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Van de Vondel L, De Winter J, Beijer D, Coarelli G, Wayand M, Palvadeau R, Pauly MG, Klein K, Rautenberg M, Guillot-Noël L, Deconinck T, Vural A, Ertan S, Dogu O, Uysal H, Brankovic V, Herzog R, Brice A, Durr A, Klebe S, Stock F, Bischoff AT, Rattay TW, Sobrido MJ, De Michele G, De Jonghe P, Klopstock T, Lohmann K, Zanni G, Santorelli FM, Timmerman V, Haack TB, Züchner S, Schüle R, Stevanin G, Synofzik M, Basak AN, Baets J. De Novo and Dominantly Inherited SPTAN1 Mutations Cause Spastic Paraplegia and Cerebellar Ataxia. Mov Disord 2022; 37:1175-1186. [PMID: 35150594 DOI: 10.1002/mds.28959] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Pathogenic variants in SPTAN1 have been linked to a remarkably broad phenotypical spectrum. Clinical presentations include epileptic syndromes, intellectual disability, and hereditary motor neuropathy. OBJECTIVES We investigated the role of SPTAN1 variants in rare neurological disorders such as ataxia and spastic paraplegia. METHODS We screened 10,000 NGS datasets across two international consortia and one local database, indicative of the level of international collaboration currently required to identify genes causative for rare disease. We performed in silico modeling of the identified SPTAN1 variants. RESULTS We describe 22 patients from 14 families with five novel SPTAN1 variants. Of six patients with cerebellar ataxia, four carry a de novo SPTAN1 variant and two show a sporadic inheritance. In this group, one variant (p.Lys2083del) is recurrent in four patients. Two patients have novel de novo missense mutations (p.Arg1098Cys, p.Arg1624Cys) associated with cerebellar ataxia, in one patient accompanied by intellectual disability and epilepsy. We furthermore report a recurrent missense mutation (p.Arg19Trp) in 15 patients with spastic paraplegia from seven families with a dominant inheritance pattern in four and a de novo origin in one case. One further patient carrying a de novo missense mutation (p.Gln2205Pro) has a complex spastic ataxic phenotype. Through protein modeling we show that mutated amino acids are located at crucial interlinking positions, interconnecting the three-helix bundle of a spectrin repeat. CONCLUSIONS We show that SPTAN1 is a relevant candidate gene for ataxia and spastic paraplegia. We suggest that for the mutations identified in this study, disruption of the interlinking of spectrin helices could be a key feature of the pathomechanism. © 2022 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Liedewei Van de Vondel
- Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.,Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Jonathan De Winter
- Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.,Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.,Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Danique Beijer
- Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.,Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.,Dr John T. Macdonald Foundation Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Giulia Coarelli
- Sorbonne University, ICM-Paris Brain Institute, INSERM, CNRS, APHP, Pitié Salpêtrière Hospital, Paris, France
| | - Melanie Wayand
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research (HIH), Center of Neurology, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Tübingen, Germany
| | - Robin Palvadeau
- Koc University, School of Medicine, Suna and Inan Kirac Foundation, Istanbul, Turkey
| | - Martje G Pauly
- Department of Neurology, University Hospital Schleswig Holstein, Lübeck, Germany.,Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Katrin Klein
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, Germany
| | - Maren Rautenberg
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, Germany
| | - Léna Guillot-Noël
- Sorbonne University, ICM-Paris Brain Institute, INSERM, CNRS, APHP, Pitié Salpêtrière Hospital, Paris, France
| | - Tine Deconinck
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem, Belgium
| | - Atay Vural
- School of Medicine, Department of Neurology, Koc University, Istanbul, Turkey
| | - Sibel Ertan
- School of Medicine, Department of Neurology, Koc University, Istanbul, Turkey
| | - Okan Dogu
- Department of Neurology, School of Medicine, Mersin University, Mersin, Turkey
| | - Hilmi Uysal
- Department of Neurology, School of Medicine, Akdeniz University, Antalya, Turkey
| | - Vesna Brankovic
- Clinic for Child Neurology and Psychiatry, University of Belgrade, Belgrade, Serbia
| | - Rebecca Herzog
- Department of Neurology, University Hospital Schleswig Holstein, Lübeck, Germany
| | - Alexis Brice
- Sorbonne University, ICM-Paris Brain Institute, INSERM, CNRS, APHP, Pitié Salpêtrière Hospital, Paris, France
| | - Alexandra Durr
- Sorbonne University, ICM-Paris Brain Institute, INSERM, CNRS, APHP, Pitié Salpêtrière Hospital, Paris, France
| | - Stephan Klebe
- Department of Neurology, University Hospital Essen, Essen, Germany
| | - Friedrich Stock
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | | | - Tim W Rattay
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research (HIH), Center of Neurology, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Tübingen, Germany
| | - María-Jesús Sobrido
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain.,Neurogenetics Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario, SERGAS, Santiago de Compostela, Spain
| | - Giovanna De Michele
- Department of Neurosciences and Reproductive and Odontostomatological Sciences, Federico II University, Naples, Italy
| | - Peter De Jonghe
- Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.,Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute, LMU Munich, Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Ginevra Zanni
