1
|
Buchanan JA, Varghese NR, Johnston CL, Sunde M. Functional Amyloids: Where Supramolecular Amyloid Assembly Controls Biological Activity or Generates New Functionality. J Mol Biol 2023; 435:167919. [PMID: 37330295 DOI: 10.1016/j.jmb.2022.167919] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 06/19/2023]
Abstract
Functional amyloids are a rapidly expanding class of fibrillar protein structures, with a core cross-β scaffold, where novel and advantageous biological function is generated by the assembly of the amyloid. The growing number of amyloid structures determined at high resolution reveal how this supramolecular template both accommodates a wide variety of amino acid sequences and also imposes selectivity on the assembly process. The amyloid fibril can no longer be considered a generic aggregate, even when associated with disease and loss of function. In functional amyloids the polymeric β-sheet rich structure provides multiple different examples of unique control mechanisms and structures that are finely tuned to deliver assembly or disassembly in response to physiological or environmental cues. Here we review the range of mechanisms at play in natural, functional amyloids, where tight control of amyloidogenicity is achieved by environmental triggers of conformational change, proteolytic generation of amyloidogenic fragments, or heteromeric seeding and amyloid fibril stability. In the amyloid fibril form, activity can be regulated by pH, ligand binding and higher order protofilament or fibril architectures that impact the arrangement of associated domains and amyloid stability. The growing understanding of the molecular basis for the control of structure and functionality delivered by natural amyloids in nearly all life forms should inform the development of therapies for amyloid-associated diseases and guide the design of innovative biomaterials.
Collapse
Affiliation(s)
- Jessica A Buchanan
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Nikhil R Varghese
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Caitlin L Johnston
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Margaret Sunde
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| |
Collapse
|
2
|
Bowler JT, Sawaya MR, Boyer DR, Cascio D, Bali M, Eisenberg DS. Micro-electron diffraction structure of the aggregation-driving N-terminus of Drosophila neuronal protein Orb2A reveals amyloid-like β-sheets. J Biol Chem 2022; 298:102396. [PMID: 35988647 PMCID: PMC9556795 DOI: 10.1016/j.jbc.2022.102396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/26/2022] Open
Abstract
Amyloid protein aggregation is commonly associated with progressive neurodegenerative diseases, however not all amyloid fibrils are pathogenic. The neuronal cytoplasmic polyadenylation element binding (CPEB) protein is a regulator of synaptic mRNA translation, and has been shown to form functional amyloid aggregates that stabilize long-term memory. In adult Drosophila neurons, the CPEB homolog Orb2 is expressed as two isoforms, of which the Orb2B isoform is far more abundant, but the rarer Orb2A isoform is required to initiate Orb2 aggregation. The N-terminus is a distinctive feature of the Orb2A isoform and is critical for its aggregation. Intriguingly, replacement of phenylalanine in the 5th position of Orb2A with tyrosine (F5Y) in Drosophila impairs stabilization of long-term memory. The structure of endogenous Orb2B fibers was recently determined by cryo-EM, but the structure adopted by fibrillar Orb2A is less certain. Here we use micro-electron diffraction to determine the structure of the first nine N-terminal residues of Orb2A, at a resolution of 1.05 Å. We find that this segment (which we term M9I) forms an amyloid-like array of parallel in-register β-sheets, which interact through side chain interdigitation of aromatic and hydrophobic residues. Our structure provides an explanation for the decreased aggregation observed for the F5Y mutant, and offers a hypothesis for how the addition of a single atom (the tyrosyl oxygen) affects long-term memory. We also propose a structural model of Orb2A that integrates our structure of the M9I segment with the published Orb2B cryo-EM structure.
Collapse
Affiliation(s)
- Jeannette T Bowler
- Molecular Biology Institute, University of California, Los Angeles; Howard Hughes Medical Institute.
| | - Michael R Sawaya
- Molecular Biology Institute, University of California, Los Angeles; Howard Hughes Medical Institute
| | - David R Boyer
- Molecular Biology Institute, University of California, Los Angeles; Howard Hughes Medical Institute
| | - Duilio Cascio
- Molecular Biology Institute, University of California, Los Angeles; Howard Hughes Medical Institute
| | - Manya Bali
- Molecular Biology Institute, University of California, Los Angeles; Howard Hughes Medical Institute
| | - David S Eisenberg
- Molecular Biology Institute, University of California, Los Angeles; Howard Hughes Medical Institute.
| |
Collapse
|
3
|
Siemer AB. What makes functional amyloids work? Crit Rev Biochem Mol Biol 2022; 57:399-411. [PMID: 35997712 PMCID: PMC9588633 DOI: 10.1080/10409238.2022.2113030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/29/2022] [Accepted: 08/10/2022] [Indexed: 01/27/2023]
Abstract
Although first described in the context of disease, cross-β (amyloid) fibrils have also been found as functional entities in all kingdoms of life. However, what are the specific properties of the cross-β fibril motif that convey biological function, make them especially suited for their particular purpose, and distinguish them from other fibrils found in biology? This review approaches these questions by arguing that cross-β fibrils are highly periodic, stable, and self-templating structures whose formation is accompanied by substantial conformational change that leads to a multimerization of their core and framing sequences. A discussion of each of these properties is followed by selected examples of functional cross-β fibrils that show how function is usually achieved by leveraging many of these properties.
