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Dabirmanesh B, Khajeh K, Uversky VN. The hidden world of protein aggregation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:473-494. [PMID: 38811088 DOI: 10.1016/bs.pmbts.2024.03.014] [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
Though the book's journey into The Hidden World of Protein Aggregation has come to an end, the search for knowledge, the development of healthier lives, and the discovery of nature's mysteries continue, promising new horizons and discoveries yet to be discovered. The intricacies of protein misfolding and aggregation remain a mystery in cellular biology, despite advances made in unraveling them. In this chapter, we will summarize the specific conclusions from the previous chapters and explore the persistent obstacles and unanswered questions that motivate scientists to pursue exploration of protein misfolding and aggregation.
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Affiliation(s)
- Bahareh Dabirmanesh
- 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
| | - Vladimir N Uversky
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Pushchino, Moscow, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
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2
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Dabirmanesh B, Khajeh K, Uversky VN. Protein aggregation: An overview. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:1-10. [PMID: 38811077 DOI: 10.1016/bs.pmbts.2024.03.007] [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
In order for an ordered protein to perform its specific function, it must have a specific molecular structure. Information about this structure is encoded in the protein's amino acid sequence. The unique functional state is achieved as a result of a specific process, known as protein folding. However, as a result of partial or complete unfolding of the polypeptide chain, proteins may misfold and aggregate, leading to the formation of various aggregated structures, such as like amyloid aggregates with the cross-β structure. A variety of cellular biological processes can be affected by protein aggregates that consume essential factors necessary for maintaining proteostasis, which leads to the proteostasis imbalance and further accumulation of protein aggregates, often resulting in age-related neurodegenerative disease progression and aging. However, in addition to their well-established pathological effects, amyloids also play various physiological roles, and many important biological processes involve such 'functional amyloids'. This chapter represents a brief overview of the protein aggregation phenomenon outlines a timeline provides of some key discoveries in this exciting field.
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Affiliation(s)
- Bahareh Dabirmanesh
- 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
| | - Vladimir N Uversky
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Pushchino, Moscow, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.
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3
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Cross ER, Coulter SM, Pentlavalli S, Laverty G. Unravelling the antimicrobial activity of peptide hydrogel systems: current and future perspectives. SOFT MATTER 2021; 17:8001-8021. [PMID: 34525154 PMCID: PMC8442837 DOI: 10.1039/d1sm00839k] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/19/2021] [Indexed: 05/05/2023]
Abstract
The use of hydrogels has garnered significant interest as biomaterial and drug delivery platforms for anti-infective applications. For decades antimicrobial peptides have been heralded as a much needed new class of antimicrobial drugs. Self-assembling peptide hydrogels with inherent antimicrobial ability have recently come to the fore. However, their fundamental antimicrobial properties, selectivity and mechanism of action are relatively undefined. This review attempts to establish a link between antimicrobial efficacy; the self-assembly process; peptide-membrane interactions and mechanical properties by studying several reported peptide systems: β-hairpin/β-loop peptides; multidomain peptides; amphiphilic surfactant-like peptides and ultrashort/low molecular weight peptides. We also explore their role in the formation of amyloid plaques and the potential for an infection etiology in diseases such as Alzheimer's. We look briefly at innovative methods of gel characterization. These may provide useful tools for future studies within this increasingly important field.
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Affiliation(s)
- Emily R Cross
- Biofunctional Nanomaterials Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, N. Ireland, BT9 7BL, UK.
| | - Sophie M Coulter
- Biofunctional Nanomaterials Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, N. Ireland, BT9 7BL, UK.
| | - Sreekanth Pentlavalli
- Biofunctional Nanomaterials Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, N. Ireland, BT9 7BL, UK.
| | - Garry Laverty
- Biofunctional Nanomaterials Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, N. Ireland, BT9 7BL, UK.
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4
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Sprunger ML, Jackrel ME. Prion-Like Proteins in Phase Separation and Their Link to Disease. Biomolecules 2021; 11:biom11071014. [PMID: 34356638 PMCID: PMC8301953 DOI: 10.3390/biom11071014] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/28/2021] [Accepted: 07/06/2021] [Indexed: 02/01/2023] Open
Abstract
Aberrant protein folding underpins many neurodegenerative diseases as well as certain myopathies and cancers. Protein misfolding can be driven by the presence of distinctive prion and prion-like regions within certain proteins. These prion and prion-like regions have also been found to drive liquid-liquid phase separation. Liquid-liquid phase separation is thought to be an important physiological process, but one that is prone to malfunction. Thus, aberrant liquid-to-solid phase transitions may drive protein aggregation and fibrillization, which could give rise to pathological inclusions. Here, we review prions and prion-like proteins, their roles in phase separation and disease, as well as potential therapeutic approaches to counter aberrant phase transitions.
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5
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Schütz D, Read C, Groß R, Röcker A, Rode S, Annamalai K, Fändrich M, Münch J. Negatively Charged Peptide Nanofibrils from Immunoglobulin Light Chain Sequester Viral Particles but Lack Cell-Binding and Viral Transduction-Enhancing Properties. ACS OMEGA 2021; 6:7731-7738. [PMID: 33778283 PMCID: PMC7992169 DOI: 10.1021/acsomega.1c00068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/09/2021] [Indexed: 05/08/2023]
Abstract
Positively charged naturally occurring or engineered peptide nanofibrils (PNF) are effective enhancers of lentiviral and retroviral transduction, an often rate-limiting step in gene transfer and gene therapy approaches. These polycationic PNF are thought to bridge the electrostatic repulsions between negatively charged membranes of virions and cells, thereby enhancing virion attachment to and infection of target cells. Here, we analyzed PNF, which are formed by the peptide AL1, that represents a fragment of an immunoglobulin light chain that causes systemic AL amyloidosis. We found that negatively charged AL1 PNF interact with viral particles to a comparable extent as positively charged PNF. However, AL1 PNF lacked cell-binding activity, and consequently, did not enhance retroviral infection. These findings show that virion capture and cell binding of PNF are mediated by different mechanisms, offering avenues for the design of advanced PNF with selective functions.
