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Sharma A, Shah OP, Sharma L, Gulati M, Behl T, Khalid A, Mohan S, Najmi A, Zoghebi K. Molecular Chaperones as Therapeutic Target: Hallmark of Neurodegenerative Disorders. Mol Neurobiol 2024; 61:4750-4767. [PMID: 38127187 DOI: 10.1007/s12035-023-03846-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023]
Abstract
Misfolded and aggregated proteins build up in neurodegenerative illnesses, which causes neuronal dysfunction and ultimately neuronal death. In the last few years, there has been a significant upsurge in the level of interest towards the function of molecular chaperones in the control of misfolding and aggregation. The crucial molecular chaperones implicated in neurodegenerative illnesses are covered in this review article, along with a variety of their different methods of action. By aiding in protein folding, avoiding misfolding, and enabling protein breakdown, molecular chaperones serve critical roles in preserving protein homeostasis. By aiding in protein folding, avoiding misfolding, and enabling protein breakdown, molecular chaperones have integral roles in preserving regulation of protein balance. It has been demonstrated that aging, a significant risk factor for neurological disorders, affects how molecular chaperones function. The aggregation of misfolded proteins and the development of neurodegeneration may be facilitated by the aging-related reduction in chaperone activity. Molecular chaperones have also been linked to the pathophysiology of several instances of neuron withering illnesses, enumerating as Parkinson's disease, Huntington's disease, and Alzheimer's disease. Molecular chaperones have become potential therapy targets concerning with the prevention and therapeutic approach for brain disorders due to their crucial function in protein homeostasis and their connection to neurodegenerative illnesses. Protein homeostasis can be restored, and illness progression can be slowed down by methods that increase chaperone function or modify their expression. This review emphasizes the importance of molecular chaperones in the context of neuron withering disorders and their potential as therapeutic targets for brain disorders.
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Affiliation(s)
- Aditi Sharma
- School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, India
| | - Om Prakash Shah
- School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, India
| | - Lalit Sharma
- School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, India
| | - Monica Gulati
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, 1444411, India
- ARCCIM, Faculty of Health, University of Technology Sydney, Ultimo, NSW, 20227, Australia
| | - Tapan Behl
- Amity School of Pharmaceutical Sciences, Amity University, Mohali, Punjab, India, Amity University, Mohali, India.
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Centre, Jazan University, Jazan, 45142, Saudi Arabia
- Medicinal and Aromatic Plants Research Institute, National Center for Research, P.O. Box 2424, 11111, Khartoum, Sudan
| | - Syam Mohan
- Substance Abuse and Toxicology Research Centre, Jazan University, Jazan, 45142, Saudi Arabia.
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Dehradun, Uttarakhand, India.
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India.
| | - Asim Najmi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, P.O. Box 114, Jazan, Saudi Arabia
| | - Khalid Zoghebi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, P.O. Box 114, Jazan, Saudi Arabia
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Mackness BC, Morgan BR, Deveau LM, Kathuria SV, Zitzewitz JA, Massi F. A hydrophobic core stabilizes the residual structure in the RRM2 intermediate state of the ALS-linked protein TDP-43. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598648. [PMID: 38915526 PMCID: PMC11195224 DOI: 10.1101/2024.06.12.598648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Folding intermediates mediate both protein folding and the misfolding and aggregation observed in human diseases, including amyotrophic lateral sclerosis (ALS), and are prime targets for therapeutic interventions. In this study, we identified the core nucleus of structure for a folding intermediate in the second RNA recognition motif (RRM2) of the ALS-linked RNA-binding protein, TDP-43, using a combination of experimental and computational approaches. Urea equilibrium unfolding studies revealed that the RRM2 intermediate state consists of collapsed residual secondary structure localized to the N-terminal half of RRM2, while the C-terminus is largely disordered. Steered molecular dynamics simulations and mutagenesis studies yielded key stabilizing hydrophobic contacts that, when mutated to alanine, severely disrupt the overall fold of RRM2. In combination, these findings suggest a role for this RRM intermediate in normal TDP-43 function as well as serving as a template for misfolding and aggregation through the low stability and non-native secondary structure.
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Khorsand FR, Aziziyan F, Khajeh K. Factors influencing amyloid fibril formation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:55-83. [PMID: 38811089 DOI: 10.1016/bs.pmbts.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Protein aggregation is a complex process with several stages that lead to the formation of complex structures and shapes with a broad variability in stability and toxicity. The aggregation process is affected by various factors and environmental conditions that disrupt the protein's original state, including internal factors like mutations, expression levels, and polypeptide chain truncation, as well as external factors, such as dense molecular surroundings, post-translation modifications, and interactions with other proteins, nucleic acids, small molecules, metal ions, chaperones, and lipid membranes. During the aggregation process, the biological activity of an aggregating protein may be reduced or eliminated, whereas the resulting aggregates may have the potential to be immunogenic, or they may have other undesirable properties. Finding the cause(s) of protein aggregation and controlling it to an acceptable level is among the most crucial topics of research in academia and biopharmaceutical companies. This chapter aims to review intrinsic pathways of protein aggregation and potential extrinsic variables that influence this process.
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Affiliation(s)
| | - Fatemeh Aziziyan
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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Duran-Meza E, Araya-Secchi R, Romero-Hasler P, Soto-Bustamante EA, Castro-Fernandez V, Castillo-Caceres C, Monasterio O, Diaz-Espinoza R. Metal Ions Can Modulate the Self-Assembly and Activity of Catalytic Peptide Amyloids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:6094-6106. [PMID: 38470353 DOI: 10.1021/acs.langmuir.3c02983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Rational design of peptides has become a powerful tool to produce self-assembled nanostructures with the ability to catalyze different chemical reactions, paving the way to develop minimalistic enzyme-like nanomaterials. Catalytic amyloid-like assemblies have emerged among the most versatile and active, but they often require additional factors for activity. Elucidating how these factors influence the structure and activity is key for the design. Here, we showed that biologically relevant metal ions can guide and modulate the self-assembly of a small peptide into diverse amyloid architectures. The morphology and catalytic activity of the resulting fibrils were tuned by the specific metal ion decorating the surface, whereas X-ray structural analysis of the amyloids showed ion-dependent shape sizes. Molecular dynamics simulations showed that the metals can strongly affect the local conformational space, which can trigger major rearrangements of the fibrils. Our results demonstrate that the conformational landscape of catalytic amyloids is broad and tunable by external factors, which can be critical for future design strategies.
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Affiliation(s)
- Eva Duran-Meza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, General Amengual 014, Estación Central, Santiago 9170390, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile
| | - Raul Araya-Secchi
- Computational Biophysics group, Facultad de Ingenieria, Tecnologia y Diseño, Universidad San Sebastian, Bellavista 7, Recoleta, Santiago 8420524, Chile
- Centro Basal Ciencia & Vida, Universidad San Sebastian, Santiago 8420524, Chile
| | - Patricio Romero-Hasler
- Departamento de Ciencia de los Alimentos y Tecnología Química, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Dr. Carlos Lorca Tobar 964, Independencia, Santiago 81380494, Chile
| | - Eduardo Arturo Soto-Bustamante
- Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Dr. Carlos Lorca Tobar 964, Independencia, Santiago 81380494, Chile
| | - Victor Castro-Fernandez
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile
| | - Claudio Castillo-Caceres
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, General Amengual 014, Estación Central, Santiago 9170390, Chile
| | - Octavio Monasterio
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile
| | - Rodrigo Diaz-Espinoza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, General Amengual 014, Estación Central, Santiago 9170390, Chile
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Macke AC, Stump JE, Kelly MS, Rowley J, Herath V, Mullen S, Dima RI. Searching for Structure: Characterizing the Protein Conformational Landscape with Clustering-Based Algorithms. J Chem Inf Model 2024; 64:470-482. [PMID: 38173388 DOI: 10.1021/acs.jcim.3c01511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The identification and characterization of the main conformations from a protein population are a challenging and inherently high-dimensional problem. Here, we evaluate the performance of the Secondary sTructural Ensembles with machine LeArning (StELa) double-clustering method, which clusters protein structures based on the relationship between the φ and ψ dihedral angles in a protein backbone and the secondary structure of the protein, thus focusing on the local properties of protein structures. The classification of states as vectors composed of the clusters' indices arising naturally from the Ramachandran plot is followed by the hierarchical clustering of the vectors to allow for the identification of the main features of the corresponding free energy landscape (FEL). We compare the performance of StELa with the established root-mean-squared-deviation (RMSD)-based clustering algorithm, which focuses on global properties of protein structures and with Combinatorial Averaged Transient Structure (CATS), the combinatorial averaged transient structure clustering method based on distributions of the φ and ψ dihedral angle coordinates. Using ensembles of conformations from molecular dynamics simulations of intrinsically disordered proteins (IDPs) of various lengths (tau protein fragments) or short fragments from a globular protein, we show that StELa is the clustering method that identifies many of the minima and relevant energy states around the minima from the corresponding FELs. In contrast, the RMSD-based algorithm yields a large number of clusters that usually cover most of the FEL, thus being unable to distinguish between states, while CATS does not sample well the FELs for long IDPs and fragments from globular proteins.
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Affiliation(s)
- Amanda C Macke
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Jacob E Stump
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Maria S Kelly
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Jamie Rowley
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Vageesha Herath
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Sarah Mullen
- Department of Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Ruxandra I Dima
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
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Gibertini S, Ruggieri A, Cheli M, Maggi L. Protein Aggregates and Aggrephagy in Myopathies. Int J Mol Sci 2023; 24:ijms24098456. [PMID: 37176163 PMCID: PMC10179229 DOI: 10.3390/ijms24098456] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
A number of muscular disorders are hallmarked by the aggregation of misfolded proteins within muscle fibers. A specialized form of macroautophagy, termed aggrephagy, is designated to remove and degrade protein aggregates. This review aims to summarize what has been studied so far about the direct involvement of aggrephagy and the activation of the key players, among others, p62, NBR1, Alfy, Tollip, Optineurin, TAX1BP1 and CCT2 in muscular diseases. In the first part of the review, we describe the aggrephagy pathway with the involved proteins; then, we illustrate the muscular disorder histologically characterized by protein aggregates, highlighting the role of aggrephagy pathway abnormalities in these muscular disorders.