Collapse
Affiliation(s)
- Ansgar B Siemer
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
4
|
Matiiv AB, Trubitsina NP, Matveenko AG, Barbitoff YA, Zhouravleva GA, Bondarev SA. Structure and Polymorphism of Amyloid and Amyloid-Like Aggregates. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:450-463. [PMID: 35790379 DOI: 10.1134/s0006297922050066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 06/15/2023]
Abstract
Amyloids are protein aggregates with the cross-β structure. The interest in amyloids is explained, on the one hand, by their role in the development of socially significant human neurodegenerative diseases, and on the other hand, by the discovery of functional amyloids, whose formation is an integral part of cellular processes. To date, more than a hundred proteins with the amyloid or amyloid-like properties have been identified. Studying the structure of amyloid aggregates has revealed a wide variety of protein conformations. In the review, we discuss the diversity of protein folds in the amyloid-like aggregates and the characteristic features of amyloid aggregates that determine their unusual properties, including stability and interaction with amyloid-specific dyes. The review also describes the diversity of amyloid aggregates and its significance for living organisms.
Collapse
Affiliation(s)
- Anton B Matiiv
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Nina P Trubitsina
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Yury A Barbitoff
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
- Bioinformatics Institute, Saint Petersburg, 197342, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
- Laboratory of Amyloid Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia.
- Laboratory of Amyloid Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| |
Collapse
|
5
|
Qi Z, Surewicz K, Surewicz WK, Jaroniec CP. Influence of the Dynamically Disordered N-Terminal Tail Domain on the Amyloid Core Structure of Human Y145Stop Prion Protein Fibrils. Front Mol Biosci 2022; 9:841790. [PMID: 35237664 PMCID: PMC8883029 DOI: 10.3389/fmolb.2022.841790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/26/2022] [Indexed: 11/13/2022] Open
Abstract
The Y145Stop mutant of human prion protein (huPrP23-144) is associated with a familial prionopathy and provides a convenient in vitro model for investigating amyloid strains and cross-seeding barriers. huPrP23-144 fibrils feature a compact and relatively rigid parallel in-register β-sheet amyloid core spanning ∼30 C-terminal amino acid residues (∼112–141) and a large ∼90-residue dynamically disordered N-terminal tail domain. Here, we systematically evaluate the influence of this dynamic domain on the structure adopted by the huPrP23-144 amyloid core region, by investigating using magic-angle spinning solid-state nuclear magnetic resonance (NMR) spectroscopy a series of fibril samples formed by huPrP23-144 variants corresponding to deletions of large segments of the N-terminal tail. We find that deletion of the bulk of the N-terminal tail, up to residue 98, yields amyloid fibrils with native-like huPrP23-144 core structure. Interestingly, deletion of additional flexible residues in the stretch 99–106 located outside of the amyloid core yields shorter heterogenous fibrils with fingerprint NMR spectra that are clearly distinct from those for full-length huPrP23-144, suggestive of the onset of perturbations to the native structure and degree of molecular ordering for the core residues. For the deletion variant missing residues 99–106 we show that native huPrP23-144 core structure can be “restored” by seeding the fibril growth with preformed full-length huPrP23-144 fibrils.
Collapse
Affiliation(s)
- Zhe Qi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Krystyna Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, United States
| | - Witold K. Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, United States
| | - Christopher P. Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
- *Correspondence: Christopher P. Jaroniec,
| |
Collapse
|
6
|
Soria MA, Cervantes SA, Siemer AB. Calmodulin binds the N-terminus of the functional amyloid Orb2A inhibiting fibril formation. PLoS One 2022; 17:e0259872. [PMID: 35025866 PMCID: PMC8758002 DOI: 10.1371/journal.pone.0259872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/16/2021] [Indexed: 11/18/2022] Open
Abstract
The cytoplasmic polyadenylation element-binding protein Orb2 is a key regulator of long-term memory (LTM) in Drosophila. The N-terminus of the Orb2 isoform A is required for LTM and forms cross-β fibrils on its own. However, this N-terminus is not part of the core found in ex vivo fibrils. We previously showed that besides forming cross-β fibrils, the N-terminus of Orb2A binds anionic lipid membranes as an amphipathic helix. Here, we show that the Orb2A N-terminus can similarly interact with calcium activated calmodulin (CaM) and that this interaction prevents fibril formation. Because CaM is a known regulator of LTM, this interaction could potentially explain the regulatory role of Orb2A in LTM.
Collapse
Affiliation(s)
- Maria A. Soria
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Silvia A. Cervantes
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Ansgar B. Siemer
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| |
Collapse
|
7
|
Daskalov A, El Mammeri N, Lends A, Shenoy J, Lamon G, Fichou Y, Saad A, Martinez D, Morvan E, Berbon M, Grélard A, Kauffmann B, Ferber M, Bardiaux B, Habenstein B, Saupe SJ, Loquet A. Structures of Pathological and Functional Amyloids and Prions, a Solid-State NMR Perspective. Front Mol Neurosci 2021; 14:670513. [PMID: 34276304 PMCID: PMC8280340 DOI: 10.3389/fnmol.2021.670513] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022] Open
Abstract
Infectious proteins or prions are a remarkable class of pathogens, where pathogenicity and infectious state correspond to conformational transition of a protein fold. The conformational change translates into the formation by the protein of insoluble amyloid aggregates, associated in humans with various neurodegenerative disorders and systemic protein-deposition diseases. The prion principle, however, is not limited to pathogenicity. While pathological amyloids (and prions) emerge from protein misfolding, a class of functional amyloids has been defined, consisting of amyloid-forming domains under natural selection and with diverse biological roles. Although of great importance, prion amyloid structures remain challenging for conventional structural biology techniques. Solid-state nuclear magnetic resonance (SSNMR) has been preferentially used to investigate these insoluble, morphologically heterogeneous aggregates with poor crystallinity. SSNMR methods have yielded a wealth of knowledge regarding the fundamentals of prion biology and have helped to solve the structures of several prion and prion-like fibrils. Here, we will review pathological and functional amyloid structures and will discuss some of the obtained structural models. We will finish the review with a perspective on integrative approaches combining solid-state NMR, electron paramagnetic resonance and cryo-electron microscopy, which can complement and extend our toolkit to structurally explore various facets of prion biology.
