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Nanajkar N, Sahoo A, Matysiak S. Unraveling the Molecular Complexity of N-Terminus Huntingtin Oligomers: Insights into Polymorphic Structures. J Phys Chem B 2024; 128:7761-7769. [PMID: 39092631 DOI: 10.1021/acs.jpcb.4c03274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Huntington's disease (HD) is a fatal neurodegenerative disorder resulting from an abnormal expansion of polyglutamine (polyQ) repeats in the N-terminus of the huntingtin protein. When the polyQ tract surpasses 35 repeats, the mutated protein undergoes misfolding, culminating in the formation of intracellular aggregates. Research in mouse models suggests that HD pathogenesis involves the aggregation of N-terminal fragments of the huntingtin protein (htt). These early oligomeric assemblies of htt, exhibiting diverse characteristics during aggregation, are implicated as potential toxic entities in HD. However, a consensus on their specific structures remains elusive. Understanding the heterogeneous nature of htt oligomers provides crucial insights into disease mechanisms, emphasizing the need to identify various oligomeric conformations as potential therapeutic targets. Employing coarse-grained molecular dynamics, our study aims to elucidate the mechanisms governing the aggregation process and resultant aggregate architectures of htt. The polyQ tract within htt is flanked by two regions: an N-terminal domain (N17) and a short C-terminal proline-rich segment. We conducted self-assembly simulations involving five distinct N17 + polyQ systems with polyQ lengths ranging from 7 to 45, utilizing the ProMPT force field. Prolongation of the polyQ domain correlates with an increase in β-sheet-rich structures. Longer polyQ lengths favor intramolecular β-sheets over intermolecular interactions due to the folding of the elongated polyQ domain into hairpin-rich conformations. Importantly, variations in polyQ length significantly influence resulting oligomeric structures. Shorter polyQ domains lead to N17 domain aggregation, forming a hydrophobic core, while longer polyQ lengths introduce a competition between N17 hydrophobic interactions and polyQ polar interactions, resulting in densely packed polyQ cores with outwardly distributed N17 domains. Additionally, at extended polyQ lengths, we observe distinct oligomeric conformations with varying degrees of N17 bundling. These findings can help explain the toxic gain-of-function that htt with expanded polyQ acquires.
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Affiliation(s)
- Neha Nanajkar
- Department of Biology, University of Maryland, College Park, Maryland 20740, United States
| | - Abhilash Sahoo
- Center for Computational Biology, Flatiron Institute, New York, New York 10010, United States
- Center for Computational Mathematics, Flatiron Institute, New York, New York 10010, United States
| | - Silvina Matysiak
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20740, United States
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2
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Kandola T, Venkatesan S, Zhang J, Lerbakken BT, Von Schulze A, Blanck JF, Wu J, Unruh JR, Berry P, Lange JJ, Box AC, Cook M, Sagui C, Halfmann R. Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal. eLife 2023; 12:RP86939. [PMID: 37921648 PMCID: PMC10624427 DOI: 10.7554/elife.86939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Abstract
A long-standing goal of amyloid research has been to characterize the structural basis of the rate-determining nucleating event. However, the ephemeral nature of nucleation has made this goal unachievable with existing biochemistry, structural biology, and computational approaches. Here, we addressed that limitation for polyglutamine (polyQ), a polypeptide sequence that causes Huntington's and other amyloid-associated neurodegenerative diseases when its length exceeds a characteristic threshold. To identify essential features of the polyQ amyloid nucleus, we used a direct intracellular reporter of self-association to quantify frequencies of amyloid appearance as a function of concentration, conformational templates, and rational polyQ sequence permutations. We found that nucleation of pathologically expanded polyQ involves segments of three glutamine (Q) residues at every other position. We demonstrate using molecular simulations that this pattern encodes a four-stranded steric zipper with interdigitated Q side chains. Once formed, the zipper poisoned its own growth by engaging naive polypeptides on orthogonal faces, in a fashion characteristic of polymer crystals with intramolecular nuclei. We further show that self-poisoning can be exploited to block amyloid formation, by genetically oligomerizing polyQ prior to nucleation. By uncovering the physical nature of the rate-limiting event for polyQ aggregation in cells, our findings elucidate the molecular etiology of polyQ diseases.
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Affiliation(s)
- Tej Kandola
- Stowers Institute for Medical ResearchKansas CityUnited States
- The Open UniversityMilton KeynesUnited Kingdom
| | | | - Jiahui Zhang
- Department of Physics, North Carolina State UniversityRaleighUnited States
| | | | | | | | - Jianzheng Wu
- Stowers Institute for Medical ResearchKansas CityUnited States
- Department of Biochemistry and Molecular Biology, University of Kansas Medical CenterKansas CityUnited States
| | - Jay R Unruh
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Paula Berry
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Jeffrey J Lange
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Andrew C Box
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Malcolm Cook
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Celeste Sagui
- Department of Physics, North Carolina State UniversityRaleighUnited States
| | - Randal Halfmann
- Stowers Institute for Medical ResearchKansas CityUnited States
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3
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Kandola T, Venkatesan S, Zhang J, Lerbakken B, Schulze AV, Blanck JF, Wu J, Unruh J, Berry P, Lange JJ, Box A, Cook M, Sagui C, Halfmann R. Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533418. [PMID: 36993401 PMCID: PMC10055281 DOI: 10.1101/2023.03.20.533418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
A long-standing goal of amyloid research has been to characterize the structural basis of the rate-determining nucleating event. However, the ephemeral nature of nucleation has made this goal unachievable with existing biochemistry, structural biology, and computational approaches. Here, we addressed that limitation for polyglutamine (polyQ), a polypeptide sequence that causes Huntington's and other amyloid-associated neurodegenerative diseases when its length exceeds a characteristic threshold. To identify essential features of the polyQ amyloid nucleus, we used a direct intracellular reporter of self-association to quantify frequencies of amyloid appearance as a function of concentration, conformational templates, and rational polyQ sequence permutations. We found that nucleation of pathologically expanded polyQ involves segments of three glutamine (Q) residues at every other position. We demonstrate using molecular simulations that this pattern encodes a four-stranded steric zipper with interdigitated Q side chains. Once formed, the zipper poisoned its own growth by engaging naive polypeptides on orthogonal faces, in a fashion characteristic of polymer crystals with intramolecular nuclei. We further show that self-poisoning can be exploited to block amyloid formation, by genetically oligomerizing polyQ prior to nucleation. By uncovering the physical nature of the rate-limiting event for polyQ aggregation in cells, our findings elucidate the molecular etiology of polyQ diseases.
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Affiliation(s)
- Tej Kandola
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- The Open University, Milton Keyes, MK7 6AA, UK
| | | | - Jiahui Zhang
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Alex Von Schulze
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jillian F Blanck
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jianzheng Wu
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jay Unruh
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Paula Berry
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jeffrey J Lange
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Andrew Box
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Malcolm Cook
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Randal Halfmann
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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4
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Neurodegenerative diseases associated with non-coding CGG tandem repeat expansions. Nat Rev Neurol 2022; 18:145-157. [PMID: 35022573 DOI: 10.1038/s41582-021-00612-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2021] [Indexed: 02/07/2023]
Abstract
Non-coding CGG repeat expansions cause multiple neurodegenerative disorders, including fragile X-associated tremor/ataxia syndrome, neuronal intranuclear inclusion disease, oculopharyngeal myopathy with leukodystrophy, and oculopharyngodistal myopathy. The underlying genetic causes of several of these diseases have been identified only in the past 2-3 years. These expansion disorders have substantial overlapping clinical, neuroimaging and histopathological features. The shared features suggest common mechanisms that could have implications for the development of therapies for this group of diseases - similar therapeutic strategies or drugs may be effective for various neurodegenerative disorders induced by non-coding CGG expansions. In this Review, we provide an overview of clinical and pathological features of these CGG repeat expansion diseases and consider the likely pathological mechanisms, including RNA toxicity, CGG repeat-associated non-AUG-initiated translation, protein aggregation and mitochondrial impairment. We then discuss future research needed to improve the identification and diagnosis of CGG repeat expansion diseases, to improve modelling of these diseases and to understand their pathogenesis. We also consider possible therapeutic strategies. Finally, we propose that CGG repeat expansion diseases may represent manifestations of a single underlying neuromyodegenerative syndrome in which different organs are affected to different extents depending on the gene location of the repeat expansion.
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5
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Sudarshi Premawardhana DM, Zhang F, Xu J, Gage MJ. The Poly-E motif in Titin's PEVK region undergoes pH dependent conformational changes. Biochem Biophys Rep 2020; 24:100859. [PMID: 33294637 PMCID: PMC7691732 DOI: 10.1016/j.bbrep.2020.100859] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 10/21/2020] [Accepted: 11/03/2020] [Indexed: 12/03/2022] Open
Abstract
The muscle protein titin plays a crucial role in passive elasticity and the disordered PEVK region within titin is central to that function. The PEVK region is so named due to its high proline, glutamate, valine and lysine content and the high charge density in this region results in a lack of organized structure within this domain. The PEVK region is highly extensible but the molecular interactions that contribute to the elastic nature of the PEVK still remain poorly described. The PEVK region is formed by two unique sequence motifs. The PPAK motif is a 26 to 28 amino acid sequence that contains a mixture of charged and hydrophobic residues and is the primary building block for the PEVK region. Poly-E sequence motifs vary in length and contain clusters of 3–4 glutamic acids distributed throughout the motif. In this study, we derived two 28-residue peptides from the human titin protein sequence and measured their structural characteristics over a range of pHs. Our results demonstrate that the poly-E peptide undergoes a shift from a more rigid and elongated state to a more collapsed state as pH decreases with the midpoint of this transition being at pH ~5.5. Interestingly, a similar conformational shift is not observed in the PPAK peptide. These results suggest that the poly-E motif might provide a nucleating site for the PEVK when the muscle is not in an extended state. Poly-E peptides have a more extended conformation at pH 7.0 than PPAK peptides. Poly-E peptides assume a more relaxed conformation below pH 6. PPAK peptides do not show any conformational sensitivity to changes in pH.
