201
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Haimov B, Srebnik S. The Relation between α-Helical Conformation and Amyloidogenicity. Biophys J 2018; 114:1869-1877. [PMID: 29653837 DOI: 10.1016/j.bpj.2018.03.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/23/2018] [Accepted: 03/20/2018] [Indexed: 01/23/2023] Open
Abstract
Amyloid fibrils are stable aggregates of misfolded proteins and polypeptides that are insoluble and resistant to protease activity. Abnormal formation of amyloid fibrils in vivo may lead to neurodegenerative disorders and other systemic amyloidosis, such as Alzheimer's, Parkinson's, and atherosclerosis. Because of their clinical importance, amyloids are under intense scientific research. It is believed that short polypeptide segments within proteins are responsible for the transformation of correctly folded proteins into parts of larger amyloid fibrils and that this transition is modulated by environmental factors, such as pH, salt concentration, interaction with the cell membrane, and interaction with metal ions. Most studies on amyloids focus on the amyloidogenic sequences. The focus of this study is on the structure of the amyloidogenic α-helical segments because the α-helical secondary structure has been recognized to be a key player in different stages of the amyloidogenesis process. We have previously shown that the α-helical conformation may be expressed by two parameters (θ and ρ) that form orthogonal coordinates based on the Ramachandran dihedrals (φ and ψ) and provide an illuminating interpretation of the α-helical conformation. By performing statistical analysis on α-helical conformations found in the Protein Data Bank, an apparent relation between α-helical conformation, as expressed by θ and ρ, and amyloidogenicity is revealed. Remarkably, random amino acid sequences, whose helical structures were obtained from the most probable dihedral angles, revealed the same dependency of amyloidogenicity, suggesting the importance of α-helical structure as opposed to sequence.
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Affiliation(s)
- Boris Haimov
- Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa, Israel
| | - Simcha Srebnik
- Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa, Israel; Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, Israel.
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202
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Galzitskaya OV, Selivanova OM. Rosetta Stone for Amyloid Fibrils: The Key Role of Ring-Like Oligomers in Amyloidogenesis. J Alzheimers Dis 2018; 59:785-795. [PMID: 28671122 DOI: 10.3233/jad-170230] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Deeper understanding of processes of protein misfolding, aggregation, formation of oligomers, protofibrils, and fibrils is crucial for the development of future medicine in treatment of amyloid-related diseases. While numerous reports illuminate the field, the above processes are extremely complex, as they depend on many varying parameters, such as the peptide concentration, temperature, pH, presence of metal ions, lipids, and organic solvents. Different mechanisms of amyloid fibril formation have been proposed, but the process of the oligomer-to-fibril transition is the least agreed upon. Our studies of a number of amyloidogenic proteins and peptides (insulin, Aβ peptides, the Bgl2 protein from the yeast cell wall), as well as their amyloidogenic fragments, have allowed us to propose a model of the fibril structure generation. We have found that the main building block of fibrils of any morphology is a ring-like oligomer. The varying models of interaction of ring oligomers with each other revealed in our studies make it possible to explain their polymorphism. Crucially, the amino acid sequence determines the oligomer structure for the given protein/peptide.
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Affiliation(s)
- Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - Olga M Selivanova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
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203
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Huang C, Ghanati E, Schmit JD. Theory of Sequence Effects in Amyloid Aggregation. J Phys Chem B 2018; 122:5567-5578. [PMID: 29486561 DOI: 10.1021/acs.jpcb.7b11830] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We present a simple model for the effect of amino acid sequences on amyloid fibril formation. Using the HP model we find the binding lifetimes of four simple sequences by solving the first passage time for the intermolecular H-bond reaction coordinate. We find that sequences with identical binding energies have widely varying binding times depending on where the aggregation prone amino acids are located in the sequence. In general, longer binding times occur when the aggregation prone amino acids are clustered in a single "hot spot". Similarly, binding times are shortened by clustering weakly bound residues. Both of these effects are explained by an increase in the multiplicity of unbinding trajectories that comes from adding weak binding residues. Our model predicts a transition from ordered to disordered fibrils as the concentration of monomers increases. We apply our model to Aβ, IAPP, and apomyoglobin using binding energy estimates derived from bioinformatics. We find that these sequences are highly selective of the in-register state. This selectivity arises from the having strongly bound segments of varying length and separation.
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Affiliation(s)
- Caleb Huang
- Department of Physics , Kansas State University , Manhattan , Kansas 66506 , United States
| | - Elaheh Ghanati
- Department of Physics , Kansas State University , Manhattan , Kansas 66506 , United States
| | - Jeremy D Schmit
- Department of Physics , Kansas State University , Manhattan , Kansas 66506 , United States
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204
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Katina NS, Suvorina MY, Grigorashvili EI, Marchenkov VV, Ryabova NA, Nikulin AD, Surin AK. Identification of Regions in Apomyoglobin that Form Intermolecular Interactions in Amyloid Aggregates Using High-Performance Mass Spectrometry. JOURNAL OF ANALYTICAL CHEMISTRY 2018. [DOI: 10.1134/s1061934817130056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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205
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Sukumaran SD, Faraj FL, Lee VS, Othman R, Buckle MJC. 2-Aryl-3-(arylideneamino)-1,2-dihydroquinazoline-4(3 H)-ones as inhibitors of cholinesterases and self-induced β-amyloid (Aβ) aggregation: biological evaluations and mechanistic insights from molecular dynamics simulations. RSC Adv 2018; 8:7818-7831. [PMID: 35539141 PMCID: PMC9078462 DOI: 10.1039/c7ra11872d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 01/19/2018] [Indexed: 11/21/2022] Open
Abstract
A series of 2-aryl-3-(arylideneamino)-1,2-dihydroquinazoline-4(3H)-ones were evaluated as inhibitors of acetylcholinesterase (AChE), butyrylcholinesterase (BuChE) and self-induced β-amyloid (Aβ) aggregation. All the compounds were found to inhibit both forms of cholinesterase (IC50 in the range 4-32 μM) with some selectivity for BuChE. Most of the compounds also showed self-induced Aβ aggregation inhibitory activities, which were comparable or higher than those obtained for reference compounds, curcumin and myricetin. Docking and molecular dynamics (MD) simulation experiments suggested that the compounds are able to disrupt the dimer form of Aβ.
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Affiliation(s)
- Sri Devi Sukumaran
- Department of Pharmacy, Faculty of Medicine, University of Malaya 50603 Kuala Lumpur Malaysia +60-3-7967-4959
- Drug Design and Development Research Group (DDDRG), University of Malaya 50603 Kuala Lumpur Malaysia
| | - Fadhil Lafta Faraj
- Department of Chemistry, Faculty of Science, University of Diyala Diyala Governorate Iraq
| | - Vannajan Sanghiran Lee
- Drug Design and Development Research Group (DDDRG), University of Malaya 50603 Kuala Lumpur Malaysia
- Department of Chemistry, Faculty of Science, University of Malaya 50603 Kuala Lumpur Malaysia +60 163208906
| | - Rozana Othman
- Department of Pharmacy, Faculty of Medicine, University of Malaya 50603 Kuala Lumpur Malaysia +60-3-7967-4959
- Drug Design and Development Research Group (DDDRG), University of Malaya 50603 Kuala Lumpur Malaysia
| | - Michael J C Buckle
- Department of Pharmacy, Faculty of Medicine, University of Malaya 50603 Kuala Lumpur Malaysia +60-3-7967-4959
- Drug Design and Development Research Group (DDDRG), University of Malaya 50603 Kuala Lumpur Malaysia
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206
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Ribarič S. Peptides as Potential Therapeutics for Alzheimer's Disease. Molecules 2018; 23:E283. [PMID: 29385735 PMCID: PMC6017258 DOI: 10.3390/molecules23020283] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 01/26/2018] [Accepted: 01/28/2018] [Indexed: 12/22/2022] Open
Abstract
Intracellular synthesis, folding, trafficking and degradation of proteins are controlled and integrated by proteostasis. The frequency of protein misfolding disorders in the human population, e.g., in Alzheimer's disease (AD), is increasing due to the aging population. AD treatment options are limited to symptomatic interventions that at best slow-down disease progression. The key biochemical change in AD is the excessive accumulation of per-se non-toxic and soluble amyloid peptides (Aβ(1-37/44), in the intracellular and extracellular space, that alters proteostasis and triggers Aβ modification (e.g., by reactive oxygen species (ROS)) into toxic intermediate, misfolded soluble Aβ peptides, Aβ dimers and Aβ oligomers. The toxic intermediate Aβ products aggregate into progressively less toxic and less soluble protofibrils, fibrils and senile plaques. This review focuses on peptides that inhibit toxic Aβ oligomerization, Aβ aggregation into fibrils, or stabilize Aβ peptides in non-toxic oligomers, and discusses their potential for AD treatment.
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Affiliation(s)
- Samo Ribarič
- Institute of Pathophysiology, Faculty of Medicine, Zaloška 4, SI-1000 Ljubljana, Slovenia.
