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Momin AA, Mendes T, Barthe P, Faure C, Hong S, Yu P, Kadaré G, Jaremko M, Girault JA, Jaremko Ł, Arold ST. PYK2 senses calcium through a disordered dimerization and calmodulin-binding element. Commun Biol 2022; 5:800. [PMID: 35945264 PMCID: PMC9363500 DOI: 10.1038/s42003-022-03760-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 07/22/2022] [Indexed: 11/25/2022] Open
Abstract
Multidomain kinases use many ways to integrate and process diverse stimuli. Here, we investigated the mechanism by which the protein tyrosine kinase 2-beta (PYK2) functions as a sensor and effector of cellular calcium influx. We show that the linker between the PYK2 kinase and FAT domains (KFL) encompasses an unusual calmodulin (CaM) binding element. PYK2 KFL is disordered and engages CaM through an ensemble of transient binding events. Calcium increases the association by promoting structural changes in CaM that expose auxiliary interaction opportunities. KFL also forms fuzzy dimers, and dimerization is enhanced by CaM binding. As a monomer, however, KFL associates with the PYK2 FERM-kinase fragment. Thus, we identify a mechanism whereby calcium influx can promote PYK2 self-association, and hence kinase-activating trans-autophosphorylation. Collectively, our findings describe a flexible protein module that expands the paradigms for CaM binding and self-association, and their use for controlling kinase activity. Protein tyrosine kinase 2-beta is shown to function as a sensor and effector of cellular calcium influx through self-association.
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Affiliation(s)
- Afaque A Momin
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Tiago Mendes
- Inserm UMR-S 1270, Sorbonne Université, Faculty of Sciences and Engineering, Institut du Fer à Moulin, 75005, Paris, France
| | - Philippe Barthe
- Centre de Biologie Structurale (CBS), University Montpellier, INSERM U1054, CNRS UMR 5048, 34090, Montpellier, France
| | - Camille Faure
- Inserm UMR-S 1270, Sorbonne Université, Faculty of Sciences and Engineering, Institut du Fer à Moulin, 75005, Paris, France
| | - SeungBeom Hong
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Piao Yu
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Gress Kadaré
- Inserm UMR-S 1270, Sorbonne Université, Faculty of Sciences and Engineering, Institut du Fer à Moulin, 75005, Paris, France
| | - Mariusz Jaremko
- Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Jean-Antoine Girault
- Inserm UMR-S 1270, Sorbonne Université, Faculty of Sciences and Engineering, Institut du Fer à Moulin, 75005, Paris, France
| | - Łukasz Jaremko
- Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Stefan T Arold
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia. .,Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia. .,Centre de Biologie Structurale (CBS), University Montpellier, INSERM U1054, CNRS UMR 5048, 34090, Montpellier, France.
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2
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Razar RBBA, Qu Y, Gunaseelan S, Chua JJE. The importance of fasciculation and elongation protein zeta-1 in neural circuit establishment and neurological disorders. Neural Regen Res 2021; 17:1165-1171. [PMID: 34782550 PMCID: PMC8643053 DOI: 10.4103/1673-5374.327327] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The human brain contains an estimated 100 billion neurons that must be systematically organized into functional neural circuits for it to function properly. These circuits range from short-range local signaling networks between neighboring neurons to long-range networks formed between various brain regions. Compelling converging evidence indicates that alterations in neural circuits arising from abnormalities during early neuronal development or neurodegeneration contribute significantly to the etiology of neurological disorders. Supporting this notion, efforts to identify genetic causes of these disorders have uncovered an over-representation of genes encoding proteins involved in the processes of neuronal differentiation, maturation, synaptogenesis and synaptic function. Fasciculation and elongation protein zeta-1, a Kinesin-1 adapter, has emerged as a key central player involved in many of these processes. Fasciculation and elongation protein zeta-1-dependent transport of synaptic cargoes and mitochondria is essential for neuronal development and synapse establishment. Furthermore, it acts downstream of guidance cue pathways to regulate axo-dendritic development. Significantly, perturbing its function causes abnormalities in neuronal development and synapse formation both in the brain as well as the peripheral nervous system. Mutations and deletions of the fasciculation and elongation protein zeta-1 gene are linked to neurodevelopmental disorders. Moreover, altered phosphorylation of the protein contributes to neurodegenerative disorders. Together, these findings strongly implicate the importance of fasciculation and elongation protein zeta-1 in the establishment of neuronal circuits and its maintenance.
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Affiliation(s)
- Rafhanah Banu Bte Abdul Razar
- Department of Physiology, Yong Loo Lin School of Medicine; LSI Neurobiology Programme; Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
| | - Yinghua Qu
- Department of Physiology, Yong Loo Lin School of Medicine; LSI Neurobiology Programme, National University of Singapore, Singapore, Singapore
| | - Saravanan Gunaseelan
- Department of Physiology, Yong Loo Lin School of Medicine; LSI Neurobiology Programme, National University of Singapore, Singapore, Singapore
| | - John Jia En Chua
- Department of Physiology, Yong Loo Lin School of Medicine; LSI Neurobiology Programme; Institute for Health Innovation and Technology; Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
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3
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Kodera N, Noshiro D, Dora SK, Mori T, Habchi J, Blocquel D, Gruet A, Dosnon M, Salladini E, Bignon C, Fujioka Y, Oda T, Noda NN, Sato M, Lotti M, Mizuguchi M, Longhi S, Ando T. Structural and dynamics analysis of intrinsically disordered proteins by high-speed atomic force microscopy. NATURE NANOTECHNOLOGY 2021; 16:181-189. [PMID: 33230318 DOI: 10.1038/s41565-020-00798-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 10/16/2020] [Indexed: 06/11/2023]
Abstract
Intrinsically disordered proteins (IDPs) are ubiquitous proteins that are disordered entirely or partly and play important roles in diverse biological phenomena. Their structure dynamically samples a multitude of conformational states, thus rendering their structural analysis very difficult. Here we explore the potential of high-speed atomic force microscopy (HS-AFM) for characterizing the structure and dynamics of IDPs. Successive HS-AFM images of an IDP molecule can not only identify constantly folded and constantly disordered regions in the molecule, but can also document disorder-to-order transitions. Moreover, the number of amino acids contained in these disordered regions can be roughly estimated, enabling a semiquantitative, realistic description of the dynamic structure of IDPs.