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesù Children's Hospital, Rome, Italy
| | | | - Vincent Timmerman
- Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.,Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Stephan Züchner
- Dr John T. Macdonald Foundation Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Rebecca Schüle
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research (HIH), Center of Neurology, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Tübingen, Germany
| | - Giovanni Stevanin
- Sorbonne University, ICM-Paris Brain Institute, INSERM, CNRS, APHP, Pitié Salpêtrière Hospital, Paris, France.,Paris Sciences Lettres Research University, Ecole Pratique des Hautes Etudes, Paris, France
| | - Matthis Synofzik
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research (HIH), Center of Neurology, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Tübingen, Germany
| | - A Nazli Basak
- Koc University, School of Medicine, Suna and Inan Kirac Foundation, Istanbul, Turkey
| | - Jonathan Baets
- Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.,Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.,Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
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2
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Sen S, Kumar H, Udgaonkar JB. Microsecond Dynamics During the Binding-induced Folding of an Intrinsically Disordered Protein. J Mol Biol 2021; 433:167254. [PMID: 34537237 DOI: 10.1016/j.jmb.2021.167254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 11/26/2022]
Abstract
Tau is an intrinsically disordered protein implicated in many neurodegenerative diseases. The repeat domain fragment of tau, tau-K18, is known to undergo a disorder to order transition in the presence of lipid micelles and vesicles, in which helices form in each of the repeat domains. Here, the mechanism of helical structure formation, induced by a phospholipid mimetic, sodium dodecyl sulfate (SDS) at sub-micellar concentrations, has been studied using multiple biophysical probes. A study of the conformational dynamics of the disordered state, using photoinduced electron transfer coupled to fluorescence correlation spectroscopy (PET-FCS) has indicated the presence of an intermediate state, I, in equilibrium with the unfolded state, U. The cooperative binding of the ligand (L), SDS, to I has been shown to induce the formation of a compact, helical intermediate (IL5) within the dead time (∼37 µs) of a continuous flow mixer. Quantitative analysis of the PET-FCS data and the ensemble microsecond kinetic data, suggests that the mechanism of induction of helical structure can be described by a U ↔ I ↔ IL5 ↔ FL5 mechanism, in which the final helical state, FL5, forms from IL5 with a time constant of 50-200 µs. Finally, it has been shown that the helical conformation is an aggregation-competent state that can directly form amyloid fibrils.
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Affiliation(s)
- Sreemantee Sen
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India; Indian Institute of Science Education and Research, Pune, Pashan, Pune 411 008, India
| | - Harish Kumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India; Indian Institute of Science Education and Research, Pune, Pashan, Pune 411 008, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India; Indian Institute of Science Education and Research, Pune, Pashan, Pune 411 008, India.
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3
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Hale J, An X, Guo X, Gao E, Papoin J, Blanc L, Hillyer CD, Gratzer W, Baines A, Mohandas N. αI-spectrin represents evolutionary optimization of spectrin for red blood cell deformability. Biophys J 2021; 120:3588-3599. [PMID: 34352252 PMCID: PMC8456306 DOI: 10.1016/j.bpj.2021.07.027] [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] [Received: 03/22/2021] [Revised: 07/21/2021] [Accepted: 07/28/2021] [Indexed: 11/15/2022] Open
Abstract
Spectrin tetramers of the membranes of enucleated mammalian erythrocytes play a critical role in red blood cell survival in circulation. One of the spectrins, αI, emerged in mammals with enucleated red cells after duplication of the ancestral α-spectrin gene common to all animals. The neofunctionalized αI-spectrin has moderate affinity for βI-spectrin, whereas αII-spectrin, expressed in nonerythroid cells, retains ancestral characteristics and has a 10-fold higher affinity for βI-spectrin. It has been hypothesized that this adaptation allows for rapid make and break of tetramers to accommodate membrane deformation. We have tested this hypothesis by generating mice with high-affinity spectrin tetramers formed by exchanging the site of tetramer formation in αI-spectrin (segments R0 and R1) for that of αII-spectrin. Erythrocytes with αIIβI presented normal hematologic parameters yet showed increased thermostability, and their membranes were significantly less deformable; under low shear forces, they displayed tumbling behavior rather than tank treading. The membrane skeleton is more stable with αIIβI and shows significantly less remodeling under deformation than red cell membranes of wild-type mice. These data demonstrate that spectrin tetramers undergo remodeling in intact erythrocytes and that this is required for the normal deformability of the erythrocyte membrane. We conclude that αI-spectrin represents evolutionary optimization of tetramer formation: neither higher-affinity tetramers (as shown here) nor lower affinity (as seen in hemolytic disease) can support the membrane properties required for effective tissue oxygenation in circulation.