Collapse
Affiliation(s)
- Asen Daskalov
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Nadia El Mammeri
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Alons Lends
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | | | - Gaelle Lamon
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Yann Fichou
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Ahmad Saad
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Denis Martinez
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Estelle Morvan
- CNRS, INSERM, IECB, UMS 3033, University of Bordeaux, Pessac, France
| | - Melanie Berbon
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Axelle Grélard
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Brice Kauffmann
- CNRS, INSERM, IECB, UMS 3033, University of Bordeaux, Pessac, France
| | | | | | | | - Sven J. Saupe
- CNRS, IBGC UMR 5095, University of Bordeaux, Bordeaux, France
| | - Antoine Loquet
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| |
Collapse
|
8
|
Reselammal DS, Pinhero F, Sharma R, Oliyantakath Hassan MS, Srinivasula SM, Vijayan V. Mapping the Fibril Core of the Prion Subdomain of the Mammalian CPEB3 that is Involved in Long Term Memory Retention. J Mol Biol 2021; 433:167084. [PMID: 34081983 DOI: 10.1016/j.jmb.2021.167084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 11/15/2022]
Abstract
Long-term memory storage is modulated by the prion nature of CPEB3 forming the molecular basis for the maintenance of synaptic facilitation. Here we report that the first prion sub-domain PRD1 of mouse CPEB3 can autonomously form amyloid fibrils in vitro and punctate-like structures in vivo. A ninety-four amino acid sequence within the PRD1 domain, PRD1-core, displays high propensity towards aggregation and associated amyloid characteristics. PRD1-core is characterized using electron microscopy, X-ray diffraction, and solution-state NMR deuterium exchange experiments. Secondary structure elements deduced from solid-state NMR reveal a β-rich core comprising of forty amino acids at the N-terminus of PRD1-core. The synthesized twenty-three amino acid long peptide containing the longest rigid segment (E124-H145) of the PRD1-core rapidly self-aggregates and forms fibrils, indicating a limited aggregation-prone region that could potentially activate the aggregation of the full-length protein. This study provides the first step in identifying the structural trigger for the CPEB3 aggregation process.
Collapse
Affiliation(s)
- Dhanya S Reselammal
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India
| | - Faina Pinhero
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India
| | - Rahul Sharma
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India
| | | | - Srinivasa M Srinivasula
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India
| | - Vinesh Vijayan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India.
| |
Collapse
|
9
|
Ashami K, Falk AS, Hurd C, Garg S, Cervantes SA, Rawat A, Siemer AB. Droplet and fibril formation of the functional amyloid Orb2. J Biol Chem 2021; 297:100804. [PMID: 34044018 PMCID: PMC8294575 DOI: 10.1016/j.jbc.2021.100804] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/10/2021] [Accepted: 05/18/2021] [Indexed: 01/18/2023] Open
Abstract
The functional amyloid Orb2 belongs to the cytoplasmic polyadenylation element binding (CPEB) protein family and plays an important role in long-term memory formation in Drosophila. The Orb2 domain structure combines RNA recognition motifs with low-complexity sequences similar to many RNA-binding proteins shown to form protein droplets via liquid–liquid phase separation (LLPS) in vivo and in vitro. This similarity suggests that Orb2 might also undergo LLPS. However, cellular Orb2 puncta have very little internal protein mobility, and Orb2 forms fibrils in Drosophila brains that are functionally active indicating that LLPS might not play a role for Orb2. In the present work, we reconcile these two views on Orb2 droplet formation. Using fluorescence microscopy, we show that soluble Orb2 can indeed phase separate into protein droplets. However, fluorescence recovery after photobleaching (FRAP) data shows that these droplets have either no or only an extremely short-lived liquid phase and appear maturated right after formation. Orb2 fragments that lack the C-terminal RNA-binding domain (RBD) form fibrils out of these droplets. Solid-state NMR shows that these fibrils have well-ordered static domains in addition to the Gln/His-rich fibril core. Further, we find that full-length Orb2B, which is by far the major component of Orb2 fibrils in vivo, does not transition into fibrils but remains in the droplet phase. Together, our data suggest that phase separation might play a role in initiating the formation of functional Orb2 fibrils.