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Affiliation(s)
- Noriyuki Kodera
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Daisuke Noshiro
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Sujit K Dora
- Department of Physics, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Tetsuya Mori
- Department of Physics, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Johnny Habchi
- Aix-Marseille University and CNRS, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - David Blocquel
- Aix-Marseille University and CNRS, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Antoine Gruet
- Aix-Marseille University and CNRS, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Marion Dosnon
- Aix-Marseille University and CNRS, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Edoardo Salladini
- Aix-Marseille University and CNRS, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Christophe Bignon
- Aix-Marseille University and CNRS, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | | | - Takashi Oda
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | | | - Mamoru Sato
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Marina Lotti
- Department of Biotechnology and Biosciences, State University of Milano-Bicocca, Milano, Italy
| | | | - Sonia Longhi
- Aix-Marseille University and CNRS, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France.
| | - Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan.
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The Mammalian High Mobility Group Protein AT-Hook 2 (HMGA2): Biochemical and Biophysical Properties, and Its Association with Adipogenesis. Int J Mol Sci 2020; 21:ijms21103710. [PMID: 32466162 PMCID: PMC7279267 DOI: 10.3390/ijms21103710] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/30/2020] [Accepted: 05/12/2020] [Indexed: 12/11/2022] Open
Abstract
The mammalian high-mobility-group protein AT-hook 2 (HMGA2) is a small DNA-binding protein and consists of three “AT-hook” DNA-binding motifs and a negatively charged C-terminal motif. It is a multifunctional nuclear protein directly linked to obesity, human height, stem cell youth, human intelligence, and tumorigenesis. Biochemical and biophysical studies showed that HMGA2 is an intrinsically disordered protein (IDP) and could form homodimers in aqueous buffer solution. The “AT-hook” DNA-binding motifs specifically bind to the minor groove of AT-rich DNA sequences and induce DNA-bending. HMGA2 plays an important role in adipogenesis most likely through stimulating the proliferative expansion of preadipocytes and also through regulating the expression of transcriptional factor Peroxisome proliferator-activated receptor γ (PPARγ) at the clonal expansion step from preadipocytes to adipocytes. Current evidence suggests that a main function of HMGA2 is to maintain stemness and renewal capacity of stem cells by which HMGA2 binds to chromosome and lock chromosome into a specific state, to allow the human embryonic stem cells to maintain their stem cell potency. Due to the importance of HMGA2 in adipogenesis and tumorigenesis, HMGA2 is considered a potential therapeutic target for anticancer and anti-obesity drugs. Efforts are taken to identify inhibitors targeting HMGA2.
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Huang PT, Summers BJ, Xu C, Perilla JR, Malikov V, Naghavi MH, Xiong Y. FEZ1 Is Recruited to a Conserved Cofactor Site on Capsid to Promote HIV-1 Trafficking. Cell Rep 2019; 28:2373-2385.e7. [PMID: 31422020 PMCID: PMC6736649 DOI: 10.1016/j.celrep.2019.07.079] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 05/08/2019] [Accepted: 07/22/2019] [Indexed: 12/31/2022] Open
Abstract
HIV-1 uses the microtubule network to traffic the viral capsid core toward the nucleus. Viral nuclear trafficking and infectivity require the kinesin-1 adaptor protein FEZ1. Here, we demonstrate that FEZ1 directly interacts with the HIV-1 capsid and specifically binds capsid protein (CA) hexamers. FEZ1 contains multiple acidic, poly-glutamate stretches that interact with the positively charged central pore of CA hexamers. The FEZ1-capsid interaction directly competes with nucleotides and inositol hexaphosphate (IP6) that bind at the same location. In addition, all-atom molecular dynamic (MD) simulations establish the molecular details of FEZ1-capsid interactions. Functionally, mutation of the FEZ1 capsid-interacting residues significantly reduces trafficking of HIV-1 particles toward the nucleus and early infection. These findings support a model in which the central capsid hexamer pore is a general HIV-1 cofactor-binding hub and FEZ1 serves as a unique CA hexamer pattern sensor to recognize this site and promote capsid trafficking in the cell.
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Affiliation(s)
- Pei-Tzu Huang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Brady James Summers
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Chaoyi Xu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Juan R Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Viacheslav Malikov
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Mojgan H Naghavi
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.
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6
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Teixeira MB, Alborghetti MR, Kobarg J. Fasciculation and elongation zeta proteins 1 and 2: From structural flexibility to functional diversity. World J Biol Chem 2019; 10:28-43. [PMID: 30815230 PMCID: PMC6388297 DOI: 10.4331/wjbc.v10.i2.28] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/02/2019] [Accepted: 01/28/2019] [Indexed: 02/05/2023] Open
Abstract
Fasciculation and elongation zeta/zygin (FEZ) proteins are a family of hub proteins and share many characteristics like high connectivity in interaction networks, they are involved in several cellular processes, evolve slowly and in general have intrinsically disordered regions. In 1985, unc-76 gene was firstly described and involved in axonal growth in C. elegans, and in 1997 Bloom and Horvitz enrolled also the human homologues genes, FEZ1 and FEZ2, in this process. While nematodes possess one gene (unc-76), mammalians have one more copy (FEZ1 and FEZ2). Several animal models have been used to study FEZ family functions like: C. elegans, D. melanogaster, R. novergicus and human cells. Complementation assays were performed and demonstrated the function conservation between paralogues. Human FEZ1 protein is more studied followed by UNC-76 and FEZ2 proteins, respectively. While FEZ1 and UNC-76 shared interaction partners, FEZ2 evolved and increased the number of protein-protein interactions (PPI) with cytoplasmatic partners. FEZ proteins are implicated in intracellular transport, acting as bivalent cargo transport adaptors in kinesin-mediated movement. Especially in light of this cellular function, this family of proteins has been involved in several processes like neuronal development, neurological disorders, viral infection and autophagy. However, nuclear functions of FEZ proteins have been explored as well, due to high content of PPI with nuclear proteins, correlating FEZ1 expression to Sox2 and Hoxb4 gene regulation and retinoic acid signaling. These recent findings open new avenue to study FEZ proteins functions and its involvement in already described processes. This review intends to reunite aspects of evolution, structure, interaction partners and function of FEZ proteins and correlate them to physiological and pathological processes.