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Affiliation(s)
- Desiree Schütz
- Institute
of Molecular Virology, Ulm University Medical
Center, 89081 Ulm, Germany
| | - Clarissa Read
- Central
Facility for Electron Microscopy, Ulm University, 89081 Ulm, Germany
| | - Rüdiger Groß
- Institute
of Molecular Virology, Ulm University Medical
Center, 89081 Ulm, Germany
| | - Annika Röcker
- Institute
of Molecular Virology, Ulm University Medical
Center, 89081 Ulm, Germany
| | - Sascha Rode
- Institute
of Molecular Virology, Ulm University Medical
Center, 89081 Ulm, Germany
| | | | - Marcus Fändrich
- Institute
of Protein Biochemistry, Ulm University, 89081 Ulm, Germany
| | - Jan Münch
- Institute
of Molecular Virology, Ulm University Medical
Center, 89081 Ulm, Germany
- Core
Facility Functional Peptidomics, Ulm University
Medical Center, 89081 Ulm, Germany
- . Phone: +49 731 500 65154
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6
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Wu T, Lai R, Yao C, Juang J, Lin S. Supramolecular Bait to Trigger Non-Equilibrium Co-Assembly and Clearance of Aβ42. Angew Chem Int Ed Engl 2021; 60:4014-4017. [PMID: 33191624 PMCID: PMC7898541 DOI: 10.1002/anie.202013754] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Indexed: 12/20/2022]
Abstract
In living systems, non-equilibrium states that control the assembly-disassembly of cellular components underlie the gradual complexification of life, whereas in nonliving systems, most molecules follow the laws of thermodynamic equilibrium to sustain dynamic consistency. Little is known about the roles of non-equilibrium states of interactions between supramolecules in living systems. Here, a non-equilibrium state of interaction between supramolecular lipopolysaccharide (LPS) and Aβ42, an aggregate-prone protein that causes Alzheimer's disease (AD), was identified. Structurally, Aβ42 presents a specific groove that is recognized by the amphiphilicity of LPS bait in a non-equilibrium manner. Functionally, the transient complex elicits a cellular response to clear extracellular Aβ42 deposits in neuronal cells. Since the impaired clearance of toxic Aβ42 deposits correlates with AD pathology, the non-equilibrium LPS and Aβ42 could represent a useful target for developing AD therapeutics.
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Affiliation(s)
- Te‐Haw Wu
- Institute of Biomedical Engineering and NanomedicineNational Health Research Institutes (NHRI)Miaoli County35053Taiwan
| | - Rai‐Hua Lai
- Institute of Molecular and Genomic MedicineNHRITaiwan
| | - Chun‐Nien Yao
- Institute of Biomedical Engineering and NanomedicineNational Health Research Institutes (NHRI)Miaoli County35053Taiwan
| | - Jyh‐Lyh Juang
- Institute of Molecular and Genomic MedicineNHRITaiwan
| | - Shu‐Yi Lin
- Institute of Biomedical Engineering and NanomedicineNational Health Research Institutes (NHRI)Miaoli County35053Taiwan
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7
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Wu T, Lai R, Yao C, Juang J, Lin S. Supramolecular Bait to Trigger Non‐Equilibrium Co‐Assembly and Clearance of Aβ42. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202013754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Te‐Haw Wu
- Institute of Biomedical Engineering and Nanomedicine National Health Research Institutes (NHRI) Miaoli County 35053 Taiwan
| | - Rai‐Hua Lai
- Institute of Molecular and Genomic Medicine NHRI Taiwan
| | - Chun‐Nien Yao
- Institute of Biomedical Engineering and Nanomedicine National Health Research Institutes (NHRI) Miaoli County 35053 Taiwan
| | - Jyh‐Lyh Juang
- Institute of Molecular and Genomic Medicine NHRI Taiwan
| | - Shu‐Yi Lin
- Institute of Biomedical Engineering and Nanomedicine National Health Research Institutes (NHRI) Miaoli County 35053 Taiwan
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8
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Chen D, Li J, Pan T, Wu R, Tao Y, Lin H. The broad-spectrum antibiofilm activity of amyloid-forming hexapeptides. Microb Biotechnol 2020; 14:656-667. [PMID: 33248016 PMCID: PMC7936291 DOI: 10.1111/1751-7915.13721] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/12/2020] [Indexed: 01/25/2023] Open
Abstract
Evidence suggests that short amyloid-forming peptides derived from bacterial proteomes have functional roles; however, the reported activities are diverse and the underlying mechanisms remain unclear. In this study, we simulated short amyloid-forming peptides from the amyloid-forming truncated protein C123 of Streptococcus mutans (S. mutans), studied their biological functions in microbial proliferation and biofilm formation, and further investigated the underlying mechanism. Fourteen hexapeptides were simulated, 13 of which were successfully synthesized. We found that the amyloid-forming hexapeptides (AFhPs) displayed efficient broad-spectrum antibiofilm activity against the Gram-positive bacteria S. mutans, Streptococcus sanguis and Staphylococcus aureus, Gram-negative bacteria Escherichia coli and fungus Candida albicans, by aggregating into rigid amyloid fibres agglutinating microbes, whereas the non-amyloid-forming hexapeptides (non-AFhPs) did not. The AFhPs did not kill microbes and showed little or no cytotoxicity. Furthermore, a set of AFhPs displayed broad-spectrum antibiofilm activity, regardless of its source. The microbial cell wall carbohydrates, peptidoglycan (PGN), lipoteichoic acid (LTA), glucan and zymosan A, mediated AFhP binding and triggered significant AFhP fibrillation. Although amyloid fibres agglutinated lipid membrane model - large unilamellar vesicles (LUVs) - and LUVs facilitated AFhP fibrillation, the roles of lipid membranes in AFhP antibiofilm activities remain to be elucidated. We highlight the potential use of AFhPs as novel antibiofilm agents.
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Affiliation(s)
- Dongru Chen
- Guangdong Provincial Key Laboratory of Stomatology, Department of Orthodontics, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jing Li
- Guangdong Provincial Key Laboratory of Stomatology, Department of Preventive Dentistry, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ting Pan
- Guangdong Provincial Key Laboratory of Stomatology, Department of Preventive Dentistry, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ruixue Wu
- Guangdong Provincial Key Laboratory of Stomatology, Department of Preventive Dentistry, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ye Tao
- Guangdong Provincial Key Laboratory of Stomatology, Department of Preventive Dentistry, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Huancai Lin
- Guangdong Provincial Key Laboratory of Stomatology, Department of Preventive Dentistry, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
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9
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Inyushin M, Zayas-Santiago A, Rojas L, Kucheryavykh L. On the Role of Platelet-Generated Amyloid Beta Peptides in Certain Amyloidosis Health Complications. Front Immunol 2020; 11:571083. [PMID: 33123145 PMCID: PMC7567018 DOI: 10.3389/fimmu.2020.571083] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022] Open
Abstract
As do many other immunity-related blood cells, platelets release antimicrobial peptides that kill bacteria, fungi, and even certain viruses. Here we review the literature suggesting that there is a similarity between the antimicrobials released by other blood cells and the amyloid-related Aβ peptide released by platelets. Analyzing the literature, we also propose that platelet-generated Aβ amyloidosis may be more common than currently recognized. This systemic Aβ from a platelet source may participate in various forms of amyloidosis in pathologies ranging from brain cancer, glaucoma, skin Aβ accumulation, and preeclampsia to Alzheimer’s disease and late-stage Parkinson’s disease. We also discuss the advantages and disadvantages of specific animal models for studying platelet-related Aβ. This field is undergoing rapid change, as it evaluates competing ideas in the light of new experimental observations. We summarized both in order to clarify the role of platelet-generated Aβ peptides in amyloidosis-related health disorders, which may be helpful to researchers interested in this growing area of investigation.