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Affiliation(s)
- Sara Gibertini
- Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", 20133 Milan, Italy
| | - Alessandra Ruggieri
- Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", 20133 Milan, Italy
| | - Marta Cheli
- Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", 20133 Milan, Italy
| | - Lorenzo Maggi
- Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", 20133 Milan, Italy
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Menon S, Mondal J. Conformational Plasticity in α-Synuclein and How Crowded Environment Modulates It. J Phys Chem B 2023; 127:4032-4049. [PMID: 37114769 DOI: 10.1021/acs.jpcb.3c00982] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
A 140-residue intrinsically disordered protein (IDP), α-synuclein (αS), is known to adopt conformations that are vastly plastic and susceptible to environmental cues and crowders. However, the inherently heterogeneous nature of αS has precluded a clear demarcation of its monomeric precursor between aggregation-prone and functionally relevant aggregation-resistant states and how a crowded environment could modulate their mutual dynamic equilibrium. Here, we identify an optimal set of distinct metastable states of αS in aqueous media by dissecting a 73 μs-long molecular dynamics ensemble via building a comprehensive Markov state model (MSM). Notably, the most populated metastable state corroborates with the dimension obtained from PRE-NMR studies of αS monomer, and it undergoes kinetic transition at diverse time scales with a weakly populated random-coil-like ensemble and a globular protein-like state. However, subjecting αS to a crowded environment results in a nonmonotonic compaction of these metastable conformations, thereby skewing the ensemble by either introducing new tertiary contacts or by reinforcing the innate contacts. The early stage of dimerization process is found to be considerably expedited in the presence of crowders, albeit promoting nonspecific interactions. Together with this, using an extensively sampled ensemble of αS, this exposition demonstrates that crowded environments can potentially modulate the conformational preferences of IDP that can either promote or inhibit aggregation events.
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Affiliation(s)
- Sneha Menon
- Tata Institute of Fundamental Research Hyderabad, Telangana 500046, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research Hyderabad, Telangana 500046, India
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8
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Dupuy E, Van der Verren SE, Lin J, Wilson MA, Dachsbeck AV, Viela F, Latour E, Gennaris A, Vertommen D, Dufrêne YF, Iorga BI, Goemans CV, Remaut H, Collet JF. A molecular device for the redox quality control of GroEL/ES substrates. Cell 2023; 186:1039-1049.e17. [PMID: 36764293 PMCID: PMC10044410 DOI: 10.1016/j.cell.2023.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 10/27/2022] [Accepted: 01/10/2023] [Indexed: 02/11/2023]
Abstract
Hsp60 chaperonins and their Hsp10 cofactors assist protein folding in all living cells, constituting the paradigmatic example of molecular chaperones. Despite extensive investigations of their structure and mechanism, crucial questions regarding how these chaperonins promote folding remain unsolved. Here, we report that the bacterial Hsp60 chaperonin GroEL forms a stable, functionally relevant complex with the chaperedoxin CnoX, a protein combining a chaperone and a redox function. Binding of GroES (Hsp10 cofactor) to GroEL induces CnoX release. Cryoelectron microscopy provided crucial structural information on the GroEL-CnoX complex, showing that CnoX binds GroEL outside the substrate-binding site via a highly conserved C-terminal α-helix. Furthermore, we identified complexes in which CnoX, bound to GroEL, forms mixed disulfides with GroEL substrates, indicating that CnoX likely functions as a redox quality-control plugin for GroEL. Proteins sharing structural features with CnoX exist in eukaryotes, suggesting that Hsp60 molecular plugins have been conserved through evolution.
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Affiliation(s)
- Emile Dupuy
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Sander Egbert Van der Verren
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, 1050 Brussels, Belgium
| | - Jiusheng Lin
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA
| | - Mark Alan Wilson
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA
| | - Alix Vincent Dachsbeck
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Felipe Viela
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Croix du Sud 4-5, 1348 Louvain-la-neuve, Belgium
| | - Emmanuelle Latour
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Alexandra Gennaris
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Didier Vertommen
- de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Yves Frédéric Dufrêne
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Croix du Sud 4-5, 1348 Louvain-la-neuve, Belgium
| | - Bogdan Iuliu Iorga
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium; Université Paris-Saclay, CNRS UPR 2301, Institut de Chimie des Substances Naturelles, 91198 Gif-sur-Yvette, France
| | - Camille Véronique Goemans
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium; European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Han Remaut
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, 1050 Brussels, Belgium.
| | - Jean-François Collet
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium.
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Sharma R, Anupa A, Kateja N, Rathore AS. Optimization of the in-vitro refolding of biotherapeutic Fab Ranibizumab. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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10
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Tomas-Grau R, González-Lizárraga F, Ploper D, Avila CL, Socías SB, Besnault P, Tourville A, Mella RM, Villacé P, Salado C, Rose C, Seon-Méniel B, Brunel JM, Ferrié L, Raisman-Vozari R, Michel PP, Figadère B, Chehín R. Neuroprotective Effects of a Novel Demeclocycline Derivative Lacking Antibiotic Activity: From a Hit to a Promising Lead Compound. Cells 2022; 11:cells11172759. [PMID: 36078167 PMCID: PMC9454755 DOI: 10.3390/cells11172759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 12/09/2022] Open
Abstract
The antibiotic tetracycline demeclocycline (DMC) was recently reported to rescue α-synuclein (α-Syn) fibril-induced pathology. However, the antimicrobial activity of DMC precludes its potential use in long-term neuroprotective treatments. Here, we synthesized a doubly reduced DMC (DDMC) derivative with residual antibiotic activity and improved neuroprotective effects. The molecule was obtained by removal the dimethylamino substituent at position 4 and the reduction of the hydroxyl group at position 12a on ring A of DMC. The modifications strongly diminished its antibiotic activity against Gram-positive and Gram-negative bacteria. Moreover, this compound preserved the low toxicity of DMC in dopaminergic cell lines while improving its ability to interfere with α-Syn amyloid-like aggregation, showing the highest effectiveness of all tetracyclines tested. Likewise, DDMC demonstrated the ability to reduce seeding induced by the exogenous addition of α-Syn preformed fibrils (α-SynPFF) in biophysical assays and in a SH-SY5Y-α-Syn-tRFP cell model. In addition, DDMC rendered α-SynPFF less inflammogenic. Our results suggest that DDMC may be a promising drug candidate for hit-to-lead development and preclinical studies in Parkinson's disease and other synucleinopathies.
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Affiliation(s)
- Rodrigo Tomas-Grau
- Instituto de Investigación en Medicina Molecular y Celular Aplicada (IMMCA) (CONICET-UNT-SIPROSA), Pasaje Dorrego 1080, San Miguel de Tucumán 4000, Argentina
| | - Florencia González-Lizárraga
- Instituto de Investigación en Medicina Molecular y Celular Aplicada (IMMCA) (CONICET-UNT-SIPROSA), Pasaje Dorrego 1080, San Miguel de Tucumán 4000, Argentina
| | - Diego Ploper
- Instituto de Investigación en Medicina Molecular y Celular Aplicada (IMMCA) (CONICET-UNT-SIPROSA), Pasaje Dorrego 1080, San Miguel de Tucumán 4000, Argentina
| | - César L. Avila
- Instituto de Investigación en Medicina Molecular y Celular Aplicada (IMMCA) (CONICET-UNT-SIPROSA), Pasaje Dorrego 1080, San Miguel de Tucumán 4000, Argentina
| | - Sergio B. Socías
- Instituto de Investigación en Medicina Molecular y Celular Aplicada (IMMCA) (CONICET-UNT-SIPROSA), Pasaje Dorrego 1080, San Miguel de Tucumán 4000, Argentina
| | - Pierre Besnault
- Paris Brain Institute-ICM, Inserm, CNRS, Sorbonne Université APHP, Hôpital de la Pitié la Pitié-Salpêtrière, 75013 Paris, France
| | - Aurore Tourville
- Paris Brain Institute-ICM, Inserm, CNRS, Sorbonne Université APHP, Hôpital de la Pitié la Pitié-Salpêtrière, 75013 Paris, France
| | - Rosa M. Mella
- Innoprot SL, Parque Tecnológico de Bizkaia, Edificio 502, 48160 Derio, Spain
| | - Patricia Villacé
- Innoprot SL, Parque Tecnológico de Bizkaia, Edificio 502, 48160 Derio, Spain
| | - Clarisa Salado
- Innoprot SL, Parque Tecnológico de Bizkaia, Edificio 502, 48160 Derio, Spain
| | - Clémence Rose
- BioCIS, Université Paris-Saclay, CNRS, 92290 Châtenay-Malabry, France
| | | | - Jean-Michel Brunel
- UMR_MD1 “Membranes et Cibles Thérapeutiques”, U1261 INSERM, Aix-Marseille Université, 13385 Marseille, France
| | - Laurent Ferrié
- BioCIS, Université Paris-Saclay, CNRS, 92290 Châtenay-Malabry, France
| | - Rita Raisman-Vozari
- Paris Brain Institute-ICM, Inserm, CNRS, Sorbonne Université APHP, Hôpital de la Pitié la Pitié-Salpêtrière, 75013 Paris, France
| | - Patrick P. Michel
- Paris Brain Institute-ICM, Inserm, CNRS, Sorbonne Université APHP, Hôpital de la Pitié la Pitié-Salpêtrière, 75013 Paris, France
| | - Bruno Figadère
- BioCIS, Université Paris-Saclay, CNRS, 92290 Châtenay-Malabry, France
- Correspondence: (B.F.); (R.C.)
| | - Rosana Chehín
- Instituto de Investigación en Medicina Molecular y Celular Aplicada (IMMCA) (CONICET-UNT-SIPROSA), Pasaje Dorrego 1080, San Miguel de Tucumán 4000, Argentina
- Correspondence: (B.F.); (R.C.)
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Dreydoppel M, Balbach J, Weininger U. Monitoring protein unfolding transitions by NMR-spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2022; 76:3-15. [PMID: 34984658 PMCID: PMC9018662 DOI: 10.1007/s10858-021-00389-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/28/2021] [Indexed: 06/01/2023]
Abstract
NMR-spectroscopy has certain unique advantages for recording unfolding transitions of proteins compared e.g. to optical methods. It enables per-residue monitoring and separate detection of the folded and unfolded state as well as possible equilibrium intermediates. This allows a detailed view on the state and cooperativity of folding of the protein of interest and the correct interpretation of subsequent experiments. Here we summarize in detail practical and theoretical aspects of such experiments. Certain pitfalls can be avoided, and meaningful simplification can be made during the analysis. Especially a good understanding of the NMR exchange regime and relaxation properties of the system of interest is beneficial. We show by a global analysis of signals of the folded and unfolded state of GB1 how accurate values of unfolding can be extracted and what limits different NMR detection and unfolding methods. E.g. commonly used exchangeable amides can lead to a systematic under determination of the thermodynamic protein stability. We give several perspectives of how to deal with more complex proteins and how the knowledge about protein stability at residue resolution helps to understand protein properties under crowding conditions, during phase separation and under high pressure.