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Affiliation(s)
- Mariana Bertini Teixeira
- Institute of Biology, Department of Biochemistry and Tissue Biology, University of Campinas, Campinas 13083-862, Brazil
| | | | - Jörg Kobarg
- Institute of Biology, Department of Biochemistry and Tissue Biology, University of Campinas, Campinas 13083-862, Brazil
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-862, Brazil
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7
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Bertini Teixeira M, Figueira ACM, Furlan AS, Aquino B, Alborghetti MR, Paes Leme AF, Wei LN, Kobarg J. Fasciculation and elongation zeta-1 protein (FEZ1) interacts with the retinoic acid receptor and participates in transcriptional regulation of the Hoxb4 gene. FEBS Open Bio 2017; 8:4-14. [PMID: 29321952 PMCID: PMC5757173 DOI: 10.1002/2211-5463.12338] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 08/27/2017] [Accepted: 10/13/2017] [Indexed: 01/18/2023] Open
Abstract
Fasciculation and elongation zeta‐1 (FEZ1) protein is involved in axon outgrowth and is highly expressed in the brain. It has multiple interaction partners, with functions varying from the regulation of neuronal development and intracellular transport mechanisms to transcription regulation. One of its interactors is retinoic acid receptor (RAR), which is activated by retinoic acid and controls many target genes and physiological process. Based on previous evidence suggesting a possible nuclear role for FEZ1, we wanted to deepen our understanding of this function by addressing the FEZ1–RAR interaction. We performed in vitro binding experiments and assessed the interface of interaction between both proteins. We found that FEZ1–RAR interacted with a similar magnitude as RAR to its responsive element DR5 and that the interaction occurred in the coiled‐coil region of FEZ1 and in the ligand‐binding domain of RAR. Furthermore, cellular experiments were performed in order to confirm the interaction and screen for induced target genes from an 86‐gene panel. The analysis of gene expression showed that only in the presence of retinoic acid did FEZ1 induce hoxb4 gene expression. This finding is consistent with data from the literature showing the hoxb4 gene functionally involved in development and acute myeloid leukemia, as is FEZ1.
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Affiliation(s)
- Mariana Bertini Teixeira
- Department of Biochemistry and Tissue Biology Institute of Biology University of Campinas Brazil
| | - Ana Carolina M Figueira
- Spectroscopy and Calorimetry Laboratory Brazilian Biosciences National Laboratory Center for Research in Energy and Materials Campinas SP Brazil
| | | | - Bruno Aquino
- Structural Genomics Consortium University of Campinas Brazil
| | - Marcos R Alborghetti
- Department of Pharmaceutical Sciences School of Health Sciences University of Brasilia Brazil
| | - Adriana F Paes Leme
- Mass Spectrometry Laboratory Brazilian Biosciences National Laboratory Center for Research in Energy and Materials Campinas SP Brazil
| | - Li-Na Wei
- Pharmacology Department University of Minnesota Medical School Minneapolis MN USA
| | - Jörg Kobarg
- Department of Biochemistry and Tissue Biology Institute of Biology University of Campinas Brazil.,Faculty of Pharmaceutical Sciences University of Campinas Brazil
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Pastor A, Singh AK, Shukla PK, Equbal MJ, Malik ST, Singh TP, Chaudhuri TK. Role of N-terminal region of Escherichia coli maltodextrin glucosidase in folding and function of the protein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1138-1151. [PMID: 27317979 DOI: 10.1016/j.bbapap.2016.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 06/10/2016] [Accepted: 06/14/2016] [Indexed: 01/06/2023]
Abstract
Maltodextrin glucosidase (MalZ) hydrolyses short malto-oligosaccharides from the reducing end releasing glucose and maltose in Escherichia coli. MalZ is a highly aggregation prone protein and molecular chaperonins GroEL and GroES assist in the folding of this protein to a substantial level. The N-terminal region of this enzyme appears to be a unique domain as seen in sequence comparison studies with other amylases as well as through homology modelling. The sequence and homology model analysis show a probability of disorder in the N-Terminal region of MalZ. The crystal structure of this enzyme has been reported in the present communication. Based on the crystallographic structure, it has been interpreted that the N-terminal region of the enzyme (Met1-Phe131) might be unstructured or flexible. To understand the role of the N-terminal region of MalZ in its enzymatic activity, and overall stability, a truncated version (Ala111-His616) of MalZ was created. The truncated version failed to fold into an active enzyme both in E. coli cytosol and in vitro even with the assistance of chaperonins GroEL and GroES. Furthermore, the refolding effort of N-truncated MalZ in the presence of isolated N-terminal domain didn't succeed. Our studies suggest that while the structural rigidity or orientation of the N-terminal region of the MalZ protein may not be essential for its stability and function, but the said domain is likely to play an important role in the formation of the native structure of the protein when present as an integral part of the protein.
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Affiliation(s)
- Ashutosh Pastor
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Amit K Singh
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Prakash K Shukla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Md Javed Equbal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Shikha T Malik
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Tej P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Tapan K Chaudhuri
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India.
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9
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Structural biology of intrinsically disordered proteins: Revisiting unsolved mysteries. Biochimie 2016; 125:112-8. [PMID: 27004461 DOI: 10.1016/j.biochi.2016.03.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 03/17/2016] [Indexed: 01/30/2023]
Abstract
The emergence of intrinsically disordered proteins (IDPs) has challenged the classical protein structure-function paradigm by introducing a new paradigm of "coupled binding and folding". This paradigm suggests that IDPs fold upon binding to their partners. Further studies, however, revealed a novel and previously unrecognized phenomenon of "uncoupled binding and folding" suggesting that IDPs do not necessarily fold upon interaction with their lipid and protein partners. The complex and often unusual biophysics of IDPs makes structural characterization of these proteins and their complexes not only challenging but often resulting in opposite conclusions. For this reason, some crucial questions in this field remain unsolved for well over a decade. Considering an important role of IDPs in cellular regulation, signaling and control in health and disease, more efforts are needed to solve these mysteries. Here, I focus on two long-standing contradictions in the literature concerning dimerization and membrane-binding activities of IDPs. Molecular explanation of these discrepancies is provided. I also demonstrate how resolution of these critical issues in the field of IDPs results in our expanded understanding of cell function and has multiple applications in biology and medicine.
