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Kurochkina N, Sapio MR, Iadarola MJ, Hall BE, Kulkarni AB. Multiprotein Assemblies, Phosphorylation and Dephosphorylation in Neuronal Cytoskeleton. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.21.545989. [PMID: 37502949 PMCID: PMC10370197 DOI: 10.1101/2023.06.21.545989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Filament systems are comprised of fibrous and globular cytoskeletal proteins and are key elements regulating cell shape, rigidity, and dynamics. The cellular localization and assembly of neurofilaments depend on phosphorylation by kinases. The involvement of the BRCA1 (Breast cancer associated protein 1)/BARD1 (BRCA1-associated RING domain 1) pathways in Alzheimer disease (AD) is suggested by colocalization studies. In particular, BRCA1 accumulation within neurofibrillary tangles and colocalization with tau aggregates in the cytoplasm of AD patients implicates the involvement of mutant forms of BRCA1/BARD1 proteins in disease pathogenesis. The purpose of this study is to show that the location of mutations in the translated BARD1, specifically within ankyrin repeats, has strong correlation with the Cdk5 motifs for phosphorylation. Mapping of the mutation sites on the protein's three-dimensional structure and estimation of the backbone dihedral angles show transitions between the canonical helical and extended conformations of the tetrapeptide sequence of ankyrin repeats. Clustering of mutations in BARD1 ankyrin repeats near the N-termini of the helices with T/SXXH motifs provides a basis for conformational transitions that might be necessary to ensure the compatibility of the substrate with active site geometry and accessibility of the substrate to the kinase. Ankyrin repeats are interaction sites for phosphorylation-dependent dynamic assembly of proteins including those involved in transcription regulation and signaling, and present potential targets for the design of new drugs.
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Affiliation(s)
- Natalya Kurochkina
- Department of Biophysics, The School of Theoretical Modeling, Washington, DC, 20006, USA
| | - Matthew R. Sapio
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Michael J. Iadarola
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Bradford E Hall
- Functional Genomics Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Ashok B. Kulkarni
- Functional Genomics Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
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Kurochkina N, Bhaskar M, Yadav SP, Pant HC. Phosphorylation, Dephosphorylation, and Multiprotein Assemblies Regulate Dynamic Behavior of Neuronal Cytoskeleton: A Mini-Review. Front Mol Neurosci 2018; 11:373. [PMID: 30349458 PMCID: PMC6186834 DOI: 10.3389/fnmol.2018.00373] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 09/20/2018] [Indexed: 12/28/2022] Open
Abstract
Cellular localization, assembly and abnormal aggregation of neurofilaments depend on phosphorylation. Pathological processes associated with neurodegeneration exhibit aberrant accumulation of microtubule associated aggregated forms of hyperphosphorylated neuronal protein tau in cell bodies. These processes are critical for the disease progression in patients suffering from Alzheimer's disease, Parkinson's disease, and Amyotrophic Lateral Sclerosis. In healthy cells, tau is localized in axons. Topographic regulation suggests that whereas the sites of synthesis of kinases and neurofilaments are the cell bodies, and sites of their functional assemblies are axons, phosphorylation/dephosphorylation are the key processes that arrange the molecules at their precise locations. Phosphorylation sites in the dynamic developmental and degenerative processes differ. Not all these processes are well understood. New advancements identify epigenetic factors involved in AD which account for the influence of age-related environment/genome interactions leading to the disease. Progress in proteomics highlights previously found major proteins and adds more to the list of those involved in AD. New key elements of specificity provide determinants of molecular recognition important for the assembly of macromolecular complexes. In this review, we discuss aberrant spatial distribution of neuronal polypeptides observed in neuropathies: aggregation, association with proteins of the neuronal cytoskeleton, and phosphorylation dependent dynamics. Particularly, we emphasize recent advancements in understanding the function and determinants of specific association of molecules involved in Alzheimer's disease with respect to the topographic regulation of phosphorylation in neuronal cytoskeleton and implications for the design of new therapies. Further, we address the role of various filament systems in maintenance of the shape, rigidity and dynamics of the cytoskeleton.