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Affiliation(s)
- Dassanayake Mudiyanselage Sudarshi Premawardhana
- Chemistry Department, University of Massachusetts Lowell, Lowell, MA, 01854, USA
- UMass Movement Center, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Fang Zhang
- Chemistry Department, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Jin Xu
- Chemistry Department, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Matthew J. Gage
- Chemistry Department, University of Massachusetts Lowell, Lowell, MA, 01854, USA
- UMass Movement Center, University of Massachusetts Lowell, Lowell, MA, 01854, USA
- Corresponding author. Department of Chemistry University of Massachusetts Lowell Lowell, Chemistry Department, University of Massachusetts Lowell, Lowell, MA, 01854, USA.
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6
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Intrinsically disordered proteins of viruses: Involvement in the mechanism of cell regulation and pathogenesis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:1-78. [PMID: 32828463 PMCID: PMC7129803 DOI: 10.1016/bs.pmbts.2020.03.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Intrinsically disordered proteins (IDPs) possess the property of inherent flexibility and can be distinguished from other proteins in terms of lack of any fixed structure. Such dynamic behavior of IDPs earned the name "Dancing Proteins." The exploration of these dancing proteins in viruses has just started and crucial details such as correlation of rapid evolution, high rate of mutation and accumulation of disordered contents in viral proteome at least understood partially. In order to gain a complete understanding of this correlation, there is a need to decipher the complexity of viral mediated cell hijacking and pathogenesis in the host organism. Further there is necessity to identify the specific patterns within viral and host IDPs such as aggregation; Molecular recognition features (MoRFs) and their association to virulence, host range and rate of evolution of viruses in order to tackle the viral-mediated diseases. The current book chapter summarizes the aforementioned details and suggests the novel opportunities for further research of IDPs senses in viruses.
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7
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Moldovean SN, Chiş V. Molecular Dynamics Simulations Applied to Structural and Dynamical Transitions of the Huntingtin Protein: A Review. ACS Chem Neurosci 2020; 11:105-120. [PMID: 31841621 DOI: 10.1021/acschemneuro.9b00561] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Over the recent years, Huntington's disease (HD) has become widely discussed in the scientific literature especially because at the mutant level there are several contradictions regarding the aggregation mechanism. The specific role of the physiological huntingtin protein remains unknown, due to the lack of characterization of its entire crystallographic structure, making the experimental and theoretical research even harder when taking into consideration its involvement in multiple biological functions and its high affinity for different interacting partners. Different types of models, containing fewer (not more than 35 Qs) polyglutamine residues for the WT structure and above 35 Qs for the mutants, were subjected to classical or advanced MD simulations to establish the proteins' structural stability by evaluating their conformational changes. Outside the polyQ tract, there are two other regions of interest (the N17 domain and the polyP rich domain) considered to be essential for the aggregation kinetics at the mutant level. The polymerization process is considered to be dependent on the polyQ length. As the polyQ tract's dimension increases, the structures present more β-sheet conformations. Contrarily, it is also considered that the aggregation stability is not necessarily dependent on the number of Qs, while the initial stage of the aggregation seed might play the decisive role. A general assumption regarding the polyP domain is that it might preserve the polyQ structures soluble by acting as an antagonist for β-sheet formation.
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Affiliation(s)
| | - Vasile Chiş
- Babeş-Bolyai University, Faculty of Physics, Kogălniceanu 1, RO-400084 Cluj-Napoca, Romania
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8
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Rodriguez CM, Todd PK. New pathologic mechanisms in nucleotide repeat expansion disorders. Neurobiol Dis 2019; 130:104515. [PMID: 31229686 DOI: 10.1016/j.nbd.2019.104515] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/07/2019] [Accepted: 06/19/2019] [Indexed: 12/14/2022] Open
Abstract
Tandem microsatellite repeats are common throughout the human genome and intrinsically unstable, exhibiting expansions and contractions both somatically and across generations. Instability in a small subset of these repeats are currently linked to human disease, although recent findings suggest more disease-causing repeats await discovery. These nucleotide repeat expansion disorders (NREDs) primarily affect the nervous system and commonly lead to neurodegeneration through toxic protein gain-of-function, protein loss-of-function, and toxic RNA gain-of-function mechanisms. However, the lines between these categories have blurred with recent findings of unconventional Repeat Associated Non-AUG (RAN) translation from putatively non-coding regions of the genome. Here we review two emerging topics in NREDs: 1) The mechanisms by which RAN translation occurs and its role in disease pathogenesis and 2) How nucleotide repeats as RNA and translated proteins influence liquid-liquid phase separation, membraneless organelle dynamics, and nucleocytoplasmic transport. We examine these topics with a particular eye on two repeats: the CGG repeat expansion responsible for Fragile X syndrome and Fragile X-associated Tremor Ataxia Syndrome (FXTAS) and the intronic GGGGCC repeat expansion in C9orf72, the most common inherited cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Our thesis is that these emerging disease mechanisms can inform a broader understanding of the native roles of microsatellites in cellular function and that aberrations in these native processes provide clues to novel therapeutic strategies for these currently untreatable disorders.
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Affiliation(s)
- C M Rodriguez
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA; Department of Genetics, Stanford University, Stanford, CA, USA
| | - P K Todd
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA; VA Ann Arbor Healthcare System, Ann Arbor, MI, USA.
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9
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Turner AH, Holbrey JD. Investigation of glycerol hydrogen-bonding networks in choline chloride/glycerol eutectic-forming liquids using neutron diffraction. Phys Chem Chem Phys 2019; 21:21782-21789. [DOI: 10.1039/c9cp04343h] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Neutron scattering reveals the persistent three-dimensional hydrogen-bonding network between glycerol molecules in the 1 : 2 choline chloride/glycerol eutectic.
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Affiliation(s)
- Adam H. Turner
- The QUILL Research Centre
- School of Chemistry and Chemical Engineering
- Queen's University Belfast
- Belfast BT9 5AG
- UK
| | - John D. Holbrey
- The QUILL Research Centre
- School of Chemistry and Chemical Engineering
- Queen's University Belfast
- Belfast BT9 5AG
- UK
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10
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Fernández-Ramírez MDC, Hervás R, Galera-Prat A, Laurents DV, Carrión-Vázquez M. Efficient and simplified nanomechanical analysis of intrinsically disordered proteins. NANOSCALE 2018; 10:16857-16867. [PMID: 30168565 DOI: 10.1039/c8nr02785d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Intrinsically disordered proteins (IDPs) lack a tertiary structure. Amyloidogenic IDPs (aIDPs) in particular have attracted great interest due to their implication in several devastating diseases as well as in critical biological functions. However, the conformational changes that trigger amyloid formation in aIDPs are largely unknown. aIDPs' conformational polymorphism at the monomer level encumbers their study using bulk techniques. Single-molecule techniques like atomic force microscopy-based single-molecule force spectroscopy represent a promising approach and a "carrier-guest" strategy, in which the protein of interest is mechanically protected, was developed to overcome the spurious signals from the noisy proximal region. However, since the carrier and single-molecule markers have similar mechanostabilities, their signals can intermingle in the force-extension recordings, making peak selection and analysis very laborious, cumbersome and prone to error for the non-expert. Here we have developed a new carrier, the c8C module from the CipC scaffoldin, with a higher mechanostability so that the signals from the protected protein will appear at the end of the recordings. This assures an accurate, more efficient and expert-independent analysis, simplifying both the selection and analysis of the single-molecule data. Furthermore, this modular design can be integrated into any SMFS polyprotein-based vector, thus constituting a useful utensil in the growing toolbox of protein nanomechanics.
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11
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Newcombe EA, Ruff KM, Sethi A, Ormsby AR, Ramdzan YM, Fox A, Purcell AW, Gooley PR, Pappu RV, Hatters DM. Tadpole-like Conformations of Huntingtin Exon 1 Are Characterized by Conformational Heterogeneity that Persists regardless of Polyglutamine Length. J Mol Biol 2018; 430:1442-1458. [PMID: 29627459 DOI: 10.1016/j.jmb.2018.03.031] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/21/2018] [Accepted: 03/25/2018] [Indexed: 11/30/2022]
Abstract
Soluble huntingtin exon 1 (Httex1) with expanded polyglutamine (polyQ) engenders neurotoxicity in Huntington's disease. To uncover the physical basis of this toxicity, we performed structural studies of soluble Httex1 for wild-type and mutant polyQ lengths. Nuclear magnetic resonance experiments show evidence for conformational rigidity across the polyQ region. In contrast, hydrogen-deuterium exchange shows absence of backbone amide protection, suggesting negligible persistence of hydrogen bonds. The seemingly conflicting results are explained by all-atom simulations, which show that Httex1 adopts tadpole-like structures with a globular head encompassing the N-terminal amphipathic and polyQ regions and the tail encompassing the C-terminal proline-rich region. The surface area of the globular domain increases monotonically with polyQ length. This stimulates sharp increases in gain-of-function interactions in cells for expanded polyQ, and one of these interactions is with the stress-granule protein Fus. Our results highlight plausible connections between Httex1 structure and routes to neurotoxicity.
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Affiliation(s)
- Estella A Newcombe
- Department of Biochemistry and Molecular Biology, and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, VIC 3010, Australia
| | - Kiersten M Ruff
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St Louis, MO 63130, USA
| | - Ashish Sethi
- Department of Biochemistry and Molecular Biology, and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, VIC 3010, Australia
| | - Angelique R Ormsby
- Department of Biochemistry and Molecular Biology, and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, VIC 3010, Australia
| | - Yasmin M Ramdzan
- Department of Biochemistry and Molecular Biology, and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, VIC 3010, Australia
| | - Archa Fox
- School of Anatomy, Physiology and Human Biology, The University of Western Australia, Crawley, WA 6009, Australia
| | - Anthony W Purcell
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Paul R Gooley
- Department of Biochemistry and Molecular Biology, and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, VIC 3010, Australia
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St Louis, MO 63130, USA.
| | - Danny M Hatters
- Department of Biochemistry and Molecular Biology, and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, VIC 3010, Australia.