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Affiliation(s)
- Mikhail Inyushin
- Department of Physiology, Universidad Central del Caribe, Bayamon, Puerto Rico
| | - Astrid Zayas-Santiago
- Department of Pathology & Laboratory Medicine, Universidad Central del Caribe, Bayamon, Puerto Rico
| | - Legier Rojas
- Department of Physiology, Universidad Central del Caribe, Bayamon, Puerto Rico
| | - Lilia Kucheryavykh
- Department of Biochemistry, Universidad Central del Caribe, Bayamon, Puerto Rico
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10
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Moshynets O, Chernii S, Chernii V, Losytskyy M, Karakhim S, Czerwieniec R, Pekhnyo V, Yarmoluk S, Kovalska V. Fluorescent β-ketoenole AmyGreen dye for visualization of amyloid components of bacterial biofilms. Methods Appl Fluoresc 2020; 8:035006. [PMID: 32375137 DOI: 10.1088/2050-6120/ab90e0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Green-emitting water-soluble amino-ketoenole dye AmyGreen is proposed as an efficient fluorescent stain for visualization of bacterial amyloids in biofilms and the detection of pathological amyloids in vitro. This dye is almost non-fluorescent in solution, displays strong green emission in the presence of amyloid fibril of proteins. AmyGreen is also weakly fluorescent in presence to biomolecules that are components of cells, extracellular matrix or medium: nucleic acids, polysaccharides, lipids, and proteins. Thus, the luminescence turn-on behavior of AmyGreen can be utilized for visualization of amyloid components of bacterial biofilm extracellular matrix. Herein we report the application of AmyGreen for fluorescent staining of a number of amyloid-contained bacteria biofilms produced by Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Bordetella avium, and Staphylococcus aureus. The effectiveness of AmyGreen was compared to traditional amyloid sensitive dye Thioflavine T. The main advantage of AmyGreen (concentration 10-5 M) is a higher sensitivity in the visualization of amyloid biofilm components over Thioflavine T (10-4 M) as it was revealed when staining E. coli and K. pneumoniae bacterial biofilms. Besides, AmyGreen displays lower cross-selectivity to nucleic acids as demonstrated both in in-solution experiments and upon staining of eukaryotic human mesenchymal stem cells used as amyloid-free negative control over amyloid-rich bacterial biofilms. The results point to a lower risk of false-positive response upon determination of amyloid components of bacterial biofilm using AmyGreen. Co-staining of biofilm by AmyGreen and cellulose sensitive dye Calcofluor White show difference in their staining patterns and localization, indicating separation of polysaccharide-rich and amyloid-rich regions of investigated biofilms. Thus, we suggest the new AmyGreen stain for visualization and differentiation of amyloid fibrils in bacterial biofilms to be used solely and in combination with other stains for confocal and fluorescence microscopy analysis.
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Affiliation(s)
- Olena Moshynets
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
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11
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Simonson AW, Aronson MR, Medina SH. Supramolecular Peptide Assemblies as Antimicrobial Scaffolds. Molecules 2020; 25:E2751. [PMID: 32545885 PMCID: PMC7355828 DOI: 10.3390/molecules25122751] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/11/2020] [Accepted: 06/11/2020] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial discovery in the age of antibiotic resistance has demanded the prioritization of non-conventional therapies that act on new targets or employ novel mechanisms. Among these, supramolecular antimicrobial peptide assemblies have emerged as attractive therapeutic platforms, operating as both the bactericidal agent and delivery vector for combinatorial antibiotics. Leveraging their programmable inter- and intra-molecular interactions, peptides can be engineered to form higher ordered monolithic or co-assembled structures, including nano-fibers, -nets, and -tubes, where their unique bifunctionalities often emerge from the supramolecular state. Further advancements have included the formation of macroscopic hydrogels that act as bioresponsive, bactericidal materials. This systematic review covers recent advances in the development of supramolecular antimicrobial peptide technologies and discusses their potential impact on future drug discovery efforts.
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Affiliation(s)
- Andrew W. Simonson
- Department of Biomedical Engineering, The Pennsylvania State University, Suite 122, CBE Building, University Park, PA 16802-4400, USA; (A.W.S.); (M.R.A.)
| | - Matthew R. Aronson
- Department of Biomedical Engineering, The Pennsylvania State University, Suite 122, CBE Building, University Park, PA 16802-4400, USA; (A.W.S.); (M.R.A.)
| | - Scott H. Medina
- Department of Biomedical Engineering, The Pennsylvania State University, Suite 122, CBE Building, University Park, PA 16802-4400, USA; (A.W.S.); (M.R.A.)
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802-4400, USA
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12
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Dolui S, Mondal A, Roy A, Pal U, Das S, Saha A, Maiti NC. Order, Disorder, and Reorder State of Lysozyme: Aggregation Mechanism by Raman Spectroscopy. J Phys Chem B 2019; 124:50-60. [PMID: 31820990 DOI: 10.1021/acs.jpcb.9b09139] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lysozyme, like many other well-folded globular proteins, under stressful conditions produces nanoscale oligomer assembly and amyloid-like fibrillar aggregates. With engaging Raman microscopy, we made a critical structural analysis of oligomer and other assembly structures of lysozyme obtained from hen egg white and provided a quantitative estimation of a protein secondary structure in different states of its fibrillation. A strong amide I Raman band at 1660 cm-1 and a N-Cα-C stretching band at ∼930 cm-1 clearly indicated the presence of a substantial amount of α-helical folds of the protein in its oligomeric assembly state. In addition, analysis of the amide III region and Raman difference spectra suggested an ample presence of a PPII-like secondary structure in these oligomers without causing major loss of α-helical folds, which is found in the case of monomeric samples. Circular dichroism study also revealed the presence of typical α-helical folds in the oligomeric state. Nonetheless, most of the Raman bands associated with aromatic residues and disulfide (-S-S-) linkages broadened in the oligomeric state and indicated a collapse in the tertiary structure. In the fibrillar state of assembly, the amide I band became much sharper and enriched with the β-sheet secondary structure. Also, the disulfide bond vibration in matured fibrils became much weaker compared to monomer and oligomers and thus confirmed certain loss/cleavage of this bond during fibrillation. The Raman band of tryptophan and tyrosine residues indicated that some of these residues experienced a greater hydrophobic microenvironment in the fibrillar state than the protein in the oligomeric state of the assembly structure.