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Affiliation(s)
- John Hale
- The Red Cell Physiology Laboratory, The New York Blood Center, New York, New York.
| | - Xiuli An
- Membrane Biology Laboratory, The New York Blood Center, New York, New York
| | - Xinhua Guo
- Membrane Biology Laboratory, The New York Blood Center, New York, New York
| | - Erjing Gao
- The Red Cell Physiology Laboratory, The New York Blood Center, New York, New York
| | - Julien Papoin
- Nelkin Laboratory of Pediatric Oncology and Laboratory of Developmental Erythropoiesis, The Feinstein Institutes for Medical Research, Manhasset, New York
| | - Lionel Blanc
- Nelkin Laboratory of Pediatric Oncology and Laboratory of Developmental Erythropoiesis, The Feinstein Institutes for Medical Research, Manhasset, New York; Department of Molecular Medicine and Pediatrics, Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York
| | | | - Walter Gratzer
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Anthony Baines
- Department of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Narla Mohandas
- The Red Cell Physiology Laboratory, The New York Blood Center, New York, New York
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4
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Cotranslational folding cooperativity of contiguous domains of α-spectrin. Proc Natl Acad Sci U S A 2020; 117:14119-14126. [PMID: 32513720 DOI: 10.1073/pnas.1909683117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Proteins synthesized in the cell can begin to fold during translation before the entire polypeptide has been produced, which may be particularly relevant to the folding of multidomain proteins. Here, we study the cotranslational folding of adjacent domains from the cytoskeletal protein α-spectrin using force profile analysis (FPA). Specifically, we investigate how the cotranslational folding behavior of the R15 and R16 domains are affected by their neighboring R14 and R16, and R15 and R17 domains, respectively. Our results show that the domains impact each other's folding in distinct ways that may be important for the efficient assembly of α-spectrin, and may reduce its dependence on chaperones. Furthermore, we directly relate the experimentally observed yield of full-length protein in the FPA assay to the force exerted by the folding protein in piconewtons. By combining pulse-chase experiments to measure the rate at which the arrested protein is converted into full-length protein with a Bell model of force-induced rupture, we estimate that the R16 domain exerts a maximal force on the nascent chain of ∼15 pN during cotranslational folding.
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5
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Yang J, Gao M, Xiong J, Su Z, Huang Y. Features of molecular recognition of intrinsically disordered proteins via coupled folding and binding. Protein Sci 2019; 28:1952-1965. [PMID: 31441158 PMCID: PMC6798136 DOI: 10.1002/pro.3718] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/16/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022]
Abstract
The sequence-structure-function paradigm of proteins has been revolutionized by the discovery of intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). In contrast to traditional ordered proteins, IDPs/IDRs are unstructured under physiological conditions. The absence of well-defined three-dimensional structures in the free state of IDPs/IDRs is fundamental to their function. Folding upon binding is an important mode of molecular recognition for IDPs/IDRs. While great efforts have been devoted to investigating the complex structures and binding kinetics and affinities, our knowledge on the binding mechanisms of IDPs/IDRs remains very limited. Here, we review recent advances on the binding mechanisms of IDPs/IDRs. The structures and kinetic parameters of IDPs/IDRs can vary greatly, and the binding mechanisms can be highly dependent on the structural properties of IDPs/IDRs. IDPs/IDRs can employ various combinations of conformational selection and induced fit in a binding process, which can be templated by the target and/or encoded by the IDP/IDR. Further studies should provide deeper insights into the molecular recognition of IDPs/IDRs and enable the rational design of IDP/IDR binding mechanisms in the future.
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Affiliation(s)
- Jing Yang
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Meng Gao
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Junwen Xiong
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Zhengding Su
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Yongqi Huang
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
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6
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Sen S, Udgaonkar JB. Binding-induced folding under unfolding conditions: Switching between induced fit and conformational selection mechanisms. J Biol Chem 2019; 294:16942-16952. [PMID: 31582563 DOI: 10.1074/jbc.ra119.009742] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/14/2019] [Indexed: 12/11/2022] Open
Abstract
The chemistry of protein-ligand binding is the basis of virtually every biological process. Ligand binding can be essential for a protein to function in the cell by stabilizing or altering the conformation of a protein, particularly for partially or completely unstructured proteins. However, the mechanisms by which ligand binding impacts disordered proteins or influences the role of disorder in protein folding is not clear. To gain insight into this question, the mechanism of folding induced by the binding of a Pro-rich peptide ligand to the SH3 domain of phosphatidylinositol 3-kinase unfolded in the presence of urea has been studied using kinetic methods. Under strongly denaturing conditions, folding was found to follow a conformational selection (CS) mechanism. However, under mildly denaturing conditions, a ligand concentration-dependent switch in the mechanism was observed. The folding mechanism switched from being predominantly a CS mechanism at low ligand concentrations to being predominantly an induced fit (IF) mechanism at high ligand concentrations. The switch in the mechanism manifests itself as an increase in the reaction flux along the IF pathway at high ligand concentrations. The results indicate that, in the case of intrinsically disordered proteins too, the folding mechanism is determined by the concentration of the ligand that induces structure formation.