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12
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Doherty CPA, Young LM, Karamanos TK, Smith HI, Jackson MP, Radford SE, Brockwell DJ. A peptide-display protein scaffold to facilitate single molecule force studies of aggregation-prone peptides. Protein Sci 2018; 27:1205-1217. [PMID: 29417650 PMCID: PMC6032367 DOI: 10.1002/pro.3386] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/05/2018] [Accepted: 02/05/2018] [Indexed: 01/12/2023]
Abstract
Protein aggregation is linked with the onset of several neurodegenerative disorders, including Parkinson's disease (PD), which is associated with the aggregation of α‐synuclein (αSyn). The structural mechanistic details of protein aggregation, including the nature of the earliest protein–protein interactions, remain elusive. In this study, we have used single molecule force spectroscopy (SMFS) to probe the first dimerization events of the central aggregation‐prone region of αSyn (residues 71–82) that may initiate aggregation. This region has been shown to be necessary for the aggregation of full length αSyn and is capable of forming amyloid fibrils in isolation. We demonstrate that the interaction of αSyn71‐82 peptides can be studied using SMFS when inserted into a loop of protein L, a mechanically strong and soluble scaffold protein that acts as a display system for SMFS studies. The corresponding fragment of the homolog protein γ‐synuclein (γSyn), which has a lower aggregation propensity, has also been studied here. The results from SMFS, together with native mass spectrometry and aggregation assays, demonstrate that the dimerization propensity of γSyn71‐82 is lower than that of αSyn71‐82, but that a mixed αSyn71‐82: γSyn71‐82 dimer forms with a similar propensity to the αSyn71‐82 homodimer, slowing amyloid formation. This work demonstrates the utility of a novel display method for SMFS studies of aggregation‐prone peptides, which would otherwise be difficult to study.
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Affiliation(s)
- Ciaran P A Doherty
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Lydia M Young
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Hugh I Smith
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Matthew P Jackson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
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13
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Isas JM, Langen A, Isas MC, Pandey NK, Siemer AB. Formation and Structure of Wild Type Huntingtin Exon-1 Fibrils. Biochemistry 2017. [PMID: 28621522 DOI: 10.1021/acs.biochem.7b00138] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The fact that the heritable neurodegenerative disorder Huntington's disease (HD) is autosomal dominant means that there is one wild type and one mutant allele in most HD patients. The CAG repeat expansion in the exon 1 of the protein huntingtin (HTTex1) that causes the disease leads to the formation of HTT fibrils in vitro and vivo. An important question for understanding the molecular mechanism of HD is which role wild type HTT plays for the formation, propagation, and structure of these HTT fibrils. Here we report that fibrils of mutant HTTex1 are able to seed the aggregation of wild type HTTex1 into amyloid fibrils, which in turn can seed the fibril formation of mutant HTTex1. Solid-state NMR and electron paramagnetic resonance data showed that wild type HTTex1 fibrils closely resemble the structure of mutant fibrils, with small differences indicating a less extended fibril core. These data suggest that wild type fibrils can faithfully perpetuate the structure of mutant fibrils in HD. However, wild type HTTex1 monomers have a much higher equilibrium solubility compared to mutant HTTex1, and only a small fraction incorporates into fibrils.
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Affiliation(s)
- J Mario Isas
- Department of Biochemistry and Molecular Medicine, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , Los Angeles, California, United States
| | - Andreas Langen
- Department of Biochemistry and Molecular Medicine, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , Los Angeles, California, United States
| | - Myles C Isas
- Department of Biochemistry and Molecular Medicine, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , Los Angeles, California, United States
| | - Nitin K Pandey
- Department of Biochemistry and Molecular Medicine, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , Los Angeles, California, United States
| | - Ansgar B Siemer
- Department of Biochemistry and Molecular Medicine, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , Los Angeles, California, United States
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14
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Kang H, Vázquez FX, Zhang L, Das P, Toledo-Sherman L, Luan B, Levitt M, Zhou R. Emerging β-Sheet Rich Conformations in Supercompact Huntingtin Exon-1 Mutant Structures. J Am Chem Soc 2017; 139:8820-8827. [PMID: 28609090 PMCID: PMC5835228 DOI: 10.1021/jacs.7b00838] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
There exists strong correlation between the extended polyglutamines (polyQ) within exon-1 of Huntingtin protein (Htt) and age onset of Huntington's disease (HD); however, the underlying molecular mechanism is still poorly understood. Here we apply extensive molecular dynamics simulations to study the folding of Htt-exon-1 across five different polyQ-lengths. We find an increase in secondary structure motifs at longer Q-lengths, including β-sheet content that seems to contribute to the formation of increasingly compact structures. More strikingly, these longer Q-lengths adopt supercompact structures as evidenced by a surprisingly small power-law scaling exponent (0.22) between the radius-of-gyration and Q-length that is substantially below expected values for compact globule structures (∼0.33) and unstructured proteins (∼0.50). Hydrogen bond analyses further revealed that the supercompact behavior of polyQ is mainly due to the "glue-like" behavior of glutamine's side chains with significantly more side chain-side chain H-bonds than regular proteins in the Protein Data Bank (PDB). The orientation of the glutamine side chains also tend to be "buried" inside, explaining why polyQ domains are insoluble on their own.
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Affiliation(s)
- Hongsuk Kang
- Computational Biology Center, IBM Thomas J. Watson Research Center , Yorktown Heights, New York 10598, United States
| | - Francisco X Vázquez
- Computational Biology Center, IBM Thomas J. Watson Research Center , Yorktown Heights, New York 10598, United States
| | - Leili Zhang
- Computational Biology Center, IBM Thomas J. Watson Research Center , Yorktown Heights, New York 10598, United States
| | - Payel Das
- Computational Biology Center, IBM Thomas J. Watson Research Center , Yorktown Heights, New York 10598, United States
| | | | - Binquan Luan
- Computational Biology Center, IBM Thomas J. Watson Research Center , Yorktown Heights, New York 10598, United States
| | - Michael Levitt
- Department of Structural Biology, Stanford University School of Medicine , Stanford, California 94305, United States
| | - Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research Center , Yorktown Heights, New York 10598, United States
- Department of Chemistry, Columbia University , New York, New York 10027, United States
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15
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James SA, Hilal N, Wright CJ. Atomic force microscopy studies of bioprocess engineering surfaces - imaging, interactions and mechanical properties mediating bacterial adhesion. Biotechnol J 2017; 12. [PMID: 28488793 DOI: 10.1002/biot.201600698] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 03/24/2017] [Accepted: 04/10/2017] [Indexed: 12/19/2022]
Abstract
The detrimental effect of bacterial biofilms on process engineering surfaces is well documented. Thus, interest in the early stages of bacterial biofilm formation; in particular bacterial adhesion and the production of anti-fouling coatings has grown exponentially as a field. During this time, Atomic force microscopy (AFM) has emerged as a critical tool for the evaluation of bacterial adhesion. Due to its versatility AFM offers not only insight into the topographical landscape and mechanical properties of the engineering surfaces, but elucidates, through direct quantification the topographical and biomechnical properties of the foulants The aim of this review is to collate the current research on bacterial adhesion, both theoretical and practical, and outline how AFM as a technique is uniquely equipped to provide further insight into the nanoscale world at the bioprocess engineering surface.
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Affiliation(s)
- Sean A James
- Biomaterials, Biofouling and Biofilms Engineering Laboratory (B3EL, System and Process Engineering Center, College of Engineering, Swansea University, Fabian Way, Swansea, SA1 8EN, UK
| | - Nidal Hilal
- Centre for Water Advanced Technologies and Environmental Research (CWATER), College of Engineering, Swansea University, Fabian Way, Swansea, SA1 8EN, UK
| | - Chris J Wright
- Biomaterials, Biofouling and Biofilms Engineering Laboratory (B3EL, System and Process Engineering Center, College of Engineering, Swansea University, Fabian Way, Swansea, SA1 8EN, UK
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16
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Adegbuyiro A, Sedighi F, Pilkington AW, Groover S, Legleiter J. Proteins Containing Expanded Polyglutamine Tracts and Neurodegenerative Disease. Biochemistry 2017; 56:1199-1217. [PMID: 28170216 DOI: 10.1021/acs.biochem.6b00936] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Several hereditary neurological and neuromuscular diseases are caused by an abnormal expansion of trinucleotide repeats. To date, there have been 10 of these trinucleotide repeat disorders associated with an expansion of the codon CAG encoding glutamine (Q). For these polyglutamine (polyQ) diseases, there is a critical threshold length of the CAG repeat required for disease, and further expansion beyond this threshold is correlated with age of onset and symptom severity. PolyQ expansion in the translated proteins promotes their self-assembly into a variety of oligomeric and fibrillar aggregate species that accumulate into the hallmark proteinaceous inclusion bodies associated with each disease. Here, we review aggregation mechanisms of proteins with expanded polyQ-tracts, structural consequences of expanded polyQ ranging from monomers to fibrillar aggregates, the impact of protein context and post-translational modifications on aggregation, and a potential role for lipid membranes in aggregation. As the pathogenic mechanisms that underlie these disorders are often classified as either a gain of toxic function or loss of normal protein function, some toxic mechanisms associated with mutant polyQ tracts will also be discussed.
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Affiliation(s)
- Adewale Adegbuyiro
- The C. Eugene Bennett Department of Chemistry, 217 Clark Hall, West Virginia University , Morgantown, West Virginia 26506, United States
| | - Faezeh Sedighi
- The C. Eugene Bennett Department of Chemistry, 217 Clark Hall, West Virginia University , Morgantown, West Virginia 26506, United States
| | - Albert W Pilkington
- The C. Eugene Bennett Department of Chemistry, 217 Clark Hall, West Virginia University , Morgantown, West Virginia 26506, United States
| | - Sharon Groover
- The C. Eugene Bennett Department of Chemistry, 217 Clark Hall, West Virginia University , Morgantown, West Virginia 26506, United States
| | - Justin Legleiter
- The C. Eugene Bennett Department of Chemistry, 217 Clark Hall, West Virginia University , Morgantown, West Virginia 26506, United States.,Blanchette Rockefeller Neurosciences Institute, Robert C. Byrd Health Sciences Center, P.O. Box 9304, West Virginia University , Morgantown, West Virginia 26506, United States.,NanoSAFE, P.O. Box 6223, West Virginia University , Morgantown, West Virginia 26506, United States
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17
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Cordeiro TN, Herranz-Trillo F, Urbanek A, Estaña A, Cortés J, Sibille N, Bernadó P. Structural Characterization of Highly Flexible Proteins by Small-Angle Scattering. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1009:107-129. [DOI: 10.1007/978-981-10-6038-0_7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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18
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Zhang YJ, Gendron TF, Grima JC, Sasaguri H, Jansen-West K, Xu YF, Katzman RB, Gass J, Murray ME, Shinohara M, Lin WL, Garrett A, Stankowski JN, Daughrity L, Tong J, Perkerson EA, Yue M, Chew J, Castanedes-Casey M, Kurti A, Wang ZS, Liesinger AM, Baker JD, Jiang J, Lagier-Tourenne C, Edbauer D, Cleveland DW, Rademakers R, Boylan KB, Bu G, Link CD, Dickey CA, Rothstein JD, Dickson DW, Fryer JD, Petrucelli L. C9ORF72 poly(GA) aggregates sequester and impair HR23 and nucleocytoplasmic transport proteins. Nat Neurosci 2016; 19:668-677. [PMID: 26998601 PMCID: PMC5138863 DOI: 10.1038/nn.4272] [Citation(s) in RCA: 241] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 02/17/2016] [Indexed: 12/13/2022]
Abstract
Neuronal inclusions of poly(GA), a protein unconventionally translated from G4C2 repeat expansions in C9ORF72, are abundant in patients with frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) caused by this mutation. To investigate poly(GA) toxicity, we generated mice that exhibit poly(GA) pathology, neurodegeneration and behavioral abnormalities reminiscent of FTD and ALS. These phenotypes occurred in the absence of TDP-43 pathology and required poly(GA) aggregation. HR23 proteins involved in proteasomal degradation and proteins involved in nucleocytoplasmic transport were sequestered by poly(GA) in these mice. HR23A and HR23B similarly colocalized to poly(GA) inclusions in C9ORF72 expansion carriers. Sequestration was accompanied by an accumulation of ubiquitinated proteins and decreased xeroderma pigmentosum C (XPC) levels in mice, indicative of HR23A and HR23B dysfunction. Restoring HR23B levels attenuated poly(GA) aggregation and rescued poly(GA)-induced toxicity in neuronal cultures. These data demonstrate that sequestration and impairment of nuclear HR23 and nucleocytoplasmic transport proteins is an outcome of, and a contributor to, poly(GA) pathology.
