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Le NTK, Kang EJ, Park JH, Kang K. Catechol-Amyloid Interactions. Chembiochem 2023; 24:e202300628. [PMID: 37850717 DOI: 10.1002/cbic.202300628] [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: 09/13/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 10/19/2023]
Abstract
This review introduces multifaceted mutual interactions between molecules containing a catechol moiety and aggregation-prone proteins. The complex relationships between these two molecular species have previously been elucidated primarily in a unidirectional manner, as demonstrated in cases involving the development of catechol-based inhibitors for amyloid aggregation and the elucidation of the role of functional amyloid fibers in melanin biosynthesis. This review aims to consolidate scattered clues pertaining to catechol-based amyloid inhibitors, functional amyloid scaffold of melanin biosynthesis, and chemically designed peptide fibers for providing chemical insights into the role of the local three-dimensional orientation of functional groups in manifesting such interactions. These orientations may play crucial, yet undiscovered, roles in various supramolecular structures.
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Affiliation(s)
- Nghia T K Le
- Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi, 17104, South Korea
| | - Eun Joo Kang
- Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi, 17104, South Korea
| | - Ji Hun Park
- Department of Science Education, Ewha Womans University, Seoul, 03760, South Korea
| | - Kyungtae Kang
- Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi, 17104, South Korea
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2
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Kawahara R, Usami T, Arakawa S, Kamo H, Suzuki T, Komatsu R, Hara H, Niwa Y, Shimizu E, Dohmae N, Shimizu S, Simizu S. Biogenesis of fibrils requires C-mannosylation of PMEL. FEBS J 2023; 290:5373-5394. [PMID: 37552474 DOI: 10.1111/febs.16927] [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: 01/24/2023] [Revised: 07/22/2023] [Accepted: 08/07/2023] [Indexed: 08/09/2023]
Abstract
Premelanosome protein (PMEL), a melanocyte-specific glycoprotein, has an essential role in melanosome maturation, assembling amyloid fibrils for melanin deposition. PMEL undergoes several post-translational modifications, including N- and O-glycosylations, which are associated with proper melanosome development. C-mannosylation is a rare type of protein glycosylation at a tryptophan residue that might regulate the secretion and localization of proteins. PMEL has one putative C-mannosylation site in its core amyloid fragment (CAF); however, there is no report focusing on C-mannosylation of PMEL. To investigate this, we expressed recombinant PMEL in SK-MEL-28 human melanoma cells and purified the protein. Mass spectrometry analyses demonstrated that human PMEL is C-mannosylated at multiple tryptophan residues in its CAF and N-terminal fragment (NTF). In addition to the W153 or W156 residue (CAF), which lies in the consensus sequence for C-mannosylation, the W104 residue (NTF) was C-mannosylated without the consensus sequence. To determine the effects of the modifications, we deleted the PMEL gene by using CRISPR/Cas9 technology and re-expressed wild-type or C-mannosylation-defective mutants of PMEL, in which the C-mannosylated tryptophan was replaced with a phenylalanine residue (WF mutation), in SK-MEL-28 cells. Importantly, fibril-containing melanosomes were significantly decreased in W104F mutant PMEL-re-expressing cells compared with wild-type PMEL, observed using transmission electron microscopy. Furthermore, western blot and immunofluorescence analysis suggested that the W104F mutation may cause mild endoplasmic reticulumretention, possibly associated with early misfolding, and lysosomal misaggregation, thus reducing functional fibril formation. Our results demonstrate that C-mannosylation of PMEL is required for proper melanosome development by regulating PMEL-derived fibril formation.
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Affiliation(s)
- Ryota Kawahara
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Tomoko Usami
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Satoko Arakawa
- Department of Pathological Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, Japan
- Research Core, Institute of Research, Tokyo Medical and Dental University, Japan
| | - Hiroki Kamo
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Ryosuke Komatsu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Hiroyuki Hara
- Division of Anatomical Science, Department of Functional Morphology, Nihon University School of Medicine, Tokyo, Japan
| | - Yuki Niwa
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Erina Shimizu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Shigeomi Shimizu
- Department of Pathological Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, Japan
| | - Siro Simizu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan
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3
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Hodges ED, Chrystal PW, Footz T, Doucette LP, Noel NCL, Li Z, Walter MA, Allison WT. Disrupting the Repeat Domain of Premelanosome Protein (PMEL) Produces Dysamyloidosis and Dystrophic Ocular Pigment Reflective of Pigmentary Glaucoma. Int J Mol Sci 2023; 24:14423. [PMID: 37833870 PMCID: PMC10572516 DOI: 10.3390/ijms241914423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 10/15/2023] Open
Abstract
Pigmentary glaucoma has recently been associated with missense mutations in PMEL that are dominantly inherited and enriched in the protein's fascinating repeat domain. PMEL pathobiology is intriguing because PMEL forms functional amyloid in healthy eyes, and this PMEL amyloid acts to scaffold melanin deposition. This is an informative contradistinction to prominent neurodegenerative diseases where amyloid formation is neurotoxic and mutations cause a toxic gain of function called "amyloidosis". Preclinical animal models have failed to model this PMEL "dysamyloidosis" pathomechanism and instead cause recessively inherited ocular pigment defects via PMEL loss of function; they have not addressed the consequences of disrupting PMEL's repetitive region. Here, we use CRISPR to engineer a small in-frame mutation in the zebrafish homolog of PMEL that is predicted to subtly disrupt the protein's repetitive region. Homozygous mutant larvae displayed pigmentation phenotypes and altered eye morphogenesis similar to presumptive null larvae. Heterozygous mutants had disrupted eye morphogenesis and disrupted pigment deposition in their retinal melanosomes. The deficits in the pigment deposition of these young adult fish were not accompanied by any detectable glaucomatous changes in intraocular pressure or retinal morphology. Overall, the data provide important in vivo validation that subtle PMEL mutations can cause a dominantly inherited pigment pathology that aligns with the inheritance of pigmentary glaucoma patient pedigrees. These in vivo observations help to resolve controversy regarding the necessity of PMEL's repeat domain in pigmentation. The data foster an ongoing interest in an antithetical dysamyloidosis mechanism that, akin to the amyloidosis of devastating dementias, manifests as a slow progressive neurodegenerative disease.
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Affiliation(s)
- Elizabeth D. Hodges
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; (E.D.H.); (P.W.C.)
- Faculty of Science, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Paul W. Chrystal
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; (E.D.H.); (P.W.C.)
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Tim Footz
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2R3, Canada (M.A.W.)
| | - Lance P. Doucette
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; (E.D.H.); (P.W.C.)
| | - Nicole C. L. Noel
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; (E.D.H.); (P.W.C.)
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2R3, Canada (M.A.W.)
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Zixuan Li
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; (E.D.H.); (P.W.C.)
| | - Michael A. Walter
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2R3, Canada (M.A.W.)
| | - W. Ted Allison
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; (E.D.H.); (P.W.C.)
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2R3, Canada (M.A.W.)
- Centre for Prions & Protein Folding Disease, University of Alberta, Edmonton, AB T6G 2M8, Canada
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4
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Joshi R, Zhaliazka K, Holman AP, Kurouski D. Elucidation of the Role of Lipids in Late Endosomes on the Aggregation of Insulin. ACS Chem Neurosci 2023; 14:3551-3559. [PMID: 37682720 PMCID: PMC10862470 DOI: 10.1021/acschemneuro.3c00475] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Abrupt aggregation of misfolded proteins is the underlying molecular cause of numerous pathologies including diabetes type 2 and injection amyloidosis. Although the exact cause of this process is unclear, a growing body of evidence suggests that protein aggregation is linked to a high protein concentration and the presence of lipid membranes. Endosomes are cell organelles that often possess high concentrations of proteins due to their uptake from the extracellular space. However, the role of endosomes in amyloid pathologies remains unclear. In this study, we used a set of biophysical methods to determine the role of bis(monoacylglycero)phosphate (BMP), the major lipid constituent of late endosomes on the aggregation properties of insulin. We found that both saturated and unsaturated BMP accelerated protein aggregation. However, very little if any changes in the secondary structure of insulin fibrils grown in the presence of BMP were observed. Therefore, no changes in the toxicity of these aggregates compared to the fibrils formed in the lipid-free environment were observed. We also found that the toxicity of insulin oligomers formed in the presence of a 77:23 mol/mol ratio of BMP/PC, which represents the lipid composition of late endosomes, was slightly higher than the toxicity of insulin oligomers formed in the lipid-free environment. However, the toxicity of mature insulin fibrils formed in the presence of BMP/PC mixture was found to be lower or similar to the toxicity of insulin fibrils formed in the lipid-free environment. These results suggest that late endosomes are unlikely to be the source of highly toxic protein aggregates if amyloid proteins aggregate in them.
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Affiliation(s)
- Ritu Joshi
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Kiryl Zhaliazka
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Aidan P. Holman
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
- Department
of Entomology, Texas A&M University, College Station, Texas 77843, United States
| | - Dmitry Kurouski
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
- Department
of Biomedical Engineering, Texas A&M
University, College Station, Texas 77843, United States
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5
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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: 4] [Impact Index Per Article: 4.0] [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.
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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.
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6
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Mondal J, Pillarisetti S, Junnuthula V, Saha M, Hwang SR, Park IK, Lee YK. Hybrid exosomes, exosome-like nanovesicles and engineered exosomes for therapeutic applications. J Control Release 2023; 353:1127-1149. [PMID: 36528193 DOI: 10.1016/j.jconrel.2022.12.027] [Citation(s) in RCA: 63] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 12/28/2022]
Abstract
Exosomes are endosome-derived nanovesicles involved in cellular communication. They are natural nanocarriers secreted by various cells, making them suitable candidates for diverse drug delivery and therapeutic applications from a material standpoint. They have a phospholipid bilayer decorated with functional molecules and an enclosed parental matrix, which has attracted interest in developing designer/hybrid engineered exosome nanocarriers. The structural versatility of exosomes allows the modification of their original configuration using various methods, including genetic engineering, chemical procedures, physical techniques, and microfluidic technology, to load exosomes with additional cargo for expanded biomedical applications. Exosomes show enormous potential for overcoming the limitations of conventional nanoparticle-based techniques in targeted therapy. This review highlights the exosome sources, characteristics, state of the art in the field of hybrid exosomes, exosome-like nanovesicles and engineered exosomes as potential cargo delivery vehicles for therapeutic applications.