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Affiliation(s)
- Sreemantee Sen
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India Indian Institute of Science Education and Research, Pune, Pashan, Pune 411 008, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India Indian Institute of Science Education and Research, Pune, Pashan, Pune 411 008, India
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7
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Bose D, Chakrabarti A. Localizing the chaperone activity of erythroid spectrin. Cytoskeleton (Hoboken) 2019; 76:383-397. [DOI: 10.1002/cm.21556] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/31/2019] [Accepted: 08/06/2019] [Indexed: 02/05/2023]
Affiliation(s)
- Dipayan Bose
- Crystallography and Molecular Biology DivisionSaha Institute of Nuclear Physics Kolkata India
- Homi Bhabha National Institute Mumbai India
| | - Abhijit Chakrabarti
- Crystallography and Molecular Biology DivisionSaha Institute of Nuclear Physics Kolkata India
- Homi Bhabha National Institute Mumbai India
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8
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Ciferri A, Crumbliss AL. A Supramolecular Polymerization Approach to the Growth of the Myofibril. Front Chem 2019; 7:487. [PMID: 31380341 PMCID: PMC6646515 DOI: 10.3389/fchem.2019.00487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/25/2019] [Indexed: 11/13/2022] Open
Abstract
Extended linear structures self-assemble by the multi-stage-open-association mechanism of supramolecular polymerization (MSOA). Application of the model requires the identification of a repeating unit, the main-chain supramolecular bond, and the binding constant. The strength of the bond and the degree of polymerization become extremely large when multiple sites for non-covalent interactions occur. These expectations had been previously verified in the case of the neuronal axon, for which the above parameters were assessed from its known molecular structure. The more complex case of the myofibril is analyzed here. The specific interactions that connect neighboring sarcomers have been a matter of debate. Recent work has focused on the bond between titin and α-actinin localized at the terminal Z-zones of each sarcomer. Elaboration of literature data suggests that titin-α-actinin interactions do bridge neighboring sarcomers, promoting the polymerization of myofibrils that attain macroscopic dimensions consistently with the MSOA predictions. The rationale for the complex structuration of single sarcomers is discussed.
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Affiliation(s)
- Alberto Ciferri
- Chemistry Department, Duke University, Durham, NC, United States
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9
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How Robust Is the Mechanism of Folding-Upon-Binding for an Intrinsically Disordered Protein? Biophys J 2019; 114:1889-1894. [PMID: 29694866 DOI: 10.1016/j.bpj.2018.03.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 03/15/2018] [Accepted: 03/20/2018] [Indexed: 12/18/2022] Open
Abstract
The mechanism of interaction of an intrinsically disordered protein (IDP) with its physiological partner is characterized by a disorder-to-order transition in which a recognition and a binding step take place. Even if the mechanism is quite complex, IDPs tend to bind their partner in a cooperative manner such that it is generally possible to detect experimentally only the disordered unbound state and the structured complex. The interaction between the disordered C-terminal domain of the measles virus nucleoprotein (NTAIL) and the X domain (XD) of the viral phosphoprotein allows us to detect and quantify the two distinct steps of the overall reaction. Here, we analyze the robustness of the folding of NTAIL upon binding to XD by measuring the effect on both the folding and binding steps of NTAIL when the structure of XD is modified. Because it has been shown that wild-type XD is structurally heterogeneous, populating an on-pathway intermediate under native conditions, we investigated the binding to 11 different site-directed variants of NTAIL of one particular variant of XD (I504A XD) that populates only the native state. Data reveal that the recognition and the folding steps are both affected by the structure of XD, indicating a highly malleable pathway. The experimental results are briefly discussed in the light of previous experiments on other IDPs.