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Affiliation(s)
- Matthias Dreydoppel
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Jochen Balbach
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany.
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12
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Sakata T, Shiratori R, Kato M. Hydrogel-Coated Gate Field-Effect Transistor for Real-Time and Label-Free Monitoring of β-Amyloid Aggregation and Its Inhibition. Anal Chem 2022; 94:2820-2826. [PMID: 35119275 DOI: 10.1021/acs.analchem.1c04339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this paper, we propose a hydrogel-coated gate field-effect transistor (FET) for the real-time and label-free monitoring of β-amyloid (Aβ) aggregation and its inhibition. The hydrogel used in this study is composed of poly tetramethoxysilane (TMOS), in which Aβ monomers are entrapped and then aggregate, and coated on the gate insulator; that is, Aβ aggregation is induced in the vicinity of the sensing surface. With the Aβ hydrogel-coated gate FET, the steplike decrease in the surface potential of the Aβ hydrogel-coated gate electrode is electrically monitored in real time, according to the stepwise aggregation of Aβ monomers to form into fibrils through oligomers and so forth in stages. This is because the capacitance of the Aβ-hydrogel membrane decreases depending on the stage of aggregation; that is, the hydrophobicity of the Aβ-hydrogel membrane increases stepwise depending on the amount of Aβ aggregates. The formation of Aβ fibrils is also confirmed in the measurement solution using a fluorescent dye, thioflavin T, which selectively binds to the Aβ fibrils. Moreover, the addition of daunomycin, an inhibitor of Aβ aggregation, to the measurement solution suppresses the stepwise electrical response of the Aβ hydrogel-coated gate FET. Thus, a platform based on the Aβ hydrogel-coated gate FET is suitable for a simple screening system for inhibitors of Aβ aggregation, which may lead the identification of potential therapeutic agents for Alzheimer's disease.
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Affiliation(s)
- Toshiya Sakata
- Department of Materials Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Reiko Shiratori
- Department of Materials Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Masaru Kato
- Department of Bioanalytical Chemistry, School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
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13
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Hsueh SS, Wang SS(S, Chen SH, Wang CL, Wu W(J, Lin TH. Insights to Human γD-Crystallin Unfolding by NMR Spectroscopy and Molecular Dynamics Simulations. Int J Mol Sci 2022; 23:ijms23031591. [PMID: 35163513 PMCID: PMC8836049 DOI: 10.3390/ijms23031591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/13/2022] [Accepted: 01/19/2022] [Indexed: 11/16/2022] Open
Abstract
Human γD-crystallin (HGDC) is an abundant lens protein residing in the nucleus of the human lens. Aggregation of this and other structural proteins within the lens leads to the development of cataract. Much has been explored on the stability and aggregation of HGDC and where detailed investigation at the atomic resolution was needed, the X-ray structure was used as an initial starting conformer for molecular modeling. In this study, we implemented NMR-solution HGDC structures as starting conformers for molecular dynamics simulations to provide the missing pieces of the puzzle on the very early stages of HGDC unfolding leading up to the domain swap theories proposed by past studies. The high-resolution details of the conformational dynamics also revealed additional insights to possible early intervention for cataractogenesis.
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Affiliation(s)
- Shu-Shun Hsueh
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; (S.-S.H.); (S.-S.W.); (S.-H.C.)
| | - S.-S. (Steven) Wang
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; (S.-S.H.); (S.-S.W.); (S.-H.C.)
| | - Shu-Han Chen
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; (S.-S.H.); (S.-S.W.); (S.-H.C.)
| | - Chia-Lin Wang
- Laboratory of Nuclear Magnetic Resonance, Medical Research Department, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
| | - W. (Josephine) Wu
- Department of Optometry, Yuanpei University of Medical Technology, Hsinchu City 30015, Taiwan
- Correspondence: (J.W.W.); (T.-H.L.); Tel.: +886-3-538-1183 (ext. 8608) (W.W.); +886-2-28712121 (ext. 2703) (T.-H.L.)
| | - Ta-Hsien Lin
- Laboratory of Nuclear Magnetic Resonance, Medical Research Department, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Correspondence: (J.W.W.); (T.-H.L.); Tel.: +886-3-538-1183 (ext. 8608) (W.W.); +886-2-28712121 (ext. 2703) (T.-H.L.)
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14
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Stopped-flow-time-resolved SAXS for studies of ligand-driven protein dimerization. Methods Enzymol 2022; 677:251-262. [DOI: 10.1016/bs.mie.2022.08.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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15
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Basu A, Mahammad A, Das A. Inhibition of the formation of lysozyme fibrillar assemblies by the isoquinoline alkaloid coralyne. NEW J CHEM 2022. [DOI: 10.1039/d1nj06007d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The isoquinoline alkaloid coralyne can efficiently attenuate fibrillogenesis in lysozyme.
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Affiliation(s)
- Anirban Basu
- Department of Chemistry, Vidyasagar University, Midnapore 721 102, India
| | - Adil Mahammad
- Department of Chemistry, Vidyasagar University, Midnapore 721 102, India
| | - Arindam Das
- Department of Chemistry, Vidyasagar University, Midnapore 721 102, India
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16
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Schwarze B, Korn A, Höfling C, Zeitschel U, Krueger M, Roßner S, Huster D. Peptide backbone modifications of amyloid β (1-40) impact fibrillation behavior and neuronal toxicity. Sci Rep 2021; 11:23767. [PMID: 34887476 PMCID: PMC8660793 DOI: 10.1038/s41598-021-03091-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/25/2021] [Indexed: 11/23/2022] Open
Abstract
Fibril formation of amyloid β (Aβ) peptides is one of the key molecular events connected to Alzheimer's disease. The pathway of formation and mechanism of action of Aβ aggregates in biological systems is still object of very active research. To this end, systematic modifications of the Phe19-Leu34 hydrophobic contact, which has been reported in almost all structural studies of Aβ40 fibrils, helps understanding Aβ folding pathways and the underlying free energy landscape of the amyloid formation process. In our approach, a series of Aβ40 peptide variants with two types of backbone modifications, namely incorporation of (i) a methylene or an ethylene spacer group and (ii) a N-methylation at the amide functional group, of the amino acids at positions 19 or 34 was applied. These mutations are expected to challenge the inter-β-strand side chain contacts as well as intermolecular backbone β-sheet hydrogen bridges. Using a multitude of biophysical methods, it is shown that these backbone modifications lead, in most of the cases, to alterations in the fibril formation kinetics, a higher local structural heterogeneity, and a somewhat modified fibril morphology without generally impairing the fibril formation capacity of the peptides. The toxicological profile found for the variants depend on the type and extent of the modification.
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Affiliation(s)
- Benedikt Schwarze
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Alexander Korn
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Corinna Höfling
- Paul Flechsig Institute for Brain Research, Leipzig University, Liebigstr. 19, 04103, Leipzig, Germany
| | - Ulrike Zeitschel
- Paul Flechsig Institute for Brain Research, Leipzig University, Liebigstr. 19, 04103, Leipzig, Germany
| | - Martin Krueger
- Institute of Anatomy, Leipzig University, Liebigstr. 13, 04103, Leipzig, Germany
| | - Steffen Roßner
- Paul Flechsig Institute for Brain Research, Leipzig University, Liebigstr. 19, 04103, Leipzig, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16/18, 04107, Leipzig, Germany.
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17
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Meyer N, Abrao-Nemeir I, Janot JM, Torrent J, Lepoitevin M, Balme S. Solid-state and polymer nanopores for protein sensing: A review. Adv Colloid Interface Sci 2021; 298:102561. [PMID: 34768135 DOI: 10.1016/j.cis.2021.102561] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/29/2021] [Accepted: 10/31/2021] [Indexed: 01/15/2023]
Abstract
In two decades, the solid state and polymer nanopores became attractive method for the protein sensing with high specificity and sensitivity. They also allow the characterization of conformational changes, unfolding, assembly and aggregation as well the following of enzymatic reaction. This review aims to provide an overview of the protein sensing regarding the technique of detection: the resistive pulse and ionic diodes. For each strategy, we report the most significant achievement regarding the detection of peptides and protein as well as the conformational change, protein-protein assembly and aggregation process. We discuss the limitations and the recent strategies to improve the nanopore resolution and accuracy. A focus is done about concomitant problematic such as protein adsorption and nanopore lifetime.
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18
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Joshi BS, Youssef SA, Bron R, de Bruin A, Kampinga HH, Zuhorn IS. DNAJB6b-enriched small extracellular vesicles decrease polyglutamine aggregation in in vitro and in vivo models of Huntington disease. iScience 2021; 24:103282. [PMID: 34755099 PMCID: PMC8564107 DOI: 10.1016/j.isci.2021.103282] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/12/2021] [Accepted: 10/13/2021] [Indexed: 12/19/2022] Open
Abstract
Huntington disease (HD) is a devastating neurodegenerative disorder characterized by aggregation of huntingtin (HTT) protein containing expanded polyglutamine (polyQ) tracts. DNAJB6, a member of the DNAJ chaperone family, was reported to efficiently inhibit polyQ aggregation in vitro, in cell models, and in vivo in flies, xenopus, and mice. For the delivery of exogenous DNAJB6 to the brain, the DNAJB6 needs to be protected against (enzymatic) degradation and show good penetration into brain tissue. Here, we tested the potential of small extracellular vesicles (sEVs) derived from neural stem cells (NSCs) for delivery of DNAJB6 as anti-amyloidogenic cargo. Administration of sEVs isolated from DNAJB6-overexpressing cells to cells expressing expanded polyQ tracts suppressed HTT aggregation. Furthermore, intrathecal injection of DNAJB6-enriched sEVs into R6/2 transgenic HD mice significantly reduced mutant HTT aggregation in the brain. Taken together, our data suggest that sEV-mediated molecular chaperone delivery may hold potential to delay disease onset in HD.