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10
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Kikhney AG, Svergun DI. A practical guide to small angle X-ray scattering (SAXS) of flexible and intrinsically disordered proteins. FEBS Lett 2015; 589:2570-7. [PMID: 26320411 DOI: 10.1016/j.febslet.2015.08.027] [Citation(s) in RCA: 378] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 08/14/2015] [Accepted: 08/15/2015] [Indexed: 12/17/2022]
Abstract
Small-angle X-ray scattering (SAXS) is a biophysical method to study the overall shape and structural transitions of biological macromolecules in solution. SAXS provides low resolution information on the shape, conformation and assembly state of proteins, nucleic acids and various macromolecular complexes. The technique also offers powerful means for the quantitative analysis of flexible systems, including intrinsically disordered proteins (IDPs). Here, the basic principles of SAXS are presented, and profits and pitfalls of the characterization of multidomain flexible proteins and IDPs using SAXS are discussed from the practical point of view. Examples of the synergistic use of SAXS with high resolution methods like X-ray crystallography and nuclear magnetic resonance (NMR), as well as other experimental and in silico techniques to characterize completely, or partially unstructured proteins, are presented.
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Affiliation(s)
- Alexey G Kikhney
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22607 Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22607 Hamburg, Germany.
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11
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Frost L, Baez MAM, Harrilal C, Garabedian A, Fernandez-Lima F, Leng F. The Dimerization State of the Mammalian High Mobility Group Protein AT-Hook 2 (HMGA2). PLoS One 2015; 10:e0130478. [PMID: 26114780 PMCID: PMC4482583 DOI: 10.1371/journal.pone.0130478] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/20/2015] [Indexed: 01/06/2023] Open
Abstract
The mammalian high mobility group protein AT-hook 2 (HMGA2) is a chromosomal architectural transcription factor involved in cell transformation and oncogenesis. It consists of three positively charged “AT-hooks” and a negatively charged C-terminus. Sequence analyses, circular dichroism experiments, and gel-filtration studies showed that HMGA2, in the native state, does not have a defined secondary or tertiary structure. Surprisingly, using combined approaches of 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDC) chemical cross-linking, analytical ultracentrifugation, fluorescence resonance energy transfer (FRET), and mass spectrometry, we discovered that HMGA2 is capable of self-associating into homodimers in aqueous buffer solution. Our results showed that electrostatic interactions between the positively charged “AT-hooks” and the negatively charged C-terminus greatly contribute to the homodimer formation.
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Affiliation(s)
- Lorraine Frost
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Maria A. M. Baez
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Christopher Harrilal
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Alyssa Garabedian
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Francisco Fernandez-Lima
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Fenfei Leng
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
- * E-mail:
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Malikov V, da Silva ES, Jovasevic V, Bennett G, de Souza Aranha Vieira DA, Schulte B, Diaz-Griffero F, Walsh D, Naghavi MH. HIV-1 capsids bind and exploit the kinesin-1 adaptor FEZ1 for inward movement to the nucleus. Nat Commun 2015; 6:6660. [PMID: 25818806 PMCID: PMC4380233 DOI: 10.1038/ncomms7660] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 02/17/2015] [Indexed: 12/11/2022] Open
Abstract
Intracellular transport of cargos, including many viruses, involves directed movement on microtubules mediated by motor proteins. Although a number of viruses bind motors of opposing directionality, how they associate with and control these motors to accomplish directed movement remains poorly understood. Here we show that human immunodeficiency virus type 1 (HIV-1) associates with the kinesin-1 adaptor protein, Fasiculation and Elongation Factor zeta 1 (FEZ1). RNAi-mediated FEZ1 depletion blocks early infection, with virus particles exhibiting bi-directional motility but no net movement to the nucleus. Furthermore, both dynein and kinesin-1 motors are required for HIV-1 trafficking to the nucleus. Finally, the ability of exogenously expressed FEZ1 to promote early HIV-1 infection requires binding to kinesin-1. Our findings demonstrate that opposing motors both contribute to early HIV-1 movement and identify the kinesin-1 adaptor, FEZ1 as a capsid-associated host regulator of this process usurped by HIV-1 to accomplish net inward movement towards the nucleus.
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Affiliation(s)
- Viacheslav Malikov
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | - Eveline Santos da Silva
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Vladimir Jovasevic
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Geoffrey Bennett
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | | | - Bianca Schulte
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Derek Walsh
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Mojgan H Naghavi
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
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13
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Sigalov AB. Unusual biophysics of immune signaling-related intrinsically disordered proteins. SELF NONSELF 2014; 1:271-281. [PMID: 21487502 DOI: 10.4161/self.1.4.13641] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 09/15/2010] [Accepted: 09/15/2010] [Indexed: 11/19/2022]
Abstract
Intrinsically disordered (ID) regions, the regions that lack a well-defined three-dimensional structure under physiological conditions, are preferentially located in the cytoplasmic segments of plasma membrane proteins, many of which are known to be involved in cell signaling. This is in line with our studies that demonstrated that cytoplasmic domains of signaling subunits of immune receptors, including those of ζ, CD3ε, CD3δ and CD3γ chains of T cell receptor, Igα and Igβ chains of B cell receptor as well as the Fc receptor γ chain represent a novel class of ID proteins (IDPs). The domains all have one or more copies of an immunoreceptor tyrosine-based activation motif, tyrosine residues of which are phosphorylated upon receptor engagement in an early and obligatory event in the signaling cascade. Our studies of these IDPs revealed several unusual biophysical phenomena, including (1) the specific dimerization of disordered protein molecules, (2) the fast and slow dimerization equilibrium, depending on the protein, (3) no disorder-to-order transition and the lack of significant chemical shift and peak intensity changes upon dimerization or interaction with a well-folded partner protein and (4) the dual mode of binding to model membranes (with and without folding), depending on the lipid bilayer stability. Here, I highlight several of these studies that not only facilitate a rethinking process of the fundamental paradigms in protein biophysics but also open new perspectives on the molecular mechanisms involved in receptor signaling.