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10
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Residual Structure Accelerates Binding of Intrinsically Disordered ACTR by Promoting Efficient Folding upon Encounter. J Mol Biol 2018; 431:422-432. [PMID: 30528464 DOI: 10.1016/j.jmb.2018.12.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 11/10/2018] [Accepted: 12/03/2018] [Indexed: 11/21/2022]
Abstract
Intrinsically disordered proteins (IDPs) often fold into stable structures upon specific binding. The roles of residual structure of unbound IDPs in coupling binding and folding have been under much debate. While many studies emphasize the importance of conformational flexibility for IDP recognition, it was recently demonstrated that stabilization the N-terminal helix of intrinsically disordered ACTR accelerated its binding to another IDP, NCBD of the CREB-binding protein. To understand how enhancing ACTR helicity accelerates binding, we derived a series of topology-based coarse-grained models that mimicked various ACTR mutants with increasing helical contents and reproduced their NCBD binding affinities. Molecular dynamics simulations were then performed to sample hundreds of reversible coupled binding and folding transitions. The results show that increasing ACTR helicity does not alter the baseline mechanism of synergistic folding, which continues to follow "extended conformational selection" with multiple stages of selection and induced folding. Importantly, these coarse-grained models, while only calibrated based on binding thermodynamics, recapitulate the observed kinetic acceleration with increasing ACTR helicity. However, the residual helices do not enhance the association kinetics via more efficient seeding of productive collisions. Instead, they allow the nonspecific collision complexes to evolve more efficiently into the final bound and folded state, which is the primary source of accelerated association kinetics. Meanwhile, reduced dissociation kinetics with increasing ACTR helicity can be directly attributed to smaller entropic cost of forming the bound state. Altogether, this study provides important mechanistic insights into how residual structure may modulate thermodynamics and kinetics of IDP interactions.
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11
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Crabtree MD, Mendonça CATF, Bubb QR, Clarke J. Folding and binding pathways of BH3-only proteins are encoded within their intrinsically disordered sequence, not templated by partner proteins. J Biol Chem 2018; 293:9718-9723. [PMID: 29716994 PMCID: PMC6016464 DOI: 10.1074/jbc.ra118.002791] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/24/2018] [Indexed: 12/03/2022] Open
Abstract
Intrinsically disordered regions are present in one-third of eukaryotic proteins and are overrepresented in cellular processes such as signaling, suggesting that intrinsically disordered proteins (IDPs) may have a functional advantage over folded proteins. Upon interacting with a partner macromolecule, a subset of IDPs can fold and bind to form a well-defined three-dimensional conformation. For example, disordered BH3-only proteins bind promiscuously to a large number of homologous BCL-2 family proteins, where they fold to a helical structure in a groove on the BCL-2–like protein surface. As two protein chains are involved in the folding reaction, and the structure is only formed in the presence of the partner macromolecule, this raises the question of where the folding information is encoded. Here, we examine these coupled folding and binding reactions to determine which component determines the folding and binding pathway. Using Φ value analysis to compare transition state interactions between the disordered BH3-only proteins PUMA and BID and the folded BCL-2–like proteins A1 and MCL-1, we found that, even though the BH3-only protein is disordered in isolation and requires a stabilizing partner to fold, its folding and binding pathway is encoded in the IDP itself; the reaction is not templated by the folded partner. We suggest that, by encoding both its transition state and level of residual structure, an IDP can evolve a specific kinetic profile, which could be a crucial functional advantage of disorder.
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Affiliation(s)
- Michael D Crabtree
- From the Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Carolina A T F Mendonça
- From the Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Quenton R Bubb
- From the Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Jane Clarke
- From the Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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12
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Dahal L, Kwan TOC, Shammas SL, Clarke J. pKID Binds to KIX via an Unstructured Transition State with Nonnative Interactions. Biophys J 2018; 113:2713-2722. [PMID: 29262364 PMCID: PMC5770965 DOI: 10.1016/j.bpj.2017.10.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/04/2017] [Accepted: 10/10/2017] [Indexed: 02/02/2023] Open
Abstract
Understanding the detailed mechanism of interaction of intrinsically disordered proteins with their partners is crucial to comprehend their functions in signaling and transcription. Through its interaction with KIX, the disordered pKID region of CREB protein is central in the transcription of cAMP responsive genes, including those involved in long-term memory. Numerous simulation studies have investigated these interactions. Combined with experimental results, these can provide valuable and comprehensive understanding of the mechanisms involved. Here, we probe the transition state of this interaction experimentally through analyzing the kinetic effect of mutating both interface and solvent exposed residues in pKID. We show that very few specific interactions between pKID and KIX are required in the initial binding process. Only a small number of weak interactions are formed at the transition state, including nonnative interactions, and most of the folding occurs after the initial binding event. These properties are consistent with computational results and also the majority of experimental studies of intrinsically disordered protein coupled folding and binding in other protein systems, suggesting that these may be common features.
