY, Lucet IS, Chalmers JD, Patrick WM, Kannan N, Petrie EJ, Czabotar PE, Murphy JM. Distinct pseudokinase domain conformations underlie divergent activation mechanisms among vertebrate MLKL orthologues. Nat Commun 2020; 11:3060. [PMID: 32561735 PMCID: PMC7305131 DOI: 10.1038/s41467-020-16823-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/27/2020] [Indexed: 12/23/2022] Open
Abstract
The MLKL pseudokinase is the terminal effector in the necroptosis cell death pathway. Phosphorylation by its upstream regulator, RIPK3, triggers MLKL's conversion from a dormant cytoplasmic protein into oligomers that translocate to, and permeabilize, the plasma membrane to kill cells. The precise mechanisms underlying these processes are incompletely understood, and were proposed to differ between mouse and human cells. Here, we examine the divergence of activation mechanisms among nine vertebrate MLKL orthologues, revealing remarkable specificity of mouse and human RIPK3 for MLKL orthologues. Pig MLKL can restore necroptotic signaling in human cells; while horse and pig, but not rat, MLKL can reconstitute the mouse pathway. This selectivity can be rationalized from the distinct conformations observed in the crystal structures of horse and rat MLKL pseudokinase domains. These studies identify important differences in necroptotic signaling between species, and suggest that, more broadly, divergent regulatory mechanisms may exist among orthologous pseudoenzymes.
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Affiliation(s)
- Katherine A Davies
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Cheree Fitzgibbon
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Samuel N Young
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Sarah E Garnish
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Diane Coursier
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Richard W Birkinshaw
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Jarrod J Sandow
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Wil I L Lehmann
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Lung-Yu Liang
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Isabelle S Lucet
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - James D Chalmers
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Wayne M Patrick
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Emma J Petrie
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Peter E Czabotar
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
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Abstract
The purpose of this quick guide is to help new modelers who have little or no background in comparative modeling yet are keen to produce high-resolution protein 3D structures for their study by following systematic good modeling practices, using affordable personal computers or online computational resources. Through the available experimental 3D-structure repositories, the modeler should be able to access and use the atomic coordinates for building homology models. We also aim to provide the modeler with a rationale behind making a simple list of atomic coordinates suitable for computational analysis abiding to principles of physics (e.g., molecular mechanics). Keeping that objective in mind, these quick tips cover the process of homology modeling and some postmodeling computations such as molecular docking and molecular dynamics (MD). A brief section was left for modeling nonprotein molecules, and a short case study of homology modeling is discussed.
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Affiliation(s)
- Yazan Haddad
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Zbynek Heger
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
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49
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Guo X, Park JE, Gallart-Palau X, Sze SK. Oxidative Damage to the TCA Cycle Enzyme MDH1 Dysregulates Bioenergetic Enzymatic Activity in the Aged Murine Brain. J Proteome Res 2020; 19:1706-1717. [DOI: 10.1021/acs.jproteome.9b00861] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Xue Guo
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Jung Eun Park
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Xavier Gallart-Palau
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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50
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Arakhamia T, Lee CE, Carlomagno Y, Duong DM, Kundinger SR, Wang K, Williams D, DeTure M, Dickson DW, Cook CN, Seyfried NT, Petrucelli L, Fitzpatrick AWP. Posttranslational Modifications Mediate the Structural Diversity of Tauopathy Strains. Cell 2020; 180:633-644.e12. [PMID: 32032505 PMCID: PMC7491959 DOI: 10.1016/j.cell.2020.01.027] [Citation(s) in RCA: 258] [Impact Index Per Article: 64.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/23/2019] [Accepted: 01/21/2020] [Indexed: 01/21/2023]
Abstract
Tau aggregation into insoluble filaments is the defining pathological hallmark of tauopathies. However, it is not known what controls the formation and templated seeding of strain-specific structures associated with individual tauopathies. Here, we use cryo-electron microscopy (cryo-EM) to determine the structures of tau filaments from corticobasal degeneration (CBD) human brain tissue. Cryo-EM and mass spectrometry of tau filaments from CBD reveal that this conformer is heavily decorated with posttranslational modifications (PTMs), enabling us to map PTMs directly onto the structures. By comparing the structures and PTMs of tau filaments from CBD and Alzheimer's disease, it is found that ubiquitination of tau can mediate inter-protofilament interfaces. We propose a structure-based model in which cross-talk between PTMs influences tau filament structure, contributing to the structural diversity of tauopathy strains. Our approach establishes a framework for further elucidating the relationship between the structures of polymorphic fibrils, including their PTMs, and neurodegenerative disease.
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Affiliation(s)
- Tamta Arakhamia
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Christina E Lee
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Yari Carlomagno
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sean R Kundinger
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kevin Wang
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Dewight Williams
- John M. Cowley Center for High Resolution Electron Microscopy, Arizona State University, Tempe, AZ 85287, USA
| | - Michael DeTure
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Casey N Cook
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | - Anthony W P Fitzpatrick
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA.
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