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207
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Pujols J, Peña-Díaz S, Ventura S. AGGRESCAN3D: Toward the Prediction of the Aggregation Propensities of Protein Structures. Methods Mol Biol 2018; 1762:427-443. [PMID: 29594784 DOI: 10.1007/978-1-4939-7756-7_21] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Protein aggregation is responsible for the onset and spread of many human diseases, ranging from neurodegenerative disorders to cancer and diabetes. Moreover, it is one of the major bottlenecks for the production of protein-based therapeutics such as antibodies or enzymes. AGGRESCAN3D (A3D) is a web server aimed to identify and evaluate structural aggregation prone regions, overcoming the limitations of sequence-based algorithms in the prediction of the aggregation propensity of globular proteins. A3D allows the redesign of protein solubility by predicting in silico the impact of mutations and protein conformational fluctuations on the aggregation of native polypeptides.
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Affiliation(s)
- Jordi Pujols
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Samuel Peña-Díaz
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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208
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Katina NS, Grigorashvili EI, Suvorina MY, Ilyina NB, Ryabova NA, Selivanova OM, Surin AK. Amyloid Core Wild-Type Apomyoglobin and Its Mutant Variants Is Formed by Different Regions of the Polypeptide Chain. Mol Biol 2018. [DOI: 10.1134/s0026893318010089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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209
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Tikhomirova TS, Ievlev RS, Suvorina MY, Bobyleva LG, Vikhlyantsev IM, Surin AK, Galzitskaya OV. Search for Functionally Significant Motifs and Amino Acid Residues of Actin. Mol Biol 2018. [DOI: 10.1134/s0026893318010193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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210
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Katina NS, Balobanov VA, Ilyina NB, Vasiliev VD, Marchenkov VV, Glukhov AS, Nikulin AD, Bychkova VE. sw ApoMb Amyloid Aggregation under Nondenaturing Conditions: The Role of Native Structure Stability. Biophys J 2017; 113:991-1001. [PMID: 28877500 DOI: 10.1016/j.bpj.2017.07.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 07/19/2017] [Accepted: 07/20/2017] [Indexed: 12/17/2022] Open
Abstract
Investigation of the molecular mechanisms underlying amyloid-related human diseases attracts close attention. These diseases, the number of which currently is above 40, are characterized by formation of peptide or protein aggregates containing a cross-β structure. Most of the amyloidogenesis mechanisms described so far are based on experimental studies of aggregation of short peptides, intrinsically disordered proteins, or proteins under denaturing conditions, and studies of amyloid aggregate formations by structured globular proteins under conditions close to physiological ones are still in the initial stage. We investigated the effect of amino acid substitutions on propensity of the completely helical protein sperm whale apomyoglobin (sw ApoMb) for amyloid formation from its structured state in the absence of denaturing agents. Stability and aggregation of mutated sw ApoMb were studied using circular dichroism, Fourier transform infrared spectroscopy, x-ray diffraction, native electrophoresis, and electron microscopy techniques. Here, we demonstrate that stability of the protein native state determines both protein aggregation propensity and structural peculiarities of formed aggregates. Specifically, structurally stable mutants show low aggregation propensity and moderately destabilized sw ApoMb variants form amyloids, whereas their strongly destabilized mutants form both amyloids and nonamyloid aggregates.
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Affiliation(s)
- Natalya S Katina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Vitalii A Balobanov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Nelly B Ilyina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Victor D Vasiliev
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Victor V Marchenkov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Anatoly S Glukhov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Alexey D Nikulin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Valentina E Bychkova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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211
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Samson AL, Ho B, Au AE, Schoenwaelder SM, Smyth MJ, Bottomley SP, Kleifeld O, Medcalf RL. Physicochemical properties that control protein aggregation also determine whether a protein is retained or released from necrotic cells. Open Biol 2017; 6:rsob.160098. [PMID: 27810968 PMCID: PMC5133435 DOI: 10.1098/rsob.160098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 10/05/2016] [Indexed: 12/11/2022] Open
Abstract
Amyloidogenic protein aggregation impairs cell function and is a hallmark of many chronic degenerative disorders. Protein aggregation is also a major event during acute injury; however, unlike amyloidogenesis, the process of injury-induced protein aggregation remains largely undefined. To provide this insight, we profiled the insoluble proteome of several cell types after acute injury. These experiments show that the disulfide-driven process of nucleocytoplasmic coagulation (NCC) is the main form of injury-induced protein aggregation. NCC is mechanistically distinct from amyloidogenesis, but still broadly impairs cell function by promoting the aggregation of hundreds of abundant and essential intracellular proteins. A small proportion of the intracellular proteome resists NCC and is instead released from necrotic cells. Notably, the physicochemical properties of NCC-resistant proteins are contrary to those of NCC-sensitive proteins. These observations challenge the dogma that liberation of constituents during necrosis is anarchic. Rather, inherent physicochemical features including cysteine content, hydrophobicity and intrinsic disorder determine whether a protein is released from necrotic cells. Furthermore, as half of the identified NCC-resistant proteins are known autoantigens, we propose that physicochemical properties that control NCC also affect immune tolerance and other host responses important for the restoration of homeostasis after necrotic injury.
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Affiliation(s)
- Andre L Samson
- Australian Centre for Blood Diseases, Alfred Medical Research and Education Precinct (AMREP), Monash University, Melbourne, Victoria 3004, Australia .,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,Heart Research Institute, and Charles Perkins Centre, University of Sydney, Camperdown, New South Wales 2006, Australia
| | - Bosco Ho
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Amanda E Au
- Australian Centre for Blood Diseases, Alfred Medical Research and Education Precinct (AMREP), Monash University, Melbourne, Victoria 3004, Australia
| | - Simone M Schoenwaelder
- Australian Centre for Blood Diseases, Alfred Medical Research and Education Precinct (AMREP), Monash University, Melbourne, Victoria 3004, Australia.,Heart Research Institute, and Charles Perkins Centre, University of Sydney, Camperdown, New South Wales 2006, Australia
| | - Mark J Smyth
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland 4006, Australia.,School of Medicine, University of Queensland, Herston, Queensland 4006, Australia
| | - Stephen P Bottomley
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Oded Kleifeld
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Robert L Medcalf
- Australian Centre for Blood Diseases, Alfred Medical Research and Education Precinct (AMREP), Monash University, Melbourne, Victoria 3004, Australia
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212
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Nizhnikov AA, Antonets KS, Bondarev SA, Inge-Vechtomov SG, Derkatch IL. Prions, amyloids, and RNA: Pieces of a puzzle. Prion 2017; 10:182-206. [PMID: 27248002 DOI: 10.1080/19336896.2016.1181253] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Amyloids are protein aggregates consisting of fibrils rich in β-sheets. Growth of amyloid fibrils occurs by the addition of protein molecules to the tip of an aggregate with a concurrent change of a conformation. Thus, amyloids are self-propagating protein conformations. In certain cases these conformations are transmissible / infectious; they are known as prions. Initially, amyloids were discovered as pathological extracellular deposits occurring in different tissues and organs. To date, amyloids and prions have been associated with over 30 incurable diseases in humans and animals. However, a number of recent studies demonstrate that amyloids are also functionally involved in a variety of biological processes, from biofilm formation by bacteria, to long-term memory in animals. Interestingly, amyloid-forming proteins are highly overrepresented among cellular factors engaged in all stages of mRNA life cycle: from transcription and translation, to storage and degradation. Here we review rapidly accumulating data on functional and pathogenic amyloids associated with mRNA processing, and discuss possible significance of prion and amyloid networks in the modulation of key cellular functions.
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Affiliation(s)
- Anton A Nizhnikov
- a Dept. of Genetics and Biotechnology , St. Petersburg State University , St. Petersburg , Russia.,b Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg Branch , St. Petersburg , Russia.,c All-Russia Research Institute for Agricultural Microbiology , St. Petersburg , Russia
| | - Kirill S Antonets
- a Dept. of Genetics and Biotechnology , St. Petersburg State University , St. Petersburg , Russia.,b Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg Branch , St. Petersburg , Russia
| | - Stanislav A Bondarev
- a Dept. of Genetics and Biotechnology , St. Petersburg State University , St. Petersburg , Russia
| | - Sergey G Inge-Vechtomov
- a Dept. of Genetics and Biotechnology , St. Petersburg State University , St. Petersburg , Russia.,b Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg Branch , St. Petersburg , Russia
| | - Irina L Derkatch
- d Department of Neuroscience , College of Physicians and Surgeons of Columbia University, Columbia University , New York , NY , USA
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213
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Murray DT, Kato M, Lin Y, Thurber KR, Hung I, McKnight SL, Tycko R. Structure of FUS Protein Fibrils and Its Relevance to Self-Assembly and Phase Separation of Low-Complexity Domains. Cell 2017; 171:615-627.e16. [PMID: 28942918 PMCID: PMC5650524 DOI: 10.1016/j.cell.2017.08.048] [Citation(s) in RCA: 558] [Impact Index Per Article: 69.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 08/10/2017] [Accepted: 08/25/2017] [Indexed: 12/22/2022]
Abstract
Polymerization and phase separation of proteins containing low-complexity (LC) domains are important factors in gene expression, mRNA processing and trafficking, and localization of translation. We have used solid-state nuclear magnetic resonance methods to characterize the molecular structure of self-assembling fibrils formed by the LC domain of the fused in sarcoma (FUS) RNA-binding protein. From the 214-residue LC domain of FUS (FUS-LC), a segment of only 57 residues forms the fibril core, while other segments remain dynamically disordered. Unlike pathogenic amyloid fibrils, FUS-LC fibrils lack hydrophobic interactions within the core and are not polymorphic at the molecular structural level. Phosphorylation of core-forming residues by DNA-dependent protein kinase blocks binding of soluble FUS-LC to FUS-LC hydrogels and dissolves phase-separated, liquid-like FUS-LC droplets. These studies offer a structural basis for understanding LC domain self-assembly, phase separation, and regulation by post-translational modification.