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Affiliation(s)
- Jagannath Mondal
- Department of Green Bioengineering, Korea National University of Transportation, Chungju 27470, Republic of Korea
| | - Shameer Pillarisetti
- Department of Biomedical Sciences and Biomedical Science Graduate Program (BMSGP), Chonnam National University Medical School, 160 Baekseo-ro, Gwangju 61469, Republic of Korea
| | | | - Monochura Saha
- Media lab, Massachusetts Institute of Technology (MIT), 75 Amherst Street, Cambridge 02139, USA
| | - Seung Rim Hwang
- College of Pharmacy, Chosun University, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - In-Kyu Park
- Department of Biomedical Sciences and Biomedical Science Graduate Program (BMSGP), Chonnam National University Medical School, 160 Baekseo-ro, Gwangju 61469, Republic of Korea.
| | - Yong-Kyu Lee
- Department of Green Bioengineering, Korea National University of Transportation, Chungju 27470, Republic of Korea; Department of Chemical & Biological Engineering, Korea National University of Transportation, Chungju 27470, Republic of Korea.
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7
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Beyers WC, Detry AM, Di Pietro SM. OCA7 is a melanosome membrane protein that defines pigmentation by regulating early stages of melanosome biogenesis. J Biol Chem 2022; 298:102669. [PMID: 36334630 DOI: 10.1016/j.jbc.2022.102669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022] Open
Abstract
Mutations in C10orf11 (oculocutaneous albinism type 7 [OCA7]) cause OCA, a disorder that presents with hypopigmentation in skin, eyes, and hair. The OCA7 pathophysiology is unknown, and there is virtually no information on the OCA7 protein and its cellular function. Here, we discover that OCA7 localizes to the limiting membrane of melanosomes, the specialized pigment cell organelles where melanin is synthesized. We demonstrate that OCA7 is recruited through interaction with a canonical effector-binding surface of melanosome proteins Rab32 and Rab38. Using newly generated OCA7-KO MNT1 cells, we show OCA7 regulates overall melanin levels in a melanocyte autonomous manner by controlling melanosome maturation. Importantly, we found that OCA7 regulates premelanosome protein (PMEL) processing, impacting fibrillation and the striations that define transition from melanosome stage I to stage II. Furthermore, the melanosome lumen of OCA7-KO cells displays lower pH than control cells. Together, our results reveal that OCA7 regulates pigmentation through two well-established determinants of melanosome biogenesis and function, PMEL processing, and organelle pH.
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Affiliation(s)
- Wyatt C Beyers
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Anna M Detry
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Santiago M Di Pietro
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA.
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8
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The retinal pigmentation pathway in human albinism: Not so black and white. Prog Retin Eye Res 2022; 91:101091. [PMID: 35729001 DOI: 10.1016/j.preteyeres.2022.101091] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 12/16/2022]
Abstract
Albinism is a pigment disorder affecting eye, skin and/or hair. Patients usually have decreased melanin in affected tissues and suffer from severe visual abnormalities, including foveal hypoplasia and chiasmal misrouting. Combining our data with those of the literature, we propose a single functional genetic retinal signalling pathway that includes all 22 currently known human albinism disease genes. We hypothesise that defects affecting the genesis or function of different intra-cellular organelles, including melanosomes, cause syndromic forms of albinism (Hermansky-Pudlak (HPS) and Chediak-Higashi syndrome (CHS)). We put forward that specific melanosome impairments cause different forms of oculocutaneous albinism (OCA1-8). Further, we incorporate GPR143 that has been implicated in ocular albinism (OA1), characterised by a phenotype limited to the eye. Finally, we include the SLC38A8-associated disorder FHONDA that causes an even more restricted "albinism-related" ocular phenotype with foveal hypoplasia and chiasmal misrouting but without pigmentation defects. We propose the following retinal pigmentation pathway, with increasingly specific genetic and cellular defects causing an increasingly specific ocular phenotype: (HPS1-11/CHS: syndromic forms of albinism)-(OCA1-8: OCA)-(GPR143: OA1)-(SLC38A8: FHONDA). Beyond disease genes involvement, we also evaluate a range of (candidate) regulatory and signalling mechanisms affecting the activity of the pathway in retinal development, retinal pigmentation and albinism. We further suggest that the proposed pigmentation pathway is also involved in other retinal disorders, such as age-related macular degeneration. The hypotheses put forward in this report provide a framework for further systematic studies in albinism and melanin pigmentation disorders.
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9
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Kachkin DV, Volkov KV, Sopova JV, Bobylev AG, Fedotov SA, Inge-Vechtomov SG, Galzitskaya OV, Chernoff YO, Rubel AA, Aksenova AY. Human RAD51 Protein Forms Amyloid-like Aggregates In Vitro. Int J Mol Sci 2022; 23:ijms231911657. [PMID: 36232958 PMCID: PMC9570251 DOI: 10.3390/ijms231911657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 12/30/2022] Open
Abstract
RAD51 is a central protein of homologous recombination and DNA repair processes that maintains genome stability and ensures the accurate repair of double-stranded breaks (DSBs). In this work, we assessed amyloid properties of RAD51 in vitro and in the bacterial curli-dependent amyloid generator (C-DAG) system. Resistance to ionic detergents, staining with amyloid-specific dyes, polarized microscopy, transmission electron microscopy (TEM), X-ray diffraction and other methods were used to evaluate the properties and structure of RAD51 aggregates. The purified human RAD51 protein formed detergent-resistant aggregates in vitro that had an unbranched cross-β fibrillar structure, which is typical for amyloids, and were stained with amyloid-specific dyes. Congo-red-stained RAD51 aggregates demonstrated birefringence under polarized light. RAD51 fibrils produced sharp circular X-ray reflections at 4.7 Å and 10 Å, demonstrating that they had a cross-β structure. Cytoplasmic aggregates of RAD51 were observed in cell cultures overexpressing RAD51. We demonstrated that a key protein that maintains genome stability, RAD51, has amyloid properties in vitro and in the C-DAG system and discussed the possible biological relevance of this observation.
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Affiliation(s)
- Daniel V. Kachkin
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Kirill V. Volkov
- Research Resource Center “Molecular and Cell Technologies”, Research Park, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Julia V. Sopova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Center of Transgenesis and Genome Editing, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Alexander G. Bobylev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 3 Institutskaya St., 142290 Moscow, Russia
| | - Sergei A. Fedotov
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Sergei G. Inge-Vechtomov
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Oxana V. Galzitskaya
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 3 Institutskaya St., 142290 Moscow, Russia
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Yury O. Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-2000, USA
| | - Aleksandr A. Rubel
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence: (A.A.R.); (A.Y.A.)
| | - Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence: (A.A.R.); (A.Y.A.)
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10
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Park H, Jeon H, Lee MY, Jeon H, Kwon S, Hong S, Kang K. Designed Amyloid Fibers with Emergent Melanosomal Functions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:7077-7084. [PMID: 35608255 DOI: 10.1021/acs.langmuir.2c00904] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Short peptides designed to self-associate into amyloid fibers with metal ion-binding ability have been used to catalyze various types of chemical reactions. This manuscript demonstrates that one of these short-peptide fibers coordinated with CuII can exhibit melanosomal functions. The coordinated CuII and the amyloid structure itself are differentially functional in accelerating oxidative self-association of dopamine into melanin-like species and in regulating their material properties (e.g., water dispersion, morphology, and the density of unpaired electrons). The results have implications for the role of functional amyloids in melanin biosynthesis and for designing peptide-based supramolecular structures with various emergent functions.
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Affiliation(s)
- Hyeyeon Park
- Department of Applied Chemistry, Kyung Hee University, 1732 Deogyoung-daero, Yongin, Gyeonggi 17104, South Korea
| | - Hyeri Jeon
- Department of Chemistry, Sookmyung Women's University, Seoul 04310, South Korea
| | - Min Young Lee
- Department of Applied Chemistry, Kyung Hee University, 1732 Deogyoung-daero, Yongin, Gyeonggi 17104, South Korea
| | - Hyojae Jeon
- Department of Applied Chemistry, Kyung Hee University, 1732 Deogyoung-daero, Yongin, Gyeonggi 17104, South Korea
| | - Sunbum Kwon
- Department of Chemistry, Chung-Ang University, Seoul 06974, South Korea
| | - Seungwoo Hong
- Department of Chemistry, Sookmyung Women's University, Seoul 04310, South Korea
| | - Kyungtae Kang
- Department of Applied Chemistry, Kyung Hee University, 1732 Deogyoung-daero, Yongin, Gyeonggi 17104, South Korea
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11
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Zhou Y, Hua J, Ding D, Tang Y. Interrogating amyloid aggregation with aggregation-induced emission fluorescence probes. Biomaterials 2022; 286:121605. [DOI: 10.1016/j.biomaterials.2022.121605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/22/2022] [Accepted: 05/24/2022] [Indexed: 12/26/2022]
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12
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Chatterjee D, Jacob RS, Ray S, Navalkar A, Singh N, Sengupta S, Gadhe L, Kadu P, Datta D, Paul A, Arunima S, Mehra S, Pindi C, Kumar S, Singru P, Senapati S, Maji SK. Co-aggregation and secondary nucleation in the life cycle of human prolactin/galanin functional amyloids. eLife 2022; 11:73835. [PMID: 35257659 PMCID: PMC8993219 DOI: 10.7554/elife.73835] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/03/2022] [Indexed: 11/22/2022] Open
Abstract
Synergistic-aggregation and cross-seeding by two different proteins/peptides in the amyloid aggregation are well evident in various neurological disorders including Alzheimer’s disease. Here, we show co-storage of human Prolactin (PRL), which is associated with lactation in mammals, and neuropeptide galanin (GAL) as functional amyloids in secretory granules (SGs) of the female rat. Using a wide variety of biophysical studies, we show that irrespective of the difference in sequence and structure, both hormones facilitate their synergic aggregation to amyloid fibrils. Although each hormone possesses homotypic seeding ability, a unidirectional cross-seeding of GAL aggregation by PRL seeds and the inability of cross seeding by mixed fibrils suggest tight regulation of functional amyloid formation by these hormones for their efficient storage in SGs. Further, the faster release of functional hormones from mixed fibrils compared to the corresponding individual amyloid, suggests a novel mechanism of heterologous amyloid formation in functional amyloids of SGs in the pituitary. The formation of plaques of proteins called ‘amyloids’ in the brain is one of the hallmark characteristics of both Alzheimer’s and Parkinson’s disease, but amyloids can form in many tissues and organs, often disrupting normal activity. A lot of the research into amyloids has focused on their role in disease, but it turns out that amyloids can also appear in healthy tissues. For example, some protein hormones form amyloids that act as storage depots, helping cells to release the hormone when it is needed. Normally, amyloids are made mostly of a single type of protein or protein fragment associated with a particular disease like Alzheimer's. Often, this type of amyloid promotes plaque formation in other proteins, which aggravates other diseases (for example, the amyloids that form in Alzheimer’s can lead to Parkinson’s disease or type II diabetes getting worse).The plaques start growing from small amyloid fragments called seeds. In mixed amyloids – amyloids made of two types of proteins – seeds made of one protein can trigger the formation of amyloids of the other protein. This raises the question, is this true for hormones? The body often releases more than one hormone at a time from the same tissue; for example, the pituitary gland releases prolactin and galanin simultaneously. However, these hormones have completely different structures, so whether they can form a mixed amyloid is unclear. To answer this question, Chatterjee et al. first determined that, within the pituitary gland of female rats, prolactin and galanin could be found together in the same cells, forming mixed amyloids. To understand out how this happens, Chatterjee et al. tried seeding new amyloids using either prolactin or galanin. This revealed that only prolactin seeds were able to trigger the formation of galanin amyloids. Chatterjee et al. also found that the mixed amyloids could release the hormones faster than amyloids made from either protein alone. Together, these results suggest that the collaboration between these two proteins may help maintain hormone balance in the body. Problems with hormone storage and release lead to various human diseases, including prolactinoma. Understanding amyloid storage depots could reveal new ways to control hormone levels. Further research could also help to explain more about well-studied diseases linked to amyloids, like Alzheimer's.