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Homodimerization propensity of the intrinsically disordered N-terminal domain of Ultraspiracle from Aedes aegypti. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1153-66. [PMID: 24704038 DOI: 10.1016/j.bbapap.2014.03.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 03/21/2014] [Accepted: 03/25/2014] [Indexed: 11/20/2022]
Abstract
The mosquito Aedes aegypti is the principal vector of dengue, one of the most devastating arthropod-borne viral infections in humans. The isoform specific A/B region, called the N-terminal domain (NTD), is hypervariable in sequence and length and is poorly conserved within the Ultraspiracle (Usp) family. The Usp protein together with ecdysteroid receptor (EcR) forms a heterodimeric complex. Up until now, there has been little data on the molecular properties of the isolated Usp-NTD. Here, we describe the biochemical and biophysical properties of the recombinant NTD of the Usp isoform B (aaUsp-NTD) from A. aegypti. These results, in combination with in silico bioinformatics approaches, indicate that aaUsp-NTD exhibits properties of an intrinsically disordered protein (IDP). We also present the first experimental evidence describing the dimerization propensity of the isolated NTD of Usp. These characteristics also appear for other members of the Usp family in different species, for example, in the Usp-NTD from Drosophila melanogaster and Bombyx mori. However, aaUsp-NTD exhibits the strongest homodimerization potential. We postulate that the unique dimerization of the NTD might be important for Usp function by providing an additional platform for interactions, in addition to the nuclear receptor superfamily dimerization via DNA binding domains and ligand binding domains that has already been extensively documented. Furthermore, the unique NTD-NTD interaction that was observed might contribute new insight into the dimerization propensities of nuclear receptors.
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15
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Alborghetti MR, Furlan ADS, da Silva JC, Sforça ML, Honorato RV, Granato DC, dos Santos Migueleti DL, Neves JL, de Oliveira PSL, Paes-Leme AF, Zeri ACDM, de Torriani ICL, Kobarg J. Structural analysis of intermolecular interactions in the kinesin adaptor complex fasciculation and elongation protein zeta 1/ short coiled-coil protein (FEZ1/SCOCO). PLoS One 2013; 8:e76602. [PMID: 24116125 PMCID: PMC3792052 DOI: 10.1371/journal.pone.0076602] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 08/29/2013] [Indexed: 01/15/2023] Open
Abstract
Cytoskeleton and protein trafficking processes, including vesicle transport to synapses, are key processes in neuronal differentiation and axon outgrowth. The human protein FEZ1 (fasciculation and elongation protein zeta 1 / UNC-76, in C. elegans), SCOCO (short coiled-coil protein / UNC-69) and kinesins (e.g. kinesin heavy chain / UNC116) are involved in these processes. Exploiting the feature of FEZ1 protein as a bivalent adapter of transport mediated by kinesins and FEZ1 protein interaction with SCOCO (proteins involved in the same path of axonal growth), we investigated the structural aspects of intermolecular interactions involved in this complex formation by NMR (Nuclear Magnetic Resonance), cross-linking coupled with mass spectrometry (MS), SAXS (Small Angle X-ray Scattering) and molecular modelling. The topology of homodimerization was accessed through NMR (Nuclear Magnetic Resonance) studies of the region involved in this process, corresponding to FEZ1 (92-194). Through studies involving the protein in its monomeric configuration (reduced) and dimeric state, we propose that homodimerization occurs with FEZ1 chains oriented in an anti-parallel topology. We demonstrate that the interaction interface of FEZ1 and SCOCO defined by MS and computational modelling is in accordance with that previously demonstrated for UNC-76 and UNC-69. SAXS and literature data support a heterotetrameric complex model. These data provide details about the interaction interfaces probably involved in the transport machinery assembly and open perspectives to understand and interfere in this assembly and its involvement in neuronal differentiation and axon outgrowth.
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Affiliation(s)
- Marcos Rodrigo Alborghetti
- Laboratório Nacional de Biociências-LNBio, Centro Nacional de Pesquisa em Energia e Materiais-CNPEM, Campinas, SP, Brasil
| | - Ariane da Silva Furlan
- Laboratório Nacional de Biociências-LNBio, Centro Nacional de Pesquisa em Energia e Materiais-CNPEM, Campinas, SP, Brasil
- Departamento de Bioquímica-Programa de Pós-graduação em Biologia Funcional e Molecular, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - Júlio César da Silva
- Laboratório Nacional de Biociências-LNBio, Centro Nacional de Pesquisa em Energia e Materiais-CNPEM, Campinas, SP, Brasil
| | - Maurício Luís Sforça
- Laboratório Nacional de Biociências-LNBio, Centro Nacional de Pesquisa em Energia e Materiais-CNPEM, Campinas, SP, Brasil
| | - Rodrigo Vargas Honorato
- Laboratório Nacional de Biociências-LNBio, Centro Nacional de Pesquisa em Energia e Materiais-CNPEM, Campinas, SP, Brasil
| | - Daniela Campos Granato
- Laboratório Nacional de Biociências-LNBio, Centro Nacional de Pesquisa em Energia e Materiais-CNPEM, Campinas, SP, Brasil
| | - Deivid Lucas dos Santos Migueleti
- Laboratório Nacional de Biociências-LNBio, Centro Nacional de Pesquisa em Energia e Materiais-CNPEM, Campinas, SP, Brasil
- Departamento de Genética, Evolução e Bioagentes, Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - Jorge L. Neves
- Laboratório Nacional de Biociências-LNBio, Centro Nacional de Pesquisa em Energia e Materiais-CNPEM, Campinas, SP, Brasil
| | - Paulo Sergio Lopes de Oliveira
- Laboratório Nacional de Biociências-LNBio, Centro Nacional de Pesquisa em Energia e Materiais-CNPEM, Campinas, SP, Brasil
| | - Adriana Franco Paes-Leme
- Laboratório Nacional de Biociências-LNBio, Centro Nacional de Pesquisa em Energia e Materiais-CNPEM, Campinas, SP, Brasil
| | - Ana Carolina de Mattos Zeri
- Laboratório Nacional de Biociências-LNBio, Centro Nacional de Pesquisa em Energia e Materiais-CNPEM, Campinas, SP, Brasil
- Departamento de Bioquímica-Programa de Pós-graduação em Biologia Funcional e Molecular, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | | | - Jörg Kobarg
- Laboratório Nacional de Biociências-LNBio, Centro Nacional de Pesquisa em Energia e Materiais-CNPEM, Campinas, SP, Brasil
- Departamento de Bioquímica-Programa de Pós-graduação em Biologia Funcional e Molecular, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil
- Departamento de Genética, Evolução e Bioagentes, Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil
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16
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Behrens C, Binotti B, Schmidt C, Robinson CV, Chua JJE, Kühnel K. Crystal structure of the human short coiled coil protein and insights into SCOC-FEZ1 complex formation. PLoS One 2013; 8:e76355. [PMID: 24098481 PMCID: PMC3788124 DOI: 10.1371/journal.pone.0076355] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 08/23/2013] [Indexed: 01/18/2023] Open
Abstract
The short coiled coil protein (SCOC) forms a complex with fasciculation and elongation protein zeta 1 (FEZ1). This complex is involved in autophagy regulation. We determined the crystal structure of the coiled coil domain of human SCOC at 2.7 Å resolution. SCOC forms a parallel left handed coiled coil dimer. We observed two distinct dimers in the crystal structure, which shows that SCOC is conformationally flexible. This plasticity is due to the high incidence of polar and charged residues at the core a/d-heptad positions. We prepared two double mutants, where these core residues were mutated to either leucines or valines (E93V/K97L and N125L/N132V). These mutations led to a dramatic increase in stability and change of oligomerisation state. The oligomerisation state of the mutants was characterized by multi-angle laser light scattering and native mass spectrometry measurements. The E93V/K97 mutant forms a trimer and the N125L/N132V mutant is a tetramer. We further demonstrate that SCOC forms a stable homogeneous complex with the coiled coil domain of FEZ1. SCOC dimerization and the SCOC surface residue R117 are important for this interaction.