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Affiliation(s)
- Sandip Dolui
- Structural Biology and Bioinformatics Division , Indian Institute of Chemical Biology, Council of Scientific and Industrial Research , 4, Raja S.C. Mullick Road , Kolkata 700032 , India
| | - Animesh Mondal
- Structural Biology and Bioinformatics Division , Indian Institute of Chemical Biology, Council of Scientific and Industrial Research , 4, Raja S.C. Mullick Road , Kolkata 700032 , India
| | - Anupam Roy
- Structural Biology and Bioinformatics Division , Indian Institute of Chemical Biology, Council of Scientific and Industrial Research , 4, Raja S.C. Mullick Road , Kolkata 700032 , India
| | - Uttam Pal
- Structural Biology and Bioinformatics Division , Indian Institute of Chemical Biology, Council of Scientific and Industrial Research , 4, Raja S.C. Mullick Road , Kolkata 700032 , India
| | - Supriya Das
- Structural Biology and Bioinformatics Division , Indian Institute of Chemical Biology, Council of Scientific and Industrial Research , 4, Raja S.C. Mullick Road , Kolkata 700032 , India
| | - Achintya Saha
- Department of Chemical Technology , University of Calcutta , 92 Acharya Prafulla Chandra Road , Calcutta 700009 , India
| | - Nakul C Maiti
- Structural Biology and Bioinformatics Division , Indian Institute of Chemical Biology, Council of Scientific and Industrial Research , 4, Raja S.C. Mullick Road , Kolkata 700032 , India
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13
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Calcium signalling in mammalian cell lines expressing wild type and mutant human α1-Antitrypsin. Sci Rep 2019; 9:17293. [PMID: 31754242 PMCID: PMC6872872 DOI: 10.1038/s41598-019-53535-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/28/2019] [Indexed: 11/08/2022] Open
Abstract
A possible role for calcium signalling in the autosomal dominant form of dementia, familial encephalopathy with neuroserpin inclusion bodies (FENIB), has been proposed, which may point towards a mechanism by which cells could sense and respond to the accumulation of mutant serpin polymers in the endoplasmic reticulum (ER). We therefore explored possible defects in Ca2+-signalling, which may contribute to the pathology associated with another serpinopathy, α1-antitrypsin (AAT) deficiency. Using CHO K1 cell lines stably expressing a wild type human AAT (MAAT) and a disease-causing polymer-forming variant (ZAAT) and the truncated variant (NHK AAT), we measured basal intracellular free Ca2+, its responses to thapsigargin (TG), an ER Ca2+-ATPase blocker, and store-operated Ca2+-entry (SOCE). Our fura2 based Ca2+ measurements detected no differences between these 3 parameters in cell lines expressing MAAT and cell lines expressing ZAAT and NHK AAT mutants. Thus, in our cell-based models of α1-antitrypsin (AAT) deficiency, unlike the case for FENIB, we were unable to detect defects in calcium signalling.
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14
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Avni A, Swasthi HM, Majumdar A, Mukhopadhyay S. Intrinsically disordered proteins in the formation of functional amyloids from bacteria to humans. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 166:109-143. [PMID: 31521230 DOI: 10.1016/bs.pmbts.2019.05.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Amyloids are nanoscopic ordered self-assemblies of misfolded proteins that are formed via aggregation of partially unfolded or intrinsically disordered proteins (IDPs) and are commonly linked to devastating human diseases. An enlarging body of recent research has demonstrated that certain amyloids can be beneficial and participate in a wide range of physiological functions from bacteria to humans. These amyloids are termed as functional amyloids. Like disease-associated amyloids, a vast majority of functional amyloids are derived from a range of IDPs or hybrid proteins containing ordered domains and intrinsically disordered regions (IDRs). In this chapter, we describe an account of recent studies on the aggregation behavior of IDPs resulting in the formation of functional amyloids in a diverse range of organisms from bacteria to human. We also discuss the strategies that are used by these organisms to regulate the spatiotemporal amyloid assembly in their physiological functions.
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Affiliation(s)
- Anamika Avni
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, and Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Hema M Swasthi
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, and Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Anupa Majumdar
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, and Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, and Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.
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15
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Gutierrez Jauregui R, Fleige H, Bubke A, Rohde M, Weiss S, Förster R. IL-1β Promotes Staphylococcus aureus Biofilms on Implants in vivo. Front Immunol 2019; 10:1082. [PMID: 31156635 PMCID: PMC6534041 DOI: 10.3389/fimmu.2019.01082] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/29/2019] [Indexed: 12/14/2022] Open
Abstract
Implant associated infections represent a serious health burden in clinics since some microorganisms are able to colonize biological surfaces or surfaces of indwelling medical devices and form biofilms. Biofilms represent communities of microorganisms attached to hydrated surfaces and enclosed in self-produced extracellular matrix. This renders them resistant to exogenous assaults like antibiotics or immune effector mechanisms. Little is known regarding the role of the immune system in the formation of biofilms during implant associated infections, largely due to the lack of suitable mouse models. Here we use colonized osmotic pumps in mice to study the interaction of an activated immune system with biofilm-forming Staphylococcus aureus encoding Gaussia luciferase. This approach permits biofilm formation on the osmotic pumps in living animals. It also allows the continuous supply of soluble immune cell activating agents, such as cytokines to study their effect on biofilm formation in vivo. Using non-invasive imaging of the bioluminescent signal emitted by the lux expressing bacteria for quantification of bacterial load in conjunction with light and electron microscopy, we observed that pump-supplied pro-inflammatory cytokine IL-1β strongly increased biofilm formation along with a massive influx of neutrophils adjacent to the biofilm-coated pumps. Thus, our data demonstrate that immune defense mechanisms can augment biofilm formation.