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Affiliation(s)
- Bhagyashree S. Joshi
- Department of Biomedical Engineering, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, the Netherlands
| | - Sameh A. Youssef
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- Department of Molecular Genetics, Department of Pediatrics, University Medical Center Groningen, Groningen, the Netherlands
| | - Reinier Bron
- Department of Biomedical Engineering, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, the Netherlands
| | - Alain de Bruin
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- Department of Molecular Genetics, Department of Pediatrics, University Medical Center Groningen, Groningen, the Netherlands
| | - Harm H. Kampinga
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Inge S. Zuhorn
- Department of Biomedical Engineering, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, the Netherlands
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19
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Lacroix E, Pereira L, Yoo B, Coyle KM, Chandhok S, Zapf R, Marijan D, Morin RD, Vlachos S, Harden N, Audas TE. Evolutionary conservation of systemic and reversible amyloid aggregation. J Cell Sci 2021; 134:273507. [PMID: 34704593 DOI: 10.1242/jcs.258907] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 10/19/2021] [Indexed: 12/30/2022] Open
Abstract
In response to environmental stress, human cells have been shown to form reversible amyloid aggregates within the nucleus, termed amyloid bodies (A-bodies). These protective physiological structures share many of the biophysical characteristics associated with the pathological amyloids found in Alzheimer's and Parkinson's disease. Here, we show that A-bodies are evolutionarily conserved across the eukaryotic domain, with their detection in Drosophila melanogaster and Saccharomyces cerevisiae marking the first examples of these functional amyloids being induced outside of a cultured cell setting. The conditions triggering amyloidogenesis varied significantly among the species tested, with results indicating that A-body formation is a severe, but sublethal, stress response pathway that is tailored to the environmental norms of an organism. RNA-sequencing analyses demonstrate that the regulatory low-complexity long non-coding RNAs that drive A-body aggregation are both conserved and essential in human, mouse and chicken cells. Thus, the identification of these natural and reversible functional amyloids in a variety of evolutionarily diverse species highlights the physiological significance of this protein conformation, and will be informative in advancing our understanding of both functional and pathological amyloid aggregation events. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Emma Lacroix
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.,Center for Cell Biology, Development, and Disease, Burnaby, BC V5A 1S6, Canada
| | - Lionel Pereira
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.,Center for Cell Biology, Development, and Disease, Burnaby, BC V5A 1S6, Canada
| | - Byoungjoo Yoo
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Krysta M Coyle
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Sahil Chandhok
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.,Center for Cell Biology, Development, and Disease, Burnaby, BC V5A 1S6, Canada
| | - Richard Zapf
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.,Center for Cell Biology, Development, and Disease, Burnaby, BC V5A 1S6, Canada
| | - Dane Marijan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.,Center for Cell Biology, Development, and Disease, Burnaby, BC V5A 1S6, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Stephanie Vlachos
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Nicholas Harden
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.,Center for Cell Biology, Development, and Disease, Burnaby, BC V5A 1S6, Canada
| | - Timothy E Audas
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.,Center for Cell Biology, Development, and Disease, Burnaby, BC V5A 1S6, Canada
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20
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Lee MC, Liao YH, Chen SH, Chen YR. Amyloid-β40 E22K fibril in familial Alzheimer's disease is more thermostable and susceptible to seeding. IUBMB Life 2021; 74:739-747. [PMID: 34724333 DOI: 10.1002/iub.2570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/25/2021] [Accepted: 10/10/2021] [Indexed: 11/11/2022]
Abstract
Alzheimer's disease (AD) is the most prevalent and devastating neurodegenerative disease occurred in the elderly. One of the pathogenic hallmarks is senile plaques composed of amyloid-β (Aβ) fibrils. Single mutations resided in Aβ were found in familial AD (FAD) patients that have early onset of the disease. The molecular details and properties of each FAD Aβ variants are still elusive. Here, we employed collective spectroscopic techniques to examine the properties of various Aβ40 fibrils. We generated fibrils of wild type (WT) and three FAD mutants on residue E22 including E22G, E22K, and E22Q. We monitored fibril formation by thioflavin T (ThT) assay, examined secondary structure by Fourier transform infrared and far-UV circular dichroism spectroscopy, imaged fibril morphology by transmission electron microscopy, and evaluated ThT-binding kinetics. In the thermal experiments, we found E22K fibrils resisted to high temperature and retained significant β-sheet content than the others. E22K fibril seeds after high-temperature treatment still possess the seeding property, whereas WT fibril seeds are disturbed after the treatment. Therefore, in this study we demonstrated the mutation at E22K increases the thermal stability and seeding function of amyloid fibrils.
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Affiliation(s)
- Ming-Che Lee
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Yi-Hung Liao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Shih-Hui Chen
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, Taiwan
| | - Yun-Ru Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
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21
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Sulatskaya AI, Kosolapova AO, Bobylev AG, Belousov MV, Antonets KS, Sulatsky MI, Kuznetsova IM, Turoverov KK, Stepanenko OV, Nizhnikov AA. β-Barrels and Amyloids: Structural Transitions, Biological Functions, and Pathogenesis. Int J Mol Sci 2021; 22:11316. [PMID: 34768745 PMCID: PMC8582884 DOI: 10.3390/ijms222111316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 01/17/2023] Open
Abstract
Insoluble protein aggregates with fibrillar morphology called amyloids and β-barrel proteins both share a β-sheet-rich structure. Correctly folded β-barrel proteins can not only function in monomeric (dimeric) form, but also tend to interact with one another-followed, in several cases, by formation of higher order oligomers or even aggregates. In recent years, findings proving that β-barrel proteins can adopt cross-β amyloid folds have emerged. Different β-barrel proteins were shown to form amyloid fibrils in vitro. The formation of functional amyloids in vivo by β-barrel proteins for which the amyloid state is native was also discovered. In particular, several prokaryotic and eukaryotic proteins with β-barrel domains were demonstrated to form amyloids in vivo, where they participate in interspecies interactions and nutrient storage, respectively. According to recent observations, despite the variety of primary structures of amyloid-forming proteins, most of them can adopt a conformational state with the β-barrel topology. This state can be intermediate on the pathway of fibrillogenesis ("on-pathway state"), or can be formed as a result of an alternative assembly of partially unfolded monomers ("off-pathway state"). The β-barrel oligomers formed by amyloid proteins possess toxicity, and are likely to be involved in the development of amyloidoses, thus representing promising targets for potential therapy of these incurable diseases. Considering rapidly growing discoveries of the amyloid-forming β-barrels, we may suggest that their real number and diversity of functions are significantly higher than identified to date, and represent only "the tip of the iceberg". Here, we summarize the data on the amyloid-forming β-barrel proteins, their physicochemical properties, and their biological functions, and discuss probable means and consequences of the amyloidogenesis of these proteins, along with structural relationships between these two widespread types of β-folds.
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Affiliation(s)
- Anna I. Sulatskaya
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Anastasiia O. Kosolapova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Alexander G. Bobylev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 3 Institutskaya St., 142290 Moscow, Russia;
| | - Mikhail V. Belousov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Maksim I. Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia;
| | - Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Olesya V. Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
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22
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Macošek J, Mas G, Hiller S. Redefining Molecular Chaperones as Chaotropes. Front Mol Biosci 2021; 8:683132. [PMID: 34195228 PMCID: PMC8237284 DOI: 10.3389/fmolb.2021.683132] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/20/2021] [Indexed: 01/27/2023] Open
Abstract
Molecular chaperones are the key instruments of bacterial protein homeostasis. Chaperones not only facilitate folding of client proteins, but also transport them, prevent their aggregation, dissolve aggregates and resolve misfolded states. Despite this seemingly large variety, single chaperones can perform several of these functions even on multiple different clients, thus suggesting a single biophysical mechanism underlying. Numerous recently elucidated structures of bacterial chaperone–client complexes show that dynamic interactions between chaperones and their client proteins stabilize conformationally flexible non-native client states, which results in client protein denaturation. Based on these findings, we propose chaotropicity as a suitable biophysical concept to rationalize the generic activity of chaperones. We discuss the consequences of applying this concept in the context of ATP-dependent and -independent chaperones and their functional regulation.
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23
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Shafiq K, Sanghai N, Guo Y, Kong J. Implication of post-translationally modified SOD1 in pathological aging. GeroScience 2021; 43:507-515. [PMID: 33608813 PMCID: PMC8110659 DOI: 10.1007/s11357-021-00332-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 01/31/2021] [Indexed: 12/18/2022] Open
Abstract
Why certain people relish healthy aging throughout their life span while others suffer pathological consequences? In this review, we focus on some of the dominant paradigms of pathological aging, such as amyotrophic lateral sclerosis (ALS), Alzheimer's disease (AD), and Parkinson's disease (PD), and predict that the antioxidant superoxide dismutase 1 (SOD1), when post-translationally modified by aging-associated oxidative stress, acts as a mechanism to accelerated aging in these age-related neurodegenerative diseases. Oxidative modifications of natively reduced SOD1 induce pathological confirmations such as misfolding, leading to a subsequent formation of monomeric, oligomeric, and multimeric aggregates. Misfolded SOD1 propagates like prions from cell to cell. These modified conformations are detected in brain tissues in ALS, AD, and PD, and are considered a contributing factor to their initial pathogenesis. We have also elaborated on oxidative stress-induced non-native modifications of SOD1 and offered a logistic argument on their global implication in accelerated or pathological aging in the context of ALS, AD, and PD.
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Affiliation(s)
- Kashfia Shafiq
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Science, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, 27, King's College Cir, Toronto, ON, M5S, Canada
| | - Nitesh Sanghai
- College of Pharmacy, Rady Faculty of Health Science, University of Manitoba, Winnipeg, MB, R3E 0T5, Canada
| | - Ying Guo
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Science, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada.,Pathological Department, Hebei North University, Zhangjiakou, Hebei, China
| | - Jiming Kong
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Science, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada.
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24
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Response to crowded conditions reveals compact nucleus for amyloid formation of folded protein. QRB DISCOVERY 2021. [PMID: 37529678 PMCID: PMC10392690 DOI: 10.1017/qrd.2020.17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract
Although the consequences of the crowded cell environments may affect protein folding, function and misfolding reactions, these processes are often studied in dilute solutions in vitro. We here used biophysical experiments to investigate the amyloid fibril formation process of the fish protein apo-β-parvalbumin in solvent conditions that mimic steric and solvation aspects of the in vivo milieu. Apo-β-parvalbumin is a folded protein that readily adopts an amyloid state via a nucleation–elongation mechanism. Aggregation experiments in the presence of macromolecular crowding agents (probing excluded volume, entropic effects) as well as small molecule osmolytes (probing solvation, enthalpic effects) revealed that both types of agents accelerate overall amyloid formation, but the elongation step was faster with macromolecular crowding agents but slower in the presence of osmolytes. The observations can be explained by the steric effects of excluded volume favoring assembled states and that amyloid nucleation does not involve monomer unfolding. In contrast, the solvation effects due to osmolyte presence promote nucleation but not elongation. Therefore, the amyloid-competent nuclei must be compact with less osmolytes excluded from the surface than either the folded monomers or amyloid fibers. We conclude that, in contrast to other amyloidogenic folded proteins, amyloid formation of apo-β-parvalbumin is accelerated by crowded cell-like conditions due to a nucleation process that does not involve large-scale protein unfolding.