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Affiliation(s)
- Caroline Behrens
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Beyenech Binotti
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Carla Schmidt
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Carol V. Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - John Jia En Chua
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Karin Kühnel
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
- * E-mail:
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17
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Dasgupta I, Sanglas L, Enghild JJ, Lindberg I. The neuroendocrine protein 7B2 is intrinsically disordered. Biochemistry 2012; 51:7456-64. [PMID: 22947085 PMCID: PMC3457758 DOI: 10.1021/bi300871k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The small neuroendocrine protein 7B2 has been shown to
be required
for the productive maturation of proprotein convertase 2 (proPC2)
to an active enzyme form; this action is accomplished via its ability
to block aggregation of proPC2 into nonactivatable forms. Recent data
show that 7B2 can also act as a postfolding chaperone to block the
aggregation of a number of other proteins, for example, α-synuclein.
To gain insight into the mechanism of action of 7B2 in blocking protein
aggregation, we performed structural studies of this protein using
gel filtration chromatography, intrinsic tryptophan fluorescence,
1-anilino-8-naphthalenesulfonate (ANS) binding, circular dichroism
(CD), and nuclear magnetic resonance (NMR) spectroscopy. Gel filtration
studies indicated that 7B2 exists as an extended monomer, eluting
at a molecular mass higher than that expected for a globular protein
of similar size. However, chemical cross-linking showed that 7B2 exhibits
concentration-dependent oligomerization. CD experiments showed that
both full-length 27 kDa 7B2 and the C-terminally truncated 21 kDa
form lack appreciable secondary structure, although the longer protein
exhibited more structural content than the latter, as demonstrated
by intrinsic and ANS fluorescence studies. NMR spectra confirmed the
lack of structure in native 7B2, but a disorder-to-order transition
was observed upon incubation with one of its client proteins, α-synuclein.
We conclude that 7B2 is a natively disordered protein whose function
as an antiaggregant chaperone is likely facilitated by its lack of
appreciable secondary structure and tendency to form oligomers.
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Affiliation(s)
- Indrani Dasgupta
- Department of Anatomy and Neurobiology, School of Medicine, University of Maryland-Baltimore, Baltimore, MD 21201, USA
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18
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Phosphorylation-regulated axonal dependent transport of syntaxin 1 is mediated by a Kinesin-1 adapter. Proc Natl Acad Sci U S A 2012; 109:5862-7. [PMID: 22451907 DOI: 10.1073/pnas.1113819109] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Presynaptic nerve terminals are formed from preassembled vesicles that are delivered to the prospective synapse by kinesin-mediated axonal transport. However, precisely how the various cargoes are linked to the motor proteins remains unclear. Here, we report a transport complex linking syntaxin 1a (Stx) and Munc18, two proteins functioning in synaptic vesicle exocytosis at the presynaptic plasma membrane, to the motor protein Kinesin-1 via the kinesin adaptor FEZ1. Mutation of the FEZ1 ortholog UNC-76 in Caenorhabditis elegans causes defects in the axonal transport of Stx. We also show that binding of FEZ1 to Kinesin-1 and Munc18 is regulated by phosphorylation, with a conserved site (serine 58) being essential for binding. When expressed in C. elegans, wild-type but not phosphorylation-deficient FEZ1 (S58A) restored axonal transport of Stx. We conclude that FEZ1 operates as a kinesin adaptor for the transport of Stx, with cargo loading and unloading being regulated by protein kinases.