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Affiliation(s)
| | - Henrike Fleige
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Anja Bubke
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholz Center for Infection Research, Braunschweig, Germany
| | - Siegfried Weiss
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Reinhold Förster
- Institute of Immunology, Hannover Medical School, Hannover, Germany.,RESIST, Cluster of Excellence 2155, Hannover Medical School, Hannover, Germany
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16
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Bomba R, Kwiatkowski W, Sánchez-Ferrer A, Riek R, Greenwald J. Cooperative Induction of Ordered Peptide and Fatty Acid Aggregates. Biophys J 2018; 115:2336-2347. [PMID: 30503535 DOI: 10.1016/j.bpj.2018.10.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/19/2018] [Accepted: 10/31/2018] [Indexed: 01/18/2023] Open
Abstract
Interactions between biological membranes and disease-associated amyloids are well documented, and their prevalence suggests that an inherent affinity exists between these molecular assemblies. Our interest in the molecular origins of life have led us to investigate the nature of such interactions in the context of their molecular predecessors (i.e., vesicle-forming amphiphiles and small peptides). Under certain conditions, amyloidogenic peptides or fatty acids are each able to form ordered structures on their own; however, we report here on their cooperative assembly into novel, to our knowledge, highly ordered structures. We first examined an amyloidogenic eight-residue peptide, which forms amyloids at pH 11, yet because of its positive electrostatic character remains soluble at a neutral pH. In mixtures with simple fatty acids, this peptide is also able to form novel, to our knowledge, coaggregates at a neutral pH whose structures are sensitive to both the fatty acid concentration and identity. Below the critical vesicle concentration, the mixtures of fatty acid and peptide yield a flocculent precipitate with an underlying β-structure. Above the critical vesicle concentration, the mixtures yield a translucent precipitate that consists of tube-like structures. Small-angle x-ray scattering and fiber diffraction data were used to model their structures as hollow-core two-shell cylinders in which the inner shell is a bilayer of fatty acid and the outer shell alternates between amyloid and bilayers of fatty acid. The further analysis of decanoic acid with a panel of 13 other basic amyloidogenic peptides confirmed the general nature of the observed interactions. The cooperativity within this heterogeneous system is attributed to the structurally repetitive natures of the fatty acid bilayer and the cross-β-sheet motif, providing compatible scaffolds for attractive electrostatic interactions. We show these interactions to be mutually beneficial, expanding the phase space of both peptides and fatty acids while providing a simple yet robust physical connection between two distinct entities relevant for life.
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Affiliation(s)
- Radoslaw Bomba
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland
| | - Witek Kwiatkowski
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland
| | - Antoni Sánchez-Ferrer
- Department of Health Sciences and Technology, Swiss Federal Institute of Technology, IFNH, LFO, Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland.
| | - Jason Greenwald
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland.
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17
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Malekkhaiat Häffner S, Malmsten M. Influence of self-assembly on the performance of antimicrobial peptides. Curr Opin Colloid Interface Sci 2018. [DOI: 10.1016/j.cocis.2018.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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18
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Fulop T, Witkowski JM, Bourgade K, Khalil A, Zerif E, Larbi A, Hirokawa K, Pawelec G, Bocti C, Lacombe G, Dupuis G, Frost EH. Can an Infection Hypothesis Explain the Beta Amyloid Hypothesis of Alzheimer's Disease? Front Aging Neurosci 2018; 10:224. [PMID: 30087609 PMCID: PMC6066504 DOI: 10.3389/fnagi.2018.00224] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 07/02/2018] [Indexed: 12/19/2022] Open
Abstract
Alzheimer's disease (AD) is the most frequent type of dementia. The pathological hallmarks of the disease are extracellular senile plaques composed of beta-amyloid peptide (Aβ) and intracellular neurofibrillary tangles composed of pTau. These findings led to the "beta-amyloid hypothesis" that proposes that Aβ is the major cause of AD. Clinical trials targeting Aβ in the brain have mostly failed, whether they attempted to decrease Aβ production by BACE inhibitors or by antibodies. These failures suggest a need to find new hypotheses to explain AD pathogenesis and generate new targets for intervention to prevent and treat the disease. Many years ago, the "infection hypothesis" was proposed, but received little attention. However, the recent discovery that Aβ is an antimicrobial peptide (AMP) acting against bacteria, fungi, and viruses gives increased credence to an infection hypothesis in the etiology of AD. We and others have shown that microbial infection increases the synthesis of this AMP. Here, we propose that the production of Aβ as an AMP will be beneficial on first microbial challenge but will become progressively detrimental as the infection becomes chronic and reactivates from time to time. Furthermore, we propose that host measures to remove excess Aβ decrease over time due to microglial senescence and microbial biofilm formation. We propose that this biofilm aggregates with Aβ to form the plaques in the brain of AD patients. In this review, we will develop this connection between Infection - Aβ - AD and discuss future possible treatments based on this paradigm.
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Affiliation(s)
- Tamas Fulop
- Division of Geriatrics, Department of Medicine, Research Center on Aging, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Jacek M. Witkowski
- Department of Pathophysiology, Medical University of Gdańsk, Gdańsk, Poland
| | - Karine Bourgade
- Division of Geriatrics, Department of Medicine, Research Center on Aging, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Abdelouahed Khalil
- Division of Geriatrics, Department of Medicine, Research Center on Aging, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Echarki Zerif
- Division of Geriatrics, Department of Medicine, Research Center on Aging, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Anis Larbi
- Singapore Immunology Network, ASTAR, Biopolis, Singapore, Singapore
| | - Katsuiku Hirokawa
- Department of Pathology, Nitobe Memorial Nakano General Hospital, Tokyo, Japan
| | - Graham Pawelec
- Department of Internal Medicine II, Center for Medical Research, University of Tübingen, Tübingen, Germany
- Health Sciences North Research Institute, Greater Sudbury, ON, Canada
| | - Christian Bocti
- Division of Geriatrics, Department of Medicine, Research Center on Aging, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Guy Lacombe
- Division of Geriatrics, Department of Medicine, Research Center on Aging, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Gilles Dupuis
- Department of Biochemistry, Graduate Programme of Immunology, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Eric H. Frost
- Department of Microbiology and Infectious Diseases, University of Sherbrooke, Sherbrooke, QC, Canada
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19
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Müller JA, Harms M, Krüger F, Groß R, Joas S, Hayn M, Dietz AN, Lippold S, von Einem J, Schubert A, Michel M, Mayer B, Cortese M, Jang KS, Sandi-Monroy N, Deniz M, Ebner F, Vapalahti O, Otto M, Bartenschlager R, Herbeuval JP, Schmidt-Chanasit J, Roan NR, Münch J. Semen inhibits Zika virus infection of cells and tissues from the anogenital region. Nat Commun 2018; 9:2207. [PMID: 29880824 PMCID: PMC5992203 DOI: 10.1038/s41467-018-04442-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 04/26/2018] [Indexed: 02/06/2023] Open
Abstract
Zika virus (ZIKV) causes severe birth defects and can be transmitted via sexual intercourse. Semen from ZIKV-infected individuals contains high viral loads and may therefore serve as an important vector for virus transmission. Here we analyze the effect of semen on ZIKV infection of cells and tissues derived from the anogenital region. ZIKV replicates in all analyzed cell lines, primary cells, and endometrial or vaginal tissues. However, in the presence of semen, infection by ZIKV and other flaviviruses is potently inhibited. We show that semen prevents ZIKV attachment to target cells, and that an extracellular vesicle preparation from semen is responsible for this anti-ZIKV activity. Our findings suggest that ZIKV transmission is limited by semen. As such, semen appears to serve as a protector against sexual ZIKV transmission, despite the availability of highly susceptible cells in the anogenital tract and high viral loads in this bodily fluid.