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Affiliation(s)
- Liza Dahal
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Tristan O C Kwan
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Sarah L Shammas
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
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13
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Affinity of IDPs to their targets is modulated by ion-specific changes in kinetics and residual structure. Proc Natl Acad Sci U S A 2017; 114:9882-9887. [PMID: 28847960 DOI: 10.1073/pnas.1705105114] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are characterized by a lack of defined structure. Instead, they populate ensembles of rapidly interconverting conformations with marginal structural stabilities. Changes in solution conditions such as temperature and crowding agents consequently affect IDPs more than their folded counterparts. Here we reveal that the residual structure content of IDPs is modulated both by ionic strength and by the type of ions present in solution. We show that these ion-specific structural changes result in binding affinity shifts of up to sixfold, which happen through alteration of both association and dissociation rates. These effects follow the Hofmeister series, but unlike the well-established effects on the stability of folded proteins, they already occur at low, hypotonic concentrations of salt. We attribute this sensitivity to the marginal stability of IDPs, which could have physiological implications given the role of IDPs in signaling, the asymmetric ion profiles of different cellular compartments, and the role of ions in biology.
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14
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Lindström I, Dogan J. Native Hydrophobic Binding Interactions at the Transition State for Association between the TAZ1 Domain of CBP and the Disordered TAD-STAT2 Are Not a Requirement. Biochemistry 2017; 56:4145-4153. [PMID: 28707474 DOI: 10.1021/acs.biochem.7b00428] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A significant fraction of the eukaryotic proteome consists of proteins that are either partially or completely disordered under native-like conditions. Intrinsically disordered proteins (IDPs) are common in protein-protein interactions and are involved in numerous cellular processes. Although many proteins have been identified as disordered, much less is known about the binding mechanisms of the coupled binding and folding reactions involving IDPs. Here we have analyzed the rate-limiting transition state for binding between the TAZ1 domain of CREB binding protein and the intrinsically disordered transactivation domain of STAT2 (TAD-STAT2) by site-directed mutagenesis and kinetic experiments (Φ-value analysis) and found that the native protein-protein binding interface is not formed at the transition state for binding. Instead, native hydrophobic binding interactions form late, after the rate-limiting barrier has been crossed. The association rate constant in the absence of electrostatic enhancement was determined to be rather high. This is consistent with the Φ-value analysis, which showed that there are few or no obligatory native contacts. Also, linear free energy relationships clearly demonstrate that native interactions are cooperatively formed, a scenario that has usually been observed for proteins that fold according to the so-called nucleation-condensation mechanism. Thus, native hydrophobic binding interactions at the rate-limiting transition state for association between TAD-STAT2 and TAZ1 are not a requirement, which is generally in agreement with previous findings on other IDP systems and might be a common mechanism for IDPs.
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Affiliation(s)
- Ida Lindström
- Department of Biochemistry and Biophysics, Stockholm University , 10691 Stockholm, Sweden
| | - Jakob Dogan
- Department of Biochemistry and Biophysics, Stockholm University , 10691 Stockholm, Sweden
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15
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Bonetti D, Troilo F, Toto A, Brunori M, Longhi S, Gianni S. Analyzing the Folding and Binding Steps of an Intrinsically Disordered Protein by Protein Engineering. Biochemistry 2017; 56:3780-3786. [DOI: 10.1021/acs.biochem.7b00350] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniela Bonetti
- Istituto
Pasteur Italia-Fondazione Cenci Bolognetti, Istituto di Biologia e
Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche
“A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy
| | - Francesca Troilo
- Istituto
Pasteur Italia-Fondazione Cenci Bolognetti, Istituto di Biologia e
Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche
“A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy
- Aix-Marseille Univ, CNRS, Architecture et Fonction des
Macromolécules Biologiques (AFMB), UMR 7257, 13288 Marseille, France
| | - Angelo Toto
- Aix-Marseille Univ, CNRS, Architecture et Fonction des
Macromolécules Biologiques (AFMB), UMR 7257, 13288 Marseille, France
| | - Maurizio Brunori
- Istituto
Pasteur Italia-Fondazione Cenci Bolognetti, Istituto di Biologia e
Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche
“A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy
| | - Sonia Longhi
- Aix-Marseille Univ, CNRS, Architecture et Fonction des
Macromolécules Biologiques (AFMB), UMR 7257, 13288 Marseille, France
| | - Stefano Gianni
- Istituto
Pasteur Italia-Fondazione Cenci Bolognetti, Istituto di Biologia e
Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche
“A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy
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16
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Cotranslational folding of spectrin domains via partially structured states. Nat Struct Mol Biol 2017; 24:221-225. [DOI: 10.1038/nsmb.3355] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 12/07/2016] [Indexed: 11/09/2022]
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17
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Toto A, Gianni S. Mutational Analysis of the Binding-Induced Folding Reaction of the Mixed-Lineage Leukemia Protein to the KIX Domain. Biochemistry 2016; 55:3957-62. [PMID: 27341615 DOI: 10.1021/acs.biochem.6b00505] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Intrinsically disordered proteins represent a large class of proteins that lack a well-defined three-dimensional structure in isolation but can undergo a disorder to order transition upon binding to their physiological ligands. Understanding the mechanism by which these proteins fold upon binding represents a challenge. Here we present a detailed mutational study of the kinetics of the binding reaction between the transactivation domain of the mixed-lineage leukemia protein, an intrinsically disordered protein, and the KIX domain, performed under different experimental conditions. The experimental data allow us to infer the mechanism of folding upon binding and to pinpoint the key interactions present in the transition state. Furthermore, we identify a peculiar malleability of the observed mechanism upon changes in reaction conditions. This finding, which is in opposition to the robustness typically observed in the folding of globular proteins, is discussed in the context of previous work on intrinsically disordered proteins.