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Bhat S, El-Kasaby A, Freissmuth M, Sucic S. Functional and Biochemical Consequences of Disease Variants in Neurotransmitter Transporters: A Special Emphasis on Folding and Trafficking Deficits. Pharmacol Ther 2020; 222:107785. [PMID: 33310157 PMCID: PMC7612411 DOI: 10.1016/j.pharmthera.2020.107785] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/02/2020] [Indexed: 01/30/2023]
Abstract
Neurotransmitters, such as γ-aminobutyric acid, glutamate, acetyl choline, glycine and the monoamines, facilitate the crosstalk within the central nervous system. The designated neurotransmitter transporters (NTTs) both release and take up neurotransmitters to and from the synaptic cleft. NTT dysfunction can lead to severe pathophysiological consequences, e.g. epilepsy, intellectual disability, or Parkinson’s disease. Genetic point mutations in NTTs have recently been associated with the onset of various neurological disorders. Some of these mutations trigger folding defects in the NTT proteins. Correct folding is a prerequisite for the export of NTTs from the endoplasmic reticulum (ER) and the subsequent trafficking to their pertinent site of action, typically at the plasma membrane. Recent studies have uncovered some of the key features in the molecular machinery responsible for transporter protein folding, e.g., the role of heat shock proteins in fine-tuning the ER quality control mechanisms in cells. The therapeutic significance of understanding these events is apparent from the rising number of reports, which directly link different pathological conditions to NTT misfolding. For instance, folding-deficient variants of the human transporters for dopamine or GABA lead to infantile parkinsonism/dystonia and epilepsy, respectively. From a therapeutic point of view, some folding-deficient NTTs are amenable to functional rescue by small molecules, known as chemical and pharmacological chaperones.
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Affiliation(s)
- Shreyas Bhat
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Ali El-Kasaby
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Michael Freissmuth
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Sonja Sucic
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, A-1090 Vienna, Austria.
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Malakouti-Nejad M, Bardania H, Aliakbari F, Baradaran-Rafii A, Elahi E, Monti D, Morshedi D. Formulation of nanoliposome-encapsulated bevacizumab (Avastin): Statistical optimization for enhanced drug encapsulation and properties evaluation. Int J Pharm 2020; 590:119895. [PMID: 32956821 DOI: 10.1016/j.ijpharm.2020.119895] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 01/01/2023]
Abstract
Bevacizumab (Avastin®), an anti-vascular endothelial growth factor, is one of the most effective drugs widely used to inhibit ocular angiogenesis. Nanoliposomes were recruited to improve the accessibility of bevacizumab (BVZ) during treatment. To optimize drug entrapment efficiency (DEE %), the effect of some independent variables was evaluated utilizing response surface methodology. The optimized formulation containing BVZ (NLP-BVZ) was characterized, and its safety was assessed. Employingarising retinalpigment epithelial (ARPE) cells, the permeability of the nanoliposome was analyzed. Structural stability and integrity of NLP-BVZ were also estimated with different methods. Optimal condition for the maximum DEE (39.9%) was obtained with cholesterol/DPPC (1,2-Dipalimitoyl-Sn-glycero-3-phosphocholine) (%w/w) 13.64, BVZ/DPPC (%w/w) 83.78 and 9 freeze-thaw cycles. Neutral fabricated NLP-BVZ with an average size of 141.5 ± 45.8 nm showed a smooth spherical structure and released the drug in a slow and sustained fashion. The formulation exhibited no obvious effect against human umbilical vein endothelial cells (HUVECs) and ARPEs. Additionally, the pattern of the circular dichroism (CD) and intrinsic fluorescence spectra confirmed the structural integrity of protein remained conserved after encapsulation. Taken together, the analysis indicated that the process of entrapment into nanoliposome meaningfully made the drug safer, more stable, and, therefore, appropriate for treating ocular disorders.
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Affiliation(s)
- Maryam Malakouti-Nejad
- Bioprocess Engineering Department, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Hassan Bardania
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran; Clinical Research Development Unit, Imamsajad Hospital, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Farhang Aliakbari
- Bioprocess Engineering Department, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Alireza Baradaran-Rafii
- Ocular Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, No 23, Paydarfard-9th Boostan St., Pasdaran Ave, Tehran, Iran
| | - Elahe Elahi
- School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Daniela Monti
- Department of Pharmacy, University of Pisa, via Bonanno 33, 56126 Pisa, Italy
| | - Dina Morshedi
- Bioprocess Engineering Department, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.
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27
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Sun H, Calabrese EJ, Lin Z, Lian B, Zhang X. Similarities between the Yin/Yang Doctrine and Hormesis in Toxicology and Pharmacology. Trends Pharmacol Sci 2020; 41:544-556. [PMID: 32564900 PMCID: PMC7302776 DOI: 10.1016/j.tips.2020.05.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/24/2020] [Accepted: 05/25/2020] [Indexed: 01/01/2023]
Abstract
Hormesis is a generalizable dose-response relationship characterized by low-dose stimulation and high-dose inhibition. Despite debate over this biphasic dose-response curve, hormesis is challenging central beliefs in the evaluation of chemicals or drugs and has influenced biological model selection, concentration range, study design, and hypothesis testing. We integrate the traditional Chinese philosophy - Yin/Yang doctrine - into the representation of the Western hormetic dose-response relationship and review the Yin/Yang historical philosophy contained in the hormesis concept, aiming to promote general acceptance and wider applications of hormesis. We suggest that the Yin/Yang doctrine embodies the hormetic dose-response, including the relationship between the opposing components, curve shape, and time-dependence, and may afford insights that clarify the hormetic dose-response relationship in toxicology and pharmacology.
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Affiliation(s)
- Haoyu Sun
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China; Post-Doctoral Research Station, College of Civil Engineering, Tongji University, Shanghai 200092, China; Shanghai Key Laboratory of Chemical Assessment and Sustainability, Shanghai, China.
| | - Edward J Calabrese
- Department of Public Health, Environmental Health Sciences, Morrill I, N344, University of Massachusetts, Amherst, MA 01003, USA
| | - Zhifen Lin
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China; Shanghai Key Laboratory of Chemical Assessment and Sustainability, Shanghai, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences
| | - Baoling Lian
- Huadong Hospital Affiliated to Fudan University, 221 West Yan'an Road, Shanghai, China
| | - Xiaoxian Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
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Qin X, Denton WD, Huiting LN, Smith KS, Feng H. Unraveling the regulatory role of endoplasmic-reticulum-associated degradation in tumor immunity. Crit Rev Biochem Mol Biol 2020; 55:322-353. [PMID: 32633575 DOI: 10.1080/10409238.2020.1784085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
During malignant transformation and cancer progression, tumor cells face both intrinsic and extrinsic stress, endoplasmic reticulum (ER) stress in particular. To survive and proliferate, tumor cells use multiple stress response pathways to mitigate ER stress, promoting disease aggression and treatment resistance. Among the stress response pathways is ER-associated degradation (ERAD), which consists of multiple components and steps working together to ensure protein quality and quantity. In addition to its established role in stress responses and tumor cell survival, ERAD has recently been shown to regulate tumor immunity. Here we summarize current knowledge on how ERAD promotes protein degradation, regulates immune cell development and function, participates in antigen presentation, exerts paradoxical roles on tumorigenesis and immunity, and thus impacts current cancer therapy. Collectively, ERAD is a critical protein homeostasis pathway intertwined with cancer development and tumor immunity. Of particular importance is the need to further unveil ERAD's enigmatic roles in tumor immunity to develop effective targeted and combination therapy for successful treatment of cancer.
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Affiliation(s)
- Xiaodan Qin
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, Center for Cancer Research, Boston University School of Medicine, Boston, MA, USA
| | - William D Denton
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, Center for Cancer Research, Boston University School of Medicine, Boston, MA, USA
| | - Leah N Huiting
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, Center for Cancer Research, Boston University School of Medicine, Boston, MA, USA
| | - Kaylee S Smith
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, Center for Cancer Research, Boston University School of Medicine, Boston, MA, USA
| | - Hui Feng
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, Center for Cancer Research, Boston University School of Medicine, Boston, MA, USA
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29
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Rein T. Peptidylprolylisomerases, Protein Folders, or Scaffolders? The Example of FKBP51 and FKBP52. Bioessays 2020; 42:e1900250. [DOI: 10.1002/bies.201900250] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/12/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Theo Rein
- Department of Translational Science in Psychiatry, MunichMax Planck Institute of Psychiatry Munich 80804 Germany
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30
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Haque E, Kamil M, Hasan A, Irfan S, Sheikh S, Khatoon A, Nazir A, Mir SS. Advanced glycation end products (AGEs), protein aggregation and their cross talk: new insight in tumorigenesis. Glycobiology 2020; 30:49-57. [PMID: 31508802 DOI: 10.1093/glycob/cwz073] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 08/21/2019] [Accepted: 08/28/2019] [Indexed: 12/15/2022] Open
Abstract
Protein glycation and protein aggregation are two distinct phenomena being observed in cancer cells as factors promoting cancer cell viability. Protein aggregation is an abnormal interaction between proteins caused as a result of structural changes in them after any mutation or environmental assault. Protein aggregation is usually associated with neurodegenerative diseases like Alzheimer's and Parkinson's, but of late, research findings have shown its association with the development of different cancers like lung, breast and ovarian cancer. On the contrary, protein glycation is a cascade of irreversible nonenzymatic reaction of reducing sugar with the amino group of the protein resulting in the modification of protein structure and formation of advanced glycation end products (AGEs). These AGEs are reported to obstruct the normal function of proteins. Lately, it has been reported that protein aggregation occurs as a result of AGEs. This aggregation of protein promotes the transformation of healthy cells to neoplasia leading to tumorigenesis. In this review, we underline the current knowledge of protein aggregation and glycation along with the cross talk between the two, which may eventually lead to the development of cancer.