Collapse
Affiliation(s)
- Kidist Ashami
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Alexander S Falk
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Connor Hurd
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Samridhi Garg
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Silvia A Cervantes
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Anoop Rawat
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Ansgar B Siemer
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.
| |
Collapse
|
10
|
Yakupova EI, Bobyleva LG, Shumeyko SA, Vikhlyantsev IM, Bobylev AG. Amyloids: The History of Toxicity and Functionality. BIOLOGY 2021; 10:biology10050394. [PMID: 34062910 PMCID: PMC8147320 DOI: 10.3390/biology10050394] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 12/15/2022]
Abstract
Proteins can perform their specific function due to their molecular structure. Partial or complete unfolding of the polypeptide chain may lead to the misfolding and aggregation of proteins in turn, resulting in the formation of different structures such as amyloid aggregates. Amyloids are rigid protein aggregates with the cross-β structure, resistant to most solvents and proteases. Because of their resistance to proteolysis, amyloid aggregates formed in the organism accumulate in tissues, promoting the development of various diseases called amyloidosis, for instance Alzheimer's diseases (AD). According to the main hypothesis, it is considered that the cause of AD is the formation and accumulation of amyloid plaques of Aβ. That is why Aβ-amyloid is the most studied representative of amyloids. Therefore, in this review, special attention is paid to the history of Aβ-amyloid toxicity. We note the main problems with anti-amyloid therapy and write about new views on amyloids that can play positive roles in the different organisms including humans.
Collapse
Affiliation(s)
- Elmira I. Yakupova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia; (L.G.B.); (S.A.S.); (I.M.V.); (A.G.B.)
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: ; Tel.: +7-(985)687-77-27
| | - Liya G. Bobyleva
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia; (L.G.B.); (S.A.S.); (I.M.V.); (A.G.B.)
| | - Sergey A. Shumeyko
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia; (L.G.B.); (S.A.S.); (I.M.V.); (A.G.B.)
| | - Ivan M. Vikhlyantsev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia; (L.G.B.); (S.A.S.); (I.M.V.); (A.G.B.)
| | - Alexander G. Bobylev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia; (L.G.B.); (S.A.S.); (I.M.V.); (A.G.B.)
| |
Collapse
|
11
|
Liu EN, Park G, Nohara J, Guo Z. Effect of spin labelling on the aggregation kinetics of yeast prion protein Ure2. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201747. [PMID: 33959337 PMCID: PMC8074925 DOI: 10.1098/rsos.201747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/10/2021] [Indexed: 06/12/2023]
Abstract
Amyloid formation is involved in a wide range of neurodegenerative diseases including Alzheimer's and prion diseases. Structural understanding of the amyloid is critical to delineate the mechanism of aggregation and its pathological spreading. Site-directed spin labelling has emerged as a powerful structural tool in the studies of amyloid structures and provided structural evidence for the parallel in-register β-sheet structure for a wide range of amyloid proteins. It is generally accepted that spin labelling does not disrupt the structure of the amyloid fibrils, the end product of protein aggregation. The effect on the rate of protein aggregation, however, has not been well characterized. Here, we employed a scanning mutagenesis approach to study the effect of spin labelling on the aggregation rate of 79 spin-labelled variants of the Ure2 prion domain. The aggregation of Ure2 protein is the basis of yeast prion [URE3]. We found that all spin-labelled Ure2 mutants aggregated within the experimental timeframe of 15 to 40 h. Among the 79 spin-labelled positions, only five residue sites (N23, N27, S33, I35 and G42) showed a dramatic delay in the aggregation rate as a result of spin labelling. These positions may be important for fibril nucleation, a rate-limiting step in aggregation. Importantly, spin labelling at most of the sites had a muted effect on Ure2 aggregation kinetics, showing a general tolerance of spin labelling in protein aggregation studies.
Collapse
Affiliation(s)
- Emilie N. Liu
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Giovanna Park
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Junsuke Nohara
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Zhefeng Guo
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| |
Collapse
|
12
|
Oroz J, Félix SS, Cabrita EJ, Laurents DV. Structural transitions in Orb2 prion-like domain relevant for functional aggregation in memory consolidation. J Biol Chem 2020; 295:18122-18133. [PMID: 33093173 PMCID: PMC7939463 DOI: 10.1074/jbc.ra120.015211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
The recent structural elucidation of ex vivo Drosophila Orb2 fibrils revealed a novel amyloid formed by interdigitated Gln and His residue side chains belonging to the prion-like domain. However, atomic-level details on the conformational transitions associated with memory consolidation remain unknown. Here, we have characterized the nascent conformation and dynamics of the prion-like domain (PLD) of Orb2A using a nonconventional liquid-state NMR spectroscopy strategy based on 13C detection to afford an essentially complete set of 13Cα, 13Cβ, 1Hα, and backbone 13CO and 15N assignments. At pH 4, where His residues are protonated, the PLD is disordered and flexible, except for a partially populated α-helix spanning residues 55-60, and binds RNA oligos, but not divalent cations. At pH 7, in contrast, His residues are predominantly neutral, and the Q/H segments adopt minor populations of helical structure, show decreased mobility and start to self-associate. At pH 7, the His residues do not bind RNA or Ca2+, but do bind Zn2+, which promotes further association. These findings represent a remarkable case of structural plasticity, based on which an updated model for Orb2A functional amyloidogenesis is suggested.