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Affiliation(s)
- Dylan T Murray
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA; Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20892-6200, USA
| | - Masato Kato
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9152, USA
| | - Yi Lin
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9152, USA
| | - Kent R Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Ivan Hung
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Steven L McKnight
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9152, USA.
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
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214
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Burdukiewicz M, Sobczyk P, Rödiger S, Duda-Madej A, Mackiewicz P, Kotulska M. Amyloidogenic motifs revealed by n-gram analysis. Sci Rep 2017; 7:12961. [PMID: 29021608 PMCID: PMC5636826 DOI: 10.1038/s41598-017-13210-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 09/21/2017] [Indexed: 12/24/2022] Open
Abstract
Amyloids are proteins associated with several clinical disorders, including Alzheimer's, and Creutzfeldt-Jakob's. Despite their diversity, all amyloid proteins can undergo aggregation initiated by short segments called hot spots. To find the patterns defining the hot spots, we trained predictors of amyloidogenicity, using n-grams and random forest classifiers. Since the amyloidogenicity may not depend on the exact sequence of amino acids but on their more general properties, we tested 524,284 reduced amino acid alphabets of different lengths (three to six letters) to find the alphabet providing the best performance in cross-validation. The predictor based on this alphabet, called AmyloGram, was benchmarked against the most popular tools for the detection of amyloid peptides using an external data set and obtained the highest values of performance measures (AUC: 0.90, MCC: 0.63). Our results showed sequential patterns in the amyloids which are strongly correlated with hydrophobicity, a tendency to form β-sheets, and lower flexibility of amino acid residues. Among the most informative n-grams of AmyloGram we identified 15 that were previously confirmed experimentally. AmyloGram is available as the web-server: http://smorfland.uni.wroc.pl/shiny/AmyloGram/ and as the R package AmyloGram. R scripts and data used to produce the results of this manuscript are available at http://github.com/michbur/AmyloGramAnalysis .
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Affiliation(s)
| | - Piotr Sobczyk
- Faculty of Pure and Applied Mathematics, Wrocław University of Science and Technology, Wrocław, Poland
| | - Stefan Rödiger
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Anna Duda-Madej
- Department of Microbiology, Wrocław Medical University, Wrocław, Poland
| | | | - Małgorzata Kotulska
- Faculty of Fundamental Problems of Technology, Department of Biomedical Engineering, Wrocław University of Science and Technology, Wrocław, Poland.
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215
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Polyglutamine expansion diseases: More than simple repeats. J Struct Biol 2017; 201:139-154. [PMID: 28928079 DOI: 10.1016/j.jsb.2017.09.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/24/2017] [Accepted: 09/15/2017] [Indexed: 12/27/2022]
Abstract
Polyglutamine (polyQ) repeat-containing proteins are widespread in the human proteome but only nine of them are associated with highly incapacitating neurodegenerative disorders. The genetic expansion of the polyQ tract in disease-related proteins triggers a series of events resulting in neurodegeneration. The polyQ tract plays the leading role in the aggregation mechanism, but other elements modulate the aggregation propensity in the context of the full-length proteins, as implied by variations in the length of the polyQ tract required to trigger the onset of a given polyQ disease. Intrinsic features such as the presence of aggregation-prone regions (APRs) outside the polyQ segments and polyQ-flanking sequences, which synergistically participate in the aggregation process, are emerging for several disease-related proteins. The inherent polymorphic structure of polyQ stretches places the polyQ proteins in a central position in protein-protein interaction networks, where interacting partners may additionally shield APRs or reshape the aggregation course. Expansion of the polyQ tract perturbs the cellular homeostasis and contributes to neuronal failure by modulating protein-protein interactions and enhancing toxic oligomerization. Post-translational modifications further regulate self-assembly either by directly altering the intrinsic aggregation propensity of polyQ proteins, by modulating their interaction with different macromolecules or by modifying their withdrawal by the cell quality control machinery. Here we review the recent data on the multifaceted aggregation pathways of disease-related polyQ proteins, focusing on ataxin-3, the protein mutated in Machado-Joseph disease. Further mechanistic understanding of this network of events is crucial for the development of effective therapies for polyQ diseases.
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216
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Abstract
Protein aggregation is an active area of research in recent decades, since it is the most common and troubling indication of protein instability. Understanding the mechanisms governing protein aggregation and amyloidogenesis is a key component to the aetiology and pathogenesis of many devastating disorders, including Alzheimer's disease or type 2 diabetes. Protein aggregation data are currently found "scattered" in an increasing number of repositories, since advances in computational biology greatly influence this field of research. This review exploits the various resources of aggregation data and attempts to distinguish and analyze the biological knowledge they contain, by introducing protein-based, fragment-based and disease-based repositories, related to aggregation. In order to gain a broad overview of the available repositories, a novel comprehensive network maps and visualizes the current association between aggregation databases and other important databases and/or tools and discusses the beneficial role of community annotation. The need for unification of aggregation databases in a common platform is also addressed.
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Affiliation(s)
- Paraskevi L Tsiolaki
- a Section of Cell Biology and Biophysics, Department of Biology, School of Sciences , National and Kapodistrian University of Athens , Athens , Greece
| | - Katerina C Nastou
- a Section of Cell Biology and Biophysics, Department of Biology, School of Sciences , National and Kapodistrian University of Athens , Athens , Greece
| | - Stavros J Hamodrakas
- a Section of Cell Biology and Biophysics, Department of Biology, School of Sciences , National and Kapodistrian University of Athens , Athens , Greece
| | - Vassiliki A Iconomidou
- a Section of Cell Biology and Biophysics, Department of Biology, School of Sciences , National and Kapodistrian University of Athens , Athens , Greece
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217
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Sharma S, Nehru B, Saini A. Inhibition of Alzheimer's amyloid-beta aggregation in-vitro by carbenoxolone: Insight into mechanism of action. Neurochem Int 2017; 108:481-493. [DOI: 10.1016/j.neuint.2017.06.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/09/2017] [Accepted: 06/22/2017] [Indexed: 10/19/2022]
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218
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Rennegarbe M, Lenter I, Schierhorn A, Sawilla R, Haupt C. Influence of C-terminal truncation of murine Serum amyloid A on fibril structure. Sci Rep 2017; 7:6170. [PMID: 28733641 PMCID: PMC5522423 DOI: 10.1038/s41598-017-06419-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/13/2017] [Indexed: 12/18/2022] Open
Abstract
Amyloid A (AA) amyloidosis is a systemic protein misfolding disease affecting humans and other vertebrates. While the protein precursor in humans and mice is the acute-phase reactant serum amyloid A (SAA) 1.1, the deposited fibrils consist mainly of C-terminally truncated SAA fragments, termed AA proteins. For yet unknown reasons, phenotypic variations in the AA amyloid distribution pattern are clearly associated with specific AA proteins. Here we describe a bacterial expression system and chromatographic strategies to obtain significant amounts of C-terminally truncated fragments of murine SAA1.1 that correspond in truncation position to relevant pathological AA proteins found in humans. This enables us to investigate systematically structural features of derived fibrils. All fragments form fibrils under nearly physiological conditions that show similar morphological appearance and amyloid-like properties as evident from amyloid-specific dye binding, transmission electron microscopy and infrared spectroscopy. However, infrared spectroscopy suggests variations in the structural organization of the amyloid fibrils that might be derived from a modulating role of the C-terminus for the fibril structure. These results provide insights, which can help to get a better understanding of the molecular mechanisms underlying the different clinical phenotypes of AA amyloidosis.
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Affiliation(s)
- Matthies Rennegarbe
- Institute of Protein Biochemistry, Ulm University, Helmholtzstraße 8/1, 89081, Ulm, Germany
| | - Inga Lenter
- Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120, Halle (Saale), Germany
| | - Angelika Schierhorn
- Institute of Biochemistry and Biotechnology, Martin-Luther-University, Kurt-Mothes-Straße 3, 06120, Halle (Saale), Germany
| | - Romy Sawilla
- Institute of Protein Biochemistry, Ulm University, Helmholtzstraße 8/1, 89081, Ulm, Germany
| | - Christian Haupt
- Institute of Protein Biochemistry, Ulm University, Helmholtzstraße 8/1, 89081, Ulm, Germany.