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Affiliation(s)
- Janis A Müller
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Mirja Harms
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Franziska Krüger
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Rüdiger Groß
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Simone Joas
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Manuel Hayn
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Andrea N Dietz
- Institute of Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Sina Lippold
- Institute of Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Jens von Einem
- Institute of Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Axel Schubert
- Institute of Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Manuela Michel
- Institute of Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Benjamin Mayer
- Institute of Epidemiology and Medical Biometry, Ulm University, 89075, Ulm, Germany
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology, Medical Faculty, Heidelberg University, 69120, Heidelberg, Germany
| | - Karen S Jang
- Gladstone Institute of Virology and Immunology, San Francisco, CA, 94158, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | | | - Miriam Deniz
- Klinik für Frauenheilkunde und Geburtshilfe, Ulm University Medical Center, 89081, Ulm, Germany
| | - Florian Ebner
- Klinik für Frauenheilkunde und Geburtshilfe, Ulm University Medical Center, 89081, Ulm, Germany
- Frauenklinik, Helios Amper Klinik, 85221, Dachau, Germany
| | - Olli Vapalahti
- Department of Virology and Immunology, University of Helsinki and Helsinki University Hospital, 00014, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, 00014, Helsinki, Finland
| | - Markus Otto
- Department of Neurology, Ulm University, 89081, Ulm, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Medical Faculty, Heidelberg University, 69120, Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg Partner Site, Heidelberg University, 69120, Heidelberg, Germany
| | - Jean-Philippe Herbeuval
- Chemistry, Biology, Modeling and Immunotherapy (CBMIT), CNRS, UMR8601, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, CICB Paris, 75006, Paris, France
| | - Jonas Schmidt-Chanasit
- Bernhard Nocht Institute for Tropical Medicine, World Health Organization Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, 20359, Hamburg, Germany
- German Centre for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel, 20359, Hamburg, Germany
| | - Nadia R Roan
- Gladstone Institute of Virology and Immunology, San Francisco, CA, 94158, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
- Core Facility Functional Peptidomics, Ulm University Medical Center, 89081, Ulm, Germany.
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20
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Abstract
Amyloid fibrils are protein homopolymers that adopt diverse cross-β conformations. Some amyloid fibrils are associated with the pathogenesis of devastating neurodegenerative disorders, including Alzheimer's disease and Parkinson's disease. Conversely, functional amyloids play beneficial roles in melanosome biogenesis, long-term memory formation and release of peptide hormones. Here, we showcase advances in our understanding of amyloid assembly and structure, and how distinct amyloid strains formed by the same protein can cause distinct neurodegenerative diseases. We discuss how mutant steric zippers promote deleterious amyloidogenesis and aberrant liquid-to-gel phase transitions. We also highlight effective strategies to combat amyloidogenesis and related toxicity, including: (1) small-molecule drugs (e.g. tafamidis) to inhibit amyloid formation or (2) stimulate amyloid degradation by the proteasome and autophagy, and (3) protein disaggregases that disassemble toxic amyloid and soluble oligomers. We anticipate that these advances will inspire therapeutics for several fatal neurodegenerative diseases. Summary: This Review showcases important advances in our understanding of amyloid structure, assembly and disassembly, which are inspiring novel therapeutic strategies for amyloid disorders.
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Affiliation(s)
- Edward Chuang
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,Pharmacology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Acacia M Hori
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christina D Hesketh
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA .,Pharmacology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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21
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Wang YH, Zhang YG. Amyloid and immune homeostasis. Immunobiology 2018; 223:288-293. [DOI: 10.1016/j.imbio.2017.10.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 10/14/2017] [Indexed: 01/06/2023]
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22
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Qiu F, Tang C, Chen Y. Amyloid-like aggregation of designer bolaamphiphilic peptides: Effect of hydrophobic section and hydrophilic heads. J Pept Sci 2017; 24. [PMID: 29239498 DOI: 10.1002/psc.3062] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/17/2017] [Accepted: 11/21/2017] [Indexed: 02/05/2023]
Abstract
Amyloid-like aggregation of natural proteins or polypeptides is an important process involved in many human diseases as well as some normal biological functions. Plenty of works have been done on this ubiquitous phenomenon, but the molecular mechanism of amyloid-like aggregation has not been fully understood yet. In this study, we showed that a series of designer bolaamphiphilic peptides could undergo amyloid-like aggregation even though they didn't possess typical β-sheet secondary structure. Through systematic amino acid substitution, we found that for the self-assembling ability, the number and species of amino acid in hydrophobic section could be variable as long as enough hydrophobic interaction is provided, while different polar amino acids as the hydrophilic heads could change the self-assembling nanostructures with their aggregating behaviors affected by pH value change. Based on these results, novel self-assembling models and aggregating mechanisms were proposed, which might provide new insight into the molecular basis of amyloid-like aggregation.
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Affiliation(s)
- Feng Qiu
- Laboratory of Anaesthesia and Critical Care Medicine, Translational Neuroscience Centre, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Chengkang Tang
- Core Facility of West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yongzhu Chen
- Periodical Press of West China Hospital, Sichuan University, Chengdu, 610041, China
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23
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Zhao Y, Cong L, Lukiw WJ. Lipopolysaccharide (LPS) Accumulates in Neocortical Neurons of Alzheimer's Disease (AD) Brain and Impairs Transcription in Human Neuronal-Glial Primary Co-cultures. Front Aging Neurosci 2017; 9:407. [PMID: 29311897 PMCID: PMC5732913 DOI: 10.3389/fnagi.2017.00407] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/24/2017] [Indexed: 11/26/2022] Open
Abstract
Several independent laboratories have recently reported the detection of bacterial nucleic acid sequences or bacterial-derived neurotoxins, such as highly inflammatory lipopolysaccharide (LPS), within Alzheimer’s disease (AD) affected brain tissues. Whether these bacterial neurotoxins originate from the gastrointestinal (GI) tract microbiome, a possible brain microbiome or some dormant pathological microbiome is currently not well understood. Previous studies indicate that the co-localization of pro-inflammatory LPS with AD-affected brain cell nuclei suggests that there may be a contribution of this neurotoxin to genotoxic events that support inflammatory neurodegeneration and failure in homeostatic gene expression. In this report we provide evidence that in sporadic AD, LPS progressively accumulates in neuronal parenchyma and appears to preferentially associate with the periphery of neuronal nuclei. Run-on transcription studies utilizing [α-32P]-uridine triphosphate incorporation into newly synthesized total RNA further indicates that human neuronal-glial (HNG) cells in primary co-culture incubated with LPS exhibit significantly reduced output of DNA transcription products. These studies suggest that in AD LPS may impair the efficient readout of neuronal genetic information normally required for the homeostatic operation of brain cell function and may contribute to a progressive disruption in the read-out of genetic information.