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Affiliation(s)
- Ejazul Haque
- Department of Biosciences, Faculty of Science, Integral University, Kursi Road, Lucknow 226026, India.,Department of Immunology and Medical Genetics, School of Medicine, University of Split, Soltanskaul. 2, 21000, Split, Croatia
| | - Mohd Kamil
- Department of Biosciences, Faculty of Science, Integral University, Kursi Road, Lucknow 226026, India.,Department of Immunology and Medical Genetics, School of Medicine, University of Split, Soltanskaul. 2, 21000, Split, Croatia.,Department of Microbiology, Beykoz Life Sciences and Biotechnology Institute (BILSAB), Bezmialem Vakif University, Istanbul, Turkey
| | - Adria Hasan
- Department of Bioengineering, Faculty of Engineering, Integral University, Kursi Road, Lucknow 226026, India
| | - Safia Irfan
- Department of Bioengineering, Faculty of Engineering, Integral University, Kursi Road, Lucknow 226026, India
| | - Saba Sheikh
- Department of Biosciences, Faculty of Science, Integral University, Kursi Road, Lucknow 226026, India
| | - Aisha Khatoon
- Department of Bioengineering, Faculty of Engineering, Integral University, Kursi Road, Lucknow 226026, India
| | - Aamir Nazir
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram extension, Sitapur Road, Lucknow, 226031, India
| | - Snober S Mir
- Department of Bioengineering, Faculty of Engineering, Integral University, Kursi Road, Lucknow 226026, India
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31
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Yadav K, Yadav A, Vashistha P, Pandey VP, Dwivedi UN. Protein Misfolding Diseases and Therapeutic Approaches. Curr Protein Pept Sci 2020; 20:1226-1245. [PMID: 31187709 DOI: 10.2174/1389203720666190610092840] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/01/2019] [Accepted: 02/24/2019] [Indexed: 12/12/2022]
Abstract
Protein folding is the process by which a polypeptide chain acquires its functional, native 3D structure. Protein misfolding, on the other hand, is a process in which protein fails to fold into its native functional conformation. This misfolding of proteins may lead to precipitation of a number of serious diseases such as Cystic Fibrosis (CF), Alzheimer's Disease (AD), Parkinson's Disease (PD), and Amyotrophic Lateral Sclerosis (ALS) etc. Protein Quality-control (PQC) systems, consisting of molecular chaperones, proteases and regulatory factors, help in protein folding and prevent its aggregation. At the same time, PQC systems also do sorting and removal of improperly folded polypeptides. Among the major types of PQC systems involved in protein homeostasis are cytosolic, Endoplasmic Reticulum (ER) and mitochondrial ones. The cytosol PQC system includes a large number of component chaperones, such as Nascent-polypeptide-associated Complex (NAC), Hsp40, Hsp70, prefoldin and T Complex Protein-1 (TCP-1) Ring Complex (TRiC). Protein misfolding diseases caused due to defective cytosolic PQC system include diseases involving keratin/collagen proteins, cardiomyopathies, phenylketonuria, PD and ALS. The components of PQC system of Endoplasmic Reticulum (ER) include Binding immunoglobulin Protein (BiP), Calnexin (CNX), Calreticulin (CRT), Glucose-regulated Protein GRP94, the thiol-disulphide oxidoreductases, Protein Disulphide Isomerase (PDI) and ERp57. ER-linked misfolding diseases include CF and Familial Neurohypophyseal Diabetes Insipidus (FNDI). The components of mitochondrial PQC system include mitochondrial chaperones such as the Hsp70, the Hsp60/Hsp10 and a set of proteases having AAA+ domains similar to the proteasome that are situated in the matrix or the inner membrane. Protein misfolding diseases caused due to defective mitochondrial PQC system include medium-chain acyl-CoA dehydrogenase (MCAD)/Short-chain Acyl-CoA Dehydrogenase (SCAD) deficiency diseases, hereditary spastic paraplegia. Among therapeutic approaches towards the treatment of various protein misfolding diseases, chaperones have been suggested as potential therapeutic molecules for target based treatment. Chaperones have been advantageous because of their efficient entry and distribution inside the cells, including specific cellular compartments, in therapeutic concentrations. Based on the chemical nature of the chaperones used for therapeutic purposes, molecular, chemical and pharmacological classes of chaperones have been discussed.
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Affiliation(s)
- Kusum Yadav
- Department of Biochemistry, University of Lucknow, Lucknow, U.P, India
| | - Anurag Yadav
- Department of Microbiology, College of Basic Sciences and Humanities, Sardar Krushinagar Dantiwada Agricultural University, Banaskantha, Gujarat, India
| | | | - Veda P Pandey
- Department of Biochemistry, University of Lucknow, Lucknow, U.P, India
| | - Upendra N Dwivedi
- Department of Biochemistry, University of Lucknow, Lucknow, U.P, India.,Institute for Development of Advanced Computing, ONGC Centre for Advanced Studies, University of Lucknow, Lucknow, U.P., India
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32
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Da Silva JD, Teixeira-Castro A, Maciel P. From Pathogenesis to Novel Therapeutics for Spinocerebellar Ataxia Type 3: Evading Potholes on the Way to Translation. Neurotherapeutics 2019; 16:1009-1031. [PMID: 31691128 PMCID: PMC6985322 DOI: 10.1007/s13311-019-00798-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Spinocerebellar ataxia type 3 (SCA3), also known as Machado-Joseph disease (MJD), is a neurodegenerative disorder caused by a polyglutamine expansion in the ATXN3 gene. In spite of the identification of a clear monogenic cause 25 years ago, the pathological process still puzzles researchers, impairing prospects for an effective therapy. Here, we propose the disruption of protein homeostasis as the hub of SCA3 pathogenesis, being the molecular mechanisms and cellular pathways that are deregulated in SCA3 downstream consequences of the misfolding and aggregation of ATXN3. Moreover, we attempt to provide a realistic perspective on how the translational/clinical research in SCA3 should evolve. This was based on molecular findings, clinical and epidemiological characteristics, studies of proposed treatments in other conditions, and how that information is essential for their (re-)application in SCA3. This review thus aims i) to critically evaluate the current state of research on SCA3, from fundamental to translational and clinical perspectives; ii) to bring up the current key questions that remain unanswered in this disorder; and iii) to provide a frame on how those answers should be pursued.
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Affiliation(s)
- Jorge Diogo Da Silva
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Andreia Teixeira-Castro
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Patrícia Maciel
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.
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33
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Lyon MS, Milligan C. Extracellular heat shock proteins in neurodegenerative diseases: New perspectives. Neurosci Lett 2019; 711:134462. [PMID: 31476356 DOI: 10.1016/j.neulet.2019.134462] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/23/2019] [Accepted: 08/24/2019] [Indexed: 01/20/2023]
Abstract
One pathological hallmark of neurodegenerative diseases and CNS trauma is accumulation of insoluble, hydrophobic molecules and protein aggregations found both within and outside cells. These may be the consequences of an inadequate or overburdened cellular response to stresses resulting from potentially toxic changes in extra- and intracellular environments. The upregulated expression of heat shock proteins (HSPs) is one example of a highly conserved cellular response to both internal and external stress. Intracellularly these proteins act as chaperones, playing vital roles in the folding of nascent polypeptides, the translocation of proteins between subcellular locations, and the disaggregation of misfolded or aggregated proteins in an attempt to maintain cellular proteostasis during both homeostatic and stressful conditions. While the predominant study of the HSPs has focused on their intracellular chaperone functions, it remains unclear if all neuronal populations can mount a complete stress response. Alternately, it is now well established that some members of this family of proteins can be secreted by nearby, non-neuronal cells to act in the extracellular environment. This review addresses the current literature detailing the use of exogenous and extracellular HSPs in the treatment of cellular and animal models of neurodegenerative disease. These findings offer a new measure of therapeutic potential to the HSPs, but obstacles must be overcome before they can be efficiently used in a clinical setting.
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Affiliation(s)
- Miles S Lyon
- Department of Neurobiology and Anatomy, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States
| | - Carol Milligan
- Department of Neurobiology and Anatomy, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States.
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34
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Coglitore D, Janot JM, Balme S. Protein at liquid solid interfaces: Toward a new paradigm to change the approach to design hybrid protein/solid-state materials. Adv Colloid Interface Sci 2019; 270:278-292. [PMID: 31306853 DOI: 10.1016/j.cis.2019.07.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/04/2019] [Accepted: 07/05/2019] [Indexed: 10/26/2022]
Abstract
This review gives an overview of protein adsorption at solid/liquid interface. Compared to the other ones, we have focus on three main questions with the point of view of the protein. The first question is related to the kinetic and especially the using of Langmuir model to describe the protein adsorption. The second question is about the concept of hard and soft protein. In this part, we report the protein structural modification induced by adsorption regarding their intrinsic structure. This allows formulating of a new concept to classify the protein to predict their behavior at solid/liquid interface. The last question is related to the protein corona. We give an overview about the soft/hard corona and attempt to make correlation with the concept of hard/soft protein.
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35
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Kuhn AJ, Raskatov JA. Using mirror-image peptides to enhance robustness and reproducibility in studying the amyloid β-protein. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 168:57-67. [PMID: 31699327 DOI: 10.1016/bs.pmbts.2019.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Alzheimer's disease, the most common form of dementia, is a devastating disease that affects over 44 million people worldwide. One etiological agent of Alzheimer's, the amyloid β-protein (Aβ), is an aggregation-prone, intrinsically disordered peptide that can form a wide variety of aggregates. The pathways by which Aβ aggregates in order to exert its toxicity, referred to as the Amyloid Cascade, remains largely elusive despite substantial deconvolution efforts. Preparing high-quality material that exhibits reproducible biophysical characteristics has proven challenging. Herein, we propose that mirror-image peptides can be used to rigorously control Aβ preparation quality.
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Affiliation(s)
- Ariel J Kuhn
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, United States
| | - Jevgenij A Raskatov
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, United States.