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Affiliation(s)
- Debdeep Chatterjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Reeba S Jacob
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Soumik Ray
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Ambuja Navalkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Namrata Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Shinjinee Sengupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Laxmikant Gadhe
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Debalina Datta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Ajoy Paul
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sakunthala Arunima
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Surabhi Mehra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Chinmai Pindi
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Santosh Kumar
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India
| | - Praful Singru
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India
| | - Sanjib Senapati
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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13
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Ha D, Kang K. Nucleophilic Regulation of the Formation of Melanin-like Species by Amyloid Fibers. ACS OMEGA 2022; 7:773-779. [PMID: 35036743 PMCID: PMC8757343 DOI: 10.1021/acsomega.1c05399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
This work examines the influences of amyloid fibers of hen egg white lysozyme (HEWL) on the formation of melanin-like species (MLS) with a rationally selected set of catechol derivatives. Catechol-amyloid interactions, which are central in melanogenesis, are complex and multifaceted, making them difficult to understand at the molecular level. The catechol derivatives are set to interact with HEWL amyloid fibers upon altering pH, and the resultant formation of MLS is characterized. For obtaining clues for the molecular mechanism by which HEWL fibers regulate the formation of MLS, putative intermolecular interactions are individually perturbed and their ramifications are analyzed. With the entire data set, we could conclude that the externally presented nucleophilic moieties of HEWL fibers play a major role in regulating the material and kinetic properties of MLS and their formation, respectively.
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14
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Sprunger ML, Jackrel ME. Prion-Like Proteins in Phase Separation and Their Link to Disease. Biomolecules 2021; 11:biom11071014. [PMID: 34356638 PMCID: PMC8301953 DOI: 10.3390/biom11071014] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/28/2021] [Accepted: 07/06/2021] [Indexed: 02/01/2023] Open
Abstract
Aberrant protein folding underpins many neurodegenerative diseases as well as certain myopathies and cancers. Protein misfolding can be driven by the presence of distinctive prion and prion-like regions within certain proteins. These prion and prion-like regions have also been found to drive liquid-liquid phase separation. Liquid-liquid phase separation is thought to be an important physiological process, but one that is prone to malfunction. Thus, aberrant liquid-to-solid phase transitions may drive protein aggregation and fibrillization, which could give rise to pathological inclusions. Here, we review prions and prion-like proteins, their roles in phase separation and disease, as well as potential therapeutic approaches to counter aberrant phase transitions.
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15
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Functional Domains and Evolutionary History of the PMEL and GPNMB Family Proteins. Molecules 2021; 26:molecules26123529. [PMID: 34207849 PMCID: PMC8273697 DOI: 10.3390/molecules26123529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 11/17/2022] Open
Abstract
The ancient paralogs premelanosome protein (PMEL) and glycoprotein nonmetastatic melanoma protein B (GPNMB) have independently emerged as intriguing disease loci in recent years. Both proteins possess common functional domains and variants that cause a shared spectrum of overlapping phenotypes and disease associations: melanin-based pigmentation, cancer, neurodegenerative disease and glaucoma. Surprisingly, these proteins have yet to be shown to physically or genetically interact within the same cellular pathway. This juxtaposition inspired us to compare and contrast this family across a breadth of species to better understand the divergent evolutionary trajectories of two related, but distinct, genes. In this study, we investigated the evolutionary history of PMEL and GPNMB in clade-representative species and identified TMEM130 as the most ancient paralog of the family. By curating the functional domains in each paralog, we identified many commonalities dating back to the emergence of the gene family in basal metazoans. PMEL and GPNMB have gained functional domains since their divergence from TMEM130, including the core amyloid fragment (CAF) that is critical for the amyloid potential of PMEL. Additionally, the PMEL gene has acquired the enigmatic repeat domain (RPT), composed of a variable number of imperfect tandem repeats; this domain acts in an accessory role to control amyloid formation. Our analyses revealed the vast variability in sequence, length and repeat number in homologous RPT domains between craniates, even within the same taxonomic class. We hope that these analyses inspire further investigation into a gene family that is remarkable from the evolutionary, pathological and cell biology perspectives.
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16
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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.
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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.)
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17
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Identification of critical amino acid residues in the regulatory N-terminal domain of PMEL. Sci Rep 2021; 11:7730. [PMID: 33833328 PMCID: PMC8032716 DOI: 10.1038/s41598-021-87259-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/26/2021] [Indexed: 01/22/2023] Open
Abstract
The pigment cell-specific protein PMEL forms a functional amyloid matrix in melanosomes onto which the pigment melanin is deposited. The amyloid core consists of a short proteolytic fragment, which we have termed the core-amyloid fragment (CAF) and perhaps additional parts of the protein, such as the PKD domain. A highly O-glycosylated repeat (RPT) domain also derived from PMEL proteolysis associates with the amyloid and is necessary to establish the sheet-like morphology of the assemblies. Excluded from the aggregate is the regulatory N-terminus, which nevertheless must be linked in cis to the CAF in order to drive amyloid formation. The domain is then likely cleaved away immediately before, during, or immediately after the incorporation of a new CAF subunit into the nascent amyloid. We had previously identified a 21 amino acid long region, which mediates the regulatory activity of the N-terminus towards the CAF. However, many mutations in the respective segment caused misfolding and/or blocked PMEL export from the endoplasmic reticulum, leaving their phenotype hard to interpret. Here, we employ a saturating mutagenesis approach targeting the motif at single amino acid resolution. Our results confirm the critical nature of the PMEL N-terminal region and identify several residues essential for PMEL amyloidogenesis.
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18
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Matiiv AB, Trubitsina NP, Matveenko AG, Barbitoff YA, Zhouravleva GA, Bondarev SA. Amyloid and Amyloid-Like Aggregates: Diversity and the Term Crisis. BIOCHEMISTRY (MOSCOW) 2021; 85:1011-1034. [PMID: 33050849 DOI: 10.1134/s0006297920090035] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Active accumulation of the data on new amyloids continuing nowadays dissolves boundaries of the term "amyloid". Currently, it is most often used to designate aggregates with cross-β structure. At the same time, amyloids also exhibit a number of other unusual properties, such as: detergent and protease resistance, interaction with specific dyes, and ability to induce transition of some proteins from a soluble form to an aggregated one. The same features have been also demonstrated for the aggregates lacking cross-β structure, which are commonly called "amyloid-like" and combined into one group, although they are very diverse. We have collected and systematized information on the properties of more than two hundred known amyloids and amyloid-like proteins with emphasis on conflicting examples. In particular, a number of proteins in membraneless organelles form aggregates with cross-β structure that are morphologically indistinguishable from the other amyloids, but they can be dissolved in the presence of detergents, which is not typical for amyloids. Such paradoxes signify the need to clarify the existing definition of the term amyloid. On the other hand, the demonstrated structural diversity of the amyloid-like aggregates shows the necessity of their classification.
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Affiliation(s)
- A B Matiiv
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - N P Trubitsina
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - A G Matveenko
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Y A Barbitoff
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia.,Bioinformatics Institute, St. Petersburg, 197342, Russia
| | - G A Zhouravleva
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - S A Bondarev
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia. .,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
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19
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Bobyleva LG, Shumeyko SA, Yakupova EI, Surin AK, Galzitskaya OV, Kihara H, Timchenko AA, Timchenko MA, Penkov NV, Nikulin AD, Suvorina MY, Molochkov NV, Lobanov MY, Fadeev RS, Vikhlyantsev IM, Bobylev AG. Myosin Binding Protein-C Forms Amyloid-Like Aggregates In Vitro. Int J Mol Sci 2021; 22:ijms22020731. [PMID: 33450960 PMCID: PMC7828380 DOI: 10.3390/ijms22020731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/06/2021] [Accepted: 01/10/2021] [Indexed: 11/17/2022] Open
Abstract
This work investigated in vitro aggregation and amyloid properties of skeletal myosin binding protein-C (sMyBP-C) interacting in vivo with proteins of thick and thin filaments in the sarcomeric A-disc. Dynamic light scattering (DLS) and transmission electron microscopy (TEM) found a rapid (5–10 min) formation of large (>2 μm) aggregates. sMyBP-C oligomers formed both at the initial 5–10 min and after 16 h of aggregation. Small angle X-ray scattering (SAXS) and DLS revealed sMyBP-C oligomers to consist of 7–10 monomers. TEM and atomic force microscopy (AFM) showed sMyBP-C to form amorphous aggregates (and, to a lesser degree, fibrillar structures) exhibiting no toxicity on cell culture. X-ray diffraction of sMyBP-C aggregates registered reflections attributed to a cross-β quaternary structure. Circular dichroism (CD) showed the formation of the amyloid-like structure to occur without changes in the sMyBP-C secondary structure. The obtained results indicating a high in vitro aggregability of sMyBP-C are, apparently, a consequence of structural features of the domain organization of proteins of this family. Formation of pathological amyloid or amyloid-like sMyBP-C aggregates in vivo is little probable due to amino-acid sequence low identity (<26%), alternating ordered/disordered regions in the protein molecule, and S–S bonds providing for general stability.
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Affiliation(s)
- Liya G. Bobyleva
- Laboratory of the Structure and Functions of Muscle Proteins, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia; (L.G.B.); (S.A.S.); (E.I.Y.); (O.V.G.)
| | - Sergey A. Shumeyko
- Laboratory of the Structure and Functions of Muscle Proteins, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia; (L.G.B.); (S.A.S.); (E.I.Y.); (O.V.G.)
| | - Elmira I. Yakupova
- Laboratory of the Structure and Functions of Muscle Proteins, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia; (L.G.B.); (S.A.S.); (E.I.Y.); (O.V.G.)
| | - Alexey K. Surin
- Laboratory of Bioinformatics and Proteomics, Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (A.K.S.); (M.Y.S.); (M.Y.L.)