Collapse
Affiliation(s)
- Javier Oroz
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Madrid, Spain
| | - Sara S Félix
- Departamento de Química Faculdade de Ciências e Tecnologia, UCIBIO, Universidade Nova de Lisboa, Caparica, Portugal
| | - Eurico J Cabrita
- Departamento de Química Faculdade de Ciências e Tecnologia, UCIBIO, Universidade Nova de Lisboa, Caparica, Portugal
| | | |
Collapse
|
13
|
Implications of the Orb2 Amyloid Structure in Huntington's Disease. Int J Mol Sci 2020; 21:ijms21186910. [PMID: 32967102 PMCID: PMC7555547 DOI: 10.3390/ijms21186910] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/11/2020] [Accepted: 09/16/2020] [Indexed: 02/06/2023] Open
Abstract
Huntington’s disease is a progressive, autosomal dominant, neurodegenerative disorder caused by an expanded CAG repeat in the huntingtin gene. As a result, the translated protein, huntingtin, contains an abnormally long polyglutamine stretch that makes it prone to misfold and aggregating. Aggregation of huntingtin is believed to be the cause of Huntington’s disease. However, understanding on how, and why, huntingtin aggregates are deleterious has been hampered by lack of enough relevant structural data. In this review, we discuss our recent findings on a glutamine-based functional amyloid isolated from Drosophila brain and how this information provides plausible structural insight on the structure of huntingtin deposits in the brain.
Collapse
|
14
|
Nil Z, Hervás R, Gerbich T, Leal P, Yu Z, Saraf A, Sardiu M, Lange JJ, Yi K, Unruh J, Slaughter B, Si K. Amyloid-like Assembly Activates a Phosphatase in the Developing Drosophila Embryo. Cell 2020; 178:1403-1420.e21. [PMID: 31491385 DOI: 10.1016/j.cell.2019.08.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 05/07/2019] [Accepted: 08/08/2019] [Indexed: 12/30/2022]
Abstract
Prion-like proteins can assume distinct conformational and physical states in the same cell. Sequence analysis suggests that prion-like proteins are prevalent in various species; however, it remains unclear what functional space they occupy in multicellular organisms. Here, we report the identification of a prion-like protein, Herzog (CG5830), through a multimodal screen in Drosophila melanogaster. Herzog functions as a membrane-associated phosphatase and controls embryonic patterning, likely being involved in TGF-β/BMP and FGF/EGF signaling pathways. Remarkably, monomeric Herzog is enzymatically inactive and becomes active upon amyloid-like assembly. The prion-like domain of Herzog is necessary for both its assembly and membrane targeting. Removal of the prion-like domain impairs activity, while restoring assembly on the membrane using a heterologous prion-like domain and membrane-targeting motif can restore phosphatase activity. This study provides an example of a prion-like domain that allows an enzyme to gain essential functionality via amyloid-like assembly to control animal development.
Collapse
Affiliation(s)
- Zelha Nil
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Rubén Hervás
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA
| | - Therese Gerbich
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA
| | - Paulo Leal
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA
| | - Zulin Yu
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA
| | - Anita Saraf
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA
| | - Mihaela Sardiu
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA
| | - Jeffrey J Lange
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA
| | - Kexi Yi
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA
| | - Jay Unruh
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA
| | - Brian Slaughter
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA
| | - Kausik Si
- Stowers Institute for Medical Research, 1000E 50(th) Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA.
| |
Collapse
|
15
|
Strategies for identifying dynamic regions in protein complexes: Flexibility changes accompany methylation in chemotaxis receptor signaling states. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183312. [PMID: 32304758 DOI: 10.1016/j.bbamem.2020.183312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/24/2020] [Accepted: 04/13/2020] [Indexed: 12/11/2022]
Abstract
Bacterial chemoreceptors are organized in arrays composed of helical receptors arranged as trimers of dimers, coupled to a histidine kinase CheA and a coupling protein CheW. Ligand binding to the external domain inhibits the kinase activity, leading to a change in the swimming behavior. Adaptation to an ongoing stimulus involves reversible methylation and demethylation of specific glutamate residues. However, the exact mechanism of signal propagation through the helical receptor to the histidine kinase remains elusive. Dynamics of the receptor cytoplasmic domain is thought to play an important role in the signal transduction, and current models propose inverse dynamic changes in different regions of the receptor. We hypothesize that the adaptational modification (methylation) controls the dynamics by stabilizing a partially ordered domain, which in turn modulates the binding of the kinase, CheA. We investigated the difference in dynamics between the methylated and unmethylated states of the chemoreceptor using solid-state NMR. The unmethylated receptor (CF4E) shows increased flexibility relative to the methylated mimic (CF4Q). Methylation helix 1 (MH1) has been shown to be flexible in the methylated mimic receptor. Our analysis indicates that in addition to MH1, methylation helix 2 also becomes flexible in the unmethylated receptor. In addition, we have demonstrated that both states of the receptor have a rigid region and segments with intermediate timescale dynamics. The strategies used in this study for identifying dynamic regions are applicable to a broad class of proteins and protein complexes with intrinsic disorder and dynamics spanning multiple timescales.