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36
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Chaari A. Molecular chaperones biochemistry and role in neurodegenerative diseases. Int J Biol Macromol 2019; 131:396-411. [DOI: 10.1016/j.ijbiomac.2019.02.148] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 02/07/2023]
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37
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Menon S, Sengupta N. The Cold Thermal Response of an Amyloid Oligomer Differs from Typical Globular Protein Cold Denaturation. J Phys Chem Lett 2019; 10:2453-2457. [PMID: 31002516 DOI: 10.1021/acs.jpclett.9b00709] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In contrast with the general behavior of folded proteins, the cold thermal response of amyloid assemblies is difficult to elicit with simple models. We exploit exhaustive simulations to evaluate the thermal response of a barrel-shaped model amyloid oligomer, with a distinct hydrophobic core akin to that of folded proteins. Cumulative thermal data over the range of 210-483 K indicate a sharp inflection and rise in structural stability as the temperature is decreased below the melting temperature of the water model. This is not commensurate with the equilibrium free energy profile obtained with core packing as the order parameter. However, energetic analyses and the size of their fluctuations indicate the crucial role of hydration in mediating structural transitions, beyond the expected temperature-dependent hydrophobic effect. Structural ordering of the hydration layer over bulk water is maximized at the transition and vanishes at high temperatures. This is a first direct demonstration of the microscopic influence of hydration water on the low-temperature response of an amyloid assembly close to the cryo-regime.
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Affiliation(s)
- Sneha Menon
- Physical Chemistry Division , CSIR-National Chemical Laboratory , Pune 411008 , India
- Academy of Scientific and Innovative Research (AcSIR) , Ghaziabad 201002 , India
| | - Neelanjana Sengupta
- Department of Biological Sciences , Indian Institute of Science Education and Research Kolkata , Mohanpur 741246 , India
- Centre for Advanced Functional Materials (CAFM) , Indian Institute of Science Education and Research Kolkata , Mohanpur 741246 , India
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38
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Olzscha H. Posttranslational modifications and proteinopathies: how guardians of the proteome are defeated. Biol Chem 2019; 400:895-915. [DOI: 10.1515/hsz-2018-0458] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/13/2019] [Indexed: 01/15/2023]
Abstract
Abstract
Protein folding is one of the fundamental processes in life and therefore needs to be tightly regulated. Many cellular quality control systems are in place to ensure that proteostasis is optimally adjusted for a changing environment, facilitating protein folding, translocation and degradation. These systems include the molecular chaperones and the major protein degradation systems, namely the ubiquitin proteasome system and autophagy. However, the capacity of the quality control systems can be exhausted and protein misfolding and aggregation, including the formation of amyloids, can occur as a result of ageing, mutations or exogenous influences. There are many known diseases in which protein misfolding and aggregation can be the underlying cause of the pathological condition; these are referred to as proteinopathies. Over the last decade, it has become clear that posttranslational modifications can govern and modulate protein folding, and that aberrant posttranslational modifications can cause or contribute to proteinopathies. This review provides an overview of protein folding and misfolding and the role of the major protein quality control systems. It focusses on different posttranslational modifications and gives examples of how these posttranslational modifications can alter protein folding and cause or accompany proteinopathies.
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Affiliation(s)
- Heidi Olzscha
- Institut für Physiologische Chemie , Medizinische Fakultät, Martin-Luther-Universität Halle-Wittenberg , Hollystr. 1 , D-06114 Halle/Saale , Germany
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Aoki E, Ikeguchi M. In vitro assembly of Haemophilus influenzae adhesin transmembrane domain and studies on the electrostatic repulsion at the interface. Biophys Rev 2019; 11:303-309. [PMID: 31073957 DOI: 10.1007/s12551-019-00535-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 04/25/2019] [Indexed: 11/24/2022] Open
Abstract
Haemophilus influenzae adhesin (Hia) belongs to the trimeric autotransporter family, and it mediates the adherence of these bacteria to the epithelial cells of host organisms. Hia is composed of the passenger domain, which is a virulence factor, and the translocator domain, which anchors the passenger domain into the outer membrane. The Hia transmembrane domain forms a transmembrane β-barrel of 12 β-strands, four of which are provided from each subunit. The β-barrel has a pore that is traversed by three α-helices, one of which is provided from each subunit. This domain has a unique arginine arrangement inside the β-barrel. The side chains of the arginine residues protrude from the β-strands of three subunits toward the center of the barrel and are close to each other. Mutation of this arginine residue revealed the importance of the electrostatic repulsion between the three arginines. Electrostatic repulsion is considered to prevent misfolding and/or misassembly. The arginine clusters at the interface were found in several proteins and might generally play an important role in the assembly of the oligomer.
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Affiliation(s)
- Eriko Aoki
- Department of Bioinformatics, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo, 192-8577, Japan.
| | - Masamichi Ikeguchi
- Department of Bioinformatics, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo, 192-8577, Japan
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40
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Ahmadi S, Zhu S, Sharma R, Wu B, Soong R, Dutta Majumdar R, Wilson DJ, Simpson AJ, Kraatz HB. Aggregation of Microtubule Binding Repeats of Tau Protein is Promoted by Cu 2. ACS OMEGA 2019; 4:5356-5366. [PMID: 31001602 PMCID: PMC6463671 DOI: 10.1021/acsomega.8b03595] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/05/2019] [Indexed: 06/09/2023]
Abstract
Understanding the factors that give rise to tau aggregation and reactive oxygen species (ROS) is the key aspect in Alzheimer's disease pathogenesis. Microtubule (MT) binding repeats of tau protein were suggested to play a critical role in tau aggregation. Here, we show that the interaction of Cu2+ with full-length MT binding repeats R1-R4 leads to the aggregation, and a Cys-based redox chemistry is critically involved in tau aggregation leading to disulfide-bridge dimerization of R2 and R3 and further aggregation into a fibrillar structure. Notably, ascorbate and glutathione, the most abundant antioxidants in neurons, cannot prevent the effect of Cu2+ on R2 and R3 aggregation. Detailed ESI-MS and NMR experiments demonstrate the interaction of Cu2+ with MT binding repeats. We show that redox activity of copper increases when bound to the MT repeats leading to ROS formation, which significantly contribute to cellular damage and neuron death. Results presented here provide new insights into the molecular mechanism of tau aggregation and ROS formation and suggest a new target domain for tau aggregation inhibitors.
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Affiliation(s)
- Soha Ahmadi
- Department
of Physical and Environmental Science, University
of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 1A1, Canada
| | - Shaolong Zhu
- Chemistry
Department, York University, Toronto, Ontario M3J1P3, Canada
- The
Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J1P3, Canada
| | - Renu Sharma
- Department
of Physical and Environmental Science, University
of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
| | - Bing Wu
- Department
of Physical and Environmental Science, University
of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
| | - Ronald Soong
- Department
of Physical and Environmental Science, University
of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 1A1, Canada
| | - R. Dutta Majumdar
- Department
of Physical and Environmental Science, University
of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
| | - Derek J. Wilson
- Chemistry
Department, York University, Toronto, Ontario M3J1P3, Canada
- The
Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J1P3, Canada
| | - Andre J. Simpson
- Department
of Physical and Environmental Science, University
of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 1A1, Canada
| | - Heinz-Bernhard Kraatz
- Department
of Physical and Environmental Science, University
of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 1A1, Canada
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41
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Influence of crowding and surfaces on protein amyloidogenesis: A thermo-kinetic perspective. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:941-953. [PMID: 30928692 DOI: 10.1016/j.bbapap.2019.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 01/24/2023]
Abstract
The last few decades have irreversibly implicated protein self-assembly and aggregation leading to amyloid fibril formation in proteopathies that include several neurodegenerative diseases. Emerging studies recognize the importance of eliciting the pathways leading to protein aggregation in the context of the crowded intracellular environment rather than in conventional in vitro conditions. It is found that crowded environments can have acceleratory as well as inhibitory effects on protein aggregation, depending on the interplay of underlying factors on the crucial rate limiting steps. The aggregation mechanism and transient species formed along the pathway are further altered when they interface with natural and artificial surfaces in the cellular milieu. An increasing number of studies probe the autocatalytic nature of amyloid surfaces as well as membrane bilayer effects on amyloidogenesis. Moreover, exposure to modern nanosurfaces via nanomedicines and other sources potentially invokes beneficial or deleterious biological response that needs rigorous investigation. Mounting evidences indicate that nanoparticles can either promote or impede amyloid aggregation, spurring efforts to tune their interactions for developing effective anti-amyloid strategies. Mechanistic insights into nanoparticle mediated aggregation pathways are therefore crucial for engineering anti-amyloid nanoparticle strategies that are biocompatible and sustainable. This review is a compilation of studies that contribute to the current understanding of the altering effects of molecular crowding as well as natural and artificial surfaces on protein amyloidogenesis.
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42
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Lim KH. Diverse Misfolded Conformational Strains and Cross-seeding of Misfolded Proteins Implicated in Neurodegenerative Diseases. Front Mol Neurosci 2019; 12:158. [PMID: 31338019 PMCID: PMC6629833 DOI: 10.3389/fnmol.2019.00158] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/07/2019] [Indexed: 01/09/2023] Open
Abstract
Numerous neurodegenerative diseases including prion, Alzheimer's and Parkinson's diseases are characterized by accumulation of protein aggregates in brain. Prion disease is unique in that the natively folded prion protein forms diverse misfolded aggregates with distinct molecular conformations (strains), which underlie different disease phenotypes. In addition, the conformational strains are able to self-propagate their unique conformations by recruiting normal protein monomers and converting their conformations to misfolded conformers. There is an increasing body of evidence that suggests other aggregation-prone proteins including tau and α-synuclein associated with Alzheimer's and Parkinson's diseases, respectively, also behave like a prion that has conformational strains with self-propagation (seeding) property. Moreover, misfolded protein aggregates can promote misfolding and aggregation of different proteins through cross-seeding, which might be associated with co-occurrence of multiple neurodegenerative diseases in the same patient. Elucidation of diverse conformational strains with self-propagation capability and of molecular basis for the cross-talk between misfolded proteins is essential to the development of effective therapeutic intervention.