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219
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Roche DB, Villain E, Kajava AV. Usage of a dataset of NMR resolved protein structures to test aggregation versus solubility prediction algorithms. Protein Sci 2017; 26:1864-1869. [PMID: 28685932 DOI: 10.1002/pro.3225] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/21/2017] [Accepted: 06/29/2017] [Indexed: 01/08/2023]
Abstract
There has been an increased interest in computational methods for amyloid and (or) aggregate prediction, due to the prevalence of these aggregates in numerous diseases and their recently discovered functional importance. To evaluate these methods, several datasets have been compiled. Typically, aggregation-prone regions of proteins, which form aggregates or amyloids in vivo, are more than 15 residues long and intrinsically disordered. However, the number of such experimentally established amyloid forming and non-forming sequences are limited, not exceeding one hundred entries in existing databases. In this work, we parsed all available NMR-resolved protein structures from the PDB and assembled a new, sevenfold larger, dataset of unfolded sequences, soluble at high concentrations. We proposed to use these sequences as a negative set for evaluating methods for predicting aggregation in vivo. We also present the results of benchmarking cutting edge tools for the prediction of aggregation versus solubility propensity.
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Affiliation(s)
- Daniel B Roche
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS-UMR 5237, Montpellier, France.,Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France
| | - Etienne Villain
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS-UMR 5237, Montpellier, France.,Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS-UMR 5237, Montpellier, France.,Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France.,University ITMO, 49 Kronverksky Pr, 197101, St. Petersburg, Russia
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220
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Yadav P, Shahane G, Gaikwad S. Amaranthus caudatus lectin with polyproline II fold: conformational and functional transitions and molecular dynamics. J Biomol Struct Dyn 2017; 36:2203-2215. [DOI: 10.1080/07391102.2017.1345328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Priya Yadav
- Academy of Scientific and Innovative Research (AcSIR) NCL campus, Biochemical Sciences Division, CSIR-NCL, Pune, India
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road, Pune 411008, India
| | - Ganesh Shahane
- Institute of Bioengineering, Queen Mary University of London, Mile End Road, London, UK
| | - Sushama Gaikwad
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road, Pune 411008, India
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221
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Kumar V, Gour S, Peter OS, Gandhi S, Goyal P, Pandey J, Harsolia RS, Yadav JK. Effect of Green Tea Polyphenol Epigallocatechin-3-gallate on the Aggregation of αA(66-80) Peptide, a Major Fragment of αA-crystallin Involved in Cataract Development. Curr Eye Res 2017. [DOI: 10.1080/02713683.2017.1324628] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Vijay Kumar
- Department of Biotechnology, Central University of Rajasthan, NH-8 Bandarsindri, Kishangarh Ajmer, Rajasthan, India
| | - Shalini Gour
- Department of Biotechnology, Central University of Rajasthan, NH-8 Bandarsindri, Kishangarh Ajmer, Rajasthan, India
| | - Ocan Simon Peter
- Department of Biotechnology, Central University of Rajasthan, NH-8 Bandarsindri, Kishangarh Ajmer, Rajasthan, India
| | - Shraddha Gandhi
- Department of Biotechnology, Central University of Rajasthan, NH-8 Bandarsindri, Kishangarh Ajmer, Rajasthan, India
| | - Pankaj Goyal
- Department of Biotechnology, Central University of Rajasthan, NH-8 Bandarsindri, Kishangarh Ajmer, Rajasthan, India
| | - Janmejay Pandey
- Department of Biotechnology, Central University of Rajasthan, NH-8 Bandarsindri, Kishangarh Ajmer, Rajasthan, India
| | - Ram Swaroop Harsolia
- Department of Ophthalmology, Jawaharlal Nehru Medical College and Hospital, Ajmer, Rajasthan, India
| | - Jay Kant Yadav
- Department of Biotechnology, Central University of Rajasthan, NH-8 Bandarsindri, Kishangarh Ajmer, Rajasthan, India
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222
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Meric G, Robinson AS, Roberts CJ. Driving Forces for Nonnative Protein Aggregation and Approaches to Predict Aggregation-Prone Regions. Annu Rev Chem Biomol Eng 2017; 8:139-159. [DOI: 10.1146/annurev-chembioeng-060816-101404] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Gulsum Meric
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716
| | - Anne S. Robinson
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118
| | - Christopher J. Roberts
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716
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223
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Lakey-Beitia J, Doens D, Jagadeesh Kumar D, Murillo E, Fernandez PL, Rao KS, Durant-Archibold AA. Anti-amyloid aggregation activity of novel carotenoids: implications for Alzheimer's drug discovery. Clin Interv Aging 2017; 12:815-822. [PMID: 28553090 PMCID: PMC5440000 DOI: 10.2147/cia.s134605] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Alzheimer's disease (AD) is the leading cause of dementia, affecting approximately 33.5 million people worldwide. Aging is the main risk factor associated with AD. Drug discovery based on nutraceutical molecules for prevention and treatment of AD is a growing topic. In this sense, carotenoids are phytochemicals present mainly in fruits and vegetables with reported benefits for human health. In this research, the anti-amyloidogenic activity of three carotenoids, cryptocapsin, cryptocapsin-5,6-epoxide, and zeaxanthin, was assessed. Cryptocapsin showed the highest bioactivity, while cryptocapsin-5,6-epoxide and zeaxanthin exhibited similar activity on anti-aggregation assays. Molecular modeling analysis revealed that the evaluated carotenoids might follow two mechanisms for inhibiting Aβ aggregation: by preventing the formation of the fibril and through disruption of the Aβ aggregates. Our studies provided evidence that cryptocapsin, cryptocapsin-5,6-epoxide, and zeaxanthin have anti-amyloidogenic potential and could be used for prevention and treatment of AD.
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Affiliation(s)
- Johant Lakey-Beitia
- Center for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama.,Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
| | - Deborah Doens
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, India.,Center for Molecular and Cellular Biology of Diseases, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama
| | - D Jagadeesh Kumar
- Department of Biotechnology, Sir M Visvesvaraya Institute of Technology, Bangalore, India
| | - Enrique Murillo
- Department of Biochemistry, College of Natural, Exact Sciences and Technology, University of Panama, Panama, Republic of Panama
| | - Patricia L Fernandez
- Center for Molecular and Cellular Biology of Diseases, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama
| | - K S Rao
- Center for Neuroscience, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama
| | - Armando A Durant-Archibold
- Center for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama.,Department of Biochemistry, College of Natural, Exact Sciences and Technology, University of Panama, Panama, Republic of Panama
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224
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Coskuner O, Uversky VN. Tyrosine Regulates β-Sheet Structure Formation in Amyloid-β42: A New Clustering Algorithm for Disordered Proteins. J Chem Inf Model 2017; 57:1342-1358. [DOI: 10.1021/acs.jcim.6b00761] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Orkid Coskuner
- Department
of Chemistry and Neurosciences Institute, The University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, United States
- Institut
für Physikalische Chemie, Universität zu Köln, Luxemburger
Strasse 116, 50939 Köln, Germany
- Molecular
Biotechnology Division, Turkisch-Deutsche Universität, Sahinkaya
Caddesi, No. 71, Beykoz, Istanbul 34820, Turkey
| | - Vladimir N. Uversky
- Department
of Molecular Medicine, USF Health Byrd Alzheimer’s Research
Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Laboratory
of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow region 142290, Russia
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225
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Functionalisation of Polyvinylpyrrolidone on Gold Nanoparticles Enhances Its Anti-Amyloidogenic Propensity towards Hen Egg White Lysozyme. Biomedicines 2017; 5:biomedicines5020019. [PMID: 28536362 PMCID: PMC5489805 DOI: 10.3390/biomedicines5020019] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/13/2017] [Accepted: 04/25/2017] [Indexed: 11/17/2022] Open
Abstract
Protein amyloids are characterized by aggregates that usually consist of fibres containing misfolded proteins and having a cross β-sheet conformation. These aggregates can eventually lead to several degenerative diseases like Alzheimer’s disease, amyotrophic lateral sclerosis (ALS), Huntington’s disease and Parkinson’s disease. The present study describes the effect of chemically synthesized polyvinylpyrrolidone (PVP)-conjugated gold nanoparticles (PVP-AuNps) on hen egg white lysozyme (HEWL) amyloids. The synthesized nanoparticles have been characterized using various biophysical techniques like Ultraviolet-Visible (UV-Vis) Spectroscopy, Transmission electron microscopy (TEM), X-ray diffraction (XRD) analysis, dynamic light scattering (DLS), zeta-potential measurement and Fourier transform infrared spectroscopy (FTIR). The aggregation studies showed that PVP acts as a partial inhibitor of HEWL amyloidogenesis. However, when conjugated to gold nanoparticle surface, it leads to complete inhibition of amyloid formation. Apart from inhibition, PVP-conjugated gold nanoparticles also exhibited a significant disaggregation effect on mature amyloids and hence can be exploited as an effective therapeutic agent against hereditary systemic amyloidosis.