Collapse
|
16
|
Siemer AB. Advances in studying protein disorder with solid-state NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2020; 106:101643. [PMID: 31972419 PMCID: PMC7202078 DOI: 10.1016/j.ssnmr.2020.101643] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 05/26/2023]
Abstract
Solution NMR is a key tool to study intrinsically disordered proteins (IDPs), whose importance for biological function is widely accepted. However, disordered proteins are not limited to solution and are also found in non-soluble systems such as fibrils and membrane proteins. In this Trends article, I will discuss how solid-state NMR can be used to study disorder in non-soluble proteins. Techniques based on dipolar couplings can study static protein disorder which either occurs naturally as e.g. in spider silk or can be induced by freeze trapping IDPs or unfolded proteins. In this case, structural ensembles are directly reflected by a static distribution of dihedral angels that can be determined by the distribution of chemical shifts or other methods. Techniques based on J-couplings can detect dynamic protein disorder under MAS. In this case, only average chemical shifts are measured but disorder can be characterized with a variety of data including secondary chemical shifts, relaxation rates, paramagnetic relaxation enhancements, or residual dipolar couplings. I describe both technical aspects and examples of solid-state NMR on protein disorder and end the article with a discussion of challenges and opportunities of this emerging field.
Collapse
Affiliation(s)
- Ansgar B Siemer
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Univeristy of Southern California, 1501 San Pablo Street, Los Angeles, CA, 90033, USA.
| |
Collapse
|
17
|
Kashefi M, Malik N, Struppe JO, Thompson LK. Carbon-nitrogen REDOR to identify ms-timescale mobility in proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 305:5-15. [PMID: 31158793 PMCID: PMC6656615 DOI: 10.1016/j.jmr.2019.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 06/09/2023]
Abstract
Protein dynamics play key mechanistic roles but are difficult to measure in large proteins and protein complexes. INEPT and CP solid-state NMR experiments have often been used to obtain spectra of protein regions that are mobile and rigid, respectively, on the nanosecond timescale. To complement this approach, we have implemented 13C{15N} REDOR to detect protein regions with backbone dynamics on the millisecond time scale that average the ≈1 kHz carbon-nitrogen dipolar coupling. REDOR-filtering of carbon correlation spectra removes signals from rigid backbone carbons and retains signals from backbone carbons with ms-timescale dynamics that would be missing in dipolar-driven NCA/NCO spectra. We use these experiments to investigate functionally important dynamics within the E coli Asp receptor cytoplasmic fragment (U-13C, 15N-CF) in native-like complexes with CheA and CheW. The CF backbone carbons exhibit only 60-75% of the expected REDOR dephasing, suggesting that 40-25% of the backbone experiences significant mobility that averages the 13C15N dipolar couplings to zero. Furthermore, the extent of this mobility changes with signaling state.
Collapse
Affiliation(s)
- Maryam Kashefi
- Department of Chemistry, University of Massachusetts Amherst, 710 N Pleasant St, Amherst, MA 01003, USA
| | - Nikita Malik
- Department of Chemistry, University of Massachusetts Amherst, 710 N Pleasant St, Amherst, MA 01003, USA
| | - Jochem O Struppe
- Bruker BioSpin Corporation, 15 Fortune Drive, Billerica, MA 01821, USA
| | - Lynmarie K Thompson
- Department of Chemistry, University of Massachusetts Amherst, 710 N Pleasant St, Amherst, MA 01003, USA.
| |
Collapse
|
18
|
Sanguanini M, Cattaneo A. A continuous model of physiological prion aggregation suggests a role for Orb2 in gating long-term synaptic information. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180336. [PMID: 30662713 PMCID: PMC6304141 DOI: 10.1098/rsos.180336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 11/02/2018] [Indexed: 06/09/2023]
Abstract
The regulation of mRNA translation at the level of the synapse is believed to be fundamental in memory and learning at the cellular level. The family of cytoplasmic polyadenylation element binding (CPEB) proteins emerged as an important RNA-binding protein family during development and in adult neurons. Drosophila Orb2 (homologue of mouse CPEB3 protein and of the neural isoform of Aplysia CPEB) has been found to be involved in the translation of plasticity-dependent mRNAs and has been associated with long-term memory. Orb2 protein presents two main isoforms, Orb2A and Orb2B, which form an activity-induced amyloid-like functional aggregate, thought to be the translation-inducing state of the RNA-binding protein. Here we present a first two-states continuous differential model for Orb2A-Orb2B aggregation. This model provides new working hypotheses for studying the role of prion-like CPEB proteins in long-term synaptic plasticity. Moreover, this model can be used as a first step to integrate translation- and protein aggregation-dependent phenomena in synaptic facilitation rules.
Collapse
Affiliation(s)
| | - Antonino Cattaneo
- Scuola Normale Superiore, Piazza dei Cavalieri, 7, 56126 Pisa, Italy
| |
Collapse
|
19
|
Caulkins BG, Cervantes SA, Isas JM, Siemer AB. Dynamics of the Proline-Rich C-Terminus of Huntingtin Exon-1 Fibrils. J Phys Chem B 2018; 122:9507-9515. [PMID: 30252478 DOI: 10.1021/acs.jpcb.8b09213] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Intrinsically disordered protein domains not only are found in soluble proteins but also can be part of large protein complexes or protein aggregates. For example, several amyloid fibrils have intrinsically disordered domains framing a rigid β-sheet-rich core. These disordered domains can often be observed using solution NMR methods in combination with modest magic angle spinning and without perdeuteration. But how can these regions be detected using solution NMR methods when they are part of a fibril that is not tumbling isotropically in solution? Here we addressed this question by investigating the dynamic C-terminus of huntingtin exon-1 (HTTex1) fibrils that are important in Huntington's disease. We assigned the most dynamic regions of the C-terminus of three HTTex1 variants. On the basis of this assignment, we measured site-specific secondary chemical shifts, peak intensities, and R1, R'2, and R1ρ 15N relaxation rates. In addition, we determined the residual 1H-15N dipolar couplings of this region. Our results show that the dipolar couplings are averaged to a very high degree, resulting in an order parameter that is essentially zero. Together, our data show that the C-terminus of HTTex1 is intrinsically disordered and undergoes motions in the high picosecond to low nanosecond range.
