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Sangar D, Hill E, Jack K, Batchelor M, Mistry B, Ribes JM, Jackson GS, Mead S, Bieschke J. Syntaxin-6 delays prion protein fibril formation and prolongs the presence of toxic aggregation intermediates. eLife 2024; 13:e83320. [PMID: 39109999 PMCID: PMC11377041 DOI: 10.7554/elife.83320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 07/20/2024] [Indexed: 09/06/2024] Open
Abstract
Prions replicate via the autocatalytic conversion of cellular prion protein (PrPC) into fibrillar assemblies of misfolded PrP. While this process has been extensively studied in vivo and in vitro, non-physiological reaction conditions of fibril formation in vitro have precluded the identification and mechanistic analysis of cellular proteins, which may alter PrP self-assembly and prion replication. Here, we have developed a fibril formation assay for recombinant murine and human PrP (23-231) under near-native conditions (NAA) to study the effect of cellular proteins, which may be risk factors or potential therapeutic targets in prion disease. Genetic screening suggests that variants that increase syntaxin-6 expression in the brain (gene: STX6) are risk factors for sporadic Creutzfeldt-Jakob disease. Analysis of the protein in NAA revealed, counterintuitively, that syntaxin-6 is a potent inhibitor of PrP fibril formation. It significantly delayed the lag phase of fibril formation at highly sub-stoichiometric molar ratios. However, when assessing toxicity of different aggregation time points to primary neurons, syntaxin-6 prolonged the presence of neurotoxic PrP species. Electron microscopy and super-resolution fluorescence microscopy revealed that, instead of highly ordered fibrils, in the presence of syntaxin-6 PrP formed less-ordered aggregates containing syntaxin-6. These data strongly suggest that the protein can directly alter the initial phase of PrP self-assembly and, uniquely, can act as an 'anti-chaperone', which promotes toxic aggregation intermediates by inhibiting fibril formation.
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Affiliation(s)
- Daljit Sangar
- MRC Prion Unit at UCL, Institute of Prion Diseases, London, United Kingdom
| | - Elizabeth Hill
- MRC Prion Unit at UCL, Institute of Prion Diseases, London, United Kingdom
| | - Kezia Jack
- MRC Prion Unit at UCL, Institute of Prion Diseases, London, United Kingdom
| | - Mark Batchelor
- MRC Prion Unit at UCL, Institute of Prion Diseases, London, United Kingdom
| | - Beenaben Mistry
- MRC Prion Unit at UCL, Institute of Prion Diseases, London, United Kingdom
| | - Juan M Ribes
- MRC Prion Unit at UCL, Institute of Prion Diseases, London, United Kingdom
| | - Graham S Jackson
- MRC Prion Unit at UCL, Institute of Prion Diseases, London, United Kingdom
| | - Simon Mead
- MRC Prion Unit at UCL, Institute of Prion Diseases, London, United Kingdom
| | - Jan Bieschke
- MRC Prion Unit at UCL, Institute of Prion Diseases, London, United Kingdom
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2
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O'Neill NS, Alvarez NJ, Schweitzer-Stenner R. Tuning the thermostability of GHG gels by salts at different positions on the Hofmeister scale. Sci Rep 2024; 14:14742. [PMID: 38926473 PMCID: PMC11208536 DOI: 10.1038/s41598-024-65145-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
The influence of Hofmeister cations (NH4+, Na+, Mg2+) and anions (H2PO4-, CH3COO-, Cl-, NO3-) on the thermostability of a GHG hydrogel was investigated. The combined results of UV circular dichroism (UVCD) and Small Amplitude Oscillatory Shear Rheology experiments reveal that the addition of salt reduces the stability of the gel phase and the underlying fibrils. In line with the cationic Hofmeister hierarchy, the chaotropic Mg2+ ions caused the greatest thermal destabilization of the gel phase with the gel → sol transition temperature Tgs value lowered by 10 °C. In the absence of salt, the gel → sol transition probed by the storage modulus and microscopy is biphasic. In the presence of salt, it becomes monophasic. Contrary to expectations the presence of Hofmeister anions leads to a nearly identical reduction of the gel → sol transition temperatures. However, UVCD spectra suggest that they affect the ππ-stacking between imidazole groups to a different extent. We relate the absence of ion specificity regarding the solubility of fibrils (probed by UVCD) to the observed enthalpy-entropy compensation of the dissolution process. Our results combined show how CD spectroscopy and rheology combined yields a more nuanced picture of the processes underlying the gel → sol transition.