- Biological Testing Laboratory, Branch of the Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia
- Laboratory of the Biochemistry of Pathogenic Microorganisms, State Research Centre for Applied Microbiology and Biotechnology, Obolensk, 142279 Serpukhov District, Russia
| | - Oxana V. Galzitskaya
- Laboratory of the Structure and Functions of Muscle Proteins, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia; (L.G.B.); (S.A.S.); (E.I.Y.); (O.V.G.)
- Laboratory of Bioinformatics and Proteomics, Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (A.K.S.); (M.Y.S.); (M.Y.L.)
| | - Hiroshi Kihara
- Department of Early Childhood Education, Himeji-Hinomoto College, 890 Koro, Kodera-cho, Himeji 679-2151, Japan;
| | - Alexander A. Timchenko
- Group of Experimental Research and Engineering of Oligomeric Structures, Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Maria A. Timchenko
- Laboratory of Applied Enzymology, FRC PSCBR, Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Nikita V. Penkov
- Laboratory of the Methods of Optical Spectral Analysis, Institute of Cell Biophysics, Russian Academy of Sciences, FRC PSCBR RAS, 142290 Pushchino, Russia;
| | - Alexey D. Nikulin
- Laboratory for Structural Studies of the Translational Apparatus, Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Mariya Yu. Suvorina
- Laboratory of Bioinformatics and Proteomics, Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (A.K.S.); (M.Y.S.); (M.Y.L.)
| | - Nikolay V. Molochkov
- Laboratory of NMR Investigations of Biosystems, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Mikhail Yu. Lobanov
- Laboratory of Bioinformatics and Proteomics, Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (A.K.S.); (M.Y.S.); (M.Y.L.)
| | - Roman S. Fadeev
- Laboratory of Pharmacological Regulation of Cell Resistance, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Ivan M. Vikhlyantsev
- Laboratory of the Structure and Functions of Muscle Proteins, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia; (L.G.B.); (S.A.S.); (E.I.Y.); (O.V.G.)
- Correspondence: (I.M.V.); (A.G.B.)
| | - Alexander G. Bobylev
- Laboratory of the Structure and Functions of Muscle Proteins, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia; (L.G.B.); (S.A.S.); (E.I.Y.); (O.V.G.)
- Correspondence: (I.M.V.); (A.G.B.)
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20
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Functional Amyloids Are the Rule Rather Than the Exception in Cellular Biology. Microorganisms 2020; 8:microorganisms8121951. [PMID: 33316961 PMCID: PMC7764130 DOI: 10.3390/microorganisms8121951] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 11/28/2020] [Accepted: 12/04/2020] [Indexed: 12/15/2022] Open
Abstract
Amyloids are a class of protein aggregates that have been historically characterized by their relationship with human disease. Indeed, amyloids can be the result of misfolded proteins that self-associate to form insoluble, extracellular plaques in diseased tissue. For the first 150 years of their study, the pathogen-first definition of amyloids was sufficient. However, new observations of amyloids foster an appreciation for non-pathological roles for amyloids in cellular systems. There is now evidence from all domains of life that amyloids can be non-pathogenic and functional, and that their formation can be the result of purposeful and controlled cellular processes. So-called functional amyloids fulfill an assortment of biological functions including acting as structural scaffolds, regulatory mechanisms, and storage mechanisms. The conceptual convergence of amyloids serving a functional role has been repeatedly confirmed by discoveries of additional functional amyloids. With dozens already known, and with the vigorous rate of discovery, the biology of amyloids is robustly represented by non-pathogenic amyloids.
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21
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Tian X, Cui Z, Liu S, Zhou J, Cui R. Melanosome transport and regulation in development and disease. Pharmacol Ther 2020; 219:107707. [PMID: 33075361 DOI: 10.1016/j.pharmthera.2020.107707] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/10/2020] [Accepted: 10/13/2020] [Indexed: 02/06/2023]
Abstract
Melanosomes are specialized membrane-bound organelles that synthesize and organize melanin, ultimately providing color to the skin, hair, and eyes. Disorders in melanogenesis and melanosome transport are linked to pigmentary diseases, such as Hermansky-Pudlak syndrome, Chediak-Higashi syndrome, and Griscelli syndrome. Clinical cases of these pigmentary diseases shed light on the molecular mechanisms that control melanosome-related pathways. However, only an improved understanding of melanogenesis and melanosome transport will further the development of diagnostic and therapeutic approaches. Herein, we review the current literature surrounding melanosomes with particular emphasis on melanosome membrane transport and cytoskeleton-mediated melanosome transport. We also provide perspectives on melanosome regulatory mechanisms which include hormonal action, inflammation, autophagy, and organelle interactions.
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Affiliation(s)
- Xiaoyu Tian
- Institute of Biomedical Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Ziyong Cui
- Harvard College, Cambridge, MA 02138, United States of America
| | - Song Liu
- Institute of Biomedical Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Jun Zhou
- Institute of Biomedical Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250014, China; State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Rutao Cui
- Skin Disease Research Institute, The 2nd Hospital, Zhejiang University, Hangzhou 310058, China.
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Sheng J, Olrichs NK, Gadella BM, Kaloyanova DV, Helms JB. Regulation of Functional Protein Aggregation by Multiple Factors: Implications for the Amyloidogenic Behavior of the CAP Superfamily Proteins. Int J Mol Sci 2020; 21:E6530. [PMID: 32906672 PMCID: PMC7554809 DOI: 10.3390/ijms21186530] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 12/13/2022] Open
Abstract
The idea that amyloid fibrils and other types of protein aggregates are toxic for cells has been challenged by the discovery of a variety of functional aggregates. However, an identification of crucial differences between pathological and functional aggregation remains to be explored. Functional protein aggregation is often reversible by nature in order to respond properly to changing physiological conditions of the cell. In addition, increasing evidence indicates that fast fibril growth is a feature of functional amyloids, providing protection against the long-term existence of potentially toxic oligomeric intermediates. It is becoming clear that functional protein aggregation is a complexly organized process that can be mediated by a multitude of biomolecular factors. In this overview, we discuss the roles of diverse biomolecules, such as lipids/membranes, glycosaminoglycans, nucleic acids and metal ions, in regulating functional protein aggregation. Our studies on the protein GAPR-1 revealed that several of these factors influence the amyloidogenic properties of this protein. These observations suggest that GAPR-1, as well as the cysteine-rich secretory proteins, antigen 5 and pathogenesis-related proteins group 1 (CAP) superfamily of proteins that it belongs to, require the assembly into an amyloid state to exert several of their functions. A better understanding of functional aggregate formation may also help in the prevention and treatment of amyloid-related diseases.
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Affiliation(s)
| | | | | | | | - J. Bernd Helms
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (J.S.); (N.K.O.); (B.M.G.); (D.V.K.)
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23
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Functional Mammalian Amyloids and Amyloid-Like Proteins. Life (Basel) 2020; 10:life10090156. [PMID: 32825636 PMCID: PMC7555005 DOI: 10.3390/life10090156] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/12/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023] Open
Abstract
Amyloids are highly ordered fibrous cross-β protein aggregates that are notorious primarily because of association with a variety of incurable human and animal diseases (termed amyloidoses), including Alzheimer’s disease (AD), Parkinson’s disease (PD), type 2 diabetes (T2D), and prion diseases. Some amyloid-associated diseases, in particular T2D and AD, are widespread and affect hundreds of millions of people all over the world. However, recently it has become evident that many amyloids, termed “functional amyloids,” are involved in various activities that are beneficial to organisms. Functional amyloids were discovered in diverse taxa, ranging from bacteria to mammals. These amyloids are involved in vital biological functions such as long-term memory, storage of peptide hormones and scaffolding melanin polymerization in animals, substrate attachment, and biofilm formation in bacteria and fungi, etc. Thus, amyloids undoubtedly are playing important roles in biological and pathological processes. This review is focused on functional amyloids in mammals and summarizes approaches used for identifying new potentially amyloidogenic proteins and domains.
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Shin JH, Le NTK, Jang H, Lee T, Kang K. Supramolecular Regulation of Polydopamine Formation by Amyloid Fibers. Chemistry 2020; 26:5500-5507. [PMID: 32092201 DOI: 10.1002/chem.202000437] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/19/2020] [Indexed: 11/10/2022]
Abstract
Polydopamine (PD) and melanin species are chemically complex systems, the formation and properties of which are incompletely understood. Inspired by the role of functional amyloids in melanin biosynthesis, this paper examines the influences of the supramolecular structure of amyloids on oxidative polymerization of dopamine. Kinetic analyses on the formation of PD species in the presence of hen egg white lysozyme (HEWL) fibers or soluble HEWL revealed that both forms gave rise to the total quantity of PD species, but the rate of their formation could be accelerated only by the amyloid form. PD species formed with HEWL fibers showed a morphology of bundled fibers, whereas those with soluble HEWL had a mesh-like structure. Amyloid fibers of recombinant Pmel17 had properties similar to those of HEWL fibers in modulating PD formation. The results presented here suggest how nature designs functionality with an amyloid structure and can help understand and engineer chemistries of other functional amyloids.
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Affiliation(s)
- J H Shin
- Department of Applied Chemistry, Kyung Hee University, 1732 Deogyoung-daero, Yongin, Gyeonggi, 17104, Republic of Korea
| | - Nghia T K Le
- Department of Applied Chemistry, Kyung Hee University, 1732 Deogyoung-daero, Yongin, Gyeonggi, 17104, Republic of Korea
| | - Hongje Jang
- Department of Chemistry, Kwangwoon University, 20 Gwangwoon-ro, Nowon-gu, Seoul, 01897, Republic of Korea
| | - Taehoon Lee
- Department of Applied Chemistry, Kyung Hee University, 1732 Deogyoung-daero, Yongin, Gyeonggi, 17104, Republic of Korea
| | - Kyungtae Kang
- Department of Applied Chemistry, Kyung Hee University, 1732 Deogyoung-daero, Yongin, Gyeonggi, 17104, Republic of Korea
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25
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Lahola-Chomiak AA, Footz T, Nguyen-Phuoc K, Neil GJ, Fan B, Allen KF, Greenfield DS, Parrish RK, Linkroum K, Pasquale LR, Leonhardt RM, Ritch R, Javadiyan S, Craig JE, Allison WT, Lehmann OJ, Walter MA, Wiggs JL. Non-Synonymous variants in premelanosome protein (PMEL) cause ocular pigment dispersion and pigmentary glaucoma. Hum Mol Genet 2019; 28:1298-1311. [PMID: 30561643 DOI: 10.1093/hmg/ddy429] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/04/2018] [Accepted: 12/12/2018] [Indexed: 01/25/2023] Open
Abstract
Pigmentary glaucoma (PG) is a common glaucoma subtype that results from release of pigment from the iris, called pigment dispersion syndrome (PDS), and its deposition throughout the anterior chamber of the eye. Although PG has a substantial heritable component, no causative genes have yet been identified. We used whole exome sequencing of two independent pedigrees to identify two premelanosome protein (PMEL) variants associated with heritable PDS/PG. PMEL encodes a key component of the melanosome, the organelle essential for melanin synthesis, storage and transport. Targeted screening of PMEL in three independent cohorts (n = 394) identified seven additional PDS/PG-associated non-synonymous variants. Five of the nine variants exhibited defective processing of the PMEL protein. In addition, analysis of PDS/PG-associated PMEL variants expressed in HeLa cells revealed structural changes to pseudomelanosomes indicating altered amyloid fibril formation in five of the nine variants. Introduction of 11-base pair deletions to the homologous pmela in zebrafish by the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 method caused profound pigmentation defects and enlarged anterior segments in the eye, further supporting PMEL's role in ocular pigmentation and function. Taken together, these data support a model in which missense PMEL variants represent dominant negative mutations that impair the ability of PMEL to form functional amyloid fibrils. While PMEL mutations have previously been shown to cause pigmentation and ocular defects in animals, this research is the first report of mutations in PMEL causing human disease.