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Affiliation(s)
- Yong-Jie Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | - Tania F Gendron
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | - Jonathan C Grima
- Department of Neurology, School of Medicine, Johns Hopkins University, Maryland, USA
- Brain Science Institute, School of Medicine, Johns Hopkins University, Maryland, USA
- Department of Neuroscience, School of Medicine, Johns Hopkins University, Maryland, USA
| | - Hiroki Sasaguri
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | | | - Ya-Fei Xu
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | | | - Jennifer Gass
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | - Melissa E Murray
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | | | - Wen-Lang Lin
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | - Aliesha Garrett
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | | | | | - Jimei Tong
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | | | - Mei Yue
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | - Jeannie Chew
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
- Neurobiology of Disease Graduate Program, Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | | | - Aishe Kurti
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | - Zizhao S Wang
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | | | - Jeremy D Baker
- Department of Molecular Medicine, College of Medicine, Byrd Alzheimer's Institute, University of South Florida, Tampa, Florida, USA
| | - Jie Jiang
- Ludwig Institute, University of California at San Diego, La Jolla, California, USA
| | | | - Dieter Edbauer
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Institute for Metabolic Biochemistry, Ludwig Maximilians University Munich, Munich, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Don W Cleveland
- Ludwig Institute, University of California at San Diego, La Jolla, California, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California, USA
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | - Kevin B Boylan
- Department of Neurology, Mayo Clinic, Jacksonville, Florida, USA
| | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | - Christopher D Link
- Integrative Physiology, Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, USA
| | - Chad A Dickey
- Department of Molecular Medicine, College of Medicine, Byrd Alzheimer's Institute, University of South Florida, Tampa, Florida, USA
| | - Jeffrey D Rothstein
- Department of Neurology, School of Medicine, Johns Hopkins University, Maryland, USA
- Brain Science Institute, School of Medicine, Johns Hopkins University, Maryland, USA
- Department of Neuroscience, School of Medicine, Johns Hopkins University, Maryland, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | - John D Fryer
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
- Neurobiology of Disease Graduate Program, Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
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19
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Malkovskiy AV, Wagh DA, Longo FM, Rajadas J. A strategy for analyzing bond strength and interaction kinetics between Pleckstrin homology domains and PI(4,5)P2 phospholipids using force distance spectroscopy and surface plasmon resonance. Analyst 2016; 140:4558-65. [PMID: 26040325 DOI: 10.1039/c5an00498e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phospholipids are important membrane components involved in diverse biological activities ranging from cell signaling to infection by viral particles. A thorough understanding of protein-phospholipid interaction dynamics is thus crucial for deciphering basic cellular processes as well as for targeted drug discovery. For any specific phospholipid-protein binding experiment, various groups have reported different binding constants, which are strongly dependent on applied conditions of interactions. Here, we report a method for accurate determination of the binding affinity and specificity between proteins and phospholipids using a model interaction between PLC-δ1/PH and phosphoinositide phospholipid PtdIns(4,5)P2. We developed an accurate Force Distance Spectroscopy (FDS)-based assay and have attempted to resolve the problem of variation in the observed binding constant by directly measuring the bond force. We confirm the FDS findings of a high bond strength of ∼0.19 ± 0.04 nN by Surface Plasmon Resonance (SPR) data analysis, segregating non-specific interactions, which show a significantly lower K(D) suggesting tight binding.
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Affiliation(s)
- A V Malkovskiy
- Stanford BioADD Laboratory, Stanford, California 94305, USA.
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20
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Garcia-Manyes S, Giganti D, Badilla CL, Lezamiz A, Perales-Calvo J, Beedle AEM, Fernández JM. Single-molecule Force Spectroscopy Predicts a Misfolded, Domain-swapped Conformation in human γD-Crystallin Protein. J Biol Chem 2015; 291:4226-35. [PMID: 26703476 PMCID: PMC4759196 DOI: 10.1074/jbc.m115.673871] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Indexed: 12/30/2022] Open
Abstract
Cataract is a protein misfolding disease where the size of the aggregate is directly related to the severity of the disorder. However, the molecular mechanisms that trigger the onset of aggregation remain unknown. Here we use a combination of protein engineering techniques and single-molecule force spectroscopy using atomic force microscopy to study the individual unfolding pathways of the human γD-crystallin, a multidomain protein that must remain correctly folded during the entire lifetime to guarantee lens transparency. When stretching individual polyproteins containing two neighboring HγD-crystallin monomers, we captured an anomalous misfolded conformation in which the β1 and β2 strands of the N terminus domain of two adjacent monomers swap. This experimentally elusive domain-swapped conformation is likely to be responsible for the increase in molecular aggregation that we measure in vitro. Our results demonstrate the power of force spectroscopy at capturing rare misfolded conformations with potential implications for the understanding of the molecular onset of protein aggregation.
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Affiliation(s)
- Sergi Garcia-Manyes
- From the Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, London WC2R 2LS, United Kingdom and
| | - David Giganti
- the Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Carmen L Badilla
- the Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Ainhoa Lezamiz
- From the Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, London WC2R 2LS, United Kingdom and
| | - Judit Perales-Calvo
- From the Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, London WC2R 2LS, United Kingdom and
| | - Amy E M Beedle
- From the Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, London WC2R 2LS, United Kingdom and
| | - Julio M Fernández
- the Department of Biological Sciences, Columbia University, New York, New York 10027
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21
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Nagarajan D, Deka G, Rao M. Design of symmetric TIM barrel proteins from first principles. BMC BIOCHEMISTRY 2015; 16:18. [PMID: 26264284 PMCID: PMC4531894 DOI: 10.1186/s12858-015-0047-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/21/2015] [Indexed: 12/03/2022]
Abstract
Background Computational protein design is a rapidly maturing field within structural biology, with the goal of designing proteins with custom structures and functions. Such proteins could find widespread medical and industrial applications. Here, we have adapted algorithms from the Rosetta software suite to design much larger proteins, based on ideal geometric and topological criteria. Furthermore, we have developed techniques to incorporate symmetry into designed structures. For our first design attempt, we targeted the (α/β)8 TIM barrel scaffold. We gained novel insights into TIM barrel folding mechanisms from studying natural TIM barrel structures, and from analyzing previous TIM barrel design attempts. Methods Computational protein design and analysis was performed using the Rosetta software suite and custom scripts. Genes encoding all designed proteins were synthesized and cloned on the pET20-b vector. Standard circular dichroism and gel chromatographic experiments were performed to determine protein biophysical characteristics. 1D NMR and 2D HSQC experiments were performed to determine protein structural characteristics. Results Extensive protein design simulations coupled with ab initio modeling yielded several all-atom models of ideal, 4-fold symmetric TIM barrels. Four such models were experimentally characterized. The best designed structure (Symmetrin-1) contained a polar, histidine-rich pore, forming an extensive hydrogen bonding network. Symmetrin-1 was easily expressed and readily soluble. It showed circular dichroism spectra characteristic of well-folded alpha/beta proteins. Temperature melting experiments revealed cooperative and reversible unfolding, with a Tm of 44 °C and a Gibbs free energy of unfolding (ΔG°) of 8.0 kJ/mol. Urea denaturing experiments confirmed these observations, revealing a Cm of 1.6 M and a ΔG° of 8.3 kJ/mol. Symmetrin-1 adopted a monomeric conformation, with an apparent molecular weight of 32.12 kDa, and displayed well resolved 1D-NMR spectra. However, the HSQC spectrum revealed somewhat molten characteristics. Conclusions Despite the detection of molten characteristics, the creation of a soluble, cooperatively folding protein represents an advancement over previous attempts at TIM barrel design. Strategies to further improve Symmetrin-1 are elaborated. Our techniques may be used to create other large, internally symmetric proteins. Electronic supplementary material The online version of this article (doi:10.1186/s12858-015-0047-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Deepesh Nagarajan
- Biochemistry Department, Indian Institute of Science, Bangalore, India.
| | - Geeta Deka
- Molecular Biology Unit, Indian Institute of Science, Bangalore, India.
| | - Megha Rao
- Biochemistry Department, Indian Institute of Science, Bangalore, India.