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Affiliation(s)
- Nichole S O'Neill
- Department of Chemistry, Drexel University, Philadelphia, PA, 19104, USA
| | - Nicolas J Alvarez
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA, 19104, USA.
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3
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Li T, Wang D, Zhang X, Chen Z, Wang L. Specific ions effect on aggregation behaviors and structural changes of amyloid fibrils from rice glutelin. Food Chem 2024; 441:138351. [PMID: 38218147 DOI: 10.1016/j.foodchem.2023.138351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/26/2023] [Accepted: 12/31/2023] [Indexed: 01/15/2024]
Abstract
Metal ions have been considered as an important factor on fibrils assembly. Herein, a comprehensive analysis of specific ions effect on fibril formation and structural changes was investigated. The addition of ions (except Zn2+) accelerated the aggregation kinetics of rice glutelin fibrils (RGFs) from 0.93 to 1.28-2.19 h-1. In addition, the fibrillization rate followed the order of NH4+ > Li+ > Na+ > K+ > Cu2+ > Mg2+ > Ca2+ > Zn2+. The highest yield and length of fibrils were observed with Ca2+, probably due to the ionic bridging effect and hydrated capacity of Ca2+. However, Cu2+ reduced the fibrils yield, which was attributable to the fact that Cu2+ disrupted β-sheet structure and inhibited the transition of monomer to fibrils. The polymorphism of fibrils was observed with different salts, and the light metals presented a superior effect on fibrils formation than heavy metals. Overall, this work will provide a further information into how to tune the structure of RGFs using various ions.
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Affiliation(s)
- Ting Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
| | - Dong Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
| | - Xinxia Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
| | - Zhengxing Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
| | - Li Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China.
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4
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Behera DP, Subadini S, Freudenberg U, Sahoo H. Sulfation of hyaluronic acid reconfigures the mechanistic pathway of bone morphogenetic protein-2 aggregation. Int J Biol Macromol 2024; 263:130128. [PMID: 38350587 DOI: 10.1016/j.ijbiomac.2024.130128] [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: 11/22/2023] [Revised: 02/03/2024] [Accepted: 02/09/2024] [Indexed: 02/15/2024]
Abstract
Bone morphogenetic protein-2 (BMP-2) is a critical growth factor of bone extracellular matrix (ECM), pivotal for osteogenesis. Glycosaminoglycans (GAGs), another vital ECM biomolecules, interact with growth factors, affecting signal transduction. Our study primarily focused on hyaluronic acid (HA), a prevalent GAG, and its sulfated derivative (SHA). We explored their impact on BMP-2's conformation, aggregation, and mechanistic pathways of aggregation using diverse optical and rheological methods. In the presence of HA and SHA, the secondary structure of BMP-2 underwent a structured transformation, characterized by a substantial increase in beta sheet content, and a detrimental alteration, manifesting as a shift towards unstructured content, respectively. Although both HA and SHA induced BMP-2 aggregation, their mechanisms differed. SHA led to rapid amorphous aggregates, while HA promoted amyloid fibrils with a lag phase and sigmoidal kinetics. Aggregate size and shape varied; HA produced larger structures, SHA smaller. Each aggregation type followed distinct pathways influenced by viscosity and excluded volume. Higher viscosity, low diffusivity of protein and higher excluded volume In the presence of HA promotes fibrillation having size in micrometer range. Low viscosity, high diffusivity of protein and lesser excluded volume leads to amorphous aggregate of size in nanometer range.