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Affiliation(s)
| | - Tim Footz
- Department of Medical Genetics, University of Alberta, Edmonton AB, Canada
| | - Kim Nguyen-Phuoc
- Department of Medical Genetics, University of Alberta, Edmonton AB, Canada
| | - Gavin J Neil
- Department of Biological Sciences, University of Alberta, Edmonton AB, Canada
| | - Baojian Fan
- Ocular Genomics Institute and Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Keri F Allen
- Ocular Genomics Institute and Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - David S Greenfield
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Palm Beach Gardens, FL, USA
| | - Richard K Parrish
- Anne Bates Leach Eye Hospital, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Kevin Linkroum
- Ocular Genomics Institute and Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Louis R Pasquale
- Ocular Genomics Institute and Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Ralf M Leonhardt
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Robert Ritch
- Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, NY, USA
| | - Shari Javadiyan
- Department of Ophthalmology, Flinders Medical Centre, Adelaide, South Australia, Australia
| | - Jamie E Craig
- Department of Ophthalmology, Flinders Medical Centre, Adelaide, South Australia, Australia
| | - W T Allison
- Department of Medical Genetics, University of Alberta, Edmonton AB, Canada.,Department of Biological Sciences, University of Alberta, Edmonton AB, Canada
| | - Ordan J Lehmann
- Department of Medical Genetics, University of Alberta, Edmonton AB, Canada.,Department of Ophthalmology, University of Alberta, Edmonton AB, Canada
| | - Michael A Walter
- Department of Medical Genetics, University of Alberta, Edmonton AB, Canada
| | - Janey L Wiggs
- Ocular Genomics Institute and Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
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26
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Graham M, Tzika AC, Mitchell SM, Liu X, Leonhardt RM. Repeat domain-associated O-glycans govern PMEL fibrillar sheet architecture. Sci Rep 2019; 9:6101. [PMID: 30988362 PMCID: PMC6465243 DOI: 10.1038/s41598-019-42571-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/06/2019] [Indexed: 12/20/2022] Open
Abstract
PMEL is a pigment cell-specific protein that forms a functional amyloid matrix in melanosomes. The matrix consists of well-separated fibrillar sheets on which the pigment melanin is deposited. Using electron tomography, we demonstrate that this sheet architecture is governed by the PMEL repeat (RPT) domain, which associates with the amyloid as an accessory proteolytic fragment. Thus, the RPT domain is dispensable for amyloid formation as such but shapes the morphology of the matrix, probably in order to maximize the surface area available for pigment adsorption. Although the primary amino acid sequence of the RPT domain differs vastly among various vertebrates, we show that it is a functionally conserved, interchangeable module. RPT domains of all species are predicted to be very highly O-glycosylated, which is likely the common defining feature of this domain. O-glycosylation is indeed essential for RPT domain function and the establishment of the PMEL sheet architecture. Thus, O-glycosylation, not amino acid sequence, appears to be the major factor governing the characteristic PMEL amyloid morphology.
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Affiliation(s)
- Morven Graham
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06519, USA
| | - Athanasia C Tzika
- Department of Genetics & Evolution, Laboratory of Artificial & Natural Evolution (LANE), Sciences III Building, 1211, Geneva, 4, Switzerland
| | - Susan M Mitchell
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT, 06519, USA
| | - Xinran Liu
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06519, USA
| | - Ralf M Leonhardt
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT, 06519, USA.
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27
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Bissig C, Croisé P, Heiligenstein X, Hurbain I, Lenk GM, Kaufman E, Sannerud R, Annaert W, Meisler MH, Weisman LS, Raposo G, van Niel G. The PIKfyve complex regulates the early melanosome homeostasis required for physiological amyloid formation. J Cell Sci 2019; 132:jcs.229500. [PMID: 30709920 DOI: 10.1242/jcs.229500] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/14/2019] [Indexed: 12/23/2022] Open
Abstract
The metabolism of PI(3,5)P2 is regulated by the PIKfyve, VAC14 and FIG4 complex, mutations in which are associated with hypopigmentation in mice. These pigmentation defects indicate a key, but as yet unexplored, physiological relevance of this complex in the biogenesis of melanosomes. Here, we show that PIKfyve activity regulates formation of amyloid matrix composed of PMEL protein within the early endosomes in melanocytes, called stage I melanosomes. PIKfyve activity controls the membrane remodeling of stage I melanosomes, which regulates PMEL abundance, sorting and processing. PIKfyve activity also affects stage I melanosome kiss-and-run interactions with lysosomes, which are required for PMEL amyloidogenesis and the establishment of melanosome identity. Mechanistically, PIKfyve activity promotes both the formation of membrane tubules from stage I melanosomes and their release by modulating endosomal actin branching. Taken together, our data indicate that PIKfyve activity is a key regulator of the melanosomal import-export machinery that fine tunes the formation of functional amyloid fibrils in melanosomes and the maintenance of melanosome identity.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Christin Bissig
- Structure and Membrane Compartments, Institut Curie, Paris Sciences & Lettres Research University, Centre National de la Recherche Scientifique, UMR144, 75005 Paris, France
| | - Pauline Croisé
- IPNP, Institute of Psychiatry and Neuroscience of Paris, Hopital Saint-Anne, Université Paris Descartes, INSERM U894, 75014 Paris, France
| | - Xavier Heiligenstein
- Structure and Membrane Compartments, Institut Curie, Paris Sciences & Lettres Research University, Centre National de la Recherche Scientifique, UMR144, 75005 Paris, France.,Cell and Tissue Imaging Facility, Institut Curie, Paris Sciences & Lettres Research University, Centre National de la Recherche Scientifique, UMR144, 75005 Paris, France
| | - Ilse Hurbain
- Structure and Membrane Compartments, Institut Curie, Paris Sciences & Lettres Research University, Centre National de la Recherche Scientifique, UMR144, 75005 Paris, France.,Cell and Tissue Imaging Facility, Institut Curie, Paris Sciences & Lettres Research University, Centre National de la Recherche Scientifique, UMR144, 75005 Paris, France
| | - Guy M Lenk
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - Emily Kaufman
- Life Science Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Ragna Sannerud
- VIB Center for Brain & Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Neurosciences, 3000 Leuven, Belgium
| | - Wim Annaert
- VIB Center for Brain & Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Neurosciences, 3000 Leuven, Belgium
| | - Miriam H Meisler
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - Lois S Weisman
- Life Science Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Graça Raposo
- Structure and Membrane Compartments, Institut Curie, Paris Sciences & Lettres Research University, Centre National de la Recherche Scientifique, UMR144, 75005 Paris, France.,Cell and Tissue Imaging Facility, Institut Curie, Paris Sciences & Lettres Research University, Centre National de la Recherche Scientifique, UMR144, 75005 Paris, France
| | - Guillaume van Niel
- Structure and Membrane Compartments, Institut Curie, Paris Sciences & Lettres Research University, Centre National de la Recherche Scientifique, UMR144, 75005 Paris, France .,IPNP, Institute of Psychiatry and Neuroscience of Paris, Hopital Saint-Anne, Université Paris Descartes, INSERM U894, 75014 Paris, France.,Cell and Tissue Imaging Facility, Institut Curie, Paris Sciences & Lettres Research University, Centre National de la Recherche Scientifique, UMR144, 75005 Paris, France
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28
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Dean DN, Lee JC. pH-Dependent fibril maturation of a Pmel17 repeat domain isoform revealed by tryptophan fluorescence. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:961-969. [PMID: 30716507 DOI: 10.1016/j.bbapap.2019.01.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/24/2019] [Accepted: 01/28/2019] [Indexed: 11/19/2022]
Abstract
The pre-melanosomal protein (Pmel17) aggregates within melanosomes to form functional amyloid fibrils that facilitate melanin polymerization. The repeat domain (RPT) of Pmel17 fibrillates under strict acidic melanosomal pH. Alternative splicing results in a shortened repeat domain (sRPT), which also forms amyloid fibrils. Here, we explored the effects of pH and protein concentration on sRPT aggregation by monitoring the intrinsic fluorescence of the sole tryptophan at position 381 (381W). 381W emission properties revealed changes of local environment polarity for sRPT fibrils formed at different pH. At pH 4, fibrils formed rapidly with no lag phase. A high 381W intensity was observed with a slight blue shift (10 nm). These fibrils underwent further structural rearrangements at intermediate pH (5-6), mirroring that of melanosome maturation, which initiates at pH 4 and increases to near neutral pH. In contrast, typical sigmoidal kinetics were observed at pH 6 with slower rates and 381W exhibited quenched emission. Interestingly, biphasic kinetics were observed at pH 5 in a protein concentration-dependent manner. A large 381W blue shift (23 nm) was measured, indicating a more hydrophobic environment for fibrils made at pH 5. Consistent with 381W fluorescence, Raman spectroscopy revealed molecular level perturbations in sRPT fibrils that were not evident from circular dichroism, transmission electron microscopy, or limited proteolysis analysis. Finally, sRPT fibrils did not form at pH ≥7 and preformed fibrils rapidly disaggregated under these solution conditions. Collectively, this work yields mechanistic insights into pH-dependent sRPT aggregation in the context of melanosome maturation.
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Affiliation(s)
- Dexter N Dean
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Jennifer C Lee
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, United States.