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Affiliation(s)
- Natalya Kurochkina
- Department of Biophysics, The School of Theoretical Modeling, Washington, DC, United States
| | - Manju Bhaskar
- Neuronal Cytoskeletal Protein Regulation Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Sharda Prasad Yadav
- Neuronal Cytoskeletal Protein Regulation Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Harish C. Pant
- Neuronal Cytoskeletal Protein Regulation Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
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Hall BE, Prochazkova M, Sapio MR, Minetos P, Kurochkina N, Binukumar BK, Amin ND, Terse A, Joseph J, Raithel SJ, Mannes AJ, Pant HC, Chung MK, Iadarola MJ, Kulkarni AB. Phosphorylation of the Transient Receptor Potential Ankyrin 1 by Cyclin-dependent Kinase 5 affects Chemo-nociception. Sci Rep 2018; 8:1177. [PMID: 29352128 PMCID: PMC5775258 DOI: 10.1038/s41598-018-19532-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 01/04/2018] [Indexed: 12/25/2022] Open
Abstract
Cyclin-dependent kinase 5 (Cdk5) is a key neuronal kinase that is upregulated during inflammation, and can subsequently modulate sensitivity to nociceptive stimuli. We conducted an in silico screen for Cdk5 phosphorylation sites within proteins whose expression was enriched in nociceptors and identified the chemo-responsive ion channel Transient Receptor Potential Ankyrin 1 (TRPA1) as a possible Cdk5 substrate. Immunoprecipitated full length TRPA1 was shown to be phosphorylated by Cdk5 and this interaction was blocked by TFP5, an inhibitor that prevents activation of Cdk5. In vitro peptide-based kinase assay revealed that four of six TRPA1 Cdk5 consensus sites acted as substrates for Cdk5, and modeling of the ankyrin repeats disclosed that phosphorylation would occur at characteristic pockets within the (T/S)PLH motifs. Calcium imaging of trigeminal ganglion neurons from genetically engineered mice overexpressing or lacking the Cdk5 activator p35 displayed increased or decreased responsiveness, respectively, to stimulation with the TRPA1 agonist allylisothiocyanate (AITC). AITC-induced chemo-nociceptive behavior was also heightened in vivo in mice overexpressing p35 while being reduced in p35 knockout mice. Our findings demonstrate that TRPA1 is a substrate of Cdk5 and that Cdk5 activity is also able to modulate TRPA1 agonist-induced calcium influx and chemo-nociceptive behavioral responses.
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Affiliation(s)
- Bradford E Hall
- Functional Genomics Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Michaela Prochazkova
- Functional Genomics Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Matthew R Sapio
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Paul Minetos
- Functional Genomics Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA.,Tulane University School of Medicine, New Orleans, LA, USA
| | | | - B K Binukumar
- Institute of Genomics and Integrative Biology, New Delhi, India
| | - Niranjana D Amin
- Neuronal Cytoskeletal Protein Regulation Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Anita Terse
- Functional Genomics Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - John Joseph
- University of Maryland, School of Dentistry, Baltimore, MD, USA
| | - Stephen J Raithel
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Andrew J Mannes
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Harish C Pant
- Neuronal Cytoskeletal Protein Regulation Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Man-Kyo Chung
- University of Maryland, School of Dentistry, Baltimore, MD, USA
| | - Michael J Iadarola
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Ashok B Kulkarni
- Functional Genomics Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA.
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Persi E, Wolf YI, Koonin EV. Positive and strongly relaxed purifying selection drive the evolution of repeats in proteins. Nat Commun 2016; 7:13570. [PMID: 27857066 PMCID: PMC5120217 DOI: 10.1038/ncomms13570] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/17/2016] [Indexed: 01/21/2023] Open
Abstract
Protein repeats are considered hotspots of protein evolution, associated with acquisition of new functions and novel phenotypic traits, including disease. Paradoxically, however, repeats are often strongly conserved through long spans of evolution. To resolve this conundrum, it is necessary to directly compare paralogous (horizontal) evolution of repeats within proteins with their orthologous (vertical) evolution through speciation. Here we develop a rigorous methodology to identify highly periodic repeats with significant sequence similarity, for which evolutionary rates and selection (dN/dS) can be estimated, and systematically characterize their evolution. We show that horizontal evolution of repeats is markedly accelerated compared with their divergence from orthologues in closely related species. This observation is universal across the diversity of life forms and implies a biphasic evolutionary regime whereby new copies experience rapid functional divergence under combined effects of strongly relaxed purifying selection and positive selection, followed by fixation and conservation of each individual repeat.
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Affiliation(s)
- Erez Persi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
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