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Affiliation(s)
- Yuhai Zhao
- Neuroscience Center, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States.,Departments of Anatomy and Cell Biology, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Lin Cong
- Neuroscience Center, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States.,Department of Neurology, Shengjing Hospital, China Medical University, Shenyang, China
| | - Walter J Lukiw
- Neuroscience Center, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States.,Department of Neurology, Shengjing Hospital, China Medical University, Shenyang, China.,Department of Neurology, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States.,Department of Ophthalmology, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
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24
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Bosso M, Ständker L, Kirchhoff F, Münch J. Exploiting the human peptidome for novel antimicrobial and anticancer agents. Bioorg Med Chem 2017; 26:2719-2726. [PMID: 29122440 DOI: 10.1016/j.bmc.2017.10.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 10/28/2017] [Indexed: 12/22/2022]
Abstract
Infectious diseases and cancers are leading causes of death and pose major challenges to public health. The human peptidome encompasses millions of compounds that display an enormous structural and functional diversity and represents an excellent source for the discovery of endogenous agents with antimicrobial and/or anticancer activity. Here, we discuss how to exploit the human peptidome for novel antimicrobial and anticancer agents through the generation of peptide libraries from human body fluids and tissues and stepwise purification of bioactive compounds.
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Affiliation(s)
- Matteo Bosso
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstrasse 1, 89081 Ulm, Germany
| | - Ludger Ständker
- Ulm Peptide Pharmaceuticals, Ulm University, Albert-Einstein-Allee 47, 89081 Ulm, Germany; Core Facility Functional Peptidomics, Ulm University Medical Center, Albert-Einstein-Allee 47, 89081 Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstrasse 1, 89081 Ulm, Germany; Ulm Peptide Pharmaceuticals, Ulm University, Albert-Einstein-Allee 47, 89081 Ulm, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstrasse 1, 89081 Ulm, Germany; Ulm Peptide Pharmaceuticals, Ulm University, Albert-Einstein-Allee 47, 89081 Ulm, Germany; Core Facility Functional Peptidomics, Ulm University Medical Center, Albert-Einstein-Allee 47, 89081 Ulm, Germany.
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25
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Zhao Y, Cong L, Jaber V, Lukiw WJ. Microbiome-Derived Lipopolysaccharide Enriched in the Perinuclear Region of Alzheimer's Disease Brain. Front Immunol 2017; 8:1064. [PMID: 28928740 PMCID: PMC5591429 DOI: 10.3389/fimmu.2017.01064] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 08/16/2017] [Indexed: 12/16/2022] Open
Abstract
Abundant clinical, epidemiological, imaging, genetic, molecular, and pathophysiological data together indicate that there occur an unusual inflammatory reaction and a disruption of the innate-immune signaling system in Alzheimer’s disease (AD) brain. Despite many years of intense study, the origin and molecular mechanics of these AD-relevant pathogenic signals are still not well understood. Here, we provide evidence that an intensely pro-inflammatory bacterial lipopolysaccharide (LPS), part of a complex mixture of pro-inflammatory neurotoxins arising from abundant Gram-negative bacilli of the human gastrointestinal (GI) tract, are abundant in AD-affected brain neocortex and hippocampus. For the first time, we provide evidence that LPS immunohistochemical signals appear to aggregate in clumps in the parenchyma in control brains, and in AD, about 75% of anti-LPS signals were clustered around the periphery of DAPI-stained nuclei. As LPS is an abundant secretory product of Gram-negative bacilli resident in the human GI-tract, these observations suggest (i) that a major source of pro-inflammatory signals in AD brain may originate from internally derived noxious exudates of the GI-tract microbiome; (ii) that due to aging, vascular deficits or degenerative disease these neurotoxic molecules may “leak” into the systemic circulation, cerebral vasculature, and on into the brain; and (iii) that this internal source of microbiome-derived neurotoxins may play a particularly strong role in shaping the human immune system and contributing to neural degeneration, particularly in the aging CNS. This “Perspectives” paper will further highlight some very recent developments that implicate GI-tract microbiome-derived LPS as an important contributor to inflammatory-neurodegeneration in the AD brain.
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Affiliation(s)
- Yuhai Zhao
- Neuroscience Center, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States.,Department of Anatomy and Cell Biology, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Lin Cong
- Neuroscience Center, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States.,Department of Neurology, Shengjing Hospital, China Medical University, Heping District, Shenyang, China
| | - Vivian Jaber
- Neuroscience Center, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Walter J Lukiw
- Neuroscience Center, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States.,Department of Neurology, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States.,Department of Ophthalmology, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
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26
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Roan NR, Sandi-Monroy N, Kohgadai N, Usmani SM, Hamil KG, Neidleman J, Montano M, Ständker L, Röcker A, Cavrois M, Rosen J, Marson K, Smith JF, Pilcher CD, Gagsteiger F, Sakk O, O'Rand M, Lishko PV, Kirchhoff F, Münch J, Greene WC. Semen amyloids participate in spermatozoa selection and clearance. eLife 2017; 6. [PMID: 28653619 PMCID: PMC5487211 DOI: 10.7554/elife.24888] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 05/24/2017] [Indexed: 12/22/2022] Open
Abstract
Unlike other human biological fluids, semen contains multiple types of amyloid fibrils in the absence of disease. These fibrils enhance HIV infection by promoting viral fusion to cellular targets, but their natural function remained unknown. The similarities shared between HIV fusion to host cell and sperm fusion to oocyte led us to examine whether these fibrils promote fertilization. Surprisingly, the fibrils inhibited fertilization by immobilizing sperm. Interestingly, however, this immobilization facilitated uptake and clearance of sperm by macrophages, which are known to infiltrate the female reproductive tract (FRT) following semen exposure. In the presence of semen fibrils, damaged and apoptotic sperm were more rapidly phagocytosed than healthy ones, suggesting that deposition of semen fibrils in the lower FRT facilitates clearance of poor-quality sperm. Our findings suggest that amyloid fibrils in semen may play a role in reproduction by participating in sperm selection and facilitating the rapid removal of sperm antigens. DOI:http://dx.doi.org/10.7554/eLife.24888.001 Seminal plasma, the fluid portion of semen, helps to transport sperm cells to the egg during sexual reproduction. Seminal plasma contains numerous proteins that help the sperm to survive and, in recent years, researchers discovered that it also harbours protein deposits known as amyloid fibrils. Such protein deposits are generally associated with neurodegenerative diseases such as Alzheimer's and Parkinson’s disease, where a build-up of fibrils can damage the nervous system. Semen amyloids, however, are present in the absence of disease, but can boost infection by HIV and other sexually transmitted viruses, by shuttling virus particles to their target cells. Despite these damaging effects, some researchers had suggested that amyloids in semen could be beneficial for humans, though it was unclear what these benefits might be. Roan et al. now set out to assess how semen amyloids affect human sperm activity. The results show that semen amyloids bind to damaged sperm cells and immobilize them, which are then quickly cleared away by immune cells. This could ensure that only the fittest sperm cells reach the egg. These findings suggest that amyloids can potentially serve beneficial roles for reproduction. A next step will be to investigate how semen amyloids trap unwanted sperm and how immune cells know when to remove it. More research is needed to investigate if problems in these processes could lead to infertility in men. DOI:http://dx.doi.org/10.7554/eLife.24888.002