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29
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Christensen LFB, Hansen LM, Finster K, Christiansen G, Nielsen PH, Otzen DE, Dueholm MS. The Sheaths of Methanospirillum Are Made of a New Type of Amyloid Protein. Front Microbiol 2018; 9:2729. [PMID: 30483237 PMCID: PMC6242892 DOI: 10.3389/fmicb.2018.02729] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/25/2018] [Indexed: 12/12/2022] Open
Abstract
The genera Methanospirillum and Methanosaeta contain species of anaerobic archaea that grow and divide within proteinaceous tubular sheaths that protect them from environmental stressors. The sheaths of Methanosaeta thermophila PT are composed of the 60.9 kDa major sheath protein MspA. In this study we show that sheaths purified from Methanospirillum hungatei JF-1 are regularly striated tubular structures with amyloid-like properties similar to those of M. thermophila PT. Depolymerizing the sheaths from M. hungatei JF-1 allowed us to identify a 40.6 kDa protein (WP_011449234.1) that shares 23% sequence similarity to MspA from M. thermophila PT (ABK14853.1), indicating that they might be distant homologs. The genome of M. hungatei JF-1 encodes six homologs of the identified MspA protein. Several homologs also exist in the related strains Methanospirillum stamsii Pt1 (7 homologs, 28–66% sequence identity), M. lacunae Ki8-1 C (15 homologs, 29–60% sequence identity) and Methanolinea tarda NOBI-1 (2 homologs, 31% sequence identity). The MspA protein discovered here could accordingly represent a more widely found sheath protein than the MspA from M. thermophila PT, which currently has no homologs in the NCBI Reference Sequence database (RefSeq).
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Affiliation(s)
- Line Friis Bakmann Christensen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Lonnie Maria Hansen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Kai Finster
- Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Gunna Christiansen
- Section for Medical Microbiology and Immunology, Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Morten Simonsen Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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30
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Mason TO, Shimanovich U. Fibrous Protein Self-Assembly in Biomimetic Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1706462. [PMID: 29883013 DOI: 10.1002/adma.201706462] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/28/2018] [Indexed: 05/22/2023]
Abstract
Protein self-assembly processes, by which polypeptides interact and independently form multimeric structures, lead to a wide array of different endpoints. Structures formed range from highly ordered molecular crystals to amorphous aggregates. Order arises in the system from a balance between many low-energy processes occurring due to a set of interactions between residues in a chain, between residues in different chains, and between solute and solvent. In Nature, self-assembling protein systems have evolved over millions of years to organize into supramolecular structures, optimized for specific functions, with this propensity determined by the sequence of their constituent amino acids, of which only 20 are encoded in DNA. The structural materials that arise from biological self-assembly can display remarkable mechanical properties, often as a result of hierarchical structure on the nano- and microscales, and much research has been devoted to mimicking and exploiting these properties for a variety of end uses. This work presents a review of a range of studies in which biological functions are effectively reproduced through the design of self-assembling fibrous protein systems.
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Affiliation(s)
- Thomas O Mason
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ulyana Shimanovich
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot, 7610001, Israel
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31
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Bergam P, Reisecker JM, Rakvács Z, Kucsma N, Raposo G, Szakacs G, van Niel G. ABCB6 Resides in Melanosomes and Regulates Early Steps of Melanogenesis Required for PMEL Amyloid Matrix Formation. J Mol Biol 2018; 430:3802-3818. [PMID: 29940187 DOI: 10.1016/j.jmb.2018.06.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 06/11/2018] [Accepted: 06/15/2018] [Indexed: 01/08/2023]
Abstract
Genetically inheritable pigmentation defects provide a unique opportunity to reveal the function of proteins contributing to melanogenesis. Dyschromatosis universalis hereditaria (DUH) is a rare pigmentary genodermatosis associated with mutations in the ABCB6 gene. Here we use optical and electron microscopy imaging combined with biochemical tools to investigate the localization and function of ABCB6 in pigment cells. We show that ABCB6 localizes to the membrane of early melanosomes and lysosomes of the human melanocytic cell line MNT-1. Depletion of ABCB6 by siRNA impaired PMEL amyloidogenesis in early melanosomes and induced aberrant accumulation of multilamellar aggregates in pigmented melanosomes. PMEL fibril formation and normal maturation of pigmented melanosomes could be restored by the overexpression of wild-type ABCB6 but not by variants containing an inactivating catalytic mutation (K629M) or the G579E DUH mutation. In line with the impairment of PMEL matrix formation in the absence of ABCB6, morphological analysis of the retinal pigment epithelium of ABCB6 knockout mice revealed a significant decrease of melanosome numbers. Our study extends the localization of ABCB6 to melanosomes, suggesting a potential link between the function of ABCB6 and the etiology of DUH to amyloid formation in pigment cells.
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Affiliation(s)
- Ptissam Bergam
- Institut Curie, PSL Research University, UMR144, Centre de Recherche, 26 rue d'Ulm, 75231 Paris, France; Centre National de la Recherche Scientifique, UMR144, Paris F-75248, France; Cell and Tissue Imaging Core Facility PICT-IBiSA, Institut Curie, Paris, France
| | | | - Zsófia Rakvács
- Institute of Enzymology, Research Centre for National Sciences, HAS, Budapest 1117, Hungary
| | - Nóra Kucsma
- Institute of Enzymology, Research Centre for National Sciences, HAS, Budapest 1117, Hungary
| | - Graça Raposo
- Institut Curie, PSL Research University, UMR144, Centre de Recherche, 26 rue d'Ulm, 75231 Paris, France; Centre National de la Recherche Scientifique, UMR144, Paris F-75248, France; Cell and Tissue Imaging Core Facility PICT-IBiSA, Institut Curie, Paris, France
| | - Gergely Szakacs
- Institute of Cancer Research, Medical University Vienna, Vienna, Austria; Institute of Enzymology, Research Centre for National Sciences, HAS, Budapest 1117, Hungary.
| | - Guillaume van Niel
- Institut Curie, PSL Research University, UMR144, Centre de Recherche, 26 rue d'Ulm, 75231 Paris, France; Centre National de la Recherche Scientifique, UMR144, Paris F-75248, France; Cell and Tissue Imaging Core Facility PICT-IBiSA, Institut Curie, Paris, France; Center for Psychiatry and Neuroscience, Hopital Saint-Anne, Université Descartes, INSERM U894, Paris, France.
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32
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Why Study Functional Amyloids? Lessons from the Repeat Domain of Pmel17. J Mol Biol 2018; 430:3696-3706. [PMID: 29886018 DOI: 10.1016/j.jmb.2018.06.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/18/2018] [Accepted: 06/04/2018] [Indexed: 11/24/2022]
Abstract
One of the current challenges facing biomedical researchers is the need to develop new approaches in preventing amyloid formation that is associated with disease. While amyloid is generally considered detrimental to the cell, examples of amyloids that maintain a benign nature and serve a specific function exist. Here, we review our work on the repeat domain (RPT) of the functional amyloid Pmel17. Specifically, the RPT domain contributes in generating amyloid fibrils in melanosomes upon which melanin biosynthesis occurs. Amyloid formation of RPT was shown to be pH sensitive, aggregating only under acidic conditions associated with melanosomal pH. Furthermore, preformed fibrils rapidly dissolved at neutral pH to generate benign monomeric species. From a biological perspective, this unique reversible aggregation/disaggregation is a safeguard against an event of releasing RPT fibrils in the cytosol, resulting in rapid fibril unfolding and circumventing cytotoxicity. Understanding how melanosomes preserve a safe environment will address vital questions that remain unanswered with pathological amyloids.
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33
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Abstract
Amyloid fibrils are protein homopolymers that adopt diverse cross-β conformations. Some amyloid fibrils are associated with the pathogenesis of devastating neurodegenerative disorders, including Alzheimer's disease and Parkinson's disease. Conversely, functional amyloids play beneficial roles in melanosome biogenesis, long-term memory formation and release of peptide hormones. Here, we showcase advances in our understanding of amyloid assembly and structure, and how distinct amyloid strains formed by the same protein can cause distinct neurodegenerative diseases. We discuss how mutant steric zippers promote deleterious amyloidogenesis and aberrant liquid-to-gel phase transitions. We also highlight effective strategies to combat amyloidogenesis and related toxicity, including: (1) small-molecule drugs (e.g. tafamidis) to inhibit amyloid formation or (2) stimulate amyloid degradation by the proteasome and autophagy, and (3) protein disaggregases that disassemble toxic amyloid and soluble oligomers. We anticipate that these advances will inspire therapeutics for several fatal neurodegenerative diseases. Summary: This Review showcases important advances in our understanding of amyloid structure, assembly and disassembly, which are inspiring novel therapeutic strategies for amyloid disorders.
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Affiliation(s)
- Edward Chuang
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,Pharmacology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Acacia M Hori
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christina D Hesketh
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA .,Pharmacology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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34
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O’Neill BT, Beck EM, Butler CR, Nolan CE, Gonzales C, Zhang L, Doran SD, Lapham K, Buzon LM, Dutra JK, Barreiro G, Hou X, Martinez-Alsina LA, Rogers BN, Villalobos A, Murray JC, Ogilvie K, LaChapelle EA, Chang C, Lanyon LF, Steppan CM, Robshaw A, Hales K, Boucher GG, Pandher K, Houle C, Ambroise CW, Karanian D, Riddell D, Bales KR, Brodney MA. Design and Synthesis of Clinical Candidate PF-06751979: A Potent, Brain Penetrant, β-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1) Inhibitor Lacking Hypopigmentation. J Med Chem 2018; 61:4476-4504. [DOI: 10.1021/acs.jmedchem.8b00246] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Brian T. O’Neill
- Medicine Design, Medicinal Chemistry, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Elizabeth M. Beck
- Medicine Design, Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Christopher R. Butler
- Medicine Design, Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Charles E. Nolan
- Internal Medicine, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Cathleen Gonzales
- Internal Medicine, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Lei Zhang
- Medicine Design, Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Shawn D. Doran
- Medicine Design, Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Kimberly Lapham
- Medicine Design, Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Leanne M. Buzon
- Medicine Design, Medicinal Chemistry, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Jason K. Dutra
- Medicine Design, Medicinal Chemistry, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Gabriela Barreiro
- Medicine Design, Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Xinjun Hou
- Medicine Design, Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | | | - Bruce N. Rogers
- Medicine Design, Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Anabella Villalobos
- Medicine Design, Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - John C. Murray
- Medicine Design, Medicinal Chemistry, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Kevin Ogilvie
- Medicine Design, Medicinal Chemistry, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Erik A. LaChapelle
- Medicine Design, Medicinal Chemistry, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Cheng Chang
- Medicine Design, Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Lorraine F. Lanyon
- Discovery Sciences, Primary Pharmacology, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Claire M. Steppan
- Discovery Sciences, Primary Pharmacology, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Ashley Robshaw
- Internal Medicine, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Katherine Hales
- Internal Medicine, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Germaine G. Boucher
- Drug Safety Research and Development, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Karamjeet Pandher
- Drug Safety Research and Development, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Christopher Houle
- Drug Safety Research and Development, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Claude W. Ambroise
- Internal Medicine, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - David Karanian
- Drug Safety Research and Development, Pfizer Inc., Groton, Connecticut 06340, United States
| | - David Riddell
- Internal Medicine, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Kelly R. Bales
- Internal Medicine, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Michael A. Brodney
- Medicine Design, Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts 02139, United States
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35
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Lee J, Lee JH, Yeom B, Char K. Layer-by-Layer Assembly of κ-Casein Amyloid Fibrils for the Preparation of Hollow Microcapsules. MACROMOL CHEM PHYS 2017. [DOI: 10.1002/macp.201700382] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Jubong Lee
- The National Creative Research Initiative Center for Intelligent Hybrids; The WCU Program of Chemical Convergence for Energy & Environment; School of Chemical & Biological Engineering; Seoul National University; Seoul 08826 Korea
| | - Ji-Hye Lee
- The National Creative Research Initiative Center for Intelligent Hybrids; The WCU Program of Chemical Convergence for Energy & Environment; School of Chemical & Biological Engineering; Seoul National University; Seoul 08826 Korea
| | - Bongjun Yeom
- Department of Chemical Engineering; Myongji University; Yongin 17058 Korea
| | - Kookheon Char
- The National Creative Research Initiative Center for Intelligent Hybrids; The WCU Program of Chemical Convergence for Energy & Environment; School of Chemical & Biological Engineering; Seoul National University; Seoul 08826 Korea
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36
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Using chirality to probe the conformational dynamics and assembly of intrinsically disordered amyloid proteins. Sci Rep 2017; 7:12433. [PMID: 28970487 PMCID: PMC5624888 DOI: 10.1038/s41598-017-10525-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/09/2017] [Indexed: 12/22/2022] Open
Abstract
Intrinsically disordered protein (IDP) conformers occupy large regions of conformational space and display relatively flat energy surfaces. Amyloid-forming IDPs, unlike natively folded proteins, have folding trajectories that frequently involve movements up shallow energy gradients prior to the “downhill” folding leading to fibril formation. We suggest that structural perturbations caused by chiral inversions of amino acid side-chains may be especially valuable in elucidating these pathways of IDP folding. Chiral inversions are subtle in that they do not change side-chain size, flexibility, hydropathy, charge, or polarizability. They allow focus to be placed solely on the question of how changes in amino acid side-chain orientation, and the resultant alterations in peptide backbone structure, affect a peptide’s conformational landscape (Ramachandran space). If specific inversions affect folding and assembly, then the sites involved likely are important in mediating these processes. We suggest here a “focused chiral mutant library” approach for the unbiased study of amyloid-forming IDPs.