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43
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Wang T, Chen J, Hou Y, Yu Y, Wang B. BAP31 deficiency contributes to the formation of amyloid‐β plaques in Alzheimer's disease by reducing the stability of RTN3. FASEB J 2018; 33:4936-4946. [DOI: 10.1096/fj.201801702r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Tianyi Wang
- College of Life Science and HealthNortheastern University Shenyang China
| | - Jing Chen
- College of Life Science and HealthNortheastern University Shenyang China
| | - Yue Hou
- College of Life Science and HealthNortheastern University Shenyang China
| | - Yang Yu
- College of Life Science and HealthNortheastern University Shenyang China
| | - Bing Wang
- College of Life Science and HealthNortheastern University Shenyang China
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Cofactors are essential constituents of stable and seeding-active tau fibrils. Proc Natl Acad Sci U S A 2018; 115:13234-13239. [PMID: 30538196 DOI: 10.1073/pnas.1810058115] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Amyloid fibrils are cross-β-rich aggregates that are exceptionally stable forms of protein assembly. Accumulation of tau amyloid fibrils is involved in many neurodegenerative diseases, including Alzheimer's disease (AD). Heparin-induced aggregates have been widely used and assumed to be a good tau amyloid fibril model for most biophysical studies. Here we show that mature fibrils made of 4R tau variants, prepared with heparin or RNA, spontaneously depolymerize and release monomers when their cofactors are removed. We demonstrate that the cross-β-sheet assembly formed in vitro with polyanion addition is unstable at room temperature. We furthermore demonstrate high seeding capacity with transgenic AD mouse brain-extracted tau fibrils in vitro that, however, is exhausted after one generation, while supplementation with RNA cofactors resulted in sustained seeding over multiple generations. We suggest that tau fibrils formed in brains are supported by unknown cofactors and inhere higher-quality packing, as reflected in a more distinct conformational arrangement in the mouse fibril-seeded, compared with heparin-induced, tau fibrils. Our study suggests that the role of cofactors in tauopathies is a worthy focus of future studies, as they may be viable targets for diagnosis and therapeutics.
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45
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Bhasne K, Mukhopadhyay S. Formation of Heterotypic Amyloids: α-Synuclein in Co-Aggregation. Proteomics 2018; 18:e1800059. [PMID: 30216674 DOI: 10.1002/pmic.201800059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/28/2018] [Indexed: 12/13/2022]
Abstract
Protein misfolding resulting in the formation of ordered amyloid aggregates is associated with a number of devastating human diseases. Intrinsically disordered proteins (IDPs) do not autonomously fold up into a unique stable conformation and remain as an ensemble of rapidly fluctuating conformers. Many IDPs are prone to convert into the β-rich amyloid state. One such amyloidogenic IDP is α-synuclein that is involved in Parkinson's disease. Recent studies have indicated that other neuronal proteins, especially IDPs, can co-aggregate with α-synuclein in many pathological ailments. This article describes several such observations highlighting the role of heterotypic protein-protein interactions in the formation of hetero-amyloids. It is believed that the characterizations of molecular cross talks between amyloidogenic proteins as well as the mechanistic studies of heterotypic protein aggregation will allow us to decipher the role of the interacting proteins in amyloid proteomics.
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Affiliation(s)
- Karishma Bhasne
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab 140306, India.,Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab 140306, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab 140306, India.,Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab 140306, India
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46
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Rangachari V, Dean DN, Rana P, Vaidya A, Ghosh P. Cause and consequence of Aβ - Lipid interactions in Alzheimer disease pathogenesis. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2018; 1860:1652-1662. [PMID: 29526709 PMCID: PMC6133763 DOI: 10.1016/j.bbamem.2018.03.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 02/28/2018] [Accepted: 03/02/2018] [Indexed: 12/14/2022]
Abstract
Self-templating propagation of protein aggregate conformations is increasingly becoming a significant factor in many neurological diseases. In Alzheimer disease (AD), intrinsically disordered amyloid-β (Aβ) peptides undergo aggregation that is sensitive to environmental conditions. High-molecular weight aggregates of Aβ that form insoluble fibrils are deposited as senile plaques in AD brains. However, low-molecular weight aggregates called soluble oligomers are known to be the primary toxic agents responsible for neuronal dysfunction. The aggregation process is highly stochastic involving both homotypic (Aβ-Aβ) and heterotypic (Aβ with interacting partners) interactions. Two of the important members of interacting partners are membrane lipids and surfactants, to which Aβ shows a perpetual association. Aβ-membrane interactions have been widely investigated for more than two decades, and this research has provided a wealth of information. Although this has greatly enriched our understanding, the objective of this review is to consolidate the information from the literature that collectively showcases the unique phenomenon of lipid-mediated Aβ oligomer generation, which has largely remained inconspicuous. This is especially important because Aβ aggregate "strains" are increasingly becoming relevant in light of the correlations between the structure of aggregates and AD phenotypes. Here, we will focus on aspects of Aβ-lipid interactions specifically from the context of how lipid modulation generates a wide variety of biophysically and biochemically distinct oligomer sub-types. This, we believe, will refocus our thinking on the influence of lipids and open new approaches in delineating the mechanisms of AD pathogenesis. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
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Affiliation(s)
- Vijayaraghavan Rangachari
- Department of Chemistry & Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406, USA.
| | - Dexter N Dean
- Department of Chemistry & Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Pratip Rana
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Ashwin Vaidya
- Department of Mathematical Science, Montclair State University, Montclair, NJ 07043, USA
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
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47
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Gil-Garcia M, Bañó-Polo M, Varejão N, Jamroz M, Kuriata A, Díaz-Caballero M, Lascorz J, Morel B, Navarro S, Reverter D, Kmiecik S, Ventura S. Combining Structural Aggregation Propensity and Stability Predictions To Redesign Protein Solubility. Mol Pharm 2018; 15:3846-3859. [DOI: 10.1021/acs.molpharmaceut.8b00341] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Marcos Gil-Garcia
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain
| | - Manuel Bañó-Polo
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain
| | - Nathalia Varejão
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain
| | - Michal Jamroz
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, 00-927 Warsaw, Poland
| | - Aleksander Kuriata
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, 00-927 Warsaw, Poland
| | - Marta Díaz-Caballero
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain
| | - Jara Lascorz
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain
| | - Bertrand Morel
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Susanna Navarro
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain
| | - David Reverter
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain
| | - Sebastian Kmiecik
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, 00-927 Warsaw, Poland
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain
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48
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Abstract
The formation of ordered nanostructures by molecular self-assembly of proteins and peptides represents one of the principal directions in nanotechnology. Indeed, polyamides provide superior features as materials with diverse physical properties. A reductionist approach allowed the identification of extremely short peptide sequences, as short as dipeptides, which could form well-ordered amyloid-like β-sheet-rich assemblies comparable to supramolecular structures made of much larger proteins. Some of the peptide assemblies show remarkable mechanical, optical, and electrical characteristics. Another direction of reductionism utilized a natural noncoded amino acid, α-aminoisobutryic acid, to form short superhelical assemblies. The use of this exceptional helix inducer motif allowed the fabrication of single heptad repeats used in various biointerfaces, including their use as surfactants and DNA-binding agents. Two additional directions of the reductionist approach include the use of peptide nucleic acids (PNAs) and coassembly techniques. The diversified accomplishments of the reductionist approach, as well as the exciting future advances it bears, are discussed.
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Affiliation(s)
- Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, Department of Materials Science and Engineering, Tel Aviv University, Tel Aviv 6997801, Israel;
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49
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Darling AL, Uversky VN. Intrinsic Disorder and Posttranslational Modifications: The Darker Side of the Biological Dark Matter. Front Genet 2018; 9:158. [PMID: 29780404 PMCID: PMC5945825 DOI: 10.3389/fgene.2018.00158] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/17/2018] [Indexed: 01/05/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs) are functional proteins and domains that devoid stable secondary and/or tertiary structure. IDPs/IDPRs are abundantly present in various proteomes, where they are involved in regulation, signaling, and control, thereby serving as crucial regulators of various cellular processes. Various mechanisms are utilized to tightly regulate and modulate biological functions, structural properties, cellular levels, and localization of these important controllers. Among these regulatory mechanisms are precisely controlled degradation and different posttranslational modifications (PTMs). Many normal cellular processes are associated with the presence of the right amounts of precisely activated IDPs at right places and in right time. However, wrecked regulation of IDPs/IDPRs might be associated with various human maladies, ranging from cancer and neurodegeneration to cardiovascular disease and diabetes. Pathogenic transformations of IDPs/IDPRs are often triggered by altered PTMs. This review considers some of the aspects of IDPs/IDPRs and their normal and aberrant regulation by PTMs.
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Affiliation(s)
- April L Darling
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.,Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Russia
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50
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Le Marchand T, de Rosa M, Salvi N, Sala BM, Andreas LB, Barbet-Massin E, Sormanni P, Barbiroli A, Porcari R, Sousa Mota C, de Sanctis D, Bolognesi M, Emsley L, Bellotti V, Blackledge M, Camilloni C, Pintacuda G, Ricagno S. Conformational dynamics in crystals reveal the molecular bases for D76N beta-2 microglobulin aggregation propensity. Nat Commun 2018; 9:1658. [PMID: 29695721 PMCID: PMC5916882 DOI: 10.1038/s41467-018-04078-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 03/29/2018] [Indexed: 11/09/2022] Open
Abstract
Spontaneous aggregation of folded and soluble native proteins in vivo is still a poorly understood process. A prototypic example is the D76N mutant of beta-2 microglobulin (β2m) that displays an aggressive aggregation propensity. Here we investigate the dynamics of β2m by X-ray crystallography, solid-state NMR, and molecular dynamics simulations to unveil the effects of the D76N mutation. Taken together, our data highlight the presence of minor disordered substates in crystalline β2m. The destabilization of the outer strands of D76N β2m accounts for the increased aggregation propensity. Furthermore, the computational modeling reveals a network of interactions with residue D76 as a keystone: this model allows predicting the stability of several point mutants. Overall, our study shows how the study of intrinsic dynamics in crystallo can provide crucial answers on protein stability and aggregation propensity. The comprehensive approach here presented may well be suited for the study of other folded amyloidogenic proteins. The aggregation prone D76N beta-2 microglobulin mutant causes systemic amyloidosis. Here the authors combine crystallography, solid-state NMR, and computational studies and show that the D76N mutation increases protein dynamics and destabilizes the outer strands, which leads to an exposure of amyloidogenic parts explaining its aggregation propensity.
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Affiliation(s)
- Tanguy Le Marchand
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France
| | - Matteo de Rosa
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy
| | - Nicola Salvi
- Institut de Biologie Structurale, CNRS, CEA, UGA, 30044, Grenoble, France
| | - Benedetta Maria Sala
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy
| | - Loren B Andreas
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France
| | - Emeline Barbet-Massin
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France
| | - Pietro Sormanni
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Alberto Barbiroli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, 20133, Milano, Italy
| | - Riccardo Porcari
- Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, University College London, London, NW3 2PF, UK
| | | | | | - Martino Bolognesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy.,Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, 20133, Milano, Italy
| | - Lyndon Emsley
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France
| | - Vittorio Bellotti
- Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, University College London, London, NW3 2PF, UK
| | - Martin Blackledge
- Institut de Biologie Structurale, CNRS, CEA, UGA, 30044, Grenoble, France
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy.
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France.
| | - Stefano Ricagno
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy.
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