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Affiliation(s)
- Devi Prasanna Behera
- Biophysical and Protein Chemistry Lab, Department of Chemistry, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Suchismita Subadini
- Biophysical and Protein Chemistry Lab, Department of Chemistry, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Uwe Freudenberg
- Institute of Polymer Research, Technical University Dresden, 01307 Dresden, Germany
| | - Harekrushna Sahoo
- Biophysical and Protein Chemistry Lab, Department of Chemistry, National Institute of Technology, Rourkela 769008, Odisha, India; Center for Nanomaterials, National Institute of Technology, Rourkela 769008, Odisha, India.
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5
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Sharma K, Stockert F, Shenoy J, Berbon M, Abdul-Shukkoor MB, Habenstein B, Loquet A, Schmidt M, Fändrich M. Cryo-EM observation of the amyloid key structure of polymorphic TDP-43 amyloid fibrils. Nat Commun 2024; 15:486. [PMID: 38212334 PMCID: PMC10784485 DOI: 10.1038/s41467-023-44489-0] [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: 06/20/2023] [Accepted: 12/14/2023] [Indexed: 01/13/2024] Open
Abstract
The transactive response DNA-binding protein-43 (TDP-43) is a multi-facet protein involved in phase separation, RNA-binding, and alternative splicing. In the context of neurodegenerative diseases, abnormal aggregation of TDP-43 has been linked to amyotrophic lateral sclerosis and frontotemporal lobar degeneration through the aggregation of its C-terminal domain. Here, we report a cryo-electron microscopy (cryo-EM)-based structural characterization of TDP-43 fibrils obtained from the full-length protein. We find that the fibrils are polymorphic and contain three different amyloid structures. The structures differ in the number and relative orientation of the protofilaments, although they share a similar fold containing an amyloid key motif. The observed fibril structures differ from previously described conformations of TDP-43 fibrils and help to better understand the structural landscape of the amyloid fibril structures derived from this protein.
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Affiliation(s)
- Kartikay Sharma
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany.
| | - Fabian Stockert
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | - Jayakrishna Shenoy
- University of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Mélanie Berbon
- University of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | | | - Birgit Habenstein
- University of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Antoine Loquet
- University of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Matthias Schmidt
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
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6
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Sun C, Slade L, Mbonu P, Ordner H, Mitchell C, Mitchell M, Liang FC. Membrane protein chaperone and sodium chloride modulate the kinetics and morphology of amyloid beta aggregation. FEBS J 2024; 291:158-176. [PMID: 37786925 DOI: 10.1111/febs.16967] [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: 12/13/2022] [Revised: 07/04/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
Protein aggregation is a biological phenomenon caused by the accumulation of misfolded proteins. Amyloid beta (Aβ) peptides are derived from the cleavage of a larger membrane protein molecule and accumulate to form plaques extracellularly. According to the amyloid hypothesis, accumulation of Aβ aggregates in the brain is primarily responsible for the pathogenesis of Alzheimer's disease (AD). Therefore, the disassembly of Aβ aggregates may provide opportunities for alleviating or treating AD. Here, we show that the novel protein targeting machinery from chloroplast, chloroplast signal recognition particle 43 (cpSRP43), is an ATP-independent membrane protein chaperone that can both prevent and reverse Aβ aggregation effectively. Using of thioflavin T dye, we obtained the aggregation kinetics of Aβ aggregation and determined that the chaperone prevents Aβ aggregation in a concentration-dependent manner. Size exclusion chromatography and sedimentation assays showed that 10-fold excess of cpSRP43 can keep Aβ in the soluble monomeric form. Electron microscopy showed that the fibril structure was disrupted in the presence of this chaperone. Importantly, cpSRP43 utilizes the binding energy to actively remodel the preformed Aβ aggregates without assistance by a co-chaperone and ATP, emphasizing its unique function among protein chaperones. Moreover, when sodium chloride concentration is higher than 25 mm, the Aβ aggregation rate increases drastically to form tightly associated aggregates and generate more oligomers. Our results demonstrate that the presence of cpSRP43 and low NaCl levels inhibit or retard Aβ peptide aggregation, potentially opening new avenues to strategically develop an effective treatment for AD.