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226
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Krauss U, Jäger VD, Diener M, Pohl M, Jaeger KE. Catalytically-active inclusion bodies-Carrier-free protein immobilizates for application in biotechnology and biomedicine. J Biotechnol 2017; 258:136-147. [PMID: 28465211 DOI: 10.1016/j.jbiotec.2017.04.033] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 04/25/2017] [Accepted: 04/26/2017] [Indexed: 02/08/2023]
Abstract
Bacterial inclusion bodies (IBs) consist of unfolded protein aggregates and represent inactive waste products often accumulating during heterologous overexpression of recombinant genes in Escherichia coli. This general misconception has been challenged in recent years by the discovery that IBs, apart from misfolded polypeptides, can also contain substantial amounts of active and thus correctly or native-like folded protein. The corresponding catalytically-active inclusion bodies (CatIBs) can be regarded as a biologically-active sub-micrometer sized biomaterial or naturally-produced carrier-free protein immobilizate. Fusion of polypeptide (protein) tags can induce CatIB formation paving the way towards the wider application of CatIBs in synthetic chemistry, biocatalysis and biomedicine. In the present review we summarize the history of CatIBs, present the molecular-biological tools that are available to induce CatIB formation, and highlight potential lines of application. In the second part findings regarding the formation, architecture, and structure of (Cat)IBs are summarized. Finally, an overview is presented about the available bioinformatic tools that potentially allow for the prediction of aggregation and thus (Cat)IB formation. This review aims at demonstrating the potential of CatIBs for biotechnology and hopefully contributes to a wider acceptance of this promising, yet not widely utilized, protein preparation.
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Affiliation(s)
- Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.
| | - Vera D Jäger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Martin Diener
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Martina Pohl
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany; IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
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227
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Bradshaw NJ, Yerabham ASK, Marreiros R, Zhang T, Nagel-Steger L, Korth C. An unpredicted aggregation-critical region of the actin-polymerizing protein TRIOBP-1/Tara, determined by elucidation of its domain structure. J Biol Chem 2017; 292:9583-9598. [PMID: 28438837 DOI: 10.1074/jbc.m116.767939] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 04/20/2017] [Indexed: 12/22/2022] Open
Abstract
Aggregation of specific proteins in the brains of patients with chronic mental illness as a result of disruptions in proteostasis is an emerging theme in the study of schizophrenia in particular. Proteins including DISC1 (disrupted in schizophrenia 1) and dysbindin-1B are found in insoluble forms within brain homogenates from such patients. We recently identified TRIOBP-1 (Trio-binding protein 1, also known as Tara) to be another such protein through an epitope discovery and proteomics approach by comparing post-mortem brain material from schizophrenia patients and control individuals. We hypothesized that this was likely to occur as a result of a specific subcellular process and that it, therefore, should be possible to identify a region of the TRIOBP-1 protein that is essential for its aggregation to occur. Here, we probe the domain organization of TRIOBP-1, finding it to possess two distinct coiled-coil domains: the central and C-terminal domains. The central domain inhibits the depolymerization of F-actin and is also responsible for oligomerization of TRIOBP-1. Along with an N-terminal pleckstrin homology domain, the central domain affects neurite outgrowth. In neuroblastoma cells it was found that the aggregation propensity of TRIOBP-1 arises from its central domain, with a short "linker" region narrowed to within amino acids 324-348, between its first two coiled coils, as essential for the formation of TRIOBP-1 aggregates. TRIOBP-1 aggregation, therefore, appears to occur through one or more specific cellular mechanisms, which therefore have the potential to be of physiological relevance for the biological process underlying the development of chronic mental illness.
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Affiliation(s)
| | | | | | - Tao Zhang
- the Institute of Physical Biology, Heinrich Heine University, 40225 Düsseldorf, Germany and.,the Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Luitgard Nagel-Steger
- the Institute of Physical Biology, Heinrich Heine University, 40225 Düsseldorf, Germany and.,the Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
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228
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Carija A, Navarro S, de Groot NS, Ventura S. Protein aggregation into insoluble deposits protects from oxidative stress. Redox Biol 2017; 12:699-711. [PMID: 28410533 PMCID: PMC5390671 DOI: 10.1016/j.redox.2017.03.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/06/2017] [Indexed: 12/22/2022] Open
Abstract
Protein misfolding and aggregation have been associated with the onset of neurodegenerative disorders. Recent studies demonstrate that the aggregation process can result in a high diversity of protein conformational states, however the identity of the specific species responsible for the cellular damage is still unclear. Here, we use yeast as a model to systematically analyse the intracellular effect of expressing 21 variants of the amyloid-ß-peptide, engineered to cover a continuous range of intrinsic aggregation propensities. We demonstrate the existence of a striking negative correlation between the aggregation propensity of a given variant and the oxidative stress it elicits. Interestingly, each variant generates a specific distribution of protein assemblies in the cell. This allowed us to identify the aggregated species that remain diffusely distributed in the cytosol and are unable to coalesce into large protein inclusions as those causing the highest levels of oxidative damage. Overall, our results indicate that the formation of large insoluble aggregates may act as a protective mechanism to avoid cellular oxidative stress.
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Affiliation(s)
- Anita Carija
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Susanna Navarro
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Natalia Sanchez de Groot
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.
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229
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In silico prediction of the effects of mutations in the human triose phosphate isomerase gene: Towards a predictive framework for TPI deficiency. Eur J Med Genet 2017; 60:289-298. [PMID: 28341520 DOI: 10.1016/j.ejmg.2017.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 02/27/2017] [Accepted: 03/20/2017] [Indexed: 01/24/2023]
Abstract
Triose phosphate isomerase (TPI) deficiency is a rare, but highly debilitating, inherited metabolic disease. Almost all patients suffer severe neurological effects and the most severely affected are unlikely to live beyond early childhood. Here, we describe an in silico study into well-characterised variants which are associated with the disease alongside an investigation into 79 currently uncharacterised TPI variants which are known to occur in the human population. The majority of the disease-associated mutations affected amino acid residues close to the dimer interface or the active site. However, the location of the altered amino acid residue did not predict the severity of the resulting disease. Prediction of the effect on protein stability using a range of different programs suggested a relationship between the degree of instability caused by the sequence variation and the severity of the resulting disease. Disease-associated variations tended to affect well-conserved residues in the protein's sequence. However, the degree of conservation of the residue was not predictive of disease severity. The majority of the 79 uncharacterised variants are potentially associated with disease since they were predicted to destabilise the protein and often occur in well-conserved residues. We predict that individuals homozygous for the corresponding mutations would be likely to suffer from TPI deficiency.
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230
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Trehalose and Magnesium Chloride Exert a Common Anti-amyloidogenic Effect Towards Hen Egg White Lysozyme. Protein J 2017; 36:138-146. [DOI: 10.1007/s10930-017-9705-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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231
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Abstract
Protein aggregation is involved in many diseases. Often, a unique aggregation-prone sequence polymerizes to form regular fibrils. Many oncogenic mutants of the tumor suppressor p53 rapidly aggregate but form amorphous fibrils. A peptide surrounding Ile254 is proposed to be the aggregation-driving sequence in cells. We identified several different aggregating sites from limited proteolysis of harvested aggregates and effects of mutations on kinetics and products of aggregation. We present a model whereby the amorphous nature of the aggregates results from multisite branching of polymerization after slow unfolding of the protein, which may be a common feature of aggregation of large proteins. Greatly lowering the aggregation propensity of any one single site, including the site of Ile254, by mutation did not inhibit aggregation in vitro because aggregation could still occur via the other sites. Inhibition of an individual site is, accordingly, potentially unable to prevent aggregation in vivo. However, cancer cells are specifically killed by peptides designed to inhibit the Ile254 sequence and further aggregation-driving sequences that we have found. Consistent with our proposed mechanism of aggregation, we found that such peptides did not inhibit aggregation of mutant p53 in vitro. The cytotoxicity was not eliminated by knockdown of p53 in 2D cancer cell cultures. The peptides caused rapid cell death, much faster than usually expected for p53-mediated transcription-dependent apoptosis. There may also be non-p53 targets for those peptides in cancer cells, such as p63, or the peptides may alter other interactions of partly denatured p53 with receptors.
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232
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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: 28] [Impact Index Per Article: 3.5] [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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233
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The propensity of the bacterial rodlin protein RdlB to form amyloid fibrils determines its function in Streptomyces coelicolor. Sci Rep 2017; 7:42867. [PMID: 28211492 PMCID: PMC5314377 DOI: 10.1038/srep42867] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/18/2017] [Indexed: 01/10/2023] Open
Abstract
Streptomyces bacteria form reproductive aerial hyphae that are covered with a pattern of pairwise aligned fibrils called rodlets. The presence of the rodlet layer requires two homologous rodlin proteins, RdlA and RdlB, and the functional amyloid chaplin proteins, ChpA-H. In contrast to the redundancy shared among the eight chaplins, both RdlA and RdlB are indispensable for the establishment of this rodlet structure. By using a comprehensive biophysical approach combined with in vivo characterization we found that RdlB, but not RdlA, readily assembles into amyloid fibrils. The marked difference in amyloid propensity between these highly similar proteins could be largely attributed to a difference in amino acid sequence at just three sites. Further, an engineered RdlA protein in which these three key amino acids were replaced with the corresponding residues from RdlB could compensate for loss of RdlB and restore formation of the surface-exposed amyloid layer in bacteria. Our data reveal that RdlB is a new functional amyloid and provide a biophysical basis for the functional differences between the two rodlin proteins. This study enhances our understanding of how rodlin proteins contribute to formation of an outer fibrillar layer during spore morphogenesis in streptomycetes.