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37
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McGlinchey RP, Lee JC. Reversing the amyloid trend: Mechanism of fibril assembly and dissolution of the repeat domain from a human functional amyloid. Isr J Chem 2017; 57:613-621. [PMID: 28993712 PMCID: PMC5630176 DOI: 10.1002/ijch.201600080] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Amyloids are traditionally observed in the context of disease. However, there is growing momentum that these structures can serve a beneficial role where the amyloid carries out a specific function. These so called 'functional amyloids' have all the structural hallmarks of disease-associated amyloids, raising the question as to what differentiates a well-behaved benign amyloid from a lethally destructive one. Here, we review our work on the repeat domain (RPT) from Pmel17, an important functional amyloid involved in melanin biosynthesis. Particularly, we focused our attention on the unique reversible aggregation-disaggregation process of RPT that is controlled strictly by solution pH. This pH dependence of RPT amyloid formation functions as a switch to control fibril assembly and maintains the benign nature that is associated with functional amyloids.
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Affiliation(s)
- Ryan P. McGlinchey
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Jennifer C. Lee
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, U.S.A
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38
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Melanosomal formation of PMEL core amyloid is driven by aromatic residues. Sci Rep 2017; 7:44064. [PMID: 28272432 PMCID: PMC5341037 DOI: 10.1038/srep44064] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 02/01/2017] [Indexed: 12/05/2022] Open
Abstract
PMEL is a pigment cell protein that forms physiological amyloid in melanosomes. Many amyloids and/or their oligomeric precursors are toxic, causing or contributing to severe, incurable diseases including Alzheimer’s and prion diseases. Striking similarities in intracellular formation pathways between PMEL and various pathological amyloids including Aβ and PrPSc suggest PMEL is an excellent model system to study endocytic amyloid. Learning how PMEL fibrils assemble without apparent toxicity may help developing novel therapies for amyloid diseases. Here we identify the critical PMEL domain that forms the melanosomal amyloid core (CAF). An unbiased alanine-scanning screen covering the entire region combined with quantitative electron microscopy analysis of the full set of mutants uncovers numerous essential residues. Many of these rely on aromaticity for function suggesting a role for π-stacking in melanosomal amyloid assembly. Various mutants are defective in amyloid nucleation. This extensive data set informs the first structural model of the CAF and provides insights into how the melanosomal amyloid core forms.
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39
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Louros NN, Iconomidou VA. Identification of an amyloid fibril forming segment of human Pmel17 repeat domain (RPT domain). Biopolymers 2017; 106:133-9. [PMID: 26394553 DOI: 10.1002/bip.22746] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/24/2015] [Accepted: 09/18/2015] [Indexed: 12/20/2022]
Abstract
Pmel17 is the major component of functional amyloid fibrils that have an important role during pigment deposition. Pmel17 polymerization is promoted within the mildly acidic conditions of melanosomes, organelles located in pigment-specific cells. A repeat domain (RPT domain) of Pmel17, rich in glutamic acid residues has been extensively associated with the formation of the fibrous matrix. Here, we examine the RPT domain of human Pmel17 in order to provide information on this mechanism. Specifically, we have identified an aggregation-prone peptide segment ((405) VSIVVLSGT(413) ), close to the C-terminal part of the RPT domain. Experimental results utilizing electron microscopy, X-ray fiber diffraction, Congo red staining and ATR FT-IR spectroscopy indicate that this peptide segment self-assembles forming fibrils with evident amyloidogenic properties. Conclusively, our results demonstrate that the (405) VSIVVLSGT(413) peptide segment possibly has an essential role in RPT domain fibrillogenesis.
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Affiliation(s)
- Nikolaos N Louros
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens, 157 01, Greece
| | - Vassiliki A Iconomidou
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens, 157 01, Greece
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40
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Dogra P, Bhattacharya M, Mukhopadhyay S. pH-Responsive Mechanistic Switch Regulates the Formation of Dendritic and Fibrillar Nanostructures of a Functional Amyloid. J Phys Chem B 2017; 121:412-419. [DOI: 10.1021/acs.jpcb.6b11281] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Priyanka Dogra
- Centre
for Protein Science Design and Engineering, ‡Department of Biological Sciences, and §Department of
Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar 140306, Punjab, India
| | - Mily Bhattacharya
- Centre
for Protein Science Design and Engineering, ‡Department of Biological Sciences, and §Department of
Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar 140306, Punjab, India
| | - Samrat Mukhopadhyay
- Centre
for Protein Science Design and Engineering, ‡Department of Biological Sciences, and §Department of
Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar 140306, Punjab, India
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41
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Nusrat S, Zaidi N, Zaman M, Islam S, Ajmal MR, Siddiqi MK, Santra MK, Khan RH. Repositioning nordihydroguaiaretic acid as a potent inhibitor of systemic amyloidosis and associated cellular toxicity. Arch Biochem Biophys 2016; 612:78-90. [DOI: 10.1016/j.abb.2016.10.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/14/2016] [Accepted: 10/22/2016] [Indexed: 02/06/2023]
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42
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Breydo L, Redington JM, Uversky VN. Effects of Intrinsic and Extrinsic Factors on Aggregation of Physiologically Important Intrinsically Disordered Proteins. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 329:145-185. [PMID: 28109327 DOI: 10.1016/bs.ircmb.2016.08.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Misfolding and aggregation of proteins and peptides play an important role in a number of diseases as well as in many physiological processes. Many of the proteins that misfold and aggregate in vivo are intrinsically disordered. Protein aggregation is a complex multistep process, and aggregates can significantly differ in morphology, structure, stability, cytotoxicity, and self-propagation ability. The aggregation process is influenced by both intrinsic (e.g., mutations and expression levels) and extrinsic (e.g., polypeptide chain truncation, macromolecular crowding, posttranslational modifications, as well as interaction with metal ions, other small molecules, lipid membranes, and chaperons) factors. This review examines the effect of a variety of these factors on aggregation of physiologically important intrinsically disordered proteins.
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Affiliation(s)
- L Breydo
- Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.
| | - J M Redington
- Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - V N Uversky
- Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia.
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43
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Bissig C, Rochin L, van Niel G. PMEL Amyloid Fibril Formation: The Bright Steps of Pigmentation. Int J Mol Sci 2016; 17:ijms17091438. [PMID: 27589732 PMCID: PMC5037717 DOI: 10.3390/ijms17091438] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/12/2016] [Accepted: 08/22/2016] [Indexed: 02/06/2023] Open
Abstract
In pigment cells, melanin synthesis takes place in specialized organelles, called melanosomes. The biogenesis and maturation of melanosomes is initiated by an unpigmented step that takes place prior to the initiation of melanin synthesis and leads to the formation of luminal fibrils deriving from the pigment cell-specific pre-melanosomal protein (PMEL). In the lumen of melanosomes, PMEL fibrils optimize sequestration and condensation of the pigment melanin. Interestingly, PMEL fibrils have been described to adopt a typical amyloid-like structure. In contrast to pathological amyloids often associated with neurodegenerative diseases, PMEL fibrils represent an emergent category of physiological amyloids due to their beneficial cellular functions. The formation of PMEL fibrils within melanosomes is tightly regulated by diverse mechanisms, such as PMEL traffic, cleavage and sorting. These mechanisms revealed increasing analogies between the formation of physiological PMEL fibrils and pathological amyloid fibrils. In this review we summarize the known mechanisms of PMEL fibrillation and discuss how the recent understanding of physiological PMEL amyloid formation may help to shed light on processes involved in pathological amyloid formation.
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Affiliation(s)
- Christin Bissig
- Institut Curie, Paris Sciences et Lettres Research University, UMR144, Centre de Recherche, 26 rue d'ULM, Paris F-75231, France.
- Centre National de la Recherche Scientifique, UMR144, Paris F-75248, France.
| | - Leila Rochin
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK.
| | - Guillaume van Niel
- Institut Curie, Paris Sciences et Lettres Research University, UMR144, Centre de Recherche, 26 rue d'ULM, Paris F-75231, France.
- Centre National de la Recherche Scientifique, UMR144, Paris F-75248, France.