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Affiliation(s)
- Angelo Toto
- Istituto Pasteur Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma , P. le A. Moro 5, 00185 Rome, Italy
| | - Stefano Gianni
- Istituto Pasteur Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma , P. le A. Moro 5, 00185 Rome, Italy.,Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
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18
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Umezawa K, Ohnuki J, Higo J, Takano M. Intrinsic disorder accelerates dissociation rather than association. Proteins 2016; 84:1124-33. [DOI: 10.1002/prot.25057] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 03/16/2016] [Accepted: 04/24/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Koji Umezawa
- Department of Pure and Applied Physics; Waseda University; Okubo 3-4-1, Shinjuku-Ku Tokyo 169-8555 Japan
| | - Jun Ohnuki
- Department of Pure and Applied Physics; Waseda University; Okubo 3-4-1, Shinjuku-Ku Tokyo 169-8555 Japan
| | - Junichi Higo
- Institute for Protein Research, Osaka University; Suita Osaka 565-0871 Japan
| | - Mitsunori Takano
- Department of Pure and Applied Physics; Waseda University; Okubo 3-4-1, Shinjuku-Ku Tokyo 169-8555 Japan
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19
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Cao H, Huang Y, Liu Z. Interplay between binding affinity and kinetics in protein-protein interactions. Proteins 2016; 84:920-33. [PMID: 27018856 DOI: 10.1002/prot.25041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/24/2016] [Accepted: 03/17/2016] [Indexed: 12/18/2022]
Abstract
To clarify the interplay between the binding affinity and kinetics of protein-protein interactions, and the possible role of intrinsically disordered proteins in such interactions, molecular simulations were carried out on 20 protein complexes. With bias potential and reweighting techniques, the free energy profiles were obtained under physiological affinities, which showed that the bound-state valley is deep with a barrier height of 12 - 33 RT. From the dependence of the affinity on interface interactions, the entropic contribution to the binding affinity is approximated to be proportional to the interface area. The extracted dissociation rates based on the Arrhenius law correlate reasonably well with the experimental values (Pearson correlation coefficient R = 0.79). For each protein complex, a linear free energy relationship between binding affinity and the dissociation rate was confirmed, but the distribution of the slopes for intrinsically disordered proteins showed no essential difference with that observed for ordered proteins. A comparison with protein folding was also performed. Proteins 2016; 84:920-933. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Huaiqing Cao
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.,Center for Quantitative Biology, and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing, 100871, China
| | - Yongqi Huang
- Institute of Theoretical Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, China
| | - Zhirong Liu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.,Center for Quantitative Biology, and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing, 100871, China
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20
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Molecular Recognition by Templated Folding of an Intrinsically Disordered Protein. Sci Rep 2016; 6:21994. [PMID: 26912067 PMCID: PMC4766501 DOI: 10.1038/srep21994] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/04/2016] [Indexed: 12/26/2022] Open
Abstract
Intrinsically disordered proteins often become structured upon interacting with their partners. The mechanism of this ‘folding upon binding’ process, however, has not been fully characterised yet. Here we present a study of the folding of the intrinsically disordered transactivation domain of c-Myb (c-Myb) upon binding its partner KIX. By determining the structure of the folding transition state for the binding of wild-type and three mutational variants of KIX, we found a remarkable plasticity of the folding pathway of c-Myb. To explain this phenomenon, we show that the folding of c-Myb is templated by the structure of KIX. This adaptive folding behaviour, which occurs by heterogeneous nucleation, differs from the robust homogeneous nucleation typically observed for globular proteins. We suggest that this templated folding mechanism may enable intrinsically disordered proteins to achieve specific and reliable binding with multiple partners while avoiding aberrant interactions.
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21
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DeForte S, Reddy KD, Uversky VN. Quarterly intrinsic disorder digest (January-February-March, 2014). INTRINSICALLY DISORDERED PROTEINS 2016; 4:e1153395. [PMID: 28232896 DOI: 10.1080/21690707.2016.1153395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This is the 5th issue of the Digested Disorder series that represents a reader's digest of the scientific literature on intrinsically disordered proteins. We continue to use only 2 criteria for inclusion of a paper to this digest: The publication date (a paper should be published within the covered time frame) and the topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the first quarter of 2014; i.e., during the period of January, February, and March of 2014. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included papers a short description is given on its major findings.