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234
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Trainor K, Broom A, Meiering EM. Exploring the relationships between protein sequence, structure and solubility. Curr Opin Struct Biol 2017; 42:136-146. [PMID: 28160724 DOI: 10.1016/j.sbi.2017.01.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 10/20/2022]
Abstract
Aggregation can be thought of as a form of protein folding in which intermolecular associations lead to the formation of large, insoluble assemblies. Various types of aggregates can be differentiated by their internal structures and gross morphologies (e.g., fibrillar or amorphous), and the ability to accurately predict the likelihood of their formation by a given polypeptide is of great practical utility in the fields of biology (including the study of disease), biotechnology, and biomaterials research. Here we review aggregation/solubility prediction methods and selected applications thereof. The development of increasingly sophisticated methods that incorporate knowledge of conformations possibly adopted by aggregating polypeptide monomers and predict the internal structure of aggregates is improving the accuracy of the predictions and continually expanding the range of applications.
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Affiliation(s)
- Kyle Trainor
- Department of Chemistry, University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada
| | - Aron Broom
- Department of Chemistry, University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada
| | - Elizabeth M Meiering
- Department of Chemistry, University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada.
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235
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Beuret N, Hasler F, Prescianotto-Baschong C, Birk J, Rutishauser J, Spiess M. Amyloid-like aggregation of provasopressin in diabetes insipidus and secretory granule sorting. BMC Biol 2017; 15:5. [PMID: 28122547 PMCID: PMC5267430 DOI: 10.1186/s12915-017-0347-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/04/2017] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Aggregation of peptide hormone precursors in the trans-Golgi network is an essential process in the biogenesis of secretory granules in endocrine cells. It has recently been proposed that this aggregation corresponds to the formation of functional amyloids. Our previous finding that dominant mutations in provasopressin, which cause cell degeneration and diabetes insipidus, prevent native folding and produce fibrillar aggregates in the endoplasmic reticulum (ER) might thus reflect mislocalized amyloid formation by sequences that evolved to mediate granule sorting. RESULTS Here we identified two sequences responsible for fibrillar aggregation of mutant precursors in the ER: the N-terminal vasopressin nonapeptide and the C-terminal glycopeptide. To test their role in granule sorting, the glycopeptide was deleted and/or vasopressin mutated to inactivate ER aggregation while still permitting precursor folding and ER exit. These mutations strongly reduced sorting into granules and regulated secretion in endocrine AtT20 cells. CONCLUSION The same sequences - vasopressin and the glycopeptide - mediate physiological aggregation of the wild-type hormone precursor into secretory granules and the pathological fibrillar aggregation of disease mutants in the ER. These findings support the amyloid hypothesis for secretory granule biogenesis.
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Affiliation(s)
- Nicole Beuret
- Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056, Basel, Switzerland
| | - Franziska Hasler
- Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056, Basel, Switzerland
| | | | - Julia Birk
- Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056, Basel, Switzerland
| | - Jonas Rutishauser
- Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056, Basel, Switzerland
| | - Martin Spiess
- Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056, Basel, Switzerland.
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236
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Kouza M, Banerji A, Kolinski A, Buhimschi IA, Kloczkowski A. Oligomerization of FVFLM peptides and their ability to inhibit beta amyloid peptides aggregation: consideration as a possible model. Phys Chem Chem Phys 2017; 19:2990-2999. [PMID: 28079198 PMCID: PMC5305032 DOI: 10.1039/c6cp07145g] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Preeclampsia, a pregnancy-specific disorder, shares typical pathophysiological features with protein misfolding disorders including Alzheimer's disease. Characteristic for preeclampsia is the involvement of multiple proteins of which fragments of SERPINA1 and β-amyloid co-aggregate in urine and placenta of preeclamptic women. To explore the biophysical basis of this interaction, we investigated the multidimensional efficacy of the FVFLM sequence in SERPINA1, as a model inhibitory agent of β-amyloid aggregation. After studying the oligomerization of FVFLM peptides using all-atom molecular dynamics simulations with the GROMOS43a1 force field and explicit water, we report that FVFLM can aggregate and its aggregation is spontaneous with a remarkably faster rate than that recorded for KLVFF (aggregation "hot-spot" from β-amyloid). The fast kinetics of FVFLM aggregation was found to be driven primarily by core-like aromatic interactions originating from the anti-parallel orientation of complementarily uncharged strands. The conspicuously stable aggregation mechanism observed for FVFLM peptides is found not to conform to the popular 'dock-lock' scheme. We also found high propensity of FVFLM for KLVFF binding. When present, FVFLM disrupts the β-amyloid aggregation pathway and we propose that FVFLM-like peptides might be used to prevent the assembly of full-length Aβ or other pro-amyloidogenic peptides into amyloid fibrils.
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Affiliation(s)
- M Kouza
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland. and Nationwide Children's Hospital, Battelle Center for Mathematical Medicine, Columbus, OH 43215, USA
| | - A Banerji
- Nationwide Children's Hospital, Battelle Center for Mathematical Medicine, Columbus, OH 43215, USA
| | - A Kolinski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - I A Buhimschi
- Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43215, USA and Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43215, USA
| | - A Kloczkowski
- Nationwide Children's Hospital, Battelle Center for Mathematical Medicine, Columbus, OH 43215, USA and Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43215, USA
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237
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Kouza M, Faraggi E, Kolinski A, Kloczkowski A. The GOR Method of Protein Secondary Structure Prediction and Its Application as a Protein Aggregation Prediction Tool. Methods Mol Biol 2017; 1484:7-24. [PMID: 27787816 DOI: 10.1007/978-1-4939-6406-2_2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The GOR method of protein secondary structure prediction is described. The original method was published by Garnier, Osguthorpe, and Robson in 1978 and was one of the first successful methods to predict protein secondary structure from amino acid sequence. The method is based on information theory, and an assumption that information function of a protein chain can be approximated by a sum of information from single residues and pairs of residues. The analysis of frequencies of occurrence of secondary structure for singlets and doublets of residues in a protein database enables prediction of secondary structure for new amino acid sequences. Because of these simple physical assumptions the GOR method has a conceptual advantage over other later developed methods such as PHD, PSIPRED, and others that are based on Machine Learning methods (like Neural Networks), give slightly better predictions, but have a "black box" nature. The GOR method has been continuously improved and modified for 30 years with the last GOR V version published in 2002, and the GOR V server developed in 2005. We discuss here the original GOR method and the GOR V program and the web server. Additionally we discuss new highly interesting and important applications of the GOR method to chameleon sequences in protein folding simulations, and for prediction of protein aggregation propensities. Our preliminary studies show that the GOR method is a promising and efficient alternative to other protein aggregation predicting tools. This shows that the GOR method despite being almost 40 years old is still important and has significant potential in application to new scientific problems.
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Affiliation(s)
- Maksim Kouza
- Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw, 02-093, Poland
| | - Eshel Faraggi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46032, USA.,Research and Information Systems, LLC, Indianapolis, Indiana, USA
| | - Andrzej Kolinski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw, 02-093, Poland
| | - Andrzej Kloczkowski
- Battelle Center for MathematicalMedicine, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43215, USA. .,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43215, USA.
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238
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Jadhao M, Das C, Rawat A, Kumar H, Joshi R, Maiti S, Ghosh SK. Development of multifunctional heterocyclic Schiff base as a potential metal chelator: a comprehensive spectroscopic approach towards drug discovery. J Biol Inorg Chem 2016; 22:47-59. [PMID: 27822620 DOI: 10.1007/s00775-016-1407-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 10/24/2016] [Indexed: 10/20/2022]
Abstract
Amyloid-β peptides and their metal-associated aggregated states have been implicated in the pathogenesis of Alzheimer's disease. The present paper epitomises the design and synthesis of a small, neutral, lipophilic benzothiazole Schiff base (E)-2-((6-chlorobenzo[d]thiazol-2-ylimino)methyl)-5-diethylamino)phenol (CBMDP), and explores its multifunctionalty as a potential metal chelator/fluorophore using UV-visible absorption, steady-state fluorescence, single molecule fluorescence correlation spectroscopic (FCS) techniques which is further corroborated by in silico studies. Some pharmaceutically relevant properties of the synthesized compound have also been calculated theoretically. Steady-state fluorescence and single molecule FCS reveal that the synthesized CBMDP not only recognizes oligomeric Aβ40, but could also be used as an amyloid-specific extrinsic fluorophore as it shows tremendous increase in its emission intensity in the presence of Aβ40. Molecular docking exercise and MD simulation reveal that CBMDP localizes itself in the crucial amyloidogenic and copper-binding region of Aβ40 and undergoes a strong binding interaction via H-bonding and π-π stacking. It stabilizes the solitary α-helical Aβ40 monomer by retaining the initial conformation of the Aβ central helix and mostly interacts with the hydrophilic N-terminus and the α-helical region spanning from Ala-2 to Val-24. CBMDP exhibits strong copper as well as zinc chelation ability and retards the rapid copper-induced aggregation of amyloid peptide. In addition, CBMDP shows radical scavenging activity which enriches its functionality. Overall, the consolidated in vitro and in silico results obtained for the synthesized molecule could provide a rational template for developing new multifunctional agents.