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22
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Lu X, Murphy RM. Asparagine Repeat Peptides: Aggregation Kinetics and Comparison with Glutamine Repeats. Biochemistry 2015. [PMID: 26204228 DOI: 10.1021/acs.biochem.5b00644] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amino acid repeat runs are common occurrences in eukaryotic proteins, with glutamine (Q) and asparagine (N) as particularly frequent repeats. Abnormal expansion of Q-repeat domains causes at least nine neurodegenerative disorders, most likely because expansion leads to protein misfolding, aggregation, and toxicity. The linkage between Q-repeats and disease has motivated several investigations into the mechanism of aggregation and the role of Q-repeat length in aggregation. Curiously, glutamine repeats are common in vertebrates, whereas N-repeats are virtually absent in vertebrates, but common in invertebrates. One hypothesis for the lack of N-repeats in vertebrates is biophysical; that is, there is strong selective pressure in higher organisms against aggregation-prone proteins. If true, then asparagine and glutamine repeats must differ substantially in their aggregation properties despite their chemical similarities. In this work, aggregation of peptides with asparagine repeats of variable length (12-24) were characterized and compared to that of similar peptides with glutamine repeats. As with glutamine, aggregation of N-repeat peptides was strongly length-dependent. Replacement of glutamine with asparagine caused a subtle shift in the conformation of the monomer, which strongly affected the rate of aggregation. Specifically, N-repeat peptides adopted β-turn structural elements, leading to faster self-assembly into globular oligomers and much more rapid conversion into fibrillar aggregates, compared to Q-repeat peptides. These biophysical differences may account for the differing biological roles of N- versus Q-repeat domains.
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Affiliation(s)
- Xiaomeng Lu
- †Biophysics Program and ‡Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Regina M Murphy
- †Biophysics Program and ‡Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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23
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Farrance OE, Paci E, Radford SE, Brockwell DJ. Extraction of accurate biomolecular parameters from single-molecule force spectroscopy experiments. ACS NANO 2015; 9:1315-1324. [PMID: 25646767 DOI: 10.1021/nn505135d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The atomic force microscope (AFM) is able to manipulate biomolecules and their complexes with exquisite force sensitivity and distance resolution. This capability, complemented by theoretical models, has greatly improved our understanding of the determinants of mechanical strength in proteins and revealed the diverse effects of directional forces on the energy landscape of biomolecules. In unbinding experiments, the interacting partners are usually immobilized on their respective substrates via extensible linkers. These linkers affect both the force and contour length (Lc) of the complex at rupture. Surprisingly, while the former effect is well understood, the latter is largely neglected, leading to incorrect estimations of Lc, a parameter that is often used as evidence for the detection of specific interactions and remodeling events and for the inference of interaction regions. To address this problem, a model that predicts contour length measurements from single-molecule forced-dissociation experiments is presented that considers attachment position on the AFM tip, geometric effects, and polymer dynamics of the linkers. Modeled data are compared with measured contour length distributions from several different experimental systems, revealing that current methods underestimate contour lengths. The model enables nonspecific interactions to be identified unequivocally, allows accurate determination of Lc, and, by comparing experimental and modeled distributions, enables partial unfolding events before rupture to be identified unequivocally.
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Affiliation(s)
- Oliver E Farrance
- Astbury Centre for Structural and Molecular Biology and School of Molecular and Cellular Biology, University of Leeds , Leeds, West Yorkshire, LS2 9JT, U.K
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24
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Luettmer-Strathmann J, Binder K. Transitions of tethered chain molecules under tension. J Chem Phys 2014; 141:114911. [DOI: 10.1063/1.4895729] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Jutta Luettmer-Strathmann
- Department of Physics and Department of Chemistry, The University of Akron, Akron, Ohio 44325-4001, USA
| | - Kurt Binder
- Institut für Physik, Johannes-Gutenberg-Universität, Staudinger Weg 7, D-55099 Mainz, Germany
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25
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Hoffner G, Djian P. Monomeric, oligomeric and polymeric proteins in huntington disease and other diseases of polyglutamine expansion. Brain Sci 2014; 4:91-122. [PMID: 24961702 PMCID: PMC4066239 DOI: 10.3390/brainsci4010091] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/06/2014] [Accepted: 02/18/2014] [Indexed: 01/03/2023] Open
Abstract
Huntington disease and other diseases of polyglutamine expansion are each caused by a different protein bearing an excessively long polyglutamine sequence and are associated with neuronal death. Although these diseases affect largely different brain regions, they all share a number of characteristics, and, therefore, are likely to possess a common mechanism. In all of the diseases, the causative protein is proteolyzed, becomes abnormally folded and accumulates in oligomers and larger aggregates. The aggregated and possibly the monomeric expanded polyglutamine are likely to play a critical role in the pathogenesis and there is increasing evidence that the secondary structure of the protein influences its toxicity. We describe here, with special attention to huntingtin, the mechanisms of polyglutamine aggregation and the modulation of aggregation by the sequences flanking the polyglutamine. We give a comprehensive picture of the characteristics of monomeric and aggregated polyglutamine, including morphology, composition, seeding ability, secondary structure, and toxicity. The structural heterogeneity of aggregated polyglutamine may explain why polyglutamine-containing aggregates could paradoxically be either toxic or neuroprotective.
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Affiliation(s)
- Guylaine Hoffner
- Génétique moléculaire et défense antivirale, Centre National de la Recherche Scientifique, Université Paris Descartes, 45 rue des Saints Pères, 75006 Paris, France.
| | - Philippe Djian
- Génétique moléculaire et défense antivirale, Centre National de la Recherche Scientifique, Université Paris Descartes, 45 rue des Saints Pères, 75006 Paris, France.
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26
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Brucale M, Schuler B, Samorì B. Single-molecule studies of intrinsically disordered proteins. Chem Rev 2014; 114:3281-317. [PMID: 24432838 DOI: 10.1021/cr400297g] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Marco Brucale
- Institute for the Study of Nanostructured Materials (ISMN), Italian National Council of Research (CNR) , Area della Ricerca Roma1, Via Salaria km 29.3 00015 Monterotondo (Rome), Italy
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27
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Ormsby AR, Ramdzan YM, Mok YF, Jovanoski KD, Hatters DM. A platform to view huntingtin exon 1 aggregation flux in the cell reveals divergent influences from chaperones hsp40 and hsp70. J Biol Chem 2013; 288:37192-203. [PMID: 24196953 PMCID: PMC3873573 DOI: 10.1074/jbc.m113.486944] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Our capacity for tracking how misfolded proteins aggregate inside a cell and how different aggregation states impact cell biology remains enigmatic. To address this, we built a new toolkit that enabled the high throughput tracking of individual cells enriched with polyglutamine-expanded Htt exon 1 (Httex1) monomers, oligomers, and inclusions using biosensors of aggregation state and flow cytometry pulse shape analysis. Supplemented with gel filtration chromatography and fluorescence-adapted sedimentation velocity analysis of cell lysates, we collated a multidimensional view of Httex1 aggregation in cells with respect to time, polyglutamine length, expression levels, cell survival, and overexpression of protein quality control chaperones hsp40 (DNAJB1) and hsp70 (HSPA1A). Cell death rates trended higher for Neuro2a cells containing Httex1 in inclusions than with Httex1 dispersed through the cytosol at time points of expression over 2 days. hsp40 stabilized monomers and suppressed inclusion formation but did not otherwise change Httex1 toxicity. hsp70, however, had no major effect on aggregation of Httex1 but increased the survival rate of cells with inclusions. hsp40 and hsp70 also increased levels of a second bicistronic reporter of Httex1 expression, mKate2, and increased total numbers of cells in culture, suggesting these chaperones partly rectify Httex1-induced deficiencies in quality control and growth rates. Collectively, these data suggest that Httex1 overstretches the protein quality control resources and that the defects can be partly rescued by overexpression of hsp40 and hsp70. Importantly, these effects occurred in a pronounced manner for soluble Httex1, which points to Httex1 aggregation occurring subsequently to more acute impacts on the cell.
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Affiliation(s)
- Angelique R Ormsby
- From the Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Melbourne, Victoria 3010, Australia
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28
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Almeida B, Fernandes S, Abreu IA, Macedo-Ribeiro S. Trinucleotide repeats: a structural perspective. Front Neurol 2013; 4:76. [PMID: 23801983 PMCID: PMC3687200 DOI: 10.3389/fneur.2013.00076] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 06/04/2013] [Indexed: 11/29/2022] Open
Abstract
Trinucleotide repeat (TNR) expansions are present in a wide range of genes involved in several neurological disorders, being directly involved in the molecular mechanisms underlying pathogenesis through modulation of gene expression and/or the function of the RNA or protein it encodes. Structural and functional information on the role of TNR sequences in RNA and protein is crucial to understand the effect of TNR expansions in neurodegeneration. Therefore, this review intends to provide to the reader a structural and functional view of TNR and encoded homopeptide expansions, with a particular emphasis on polyQ expansions and its role at inducing the self-assembly, aggregation and functional alterations of the carrier protein, which culminates in neuronal toxicity and cell death. Detail will be given to the Machado-Joseph Disease-causative and polyQ-containing protein, ataxin-3, providing clues for the impact of polyQ expansion and its flanking regions in the modulation of ataxin-3 molecular interactions, function, and aggregation.
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Affiliation(s)
- Bruno Almeida
- Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto , Portugal
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29
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Klein FAC, Zeder-Lutz G, Cousido-Siah A, Mitschler A, Katz A, Eberling P, Mandel JL, Podjarny A, Trottier Y. Linear and extended: a common polyglutamine conformation recognized by the three antibodies MW1, 1C2 and 3B5H10. Hum Mol Genet 2013; 22:4215-23. [PMID: 23777629 DOI: 10.1093/hmg/ddt273] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A long-standing pathomechanistic model proposes that the polyglutamine (polyQ)-length-dependent toxicity threshold observed in all polyQ diseases is triggered by a conformational change within the monomer that occurs only above a certain polyQ length. If true, this yet undefined and elusive mutant-specific toxic conformation would constitute a direct therapeutic target. Three anti-polyQ antibodies-MW1, 1C2 and 3B5H10-have been extensively used to probe the conformation of polyQ. The crystal structure of the MW1 epitope reveals a linear, non-pathogenic polyQ. In contrast, although the detailed structure of its epitope is unknown, the 3B5H10 antibody is widely advertised and used as a conformational antibody that recognizes the toxic conformation of expanded polyQ. We solved the crystal structure of the 1C2 antigen-binding domain (1C2-Fab) and performed a direct comparison between the 1C2, MW1 and 3B5H10 structures. The MW1 and 1C2 antibodies have similar sequences and structures, consistent with their binding to short polyQ and their polyQ length-discrimination properties. Unexpectedly, the 3B5H10 antibody also shares striking features with MW1 and 1C2, which prompted us to revisit its binding properties. We show that the 3B5H10 epitope is actually a short, non-pathogenic polyQ. All three antibodies MW1, 1C2 and 3B5H10 interact similarly with polyQ of various lengths, and bind small polyQ epitopes in similar linear and extended conformations. Together with studies published during the recent years, our work argues against the hypothesis that a mutant-specific conformation in monomeric polyQ molecules is the toxic entity responsible for polyQ diseases.