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Affiliation(s)
- Nadia R Roan
- Department or Urology, University of California San Francisco, San Francisco, United States.,Gladstone Institute of Virology and Immunology, University of California San Francisco, San Francisco, United States
| | - Nathallie Sandi-Monroy
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany.,Kinderwunsch-Zentrum, Ulm, Germany
| | - Nargis Kohgadai
- Department or Urology, University of California San Francisco, San Francisco, United States.,Gladstone Institute of Virology and Immunology, University of California San Francisco, San Francisco, United States
| | - Shariq M Usmani
- The Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - Katherine G Hamil
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, United States
| | - Jason Neidleman
- Department or Urology, University of California San Francisco, San Francisco, United States.,Gladstone Institute of Virology and Immunology, University of California San Francisco, San Francisco, United States
| | - Mauricio Montano
- Gladstone Institute of Virology and Immunology, University of California San Francisco, San Francisco, United States
| | - Ludger Ständker
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany.,Core Facility Functional Peptidomics, Ulm University, Ulm, Germany
| | - Annika Röcker
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Marielle Cavrois
- Gladstone Institute of Virology and Immunology, University of California San Francisco, San Francisco, United States.,Department of Medicine, University of California San Francisco, San Francisco, United States
| | - Jared Rosen
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, United States
| | - Kara Marson
- HIV / AIDS Division, San Francisco General Hospital, University of California San Francisco, San Francisco, United States
| | - James F Smith
- Department or Urology, University of California San Francisco, San Francisco, United States
| | - Christopher D Pilcher
- HIV / AIDS Division, San Francisco General Hospital, University of California San Francisco, San Francisco, United States
| | | | - Olena Sakk
- Core Facility Transgenic Mice, Medical Faculty, Ulm University, Ulm, Germany
| | - Michael O'Rand
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, United States
| | - Polina V Lishko
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, United States
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Warner C Greene
- Gladstone Institute of Virology and Immunology, University of California San Francisco, San Francisco, United States.,Department of Medicine, University of California San Francisco, San Francisco, United States.,Department of Microbiology and Immunology, University of California, San Francisco, United States
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27
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Prabakaran R, Goel D, Kumar S, Gromiha MM. Aggregation prone regions in human proteome: Insights from large-scale data analyses. Proteins 2017; 85:1099-1118. [DOI: 10.1002/prot.25276] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 02/10/2017] [Accepted: 02/24/2017] [Indexed: 12/25/2022]
Affiliation(s)
- R. Prabakaran
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences; Indian Institute of Technology Madras; Chennai 600036 India
| | - Dhruv Goel
- Department of Computer Science and Engineering; Motilal Nehru National Institute of Technology; Allahabad 211004 India
| | - Sandeep Kumar
- Biotherapeutics Pharmaceutical Sciences, Pfizer Inc; 700 Chesterfield Parkway West Chesterfield Missouri 63017, USA
| | - M. Michael Gromiha
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences; Indian Institute of Technology Madras; Chennai 600036 India
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28
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Biza KV, Nastou KC, Tsiolaki PL, Mastrokalou CV, Hamodrakas SJ, Iconomidou VA. The amyloid interactome: Exploring protein aggregation. PLoS One 2017; 12:e0173163. [PMID: 28249044 PMCID: PMC5383009 DOI: 10.1371/journal.pone.0173163] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/15/2017] [Indexed: 11/22/2022] Open
Abstract
Protein-protein interactions are the quintessence of physiological activities, but also participate in pathological conditions. Amyloid formation, an abnormal protein-protein interaction process, is a widespread phenomenon in divergent proteins and peptides, resulting in a variety of aggregation disorders. The complexity of the mechanisms underlying amyloid formation/amyloidogenicity is a matter of great scientific interest, since their revelation will provide important insight on principles governing protein misfolding, self-assembly and aggregation. The implication of more than one protein in the progression of different aggregation disorders, together with the cited synergistic occurrence between amyloidogenic proteins, highlights the necessity for a more universal approach, during the study of these proteins. In an attempt to address this pivotal need we constructed and analyzed the human amyloid interactome, a protein-protein interaction network of amyloidogenic proteins and their experimentally verified interactors. This network assembled known interconnections between well-characterized amyloidogenic proteins and proteins related to amyloid fibril formation. The consecutive extended computational analysis revealed significant topological characteristics and unraveled the functional roles of all constituent elements. This study introduces a detailed protein map of amyloidogenicity that will aid immensely towards separate intervention strategies, specifically targeting sub-networks of significant nodes, in an attempt to design possible novel therapeutics for aggregation disorders.
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Affiliation(s)
- Konstantina V. Biza
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, Athens, Greece
| | - Katerina C. Nastou
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, Athens, Greece
| | - Paraskevi L. Tsiolaki
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, Athens, Greece
| | - Chara V. Mastrokalou
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, Athens, Greece
| | - Stavros J. Hamodrakas
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, Athens, Greece
| | - Vassiliki A. Iconomidou
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, Athens, Greece
- * E-mail:
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29
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Johansson J, Olson L, Andersson J, Johansson G, Winblad B. Amyloid: a multifaceted player in human health and disease. J Intern Med 2016; 280:136-8. [PMID: 27436687 DOI: 10.1111/joim.12497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- J Johansson
- Department of Neurobiology, Care Sciences and Society (NVS), Center for Alzheimer Research, Karolinska Institutet, Huddinge, Sweden
| | - L Olson
- Department of Neuroscience, Retzius Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - J Andersson
- Department of Medicine, Center for Infectious Medicine (CIM), Karolinska Institutet, Stockholm, Sweden
| | - G Johansson
- Department of Neurobiology, Care Sciences and Society (NVS), Center for Alzheimer Research, Karolinska Institutet, Huddinge, Sweden
| | - B Winblad
- Department of Neurobiology, Care Sciences and Society (NVS), Center for Alzheimer Research, Karolinska Institutet, Huddinge, Sweden
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