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Affiliation(s)
- Shelly DeForte
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida , Tampa, FL, USA
| | - Krishna D Reddy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida , Tampa, FL, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Biology Department, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
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22
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Shammas SL, Crabtree MD, Dahal L, Wicky BIM, Clarke J. Insights into Coupled Folding and Binding Mechanisms from Kinetic Studies. J Biol Chem 2016; 291:6689-95. [PMID: 26851275 PMCID: PMC4807256 DOI: 10.1074/jbc.r115.692715] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) are characterized by a lack of persistent structure. Since their identification more than a decade ago, many questions regarding their functional relevance and interaction mechanisms remain unanswered. Although most experiments have taken equilibrium and structural perspectives, fewer studies have investigated the kinetics of their interactions. Here we review and highlight the type of information that can be gained from kinetic studies. In particular, we show how kinetic studies of coupled folding and binding reactions, an important class of signaling event, are needed to determine mechanisms.
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Affiliation(s)
- Sarah L Shammas
- From the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Michael D Crabtree
- From the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Liza Dahal
- From the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Basile I M Wicky
- From the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Jane Clarke
- From the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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23
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Gianni S, Dogan J, Jemth P. Coupled binding and folding of intrinsically disordered proteins: what can we learn from kinetics? Curr Opin Struct Biol 2016; 36:18-24. [DOI: 10.1016/j.sbi.2015.11.012] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/13/2015] [Accepted: 11/26/2015] [Indexed: 12/16/2022]
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24
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Gibbs EB, Showalter SA. Quantitative biophysical characterization of intrinsically disordered proteins. Biochemistry 2015; 54:1314-26. [PMID: 25631161 DOI: 10.1021/bi501460a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Intrinsically disordered proteins (IDPs) are broadly defined as protein regions that do not cooperatively fold into a spatially or temporally stable structure. Recent research strongly supports the hypothesis that a conserved functional role for structural disorder renders IDPs uniquely capable of functioning in biological processes such as cellular signaling and transcription. Recently, the frequency of application of rigorous mechanistic biochemistry and quantitative biophysics to disordered systems has increased dramatically. For example, the launch of the Protein Ensemble Database (pE-DB) demonstrates that the potential now exists to refine models for the native state structure of IDPs using experimental data. However, rigorous assessment of which observables place the strongest and least biased constraints on those ensembles is now needed. Most importantly, the past few years have seen strong growth in the number of biochemical and biophysical studies attempting to connect structural disorder with function. From the perspective of equilibrium thermodynamics, there is a clear need to assess the relative significance of hydrophobic versus electrostatic forces in IDP interactions, if it is possible to generalize at all. Finally, kinetic mechanisms that invoke conformational selection and/or induced fit are often used to characterize coupled IDP folding and binding, although application of these models is typically built upon thermodynamic observations. Recently, the reaction rates and kinetic mechanisms of more intrinsically disordered systems have been tested through rigorous kinetic experiments. Motivated by these exciting advances, here we provide a review and prospectus for the quantitative study of IDP structure, thermodynamics, and kinetics.
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Affiliation(s)
- Eric B Gibbs
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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25
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Affiliation(s)
- Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; and
| | - Patricia L Clark
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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26
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Rogers JM, Oleinikovas V, Shammas SL, Wong CT, De Sancho D, Baker CM, Clarke J. Interplay between partner and ligand facilitates the folding and binding of an intrinsically disordered protein. Proc Natl Acad Sci U S A 2014; 111:15420-5. [PMID: 25313042 PMCID: PMC4217413 DOI: 10.1073/pnas.1409122111] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein-protein interactions are at the heart of regulatory and signaling processes in the cell. In many interactions, one or both proteins are disordered before association. However, this disorder in the unbound state does not prevent many of these proteins folding to a well-defined, ordered structure in the bound state. Here we examine a typical system, where a small disordered protein (PUMA, p53 upregulated modulator of apoptosis) folds to an α-helix when bound to a groove on the surface of a folded protein (MCL-1, induced myeloid leukemia cell differentiation protein). We follow the association of these proteins using rapid-mixing stopped flow, and examine how the kinetic behavior is perturbed by denaturant and carefully chosen mutations. We demonstrate the utility of methods developed for the study of monomeric protein folding, including β-Tanford values, Leffler α, Φ-value analysis, and coarse-grained simulations, and propose a self-consistent mechanism for binding. Folding of the disordered protein before binding does not appear to be required and few, if any, specific interactions are required to commit to association. The majority of PUMA folding occurs after the transition state, in the presence of MCL-1. We also examine the role of the side chains of folded MCL-1 that make up the binding groove and find that many favor equilibrium binding but, surprisingly, inhibit the association process.
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Affiliation(s)
- Joseph M Rogers
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | | | - Sarah L Shammas
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Chi T Wong
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - David De Sancho
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Christopher M Baker
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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