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Affiliation(s)
- Fabrice A C Klein
- Present address: Computational Chemistry and Biology Group-DETEMA, Facultad de Química, UdelaR, Isidoro de María 1620 piso 3, CC1157, Montevideo, Uruguay
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30
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Analysis of the REJ Module of Polycystin-1 Using Molecular Modeling and Force-Spectroscopy Techniques. JOURNAL OF BIOPHYSICS 2013; 2013:525231. [PMID: 23762046 PMCID: PMC3677617 DOI: 10.1155/2013/525231] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 05/07/2013] [Indexed: 11/18/2022]
Abstract
Polycystin-1 is a large transmembrane protein, which, when mutated, causes autosomal dominant polycystic kidney disease, one of the most common life-threatening genetic diseases that is a leading cause of kidney failure. The REJ (receptor for egg lelly) module is a major component of PC1 ectodomain that extends to about 1000 amino acids. Many missense disease-causing mutations map to this module; however, very little is known about the structure or function of this region. We used a combination of homology molecular modeling, protein engineering, steered molecular dynamics (SMD) simulations, and single-molecule force spectroscopy (SMFS) to analyze the conformation and mechanical stability of the first ~420 amino acids of REJ. Homology molecular modeling analysis revealed that this region may contain structural elements that have an FNIII-like structure, which we named REJd1, REJd2, REJd3, and REJd4. We found that REJd1 has a higher mechanical stability than REJd2 (~190 pN and 60 pN, resp.). Our data suggest that the putative domains REJd3 and REJd4 likely do not form mechanically stable folds. Our experimental approach opens a new way to systematically study the effects of disease-causing mutations on the structure and mechanical properties of the REJ module of PC1.
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31
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Olivares-Quiroz L. Thermodynamics of ideal proteinogenic homopolymer chains as a function of the energy spectrum E, helical propensity ω and enthalpic energy barrier. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2013; 25:155103. [PMID: 23515207 DOI: 10.1088/0953-8984/25/15/155103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A reformulation and generalization of the Zwanzig model (ZW model) for ideal homopolymer chains poly-X, where X represents any of the twenty naturally occurring proteinogenic amino acid residues is presented. This reformulation and generalization provides a direct connection between coarse-grained parameters originally proposed in the ZW model with variables from the Lifson-Roig (LR) theory, such as the helical propensity per residue ω, and new variables introduced here, such as the energy gap Δ between unfolded and folded structures, as well as the ratio f of the energy scales involved. This enables us to discover the relevance of the energy spectrum E to the onset of configurational phase transitions. From the configurational partition function Q, thermodynamic properties such as the configurational entropy S, specific heat v and average energy <E> are calculated in terms of the number of residues K, temperature T, helical propensity ω and energy barrier ΔH for different poly-X chains in vacuo. Results obtained here provide substantial evidence that configurational phase transitions for ideal poly-X chains correspond to first-order phase transitions. An anomalous behavior of the thermodynamic functions <E>, Cv, S with respect to the number K of residues is also highlighted. On-going methods of solution are outlined.
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Affiliation(s)
- L Olivares-Quiroz
- Universidad Autónoma de la Ciudad de México, Campus Cuautepec, Av La Corona 320, Col Loma Alta CP 07160 DF, Mexico.
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32
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Hoffmann T, Tych KM, Brockwell DJ, Dougan L. Single-molecule force spectroscopy identifies a small cold shock protein as being mechanically robust. J Phys Chem B 2013; 117:1819-26. [PMID: 23293964 DOI: 10.1021/jp310442s] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Single-molecule force spectroscopy has emerged as a powerful approach to examine the stability and dynamics of single proteins. We have completed force extension experiments on the small cold shock protein B from Thermotoga maritima, using a specially constructed chimeric polyprotein. The protein's simple topology, which is distinct from the mechanically well-characterized β-grasp and immunoglobulin (Ig)-like folds, in addition to the wide range of structural homologues resulting from its ancient origin, provides an attractive model protein for single-molecule force spectroscopy studies. We have determined that the protein has mechanical stability, unfolding at greater than 70 pN at a pulling velocity of 100 nm s(-1). We reveal features of the unfolding energy landscape by measuring the dependence of the mechanical stability on pulling velocity, in combination with Monte Carlo simulations. We show that the cold shock protein has mechanically robust, yet malleable, features that may be important in providing the protein with stability and flexibility to function over a range of environmental conditions. These results provide insights into the relationship between the secondary structure and topology of a protein and its mechanical strength. This lays the foundation for the investigation of the effects of changes in environmental conditions on the mechanical and dynamic properties of cold shock proteins.
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Affiliation(s)
- Toni Hoffmann
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
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33
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Mao AH, Lyle N, Pappu RV. Describing sequence-ensemble relationships for intrinsically disordered proteins. Biochem J 2013; 449:307-18. [PMID: 23240611 PMCID: PMC4074364 DOI: 10.1042/bj20121346] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Intrinsically disordered proteins participate in important protein-protein and protein-nucleic acid interactions and control cellular phenotypes through their prominence as dynamic organizers of transcriptional, post-transcriptional and signalling networks. These proteins challenge the tenets of the structure-function paradigm and their functional mechanisms remain a mystery given that they fail to fold autonomously into specific structures. Solving this mystery requires a first principles understanding of the quantitative relationships between information encoded in the sequences of disordered proteins and the ensemble of conformations they sample. Advances in quantifying sequence-ensemble relationships have been facilitated through a four-way synergy between bioinformatics, biophysical experiments, computer simulations and polymer physics theories. In the present review we evaluate these advances and the resultant insights that allow us to develop a concise quantitative framework for describing the sequence-ensemble relationships of intrinsically disordered proteins.
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Affiliation(s)
- Albert H. Mao
- Medical Scientist Training Program, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130, U.S.A
- Computational & Molecular Biophysics Program, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130, U.S.A
| | - Nicholas Lyle
- Computational & Systems Biology Program, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130, U.S.A
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130, U.S.A
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34
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Malinovska L, Kroschwald S, Alberti S. Protein disorder, prion propensities, and self-organizing macromolecular collectives. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:918-31. [PMID: 23328411 DOI: 10.1016/j.bbapap.2013.01.003] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 12/12/2012] [Accepted: 01/03/2013] [Indexed: 12/24/2022]
Abstract
Eukaryotic cells are partitioned into functionally distinct self-organizing compartments. But while the biogenesis of membrane-surrounded compartments is beginning to be understood, the organizing principles behind large membrane-less structures, such as RNA-containing granules, remain a mystery. Here, we argue that protein disorder is an essential ingredient for the formation of such macromolecular collectives. Intrinsically disordered regions (IDRs) do not fold into a well-defined structure but rather sample a range of conformational states, depending on the local conditions. In addition to being structurally versatile, IDRs promote multivalent and transient interactions. This unique combination of features turns intrinsically disordered proteins into ideal agents to orchestrate the formation of large macromolecular assemblies. The presence of conformationally flexible regions, however, comes at a cost, for many intrinsically disordered proteins are aggregation-prone and cause protein misfolding diseases. This association with disease is particularly strong for IDRs with prion-like amino acid composition. Here, we examine how disease-causing and normal conformations are linked, and discuss the possibility that the dynamic order of the cytoplasm emerges, at least in part, from the collective properties of intrinsically disordered prion-like domains. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.
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Affiliation(s)
- Liliana Malinovska
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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35
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Kaiser CM, Bujalowski PJ, Ma L, Anderson J, Epstein HF, Oberhauser AF. Tracking UNC-45 chaperone-myosin interaction with a titin mechanical reporter. Biophys J 2012; 102:2212-9. [PMID: 22824286 DOI: 10.1016/j.bpj.2012.03.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 03/01/2012] [Accepted: 03/06/2012] [Indexed: 01/26/2023] Open
Abstract
Myosins are molecular motors that convert chemical energy into mechanical work. Allosterically coupling ATP-binding, hydrolysis, and binding/dissociation to actin filaments requires precise and coordinated structural changes that are achieved by the structurally complex myosin motor domain. UNC-45, a member of the UNC-45/Cro1/She4p family of proteins, acts as a chaperone for myosin and is essential for proper folding and assembly of myosin into muscle thick filaments in vivo. The molecular mechanisms by which UNC-45 interacts with myosin to promote proper folding of the myosin head domain are not known. We have devised a novel approach, to our knowledge, to analyze the interaction of UNC-45 with the myosin motor domain at the single molecule level using atomic force microscopy. By chemically coupling a titin I27 polyprotein to the motor domain of myosin, we introduced a mechanical reporter. In addition, the polyprotein provided a specific attachment point and an unambiguous mechanical fingerprint, facilitating our atomic force microscopy measurements. This approach enabled us to study UNC-45-motor domain interactions. After mechanical unfolding, the motor domain interfered with refolding of the otherwise robust I27 modules, presumably by recruiting them into a misfolded state. In the presence of UNC-45, I27 folding was restored. Our single molecule approach enables the study of UNC-45 chaperone interactions with myosin and their consequences for motor domain folding and misfolding in mechanistic detail.