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Affiliation(s)
- Manojkumar Jadhao
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, 440010, Maharashtra, India
| | - Chayan Das
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, 440010, Maharashtra, India
| | - Anoop Rawat
- Tata Institute of Fundamental Research (TIFR), 1-Homi Bhabha Road, Colaba, 400005, Mumbai, India
| | - Himank Kumar
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, 440010, Maharashtra, India
| | - Ritika Joshi
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, 440010, Maharashtra, India
| | - Sudipta Maiti
- Tata Institute of Fundamental Research (TIFR), 1-Homi Bhabha Road, Colaba, 400005, Mumbai, India
| | - Sujit Kumar Ghosh
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, 440010, Maharashtra, India.
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239
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Bemporad F, Ramazzotti M. From the Evolution of Protein Sequences Able to Resist Self-Assembly to the Prediction of Aggregation Propensity. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 329:1-47. [PMID: 28109326 DOI: 10.1016/bs.ircmb.2016.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Folding of polypeptide chains into biologically active entities is an astonishingly complex process, determined by the nature and the sequence of residues emerging from ribosomes. While it has been long believed that evolution has pressed genomes so that specific sequences could adopt unique, functional three-dimensional folds, it is now clear that complex protein machineries act as quality control system and supervise folding. Notwithstanding that, events such as erroneous folding, partial folding, or misfolding are frequent during the life of a cell or a whole organism, and they can escape controls. One of the possible outcomes of this misbehavior is cross-β aggregation, a super secondary structure which represents the hallmark of self-assembled, well organized, and extremely ordered structures termed amyloid fibrils. What if evolution would have not taken into account such possibilities? Twenty years of research point toward the idea that, in fact, evolution has constantly supervised the risk of errors and minimized their impact. In this review we tried to survey the major findings in the amyloid field, trying to describe what the real pitfalls of protein folding are-from an evolutionary perspective-and how sequence and structural features have evolved to balance the need for perfect, dynamic, functionally efficient structures, and the detrimental effects implicit in the dangerous process of folding. We will discuss how the knowledge obtained from these studies has been employed to produce computational methods able to assess, predict, and discriminate the aggregation properties of protein sequences.
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Affiliation(s)
- F Bemporad
- Università degli Studi di Firenze, Firenze, Italy.
| | - M Ramazzotti
- Università degli Studi di Firenze, Firenze, Italy.
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240
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Pallarès I, Ventura S. Understanding and predicting protein misfolding and aggregation: Insights from proteomics. Proteomics 2016; 16:2570-2581. [PMID: 27479752 DOI: 10.1002/pmic.201500529] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 07/08/2016] [Accepted: 07/25/2016] [Indexed: 11/09/2022]
Abstract
Protein misfolding and aggregation are being found to be associated with an increasing number of human diseases and premature aging, either because they promote a loss of protein function or, more frequently, because the aggregated species gain a toxic activity. Despite potentially harmful, aggregation seems to be a generic property of polypeptide chains and aggregation-prone protein sequences seem to be ubiquitous, which, counterintuitively, suggests that they serve evolutionary conserved functions. The in vitro study of individual aggregation reactions of a large number of proteins has provided important insights on the structural and sequential determinants of this process. However, it is clear that understanding the role played by protein aggregation and its regulation in health and disease at the cellular, developmental, and evolutionary levels require more global approaches. The use of model organisms and their proteomic analysis hold the power to provide answers to such issues. In the present review, we address how, initially, computational large-scale analysis and, more recently, experimental proteomics are helping us to rationalize how, why and when proteins aggregate, as well as to decipher the strategies organisms have developed to control proteins aggregation propensities.
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Affiliation(s)
- Irantzu Pallarès
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain. .,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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241
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Žerovnik E. Putative alternative functions of human stefin B (cystatin B): binding to amyloid-beta, membranes, and copper. J Mol Recognit 2016; 30. [PMID: 27577977 DOI: 10.1002/jmr.2562] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/25/2016] [Accepted: 07/26/2016] [Indexed: 12/17/2022]
Abstract
We describe studies performed thus far on stefin B from the family of cystatins as a model protein for folding and amyloid fibril formation studies. We also briefly mention our studies on aggregation of some of the missense EPM1 mutants of stefin B in cells, which mimic additional pathological traits (gain in toxic function) in selected patients with EPM1 disease. We collected data on the reported interactors of stefin B and discuss several hypotheses of possible cytosolic alternative functions.
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Affiliation(s)
- Eva Žerovnik
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia.,CipKeBip-Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Ljubljana, Slovenia
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242
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Surin AK, Grigorashvili EI, Suvorina MY, Selivanova OM, Galzitskaya OV. Determination of regions involved in amyloid fibril formation for Aβ(1-40) peptide. BIOCHEMISTRY (MOSCOW) 2016; 81:762-769. [DOI: 10.1134/s0006297916070130] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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243
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Selivanova OM, Gorbunova EY, Mustaeva LG, Grigorashvili EI, Suvorina MY, Surin AK, Galzitskaya OV. Peptide Aβ(16-25) forms nanofilms in the process of its aggregation. BIOCHEMISTRY (MOSCOW) 2016; 81:755-761. [DOI: 10.1134/s0006297916070129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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244
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Awasthi S, Sankaranarayanan K, Saraswathi NT. Advanced glycation end products induce differential structural modifications and fibrillation of albumin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 163:60-67. [PMID: 27037764 DOI: 10.1016/j.saa.2016.03.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 03/11/2016] [Accepted: 03/20/2016] [Indexed: 06/05/2023]
Abstract
Glycation induced amyloid fibrillation is fundamental to the development of many neurodegenerative and cardiovascular complications. Excessive non-enzymatic glycation in conditions such as hyperglycaemia results in the increased accumulation of advanced glycation end products (AGEs). AGEs are highly reactive pro-oxidants, which can lead to the activation of inflammatory pathways and development of oxidative stress. Recently, the effect of non-enzymatic glycation on protein structure has been the major research area, but the role of specific AGEs in such structural alteration and induction of fibrillation remains undefined. In this study, we determined the specific AGEs mediated structural modifications in albumin mainly considering carboxymethyllysine (CML), carboxyethyllysine (CEL), and argpyrimidine (Arg-P) which are the major AGEs formed in the body. We studied the secondary structural changes based on circular dichroism (CD) and spectroscopic analysis. The AGEs induced fibrillation was determined by Congo red binding and examination of scanning and transmission electron micrographs. The amyloidogenic regions in the sequence of BSA were determined using FoldAmyloid. It was observed that CEL modification of BSA leads to the development of fibrillar structures, which was evident from both secondary structure changes and TEM analysis.
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Affiliation(s)
- Saurabh Awasthi
- Molecular Biophysics Lab, School of Chemical and Biotechnology, SASTRA University, Thanjavur 613401, Tamilnadu, India
| | - Kamatchi Sankaranarayanan
- DST-INSPIRE Faculty, Department of Energy and Environment, National Institute of Technology, Tiruchirappalli 620015, Tamilnadu, India
| | - N T Saraswathi
- Molecular Biophysics Lab, School of Chemical and Biotechnology, SASTRA University, Thanjavur 613401, Tamilnadu, India.
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245
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Cryo-EM reveals the steric zipper structure of a light chain-derived amyloid fibril. Proc Natl Acad Sci U S A 2016; 113:6200-5. [PMID: 27185936 DOI: 10.1073/pnas.1522282113] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Amyloid fibrils are proteinaceous aggregates associated with diseases in humans and animals. The fibrils are defined by intermolecular interactions between the fibril-forming polypeptide chains, but it has so far remained difficult to reveal the assembly of the peptide subunits in a full-scale fibril. Using electron cryomicroscopy (cryo-EM), we present a reconstruction of a fibril formed from the pathogenic core of an amyloidogenic immunoglobulin (Ig) light chain. The fibril density shows a lattice-like assembly of face-to-face packed peptide dimers that corresponds to the structure of steric zippers in peptide crystals. Interpretation of the density map with a molecular model enabled us to identify the intermolecular interactions between the peptides and rationalize the hierarchical structure of the fibril based on simple chemical principles.