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44
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Bleem A, Daggett V. Structural and functional diversity among amyloid proteins: Agents of disease, building blocks of biology, and implications for molecular engineering. Biotechnol Bioeng 2016; 114:7-20. [PMID: 27474784 DOI: 10.1002/bit.26059] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 07/25/2016] [Accepted: 07/28/2016] [Indexed: 12/23/2022]
Abstract
Amyloids have long been associated with protein dysfunction and neurodegenerative diseases, but recent research has demonstrated that some organisms utilize the unique properties of the amyloid fold to create functional structures with important roles in biological processes. Additionally, new engineering approaches have taken advantage of amyloid structures for implementation in a wide variety of materials and devices. In this review, the role of amyloid in human disease is discussed and compared to the functional amyloids, which serve a largely structural purpose. We then consider the use of amyloid constructs in engineering applications, including their utility as building blocks for synthetic biology and molecular engineering. Biotechnol. Bioeng. 2017;114: 7-20. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Alissa Bleem
- Department of Bioengineering, University of Washington, Box 355013, Seattle, Washington, 98195-5013
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Box 355013, Seattle, Washington, 98195-5013
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45
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van Niel G. Study of Exosomes Shed New Light on Physiology of Amyloidogenesis. Cell Mol Neurobiol 2016; 36:327-42. [DOI: 10.1007/s10571-016-0357-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/27/2016] [Indexed: 12/18/2022]
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46
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Pharmacological BACE1 and BACE2 inhibition induces hair depigmentation by inhibiting PMEL17 processing in mice. Sci Rep 2016; 6:21917. [PMID: 26912421 PMCID: PMC4766495 DOI: 10.1038/srep21917] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/02/2016] [Indexed: 02/04/2023] Open
Abstract
Melanocytes of the hair follicle produce melanin and are essential in determining the differences in hair color. Pigment cell-specific MELanocyte Protein (PMEL17) plays a crucial role in melanogenesis. One of the critical steps is the amyloid-like functional oligomerization of PMEL17. Beta Site APP Cleaving Enzyme-2 (BACE2) and γ-secretase have been shown to be key players in generating the proteolytic fragments of PMEL17. The β-secretase (BACE1) is responsible for the generation of amyloid-β (Aβ) fragments in the brain and is therefore proposed as a therapeutic target for Alzheimer's disease (AD). Currently BACE1 inhibitors, most of which lack selectivity over BACE2, have demonstrated efficacious reduction of amyloid-β peptides in animals and the CSF of humans. BACE2 knock-out mice have a deficiency in PMEL17 proteolytic processing leading to impaired melanin storage and hair depigmentation. Here, we confirm BACE2-mediated inhibition of PMEL17 proteolytic processing in vitro in mouse and human melanocytes. Furthermore, we show that wildtype as well as bace2(+/-) and bace2(-/-) mice treated with a potent dual BACE1/BACE2 inhibitor NB-360 display dose-dependent appearance of irreversibly depigmented hair. Retinal pigmented epithelium showed no morphological changes. Our data demonstrates that BACE2 as well as additional BACE1 inhibition affects melanosome maturation and induces hair depigmentation in mice.
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47
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Abstract
Protein misfolding and aggregation underpin several fatal neurodegenerative diseases, including Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD). There are no treatments that directly antagonize the protein-misfolding events that cause these disorders. Agents that reverse protein misfolding and restore proteins to native form and function could simultaneously eliminate any deleterious loss-of-function or toxic gain-of-function caused by misfolded conformers. Moreover, a disruptive technology of this nature would eliminate self-templating conformers that spread pathology and catalyze formation of toxic, soluble oligomers. Here, we highlight our efforts to engineer Hsp104, a protein disaggregase from yeast, to more effectively disaggregate misfolded proteins connected with PD, ALS, and FTD. Remarkably subtle modifications of Hsp104 primary sequence yielded large gains in protective activity against deleterious α-synuclein, TDP-43, FUS, and TAF15 misfolding. Unusually, in many cases loss of amino acid identity at select positions in Hsp104 rather than specific mutation conferred a robust therapeutic gain-of-function. Nevertheless, the misfolding and toxicity of EWSR1, an RNA-binding protein with a prion-like domain linked to ALS and FTD, could not be buffered by potentiated Hsp104 variants, indicating that further amelioration of disaggregase activity or sharpening of substrate specificity is warranted. We suggest that neuroprotection is achievable for diverse neurodegenerative conditions via surprisingly subtle structural modifications of existing chaperones.
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Affiliation(s)
- Meredith E Jackrel
- a Department of Biochemistry and Biophysics ; Perelman School of Medicine at the University of Pennsylvania ; Philadelphia , PA USA
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48
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Louros NN, Baltoumas FA, Hamodrakas SJ, Iconomidou VA. A β-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils. J Comput Aided Mol Des 2016; 30:153-64. [PMID: 26754844 DOI: 10.1007/s10822-015-9892-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 12/21/2015] [Indexed: 10/22/2022]
Abstract
Pmel17 is a multidomain protein involved in biosynthesis of melanin. This process is facilitated by the formation of Pmel17 amyloid fibrils that serve as a scaffold, important for pigment deposition in melanosomes. A specific luminal domain of human Pmel17, containing 10 tandem imperfect repeats, designated as repeat domain (RPT), forms amyloid fibrils in a pH-controlled mechanism in vitro and has been proposed to be essential for the formation of the fibrillar matrix. Currently, no three-dimensional structure has been resolved for the RPT domain of Pmel17. Here, we examine the structure of the RPT domain by performing sequence threading. The resulting model was subjected to energy minimization and validated through extensive molecular dynamics simulations. Structural analysis indicated that the RPT model exhibits several distinct properties of β-solenoid structures, which have been proposed to be polymerizing components of amyloid fibrils. The derived model is stabilized by an extensive network of hydrogen bonds generated by stacking of highly conserved polar residues of the RPT domain. Furthermore, the key role of invariant glutamate residues is proposed, supporting a pH-dependent mechanism for RPT domain assembly. Conclusively, our work attempts to provide structural insights into the RPT domain structure and to elucidate its contribution to Pmel17 amyloid fibril formation.
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Affiliation(s)
- Nikolaos N Louros
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 157 01, Athens, Greece
| | - Fotis A Baltoumas
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 157 01, Athens, Greece
| | - Stavros J Hamodrakas
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 157 01, Athens, Greece
| | - Vassiliki A Iconomidou
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 157 01, Athens, Greece.
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49
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Ho T, Watt B, Spruce LA, Seeholzer SH, Marks MS. The Kringle-like Domain Facilitates Post-endoplasmic Reticulum Changes to Premelanosome Protein (PMEL) Oligomerization and Disulfide Bond Configuration and Promotes Amyloid Formation. J Biol Chem 2015; 291:3595-612. [PMID: 26694611 DOI: 10.1074/jbc.m115.692442] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Indexed: 11/06/2022] Open
Abstract
The formation of functional amyloid must be carefully regulated to prevent the accumulation of potentially toxic products. Premelanosome protein (PMEL) forms non-toxic functional amyloid fibrils that assemble into sheets upon which melanins ultimately are deposited within the melanosomes of pigment cells. PMEL is synthesized in the endoplasmic reticulum but forms amyloid only within post-Golgi melanosome precursors; thus, PMEL must traverse the secretory pathway in a non-amyloid form. Here, we identified two pre-amyloid PMEL intermediates that likely regulate the timing of fibril formation. Analyses by non-reducing SDS-PAGE, size exclusion chromatography, and sedimentation velocity revealed two native high Mr disulfide-bonded species that contain Golgi-modified forms of PMEL. These species correspond to disulfide bond-containing dimeric and monomeric PMEL isoforms that contain no other proteins as judged by two-dimensional PAGE of metabolically labeled/immunoprecipitated PMEL and by mass spectrometry of affinity-purified complexes. Metabolic pulse-chase analyses, small molecule inhibitor treatments, and evaluation of site-directed mutants suggest that the PMEL dimer forms around the time of endoplasmic reticulum exit and is resolved by disulfide bond rearrangement into a monomeric form within the late Golgi or a post-Golgi compartment. Mutagenesis of individual cysteine residues within the non-amyloid cysteine-rich Kringle-like domain stabilizes the disulfide-bonded dimer and impairs fibril formation as determined by electron microscopy. Our data show that the Kringle-like domain facilitates the resolution of disulfide-bonded PMEL dimers and promotes PMEL functional amyloid formation, thereby suggesting that PMEL dimers must be resolved to monomers to generate functional amyloid fibrils.
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Affiliation(s)
- Tina Ho
- From the Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 and the Cell and Molecular Biology Graduate Group, the Department of Pathology and Laboratory Medicine, and
| | - Brenda Watt
- From the Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 and the Cell and Molecular Biology Graduate Group, the Department of Pathology and Laboratory Medicine, and
| | - Lynn A Spruce
- From the Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 and
| | - Steven H Seeholzer
- From the Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 and
| | - Michael S Marks
- From the Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 and the Cell and Molecular Biology Graduate Group, the Department of Pathology and Laboratory Medicine, and the Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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50
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Pulze L, Bassani B, Gini E, D'Antona P, Grimaldi A, Luini A, Marino F, Noonan DM, Tettamanti G, Valvassori R, de Eguileor M. NET amyloidogenic backbone in human activated neutrophils. Clin Exp Immunol 2015; 183:469-79. [PMID: 26462606 DOI: 10.1111/cei.12730] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2015] [Indexed: 12/27/2022] Open
Abstract
Activated human neutrophils produce a fibrillar DNA network [neutrophil extracellular traps (NETs)] for entrapping and killing bacteria, fungi, protozoa and viruses. Our results suggest that the neutrophil extracellular traps show a resistant amyloidogenic backbone utilized for addressing reputed proteins and DNA against the non-self. The formation of amyloid fibrils in neutrophils is regulated by the imbalance of reactive oxygen species (ROS) in the cytoplasm. The intensity and source of the ROS signal is determinant for promoting stress-associated responses such as amyloidogenesis and closely related events: autophagy, exosome release, activation of the adrenocorticotrophin hormone/α-melanocyte-stimulating hormone (ACTH/α-MSH) loop and synthesis of specific cytokines. These interconnected responses in human activated neutrophils, that have been evaluated from a morphofunctional and quantitative viewpoint, represent primitive, but potent, innate defence mechanisms. In invertebrates, circulating phagocytic immune cells, when activated, show responses similar to those described previously for activated human neutrophils. Invertebrate cells within endoplasmic reticulum cisternae produce a fibrillar material which is then assembled into an amyloidogenic scaffold utilized to convey melanin close to the invader. These findings, in consideration to the critical role played by NET in the development of several pathologies, could explain the structural resistance of these scaffolds and could provide the basis for developing new diagnostic and therapeutic approaches in immunomediated diseases in which the innate branch of the immune system has a pivotal role.
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Affiliation(s)
- L Pulze
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - B Bassani
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,IRCCS MultiMedica, Scientific and Technology Park, Milano, Italy
| | - E Gini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - P D'Antona
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - A Grimaldi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - A Luini
- Center of Research in Medical Pharmacology, University of Insubria, Varese, Italy
| | - F Marino
- Center of Research in Medical Pharmacology, University of Insubria, Varese, Italy
| | - D M Noonan
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,IRCCS MultiMedica, Scientific and Technology Park, Milano, Italy
| | - G Tettamanti
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - R Valvassori
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - M de Eguileor
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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