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Affiliation(s)
- Christian M Kaiser
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
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36
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Shao Q, Zhu W, Gao YQ. Robustness in Protein Folding Revealed by Thermodynamics Calculations. J Phys Chem B 2012; 116:13848-56. [DOI: 10.1021/jp307684h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qiang Shao
- Institute of Theoretical and
Computational Chemistry, College of Chemistry and Molecular Engineering,
Beijing National Laboratory of Molecular Sciences, Peking University, Beijing 100871, China
- Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203,
China
| | - Weiliang Zhu
- Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203,
China
| | - Yi Qin Gao
- Institute of Theoretical and
Computational Chemistry, College of Chemistry and Molecular Engineering,
Beijing National Laboratory of Molecular Sciences, Peking University, Beijing 100871, China
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37
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Khan MKA, Bowler BE. Conformational properties of polyglutamine sequences in guanidine hydrochloride solutions. Biophys J 2012. [PMID: 23199927 DOI: 10.1016/j.bpj.2012.09.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Two sets of iso-1-cytochrome c variants have been prepared with N-terminal insertions of pure polyglutamine, i.e., PolyQ variants, or polyglutamine interrupted with lysine every sixth residue, i.e., Gln-rich variants. The polymer properties of these pure polyGln or Gln-rich sequences have been evaluated using equilibrium and kinetic His-heme loop formation methods for loop sizes ranging from 22 to 46 in 1.5, 3.0, and 6.0 M guanidine hydrochloride (GdnHCl). In 6.0 M GdnHCl, the scaling exponent, ν(3), for the pure polyGln sequences, is ~1.7--significantly less than ν(3) ≈ 2.15 for the Gln-rich sequences. The stability of the His-heme loops becomes progressively greater for the pure polyGln sequences relative to the Gln-rich sequences as GdnHCl concentration decreases from 6.0 to 1.5 M. Thus, the context of the sequence effects the polymer properties of Gln repeats even in denaturing concentrations of GdnHCl. Comparison of data for the Gln-rich variants with previous results for Gly-rich and Ala-rich variants shows that ν(3) ~ 2.2 for the Gln-rich, Gly-rich, and Ala-rich sequences in 6.0 M GdnHCl, whereas ν(3) remains unchanged at 3.0 M GdnHCl concentration for the Gln-rich and Ala-rich sequences but decreases to ~1.7 for the Gly-rich sequences. Thus, the polymer properties of Gln-rich and Ala-rich sequences are less sensitive to solvent quality in denaturing solutions of GdnHCl than Gly-rich sequences. Evaluation of Flory's characteristic ratio, C(n), for the Gln-rich and Ala-rich sequences relative to the Gly-rich sequences shows that Gln-rich sequences are stiffer than Ala-rich sequences at both 3.0 and 6.0 M GdnHCl.
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Affiliation(s)
- Md Khurshid Alam Khan
- Department of Chemistry and Biochemistry, and Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana, USA
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38
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Rhys NH, Soper AK, Dougan L. The Hydrogen-Bonding Ability of the Amino Acid Glutamine Revealed by Neutron Diffraction Experiments. J Phys Chem B 2012; 116:13308-19. [DOI: 10.1021/jp307442f] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- N. H. Rhys
- School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, U.K
| | - A. K. Soper
- ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, Oxon,
OX11 OQX, U.K
| | - L. Dougan
- School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, U.K
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39
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Hervás R, Oroz J, Galera-Prat A, Goñi O, Valbuena A, Vera AM, Gómez-Sicilia À, Losada-Urzáiz F, Uversky VN, Menéndez M, Laurents DV, Bruix M, Carrión-Vázquez M. Common features at the start of the neurodegeneration cascade. PLoS Biol 2012; 10:e1001335. [PMID: 22666178 PMCID: PMC3362641 DOI: 10.1371/journal.pbio.1001335] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 04/06/2012] [Indexed: 12/30/2022] Open
Abstract
A single-molecule study reveals that neurotoxic proteins share common structural features that may trigger neurodegeneration, thus identifying new targets for therapy and diagnosis. Amyloidogenic neurodegenerative diseases are incurable conditions with high social impact that are typically caused by specific, largely disordered proteins. However, the underlying molecular mechanism remains elusive to established techniques. A favored hypothesis postulates that a critical conformational change in the monomer (an ideal therapeutic target) in these “neurotoxic proteins” triggers the pathogenic cascade. We use force spectroscopy and a novel methodology for unequivocal single-molecule identification to demonstrate a rich conformational polymorphism in the monomer of four representative neurotoxic proteins. This polymorphism strongly correlates with amyloidogenesis and neurotoxicity: it is absent in a fibrillization-incompetent mutant, favored by familial-disease mutations and diminished by a surprisingly promiscuous inhibitor of the critical monomeric β-conformational change, neurotoxicity, and neurodegeneration. Hence, we postulate that specific mechanostable conformers are the cause of these diseases, representing important new early-diagnostic and therapeutic targets. The demonstrated ability to inhibit the conformational heterogeneity of these proteins by a single pharmacological agent reveals common features in the monomer and suggests a common pathway to diagnose, prevent, halt, or reverse multiple neurodegenerative diseases. Neurodegenerative diseases like Alzheimer's or Parkinson's are currently incurable. They are caused by different proteins that, under certain circumstances, aggregate and become toxic as we grow older, but the molecular events underlying this process remain unclear. The lack of a well-defined structure, and the tendency of these “neurotoxic proteins” to aggregate make them difficult to study using conventional techniques. Here, we use an established single-molecule manipulation technique combined with a new protein-engineering strategy to show that all these proteins can adopt a rich collection of structures (conformers) that includes a high proportion of mechanostable conformers, which are associated with toxicity and disease. We also find that a known drug can block the formation of these mechanostable structures in different neurotoxic proteins. We suggest that the most mechanostable conformers, or their precursors, may trigger the pathogenic cascade that results in toxicity. We thus propose that these mechanostable structures are ideal targets for early diagnosis, prevention, and treatment of these fatal diseases.
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Affiliation(s)
- Rubén Hervás
- Instituto Cajal, IC-CSIC & Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
| | - Javier Oroz
- Instituto Cajal, IC-CSIC & Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
| | - Albert Galera-Prat
- Instituto Cajal, IC-CSIC & Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
| | - Oscar Goñi
- Instituto Cajal, IC-CSIC & Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
| | - Alejandro Valbuena
- Instituto Cajal, IC-CSIC & Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
| | - Andrés M. Vera
- Instituto Cajal, IC-CSIC & Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
| | - Àngel Gómez-Sicilia
- Instituto Cajal, IC-CSIC & Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
| | - Fernando Losada-Urzáiz
- Instituto Cajal, IC-CSIC & Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
| | - Vladimir N. Uversky
- University of South Florida, College of Medicine and Byrd Alzheimer's Research Institute, Tampa, Florida, United States of America
- Institute for Biological Instrumentation. Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Margarita Menéndez
- Instituto de Química-Física Rocasolano, IQFR-CSIC & Centro de Investigación Biomédica en Red sobre Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | | | - Marta Bruix
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Madrid, Spain
| | - Mariano Carrión-Vázquez
- Instituto Cajal, IC-CSIC & Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
- * E-mail:
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40
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Dey A, Szoszkiewicz R. Complete noise analysis of a simple force spectroscopy AFM setup and its applications to study nanomechanics of mammalian Notch 1 protein. NANOTECHNOLOGY 2012; 23:175101. [PMID: 22481314 DOI: 10.1088/0957-4484/23/17/175101] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We describe a complete noise analysis and application of a custom made AFM force spectroscopy setup on pulling a recombinant protein with an NRR domain of mouse Notch 1. Our table top AFM setup is affordable, has an open architecture, and is easily transferable to other laboratories. Its calculated noise characteristics are dominated by the Brownian noise with 2% non-Brownian components integrated over the first thermally induced resonance of a typical cantilever. For a typical SiN cantilever with a force constant of ~15 pN nm(-1) and in water the force sensitivity and resolution are less than 10 pN, and the corresponding deflection sensitivities are less than 100 pm Hz(-1/2). Also, we obtain a sub-ms time resolution in detecting the protein length change, and only few ms cantilever response times as measured in the force clamp mode on a well-known protein standard. Using this setup we investigate force-induced conformational transitions in the NRR region of a mouse Notch 1. Notch is an important protein related to leukemia and breast cancers in humans. We demonstrate that it is feasible to develop AFM-based studies of the force-induced conformational transitions in Notch. Our results match recent steered molecular dynamics simulations of the NRR unfolding and constitute a first step towards a detailed study of Notch activation with AFM.
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Affiliation(s)
- Ashim Dey
- Department of Physics, Kansas State University, Manhattan, KS 66506, USA
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41
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Liu Y, Strümpfer J, Freddolino PL, Gruebele M, Schulten K. Structural Characterization of λ-Repressor Folding from All-Atom Molecular Dynamics Simulations. J Phys Chem Lett 2012; 3:1117-1123. [PMID: 22737279 PMCID: PMC3377354 DOI: 10.1021/jz300017c] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The five-helix bundle λ-repressor fragment is a fast-folding protein. A length of 80 amino acid residues puts it on the large end among all known microsecond folders and its size poses a computational challenge for molecular dynamics (MD) studies. We simulated the folding of a novel λ-repressor fast-folding mutant (λ-HG) in explicit solvent using an all-atom description. By means of a recently developed tempering method, we observed reversible folding and unfolding of λ-repressor in a 10-microsecond trajectory. The folding kinetics was also investigated through a set of MD simulations run at different temperatures that together covered more than 125 microseconds. The protein was seen to fold into a native-like topology at intermediate temperature and a slow-folding pathway was identified. The simulations suggest new experimental observables for better monitoring the folding process, and a novel mutation expected to accelerate λ-repressor folding.
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Affiliation(s)
| | | | | | - Martin Gruebele
- To whom correspondence should be addressed: ; , Phone: 217-244-1604. Fax: 217-244-6078
| | - Klaus Schulten
- To whom correspondence should be addressed: ; , Phone: 217-244-1604. Fax: 217-244-6078
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42
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Moradi M, Babin V, Roland C, Sagui C. Are long-range structural correlations behind the aggregration phenomena of polyglutamine diseases? PLoS Comput Biol 2012; 8:e1002501. [PMID: 22577357 PMCID: PMC3343152 DOI: 10.1371/journal.pcbi.1002501] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 03/18/2012] [Indexed: 02/06/2023] Open
Abstract
We have characterized the conformational ensembles of polyglutamine peptides of various lengths (ranging from to ), both with and without the presence of a C-terminal polyproline hexapeptide. For this, we used state-of-the-art molecular dynamics simulations combined with a novel statistical analysis to characterize the various properties of the backbone dihedral angles and secondary structural motifs of the glutamine residues. For (i.e., just above the pathological length for Huntington's disease), the equilibrium conformations of the monomer consist primarily of disordered, compact structures with non-negligible -helical and turn content. We also observed a relatively small population of extended structures suitable for forming aggregates including - and -strands, and - and -hairpins. Most importantly, for we find that there exists a long-range correlation (ranging for at least residues) among the backbone dihedral angles of the Q residues. For polyglutamine peptides below the pathological length, the population of the extended strands and hairpins is considerably smaller, and the correlations are short-range (at most residues apart). Adding a C-terminal hexaproline to suppresses both the population of these rare motifs and the long-range correlation of the dihedral angles. We argue that the long-range correlation of the polyglutamine homopeptide, along with the presence of these rare motifs, could be responsible for its aggregation phenomena. Nine neurodegenerative diseases are caused by polyglutamine (polyQ) expansions greater than a given threshold in proteins with little or no homology except for the polyQ regions. The diseases all share a common feature: the formation of polyQ aggregates and eventual neuronal death. Using molecular dynamics simulations, we have explored the conformations of polyQ peptides. Results indicate that for peptides (i.e., just above the pathological length for Hungtington's disease), the equilibrium conformations were found to consist primarily of disordered, compact structures with a non-negligible -helical and turn content. We also observed a small population of extended structures suitable for forming aggregates. For peptides below the pathological length, the population of these structures was found to be considerably lower. For longer peptides, we found evidence for long-range correlations among the dihedral angles. This correlation turns out to be short-range for the smaller polyQ peptides, and is suppressed (along with the extended structural motifs) when a C-terminal polyproline tail is added to the peptides. We believe that the existence of these long-range correlations in above-threshold polyQ peptides, along with the presence of rare motifs, could be responsible for the experimentally observed aggregation phenomena associated with polyQ diseases.