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Affiliation(s)
- Christopher Sun
- Department of Biology, Midwestern State University, Wichita Falls, TX, USA
| | - Leah Slade
- Department of Chemistry, Midwestern State University, Wichita Falls, TX, USA
| | - Prisca Mbonu
- Department of Biology, Midwestern State University, Wichita Falls, TX, USA
| | - Hunter Ordner
- Department of Chemistry, Midwestern State University, Wichita Falls, TX, USA
| | - Connor Mitchell
- Department of Chemistry, Midwestern State University, Wichita Falls, TX, USA
| | - Matthew Mitchell
- Department of Chemistry, Midwestern State University, Wichita Falls, TX, USA
| | - Fu-Cheng Liang
- Department of Chemistry, Midwestern State University, Wichita Falls, TX, USA
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7
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Farrell KM, Fields CR, Dicke SS, Zanni MT. Simultaneously Measured Kinetics of Two Amyloid Polymorphs Using Cross Peak Specific 2D IR Spectroscopy. J Phys Chem Lett 2023; 14:11750-11757. [PMID: 38117179 PMCID: PMC11163371 DOI: 10.1021/acs.jpclett.3c02698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The origin of in vitro amyloid fibril polymorphs is debated, in part, because few techniques can simultaneously monitor the formation kinetics of multiple amyloid polymorphs. Using a cross-peak specific polarization scheme, ⟨0°,0°,60°,-60°⟩, we resolve 22 previously unseen cross peaks in the 2D IR spectra of amyloid fibrils formed by the human islet amyloid polypeptide (hIAPP). Those cross peaks include a subset assigned to a second fibril polymorph, which forms on a slower time scale. We simulated the data with three different kinetic models for polymorph formation. Only a model based on secondary nucleation reproduces the cross peak kinetics. These experiments are evidence that fibrils formed by secondary nucleation have a different polymorphic structure than the parent fibrils and illustrate the enhanced structural resolution of this new cross peak specific polarization scheme.
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Affiliation(s)
- Kieran M Farrell
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Caitlyn R Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Sidney S Dicke
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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8
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Hovanová V, Hovan A, Humenik M, Sedlák E. Only kosmotrope anions trigger fibrillization of the recombinant core spidroin eADF4(C16) from Araneus diadematus. Protein Sci 2023; 32:e4832. [PMID: 37937854 PMCID: PMC10661072 DOI: 10.1002/pro.4832] [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: 07/18/2023] [Revised: 10/20/2023] [Accepted: 11/05/2023] [Indexed: 11/09/2023]
Abstract
Recombinant core spidroin eADF4(C16) has received increasing attention due to its ability to form micro- and nano-structured scaffolds, which are based on nanofibrils with great potential for biomedical and biotechnological applications. Phosphate anions have been demonstrated to trigger the eADF4(C16) self-assembly into cross-beta fibrils. In the present work, we systematically addressed the effect of nine sodium anions, namely SO4 2- , HPO4 2- (Pi), F- , Cl- , Br- , NO3 - , I- , SCN- , and ClO4 - from the Hofmeister series on the in vitro self-assembly kinetics of eADF4(C16). We show that besides the phosphate anions, only kosmotropic anions such as sulfate and fluoride can initiate the eADF4(C16) fibril formation. Global analysis of the self-assembly kinetics, utilizing the platform AmyloFit, showed the nucleation-based mechanism with a major role of secondary nucleation, surprisingly independent of the type of the kosmotropic anion. The rate constant of the fibril elongation in mixtures of phosphate anions with other studied anions correlated with their kosmotropic or chaotropic position in the Hofmeister series. Our findings suggest an important role of anion hydration in the eADF4(C16) fibrillization process.