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Aguado-Llera D, Bacarizo J, Gregorio-Teruel L, Taberner FJ, Cámara-Artigas A, Neira JL. Biophysical characterization of the isolated C-terminal region of the transient receptor potential vanilloid 1. FEBS Lett 2012; 586:1154-9. [DOI: 10.1016/j.febslet.2012.03.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 03/14/2012] [Accepted: 03/14/2012] [Indexed: 11/28/2022]
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20
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Sigalov AB. Interplay Between Protein Order, Disorder and Oligomericity in Receptor Signaling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 725:50-73. [DOI: 10.1007/978-1-4614-0659-4_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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21
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FERM domain interaction with myosin negatively regulates FAK in cardiomyocyte hypertrophy. Nat Chem Biol 2011; 8:102-10. [PMID: 22101605 DOI: 10.1038/nchembio.717] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 09/15/2011] [Indexed: 12/23/2022]
Abstract
Focal adhesion kinase (FAK) regulates cellular processes that affect several aspects of development and disease. The FAK N-terminal FERM (4.1 protein-ezrin-radixin-moesin homology) domain, a compact clover-leaf structure, binds partner proteins and mediates intramolecular regulatory interactions. Combined chemical cross-linking coupled to MS, small-angle X-ray scattering, computational docking and mutational analyses showed that the FAK FERM domain has a molecular cleft (~998 Å(2)) that interacts with sarcomeric myosin, resulting in FAK inhibition. Accordingly, mutations in a unique short amino acid sequence of the FERM myosin cleft, FP-1, impaired the interaction with myosin and enhanced FAK activity in cardiomyocytes. An FP-1 decoy peptide selectively inhibited myosin interaction and increased FAK activity, promoting cardiomyocyte hypertrophy through activation of the AKT-mammalian target of rapamycin pathway. Our findings uncover an inhibitory interaction between the FAK FERM domain and sarcomeric myosin that presents potential opportunities to modulate the cardiac hypertrophic response through changes in FAK activity.
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22
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Bernadó P, Svergun DI. Structural analysis of intrinsically disordered proteins by small-angle X-ray scattering. MOLECULAR BIOSYSTEMS 2011; 8:151-67. [PMID: 21947276 DOI: 10.1039/c1mb05275f] [Citation(s) in RCA: 257] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Small-angle scattering of X-rays (SAXS) is an established method to study the overall structure and structural transitions of biological macromolecules in solution. For folded proteins, the technique provides three-dimensional low resolution structures ab initio or it can be used to drive rigid-body modeling. SAXS is also a powerful tool for the quantitative analysis of flexible systems, including intrinsically disordered proteins (IDPs), and is highly complementary to the high resolution methods of X-ray crystallography and NMR. Here we present the basic principles of SAXS and review the main approaches to the characterization of IDPs and flexible multidomain proteins using SAXS. Together with the standard approaches based on the analysis of overall parameters, a recently developed Ensemble Optimization Method (EOM) is now available. The latter method allows for the co-existence of multiple protein conformations in solution compatible with the scattering data. Analysis of the selected ensembles provides quantitative information about flexibility and also offers insights into structural features. Examples of the use of SAXS and combined approaches with NMR, X-ray crystallography, and computational methods to characterize completely or partially disordered proteins are presented.
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Affiliation(s)
- Pau Bernadó
- Institute for Research in Biomedicine, Parc Científic de Barcelona, Barcelona, Spain.
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23
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Sigalov AB. Uncoupled binding and folding of immune signaling-related intrinsically disordered proteins. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2011; 106:525-36. [DOI: 10.1016/j.pbiomolbio.2011.08.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 08/10/2011] [Indexed: 10/17/2022]
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Alborghetti MR, Furlan AS, Kobarg J. FEZ2 has acquired additional protein interaction partners relative to FEZ1: functional and evolutionary implications. PLoS One 2011; 6:e17426. [PMID: 21408165 PMCID: PMC3050892 DOI: 10.1371/journal.pone.0017426] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 02/04/2011] [Indexed: 12/16/2022] Open
Abstract
Background The FEZ (fasciculation and elongation protein zeta) family designation was purposed by Bloom and Horvitz by genetic analysis of C. elegans unc-76. Similar human sequences were identified in the expressed sequence tag database as FEZ1 and FEZ2. The unc-76 function is necessary for normal axon fasciculation and is required for axon-axon interactions. Indeed, the loss of UNC-76 function results in defects in axonal transport. The human FEZ1 protein has been shown to rescue defects caused by unc-76 mutations in nematodes, indicating that both UNC-76 and FEZ1 are evolutionarily conserved in their function. Until today, little is known about FEZ2 protein function. Methodology/Principal Findings Using the yeast two-hybrid system we demonstrate here conserved evolutionary features among orthologs and non-conserved features between paralogs of the FEZ family of proteins, by comparing the interactome profiles of the C-terminals of human FEZ1, FEZ2 and UNC-76 from C. elegans. Furthermore, we correlate our data with an analysis of the molecular evolution of the FEZ protein family in the animal kingdom. Conclusions/Significance We found that FEZ2 interacted with 59 proteins and that of these only 40 interacted with FEZ1. Of the 40 FEZ1 interacting proteins, 36 (90%), also interacted with UNC-76 and none of the 19 FEZ2 specific proteins interacted with FEZ1 or UNC-76. This together with the duplication of unc-76 gene in the ancestral line of chordates suggests that FEZ2 is in the process of acquiring new additional functions. The results provide also an explanation for the dramatic difference between C. elegans and D. melanogaster unc-76 mutants on one hand, which cause serious defects in the nervous system, and the mouse FEZ1 -/- knockout mice on the other, which show no morphological and no strong behavioural phenotype. Likely, the ubiquitously expressed FEZ2 can completely compensate the lack of neuronal FEZ1, since it can interact with all FEZ1 interacting proteins and additional 19 proteins.
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Affiliation(s)
- Marcos R. Alborghetti
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brasil
- Departamento de Bioquímica-Programa de Pós-graduação em Biologia Funcional e Molecular, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
| | - Ariane S. Furlan
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brasil
- Departamento de Bioquímica-Programa de Pós-graduação em Biologia Funcional e Molecular, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
| | - Jörg Kobarg
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brasil
- Departamento de Bioquímica-Programa de Pós-graduação em Biologia Funcional e Molecular, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
- * E-mail:
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25
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Meirelles GV, Silva JC, Mendonça YDA, Ramos CHI, Torriani IL, Kobarg J. Human Nek6 is a monomeric mostly globular kinase with an unfolded short N-terminal domain. BMC STRUCTURAL BIOLOGY 2011; 11:12. [PMID: 21320329 PMCID: PMC3053220 DOI: 10.1186/1472-6807-11-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 02/14/2011] [Indexed: 12/30/2022]
Abstract
BACKGROUND The NIMA-related kinases (Neks) are widespread among eukaryotes. In mammalians they represent an evolutionarily conserved family of 11 serine/threonine kinases, with 40-45% amino acid sequence identity to the Aspergillus nidulans mitotic regulator NIMA within their catalytic domains. Neks have cell cycle-related functions and were recently described as related to pathologies, particularly cancer, consisting in potential chemotherapeutic targets. Human Nek6, -7 and -9 are involved in the control of mitotic spindle formation, acting together in a mitotic kinase cascade, but their mechanism of regulation remain elusive. RESULTS In this study we performed a biophysical and structural characterization of human Nek6 with the aim of obtaining its low resolution and homology models. SAXS experiments showed that hNek6 is a monomer of a mostly globular, though slightly elongated shape. Comparative molecular modeling together with disorder prediction analysis also revealed a flexible disordered N-terminal domain for hNek6, which we found to be important to mediate interactions with diverse partners. SEC-MALS experiments showed that hNek6 conformation is dependent on its activation/phosphorylation status, a higher phosphorylation degree corresponding to a bigger Stokes radius. Circular dichroism spectroscopy confirmed our in silico predictions of secondary structure content and thermal stability shift assays revealed a slightly higher stability of wild-type hNek6 compared to the activation loop mutant hNek6(S206A). CONCLUSIONS Our data present the first low resolution 3D structure of hNek6 protein in solution. SAXS, comparative modeling and SEC-MALS analysis revealed that hNek6 is a monomeric kinase of slightly elongated shape and a short unfolded N-terminal domain.