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Affiliation(s)
| | | | | | - Celeste Sagui
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
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Hayre NR, Singh RRP, Cox DL. Sequence-dependent stability test of a left-handed β-helix motif. Biophys J 2012; 102:1443-52. [PMID: 22455928 PMCID: PMC3309403 DOI: 10.1016/j.bpj.2012.02.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 01/25/2012] [Accepted: 02/07/2012] [Indexed: 11/18/2022] Open
Abstract
The left-handed β-helix (LHBH) is an intriguing, rare structural pattern in polypeptides that has been implicated in the formation of amyloid aggregates. We used accurate all-atom replica-exchange molecular dynamics (REMD) simulations to study the relative stability of diverse sequences in the LHBH conformation. Ensemble-average coordinates from REMD served as a scoring criterion to identify sequences and threadings optimally suited to the LHBH, as in a fold recognition paradigm. We examined the repeatability of our REMD simulations, finding that single simulations can be reliable to a quantifiable extent. We find expected behavior for the positive and negative control cases of a native LHBH and intrinsically disordered sequences, respectively. Polyglutamine and a designed hexapeptide repeat show remarkable affinity for the LHBH motif. A structural model for misfolded murine prion protein was also considered, and showed intermediate stability under the given conditions. Our technique is found to be an effective probe of LHBH stability, and promises to be scalable to broader studies of this and potentially other novel or rare motifs. The superstable character of the designed hexapeptide repeat suggests theoretical and experimental follow-ups.
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Affiliation(s)
- Natha R Hayre
- Department of Physics, University of California, Davis, California, USA.
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Effect of αB-crystallin on protein aggregation in Drosophila. J Biomed Biotechnol 2012; 2012:252049. [PMID: 22505806 PMCID: PMC3312385 DOI: 10.1155/2012/252049] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Accepted: 12/13/2011] [Indexed: 02/06/2023] Open
Abstract
Disorganisation and aggregation of proteins containing expanded polyglutamine (polyQ) repeats, or ectopic expression of α-synuclein, underlie neurodegenerative diseases including Alzheimer's, Parkinson, Huntington, Creutzfeldt diseases. Small heat-shock proteins, such as αB-crystallin, act as chaperones to prevent protein aggregation and play a key role in the prevention of such protein disorganisation diseases. In this study, we have explored the potential for chaperone activity of αB-crystallin to suppress the formation of protein aggregates. We tested the ability of αB-crystallin to suppress the aggregation of a polyQ protein and α-synuclein in Drosophila. We found that αB-crystallin suppresses both the compound eye degeneration induced by polyQ and the α-synuclein-induced rough eye phenotype. Furthermore, by using histochemical staining we have determined that αB-crystallin inhibits the aggregation of polyQ in vivo. These data provide a clue for the development of therapeutics for neurodegenerative diseases.
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Peters-Libeu C, Miller J, Rutenber E, Newhouse Y, Krishnan P, Cheung K, Hatters D, Brooks E, Widjaja K, Tran T, Mitra S, Arrasate M, Mosquera LA, Taylor D, Weisgraber KH, Finkbeiner S. Disease-associated polyglutamine stretches in monomeric huntingtin adopt a compact structure. J Mol Biol 2012; 421:587-600. [PMID: 22306738 DOI: 10.1016/j.jmb.2012.01.034] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 01/18/2012] [Accepted: 01/21/2012] [Indexed: 12/13/2022]
Abstract
Abnormal polyglutamine (polyQ) tracts are the only common feature in nine proteins that each cause a dominant neurodegenerative disorder. In Huntington's disease, tracts longer than 36 glutamines in the protein huntingtin (htt) cause degeneration. In situ, monoclonal antibody 3B5H10 binds to different htt fragments in neurons in proportion to their toxicity. Here, we determined the structure of 3B5H10 Fab to 1.9 Å resolution by X-ray crystallography. Modeling demonstrates that the paratope forms a groove suitable for binding two β-rich polyQ strands. Using small-angle X-ray scattering, we confirmed that the polyQ epitope recognized by 3B5H10 is a compact two-stranded hairpin within monomeric htt and is abundant in htt fragments unbound to antibody. Thus, disease-associated polyQ stretches preferentially adopt compact conformations. Since 3B5H10 binding predicts degeneration, this compact polyQ structure may be neurotoxic.
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Affiliation(s)
- Clare Peters-Libeu
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
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Wetzel R. Physical chemistry of polyglutamine: intriguing tales of a monotonous sequence. J Mol Biol 2012; 421:466-90. [PMID: 22306404 DOI: 10.1016/j.jmb.2012.01.030] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 01/18/2012] [Indexed: 01/08/2023]
Abstract
Polyglutamine (polyQ) sequences of unknown normal function are present in a significant number of proteins, and their repeat expansion is associated with a number of genetic neurodegenerative diseases. PolyQ solution structure and properties are important not only because of the normal and abnormal biology associated with these sequences but also because they represent an interesting case of a biologically relevant homopolymer. As the common thread in expanded polyQ repeat diseases, it is important to understand the structure and properties of simple polyQ sequences. At the same time, experience has shown that sequences attached to polyQ, whether in artificial constructs or in disease proteins, can influence structure and properties. The two major contenders for the molecular source of the neurotoxicity implicit in polyQ expansion within disease proteins are a populated toxic conformation in the monomer ensemble and a toxic aggregated species. This review summarizes experimental and computational studies on the solution structure and aggregation properties of both simple and complex polyQ sequences, and their repeat-length dependence. As a representative of complex polyQ proteins, the behavior of huntingtin N-terminal fragments, such as exon-1, receives special attention.
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Affiliation(s)
- Ronald Wetzel
- Department of Structural Biology and Pittsburgh Institute for Neurodegenerative Disease, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
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Polling S, Hill AF, Hatters DM. Polyglutamine aggregation in Huntington and related diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 769:125-40. [PMID: 23560308 DOI: 10.1007/978-1-4614-5434-2_8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Polyglutamine (polyQ)-expansions in different proteins cause nine neurodegenerative diseases. While polyQ aggregation is a key pathological hallmark of these diseases, how aggregation relates to pathogenesis remains contentious. In this chapter, we review what is known about the aggregation process and how cells respond and interact with the polyQ-expanded proteins. We cover detailed biophysical and structural studies to uncover the intrinsic features of polyQ aggregates and concomitant effects in the cellular environment. We also examine the functional consequences ofpolyQ aggregation and how cells may attempt to intervene and guide the aggregation process.
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Affiliation(s)
- Saskia Polling
- Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Victoria, Australia
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Hoffmann T, Dougan L. Single molecule force spectroscopy using polyproteins. Chem Soc Rev 2012; 41:4781-96. [DOI: 10.1039/c2cs35033e] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Lyubchenko YL, Krasnoslobodtsev AV, Luca S. Fibrillogenesis of huntingtin and other glutamine containing proteins. Subcell Biochem 2012; 65:225-51. [PMID: 23225006 PMCID: PMC4226413 DOI: 10.1007/978-94-007-5416-4_10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This chapter focuses on the aggregation of glutamine containing peptides and proteins with an emphasis on huntingtin protein, whose aggregation leads to the development of Huntington's disease. The kinetics that leads to the formation of amyloids, the structure of aggregates of various types and the morphological mechanical properties of amyloid fibrils are described. The kinetics of amyloid fibril formation has been proposed to follow a nucleation dependent polymerization model, dependent upon the size of the nucleus. This model and the effect of the polyglutamine length on the nucleus size are reviewed. Aggregate structure is characterized at two different levels. The atomic-scale resolution structure of fibrillar and crystalline aggregates of polyglutamine containing proteins and peptides was determined by X-ray crystallography and solid-state nuclear magnetic resonance (NMR). The chapter outlines the results obtained by both these techniques. Atomic force microscopy (AFM) was instrumental in elucidating the morphology of fibrils, their organization and assembly. The chapter also discusses the high stability of amyloid fibrils, including their mechanical properties as revealed by AFM.
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Affiliation(s)
- Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, Nanoimaging Core Facility College of Pharmacy, University of Nebraska Medical Center, COP 1012, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Alexey V. Krasnoslobodtsev
- Department of Pharmaceutical Sciences, Nanoimaging Core Facility College of Pharmacy, University of Nebraska Medical Center, COP 1012, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Sorin Luca
- Department of Pharmaceutical Sciences, Nanoimaging Core Facility College of Pharmacy, University of Nebraska Medical Center, COP 1012, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
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Uversky VN, Santambrogio C, Brocca S, Grandori R. Length-dependent compaction of intrinsically disordered proteins. FEBS Lett 2011; 586:70-3. [PMID: 22138473 DOI: 10.1016/j.febslet.2011.11.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 11/08/2011] [Accepted: 11/20/2011] [Indexed: 12/14/2022]
Abstract
This work investigates the effect of chain length on the degree of compaction of intrinsically disordered proteins (IDPs). The three main IDP types, native coil (NC), pre-molten globule (PMG) and molten globule (MG), are compared by means of a compaction index (CI) normalized for chain length. The results point out a strong variability of compactness as a function of chain length within each group, with larger proteins populating more compact states. While qualitative sequence features are responsible for the main differences among groups, chain length seems to have an unspecific effect modulating the extent of compaction within each group. The results are consistent with a cooperative character of the weak interactions responsible for chain collapse.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine, College of Medicine, University of South Florida, Tampa, FL 33612, USA
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