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246
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Niroula A, Vihinen M. Variation Interpretation Predictors: Principles, Types, Performance, and Choice. Hum Mutat 2016; 37:579-97. [DOI: 10.1002/humu.22987] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/07/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Abhishek Niroula
- Department of Experimental Medical Science; Lund University; BMC B13 Lund SE-22184 Sweden
| | - Mauno Vihinen
- Department of Experimental Medical Science; Lund University; BMC B13 Lund SE-22184 Sweden
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247
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Chang EP, Roncal-Herrero T, Morgan T, Dunn KE, Rao A, Kunitake JAMR, Lui S, Bilton M, Estroff LA, Kröger R, Johnson S, Cölfen H, Evans JS. Synergistic Biomineralization Phenomena Created by a Combinatorial Nacre Protein Model System. Biochemistry 2016; 55:2401-10. [PMID: 27072850 DOI: 10.1021/acs.biochem.6b00163] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In the nacre or aragonite layer of the mollusk shell, proteomes that regulate both the early stages of nucleation and nano-to-mesoscale assembly of nacre tablets from mineral nanoparticle precursors exist. Several approaches have been developed to understand protein-associated mechanisms of nacre formation, yet we still lack insight into how protein ensembles or proteomes manage nucleation and crystal growth. To provide additional insights, we have created a proportionally defined combinatorial model consisting of two nacre-associated proteins, C-RING AP7 (shell nacre, Haliotis rufescens) and pseudo-EF hand PFMG1 (oyster pearl nacre, Pinctada fucata), whose individual in vitro mineralization functionalities are well-documented and distinct from one another. Using scanning electron microscopy, flow cell scanning transmission electron microscopy, atomic force microscopy, Ca(II) potentiometric titrations, and quartz crystal microbalance with dissipation monitoring quantitative analyses, we find that both nacre proteins are functionally active within the same mineralization environments and, at 1:1 molar ratios, synergistically create calcium carbonate mesoscale structures with ordered intracrystalline nanoporosities, extensively prolong nucleation times, and introduce an additional nucleation event. Further, these two proteins jointly create nanoscale protein aggregates or phases that under mineralization conditions further assemble into protein-mineral polymer-induced liquid precursor-like phases with enhanced ACC stabilization capabilities, and there is evidence of intermolecular interactions between AP7 and PFMG1 under these conditions. Thus, a combinatorial model system consisting of more than one defined biomineralization protein dramatically changes the outcome of the in vitro biomineralization process.
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Affiliation(s)
- Eric P Chang
- Center for Skeletal Biology, Laboratory for Chemical Physics, New York University College of Dentistry , New York, New York 10010, United States
| | | | - Tamara Morgan
- Department of Electronics, University of York , Heslington, York, United Kingdom
| | - Katherine E Dunn
- Department of Electronics, University of York , Heslington, York, United Kingdom
| | - Ashit Rao
- Department of Chemistry, Universitat Konstanz , Konstanz, Germany
| | - Jennie A M R Kunitake
- Department of Materials Science and Engineering, Cornell University , Ithaca, New York 14853-1501, United States
| | - Susan Lui
- Center for Skeletal Biology, Laboratory for Chemical Physics, New York University College of Dentistry , New York, New York 10010, United States
| | - Matthew Bilton
- Department of Physics, University of York , Heslington, York, United Kingdom
| | - Lara A Estroff
- Department of Materials Science and Engineering, Cornell University , Ithaca, New York 14853-1501, United States
| | - Roland Kröger
- Department of Physics, University of York , Heslington, York, United Kingdom
| | - Steven Johnson
- Department of Electronics, University of York , Heslington, York, United Kingdom
| | - Helmut Cölfen
- Department of Chemistry, Universitat Konstanz , Konstanz, Germany
| | - John Spencer Evans
- Center for Skeletal Biology, Laboratory for Chemical Physics, New York University College of Dentistry , New York, New York 10010, United States
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248
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Rebelo AP, Abrams AJ, Cottenie E, Horga A, Gonzalez M, Bis DM, Sanchez-Mejias A, Pinto M, Buglo E, Markel K, Prince J, Laura M, Houlden H, Blake J, Woodward C, Sweeney MG, Holton JL, Hanna M, Dallman JE, Auer-Grumbach M, Reilly MM, Zuchner S. Cryptic Amyloidogenic Elements in the 3' UTRs of Neurofilament Genes Trigger Axonal Neuropathy. Am J Hum Genet 2016; 98:597-614. [PMID: 27040688 PMCID: PMC4833435 DOI: 10.1016/j.ajhg.2016.02.022] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 02/16/2016] [Indexed: 12/14/2022] Open
Abstract
Abnormal protein aggregation is observed in an expanding number of neurodegenerative diseases. Here, we describe a mechanism for intracellular toxic protein aggregation induced by an unusual mutation event in families affected by axonal neuropathy. These families carry distinct frameshift variants in NEFH (neurofilament heavy), leading to a loss of the terminating codon and translation of the 3' UTR into an extra 40 amino acids. In silico aggregation prediction suggested the terminal 20 residues of the altered NEFH to be amyloidogenic, which we confirmed experimentally by serial deletion analysis. The presence of this amyloidogenic motif fused to NEFH caused prominent and toxic protein aggregates in transfected cells and disrupted motor neurons in zebrafish. We identified a similar aggregation-inducing mechanism in NEFL (neurofilament light) and FUS (fused in sarcoma), in which mutations are known to cause aggregation in Charcot-Marie-Tooth disease and amyotrophic lateral sclerosis, respectively. In summary, we present a protein-aggregation-triggering mechanism that should be taken into consideration during the evaluation of stop-loss variants.
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Affiliation(s)
- Adriana P Rebelo
- Dr. John T. Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Alexander J Abrams
- Dr. John T. Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ellen Cottenie
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Molecular Neurosciences, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Alejandro Horga
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Molecular Neurosciences, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Michael Gonzalez
- Dr. John T. Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Dana M Bis
- Dr. John T. Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Avencia Sanchez-Mejias
- Dr. John T. Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Milena Pinto
- Dr. John T. Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Elena Buglo
- Dr. John T. Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Kasey Markel
- Department of Biology, University of Miami, Miami, FL 33146, USA
| | - Jeffrey Prince
- Department of Biology, University of Miami, Miami, FL 33146, USA
| | - Matilde Laura
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Molecular Neurosciences, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Henry Houlden
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Molecular Neurosciences, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Neurogenetics Laboratory, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Julian Blake
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Clinical Neurophysiology, Norfolk and Norwich University Hospital, Norwich NR4 7UY, UK
| | - Cathy Woodward
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Molecular Neurosciences, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Mary G Sweeney
- Neurogenetics Laboratory, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Janice L Holton
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Molecular Neurosciences, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Michael Hanna
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Molecular Neurosciences, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Julia E Dallman
- Department of Biology, University of Miami, Miami, FL 33146, USA
| | | | - Mary M Reilly
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Molecular Neurosciences, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Stephan Zuchner
- Dr. John T. Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA.
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Garg DK, Kundu B. Clues for divergent, polymorphic amyloidogenesis through dissection of amyloid forming steps of bovine carbonic anhydrase and its critical amyloid forming stretch. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:794-804. [PMID: 27045222 DOI: 10.1016/j.bbapap.2016.03.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/12/2016] [Accepted: 03/31/2016] [Indexed: 01/23/2023]
Abstract
Certain amino acid stretches are considered 'critical' to trigger amyloidogenesis in a protein. Synthetic peptides corresponding to these stretches are often used as experimental mimics for studying the amyloidogenesis of their parent protein. Here we provide evidence that such simple extrapolation is misleading. We scrutinized each step of amyloid progression of full length bovine carbonic anhydrase (BCA) and compared it with the amyloidogenic process of its critical peptide stretch 201-227 (PepB). We found that under similar solution conditions amyloidogenesis of BCA followed surface-catalyzed secondary nucleation, whereas, that of PepB followed classical nucleation-dependent pathway. AFM images showed that while BCA formed short, thick and branched fibrils, PepB formed thin, long and unbranched fibrils. Structural information obtained by ATR-FTIR spectroscopy suggested parallel arrangement of intermolecular β-sheet in BCA amyloids in contrast to PepB amyloids which arranged into antiparallel β sheets. Amyloids formed by BCA were unable to seed the fibrillation of PepB and vice versa. Even the intermediates formed during lag phase revealed contrasting FTIR and far UV CD signature, hydrophobicity, morphology and cell cytotoxicity. Thus, we propose that sequences other than critical amyloidogenic stretches may significantly influence the initiation, polymerization and final fibrillar morphology of amyloid forming protein. The results have been discussed in light of primary sequence mediated amyloid polymorphism and its importance in the rational design of amyloid nanomaterials possessing desired physico-chemical properties.
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Affiliation(s)
- Dushyant Kumar Garg
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Bishwajit Kundu
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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Berthelot K, Lecomte S, Coulary-Salin B, Bentaleb A, Peruch F. Hevea brasiliensis prohevein possesses a conserved C-terminal domain with amyloid-like properties in vitro. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:388-99. [DOI: 10.1016/j.bbapap.2016.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 01/05/2016] [Accepted: 01/11/2016] [Indexed: 11/30/2022]
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