Collapse
Affiliation(s)
- Bethany G Caulkins
- Department of Physiology & Neuroscience, Zilkha Neurogenetic Institute , Keck School of Medicine of USC , 1501 San Pablo St. , Los Angeles , California 90033 , United States
| | - Silvia A Cervantes
- Department of Physiology & Neuroscience, Zilkha Neurogenetic Institute , Keck School of Medicine of USC , 1501 San Pablo St. , Los Angeles , California 90033 , United States
| | - J Mario Isas
- Department of Physiology & Neuroscience, Zilkha Neurogenetic Institute , Keck School of Medicine of USC , 1501 San Pablo St. , Los Angeles , California 90033 , United States
| | - Ansgar B Siemer
- Department of Physiology & Neuroscience, Zilkha Neurogenetic Institute , Keck School of Medicine of USC , 1501 San Pablo St. , Los Angeles , California 90033 , United States
| |
Collapse
|
20
|
Matlahov I, van der Wel PCA. Hidden motions and motion-induced invisibility: Dynamics-based spectral editing in solid-state NMR. Methods 2018; 148:123-135. [PMID: 29702226 DOI: 10.1016/j.ymeth.2018.04.015] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/05/2018] [Accepted: 04/16/2018] [Indexed: 10/17/2022] Open
Abstract
Solid-state nuclear magnetic resonance (ssNMR) spectroscopy enables the structural characterization of a diverse array of biological assemblies that include amyloid fibrils, non-amyloid aggregates, membrane-associated proteins and viral capsids. Such biological samples feature functionally relevant molecular dynamics, which often affect different parts of the sample in different ways. Solid-state NMR experiments' sensitivity to dynamics represents a double-edged sword. On the one hand, it offers a chance to measure dynamics in great detail. On the other hand, certain types of motion lead to signal loss and experimental inefficiencies that at first glance interfere with the application of ssNMR to overly dynamic proteins. Dynamics-based spectral editing (DYSE) ssNMR methods leverage motion-dependent signal losses to simplify spectra and enable the study of sub-structures with particular motional properties.
Collapse
Affiliation(s)
- Irina Matlahov
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15213, USA
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15213, USA; Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
| |
Collapse
|
21
|
van der Wel PCA. Insights into protein misfolding and aggregation enabled by solid-state NMR spectroscopy. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 88:1-14. [PMID: 29035839 PMCID: PMC5705391 DOI: 10.1016/j.ssnmr.2017.10.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/03/2017] [Accepted: 10/03/2017] [Indexed: 05/17/2023]
Abstract
The aggregation of proteins and peptides into a variety of insoluble, and often non-native, aggregated states plays a central role in many devastating diseases. Analogous processes undermine the efficacy of polypeptide-based biological pharmaceuticals, but are also being leveraged in the design of biologically inspired self-assembling materials. This Trends article surveys the essential contributions made by recent solid-state NMR (ssNMR) studies to our understanding of the structural features of polypeptide aggregates, and how such findings are informing our thinking about the molecular mechanisms of misfolding and aggregation. A central focus is on disease-related amyloid fibrils and oligomers involved in neurodegenerative diseases such as Alzheimer's, Parkinson's and Huntington's disease. SSNMR-enabled structural and dynamics-based findings are surveyed, along with a number of resulting emerging themes that appear common to different amyloidogenic proteins, such as their compact alternating short-β-strand/β-arc amyloid core architecture. Concepts, methods, future prospects and challenges are discussed.
Collapse
Affiliation(s)
- Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
| |
Collapse
|
22
|
Kashefi M, Thompson LK. Signaling-Related Mobility Changes in Bacterial Chemotaxis Receptors Revealed by Solid-State NMR. J Phys Chem B 2017; 121:8693-8705. [PMID: 28816463 PMCID: PMC5613836 DOI: 10.1021/acs.jpcb.7b06475] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Bacteria employ remarkable
membrane-bound nanoarrays to sense their
environment and direct their swimming. Arrays consist of chemotaxis
receptor trimers of dimers that are bridged at their membrane-distal
tips by rings of two cytoplasmic proteins, a kinase CheA and a coupling
protein CheW. It is not clear how ligand binding to the periplasmic
domain of the receptor deactivates the CheA kinase bound to the cytoplasmic
tip ∼300 Å away, but the mechanism is thought to involve
changes in dynamics within the cytoplasmic domain. To test these proposals,
we applied solid-state NMR mobility-filtered experiments to functional
complexes of the receptor cytoplasmic fragment (U–13C,15N-CF), CheA, and CheW. Assembly of these proteins
into native-like, homogeneous arrays is mediated by either vesicle
binding or molecular crowding agents, and paramagnetic relaxation
enhancement is used to overcome sensitivity challenges in these large
complexes. INEPT spectra reveal that a significant fraction of the
receptor is dynamic on the nanosecond or shorter time scale, and these
dynamics change with signaling state. The mobile regions are identified
through a combination of biochemical and NMR approaches (protein truncations
and unique chemical shifts). The INEPT spectra are consistent with
an asymmetric mobility in the methylation region (N-helix mobility
≫ C-helix mobility) and reveal an increase in the mobility
of the N-helix in the kinase-off state. This finding identifies functionally
relevant dynamics in the receptor, and suggests that this N-helix
segment plays a key role in propagating the signal.