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Affiliation(s)
- Gabriela V Meirelles
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
- Departamento de Bioquímica-Programa de Pós-graduação em Biologia Funcional e Molecular, Instituto de Biologia, Universidade Estadual de Campinas, 13083-970 Campinas, SP, Brazil
| | - Júlio C Silva
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Yuri de A Mendonça
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
- Departamento de Bioquímica-Programa de Pós-graduação em Biologia Funcional e Molecular, Instituto de Biologia, Universidade Estadual de Campinas, 13083-970 Campinas, SP, Brazil
- Instituto de Química, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Carlos HI Ramos
- Departamento de Bioquímica-Programa de Pós-graduação em Biologia Funcional e Molecular, Instituto de Biologia, Universidade Estadual de Campinas, 13083-970 Campinas, SP, Brazil
- Instituto de Química, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Iris L Torriani
- Laboratório Nacional de Luz Síncrotron, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
- Instituto de Física "Gleb Wataghin", Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Jörg Kobarg
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
- Departamento de Bioquímica-Programa de Pós-graduação em Biologia Funcional e Molecular, Instituto de Biologia, Universidade Estadual de Campinas, 13083-970 Campinas, SP, Brazil
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Sigalov AB. The SCHOOL of nature: II. Protein order, disorder and oligomericity in transmembrane signaling. SELF/NONSELF 2010; 1:89-102. [PMID: 21487511 PMCID: PMC3065667 DOI: 10.4161/self.1.2.11590] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 02/20/2010] [Accepted: 02/22/2010] [Indexed: 11/19/2022]
Abstract
Recent reports have revealed that many proteins that do not adopt globular structures under native conditions, thus termed intrinsically disordered proteins (IDPs), are involved in cell signaling. Intriguingly, physiologically relevant oligomerization of IDPs has been recently observed and shown to exhibit unique biophysical characteristics, including the lack of significant changes in chemical shift and peak intensity upon binding. In this work, I summarize several distinct features of protein disorder that are especially important as related to receptor-mediated transmembrane signal transduction. I also hypothesize that interactions of IDPs with their protein or lipid partners represent a general biphasic process with the "no disorder-to-order" fast interaction which, depending on the interacting partner, may or may not be accompanied by the slow formation of a secondary structure. Further, I suggest signaling-related functional connections between protein order, disorder, and oligomericity and hypothesize that receptor oligomerization induced or tuned upon ligand binding outside the cell is translated across the membrane into protein oligomerization inside the cell, thus providing a general platform, the Signaling Chain HOmoOLigomerization (SCHOOL) platform, for receptor-mediated signaling. This structures our current multidisciplinary knowledge and views of the mechanisms governing the coupling of recognition to signal transduction and cell response. Importantly, this approach not only reveals previously unrecognized striking similarities in the basic mechanistic principles of function of numerous functionally diverse and unrelated surface membrane receptors, but also suggests the similarity between therapeutic targets, thus opening new horizons for both fundamental and clinically relevant studies.
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Sigalov AB. Protein intrinsic disorder and oligomericity in cell signaling. ACTA ACUST UNITED AC 2010; 6:451-61. [DOI: 10.1039/b916030m] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Lanza DCF, Meirelles GV, Alborghetti MR, Abrile CH, Lenz G, Kobarg J. FEZ1 interacts with CLASP2 and NEK1 through coiled-coil regions and their cellular colocalization suggests centrosomal functions and regulation by PKC. Mol Cell Biochem 2009; 338:35-45. [PMID: 19924516 DOI: 10.1007/s11010-009-0317-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 11/03/2009] [Indexed: 01/02/2023]
Abstract
FEZ1 was initially described as a neuronal protein that influences axonal development and cell polarization. CLASP2 and NEK1 proteins are present in a centrosomal complex and participate in cell cycle and cell division mechanisms, but their functions were always described individually. Here, we report that NEK1 and CLASP2 colocalize with FEZ1 in a perinuclear region in mammalian cells, and observed that coiled-coil interactions occur between FEZ1/CLASP2 and FEZ1/NEK1 in vitro. These three proteins colocalize and interact with endogenous gamma-tubulin. Furthermore, we found that CLASP2 is phosphorylated and interacts with active PKC isoforms, and that FEZ1/CLASP2 colocalization is inhibited by PMA treatment. Our results provide evidence that these three proteins cooperate in centrosomal functions and open new directions for future studies.
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Affiliation(s)
- Daniel C F Lanza
- Centro de Biologia Molecular Estrutural, Associação Brasileira de Tecnologia de Luz Síncrotron, Rua Giuseppe Máximo Scolfaro, Campinas, SP, Brazil
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Quaresma AJ, Bressan G, Gava L, Lanza D, Ramos C, Kobarg J. Human hnRNP Q re-localizes to cytoplasmic granules upon PMA, thapsigargin, arsenite and heat-shock treatments. Exp Cell Res 2009; 315:968-80. [DOI: 10.1016/j.yexcr.2009.01.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Revised: 01/13/2009] [Accepted: 01/17/2009] [Indexed: 12/15/2022]
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