Collapse
Affiliation(s)
- Maryam Kashefi
- Department of Chemistry, ‡Program in Molecular and Cellular Biology, University of Massachusetts Amherst , Amherst, Massachusetts 01003, United States
| | - Lynmarie K Thompson
- Department of Chemistry, ‡Program in Molecular and Cellular Biology, University of Massachusetts Amherst , Amherst, Massachusetts 01003, United States
| |
Collapse
|
23
|
Soria MA, Cervantes SA, Bajakian TH, Siemer AB. The Functional Amyloid Orb2A Binds to Lipid Membranes. Biophys J 2017; 113:37-47. [PMID: 28700922 DOI: 10.1016/j.bpj.2017.05.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 05/18/2017] [Accepted: 05/23/2017] [Indexed: 02/08/2023] Open
Abstract
Lipid membranes interact with and influence the aggregation of many amyloid-forming proteins. Orb2 is a cytoplasmic polyadenylation element-binding protein homolog in Drosophila melanogaster that forms functional amyloids necessary for long-term memory. One isoform, Orb2A, has a unique N-terminus that has been shown to be important for the formation of amyloid-like aggregates and long-term memory in vivo. Orb2A is also found enriched in the synaptic membrane fraction. Our sequence and hydropathy analysis suggests that it can form an amphipathic helix, which is ideal for lipid membrane interaction. We used circular dichroism and site-directed spin labeling coupled with electron paramagnetic resonance to test the first 88 amino acids of Orb2A for lipid interaction. We show that Orb2A1-88 interacts with anionic lipid membranes using an amphipathic helix at its unique N-terminus. This interaction depends on the charge of the lipid membrane and the degree of membrane curvature. We used transmission electron microscopy and electron paramagnetic resonance to show that the presence of anionic small unilamellar vesicles inhibits amyloid fibril formation by Orb2A. This inhibition by anionic membranes could be a potential mechanism regulating Orb2A amyloid formation in vivo.
Collapse
Affiliation(s)
- Maria A Soria
- Department of Biochemistry and Molecular Medicine, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Silvia A Cervantes
- Department of Biochemistry and Molecular Medicine, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Thalia H Bajakian
- Department of Biochemistry and Molecular Medicine, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ansgar B Siemer
- Department of Biochemistry and Molecular Medicine, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California.
| |
Collapse
|
24
|
Metal Binding Properties of the N-Terminus of the Functional Amyloid Orb2. Biomolecules 2017; 7:biom7030057. [PMID: 28763009 PMCID: PMC5618238 DOI: 10.3390/biom7030057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 07/14/2017] [Accepted: 07/21/2017] [Indexed: 12/18/2022] Open
Abstract
The cytoplasmic polyadenylation element binding protein (CPEB) homologue Orb2 is a functional amyloid that plays a key regulatory role for long-term memory in Drosophila. Orb2 has a glutamine, histidine-rich (Q/H-rich) domain that resembles the Q/H-rich, metal binding domain of the Hpn-like protein (Hpnl) found in Helicobacter pylori. In the present study, we used chromatography and isothermal titration calorimetry (ITC) to show that the Q/H-rich domain of Orb2 binds Ni2+ and other transition metals ions with μM affinity. Using site directed mutagenesis, we show that several histidine residues are important for binding. In particular, the H61Y mutation, which was previously shown to affect the aggregation of Orb2 in cell culture, completely inhibited metal binding of Orb2. Finally, we used thioflavin T fluorescence and electron microscopy images to show that Ni2+ binding induces the aggregating of Orb2 into structures that are distinct from the amyloid fibrils formed in the absence of Ni2+. These data suggest that transition metal binding might be important for the function of Orb2 and potentially long-term memory in Drosophila.
Collapse
|
25
|
Hewetson A, Do HQ, Myers C, Muthusubramanian A, Sutton RB, Wylie BJ, Cornwall GA. Functional Amyloids in Reproduction. Biomolecules 2017; 7:biom7030046. [PMID: 28661450 PMCID: PMC5618227 DOI: 10.3390/biom7030046] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 06/20/2017] [Accepted: 06/23/2017] [Indexed: 11/16/2022] Open
Abstract
Amyloids are traditionally considered pathological protein aggregates that play causative roles in neurodegenerative disease, diabetes and prionopathies. However, increasing evidence indicates that in many biological systems nonpathological amyloids are formed for functional purposes. In this review, we will specifically describe amyloids that carry out biological roles in sexual reproduction including the processes of gametogenesis, germline specification, sperm maturation and fertilization. Several of these functional amyloids are evolutionarily conserved across several taxa, including human, emphasizing the critical role amyloids perform in reproduction. Evidence will also be presented suggesting that, if altered, some functional amyloids may become pathological.
Collapse
Affiliation(s)
- Aveline Hewetson
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
| | - Hoa Quynh Do
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
| | - Caitlyn Myers
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
| | - Archana Muthusubramanian
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
| | - Roger Bryan Sutton
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
| | - Benjamin J Wylie
- Department of Chemistry, Texas Tech University, Lubbock, TX 79409, USA.
| | - Gail A Cornwall
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
| |
Collapse
|