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Affiliation(s)
- Veronika Hovanová
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
- Department of Biophysics, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Andrej Hovan
- Department of Biophysics, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Martin Humenik
- Department of Biomaterials, Faculty of Engineering ScienceUniversity BayreuthBayreuthGermany
| | - Erik Sedlák
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
- Department of Biochemistry, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
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9
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Havemeister F, Ghaeidamini M, Esbjörner EK. Monovalent cations have different effects on the assembly kinetics and morphology of α-synuclein amyloid fibrils. Biochem Biophys Res Commun 2023; 679:31-36. [PMID: 37660641 DOI: 10.1016/j.bbrc.2023.08.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 08/29/2023] [Indexed: 09/05/2023]
Abstract
Formation of α-synuclein amyloid fibrils is a pathological hallmark of Parkinson's disease and a phenomenon that is strongly modulated by environmental factors. Here, we compared effects of different monovalent cations (Li+, Na+, K+) on the formation and properties of α-synuclein amyloid fibrils. Na+ > Li+ were found to have concentration-dependent catalytic effects on primary nucleation whereas K+ ions acted inhibitory. We discuss this discrepancy in terms of a superior affinity of Na+ and Li+ to carboxylic protein groups, resulting in reduced Columbic repulsion and by considering K+ as an ion with poor protein binding and slight chaotropic character, which could promote random coil protein structure. K+ ions, furthermore, appeared to lower the β-sheet content of the fibrils and increase their persistence lengths, the latter we interpret as a consequence of lesser ion binding and hence higher line charge of the fibrils. The finding that Na+ and K+ have opposite effects on α-synuclein aggregation is intriguing in relation to the significant transient gradients of these ions across axonal membranes, but also important for the design and interpretation of biophysical assays where buffers containing these monovalent cations have been intermixedly used.
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Affiliation(s)
- Fritjof Havemeister
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, S-41296, Gothenburg, Sweden
| | - Marziyeh Ghaeidamini
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, S-41296, Gothenburg, Sweden
| | - Elin K Esbjörner
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, S-41296, Gothenburg, Sweden.
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10
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Sudhakar S, Manohar A, Mani E. Liquid-Liquid Phase Separation (LLPS)-Driven Fibrilization of Amyloid-β Protein. ACS Chem Neurosci 2023; 14:3655-3664. [PMID: 37718544 DOI: 10.1021/acschemneuro.3c00286] [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] [Indexed: 09/19/2023] Open
Abstract
Amyloid-β [Aβ(1-40)] aggregation into a fibrillar network is one of the major hallmarks of Alzheimer's disease (AD). Recently, a few studies reported that polyphosphate (polyP), an anionic biopolymer that participates in various cellular physiological processes in humans, induces fibrilization in many amyloidogenic proteins [ 2020 Alzheimer's Disease Facts and Figures; John Wiley and Sons Inc., 2020; Tanzi, R. E.; Bertram, L. Cell 2005, 120, 545-555; Selkoe, D. J. Proc. Natl. Acad. Sci. U.S.A. 1995, 275, 630-631; and Rambaran, R. N.; Serpell, L. C. Prion 2008, 2, 112-117]. However, the role of polyP in Aβ(1-40) fibrilization and the underlying mechanism are unclear. In this study, we report experimental investigations on the role of polyP in the fibrilization kinetics of Aβ(1-40). It is found that polyP exhibits a dual effect depending upon the pH value. At pH = 7 (neutral), polyP inhibits amyloid fibrilization in a dose-dependent manner similar to negatively charged nanoparticles. On the contrary, at pH = 3 (acidic), polyP accelerates amyloid fibrilization kinetics via liquid-liquid phase separation (LLPS), wherein the protein-rich droplets contain mature fibrils. In the parameter space spanned by concentrations of Aβ(1-40) and polyP, a phase diagram is constructed to demark the domain where LLPS is observed at pH = 3. Characterization of the protein aggregates, secondary structure content in the aggregates, and cell viability studies in the presence of aggregates are discussed at both pH values. This study reveals that anionic biopolymers can modulate amyloid fibrilization kinetics, linked to neurodegenerative diseases, depending upon their local concentrations and pH.
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Affiliation(s)
- Swathi Sudhakar
- Department of Applied Mechanics, Indian Institute of Technology Madras, Chennai 600036, India
- Center for Soft and Biological Matter, Indian Institute of Technology Madras, Chennai 600036, India
| | - Anagha Manohar
- Department of Applied Mechanics, Indian Institute of Technology Madras, Chennai 600036, India
| | - Ethayaraja Mani
- Polymer Engineering and Colloid Science Lab, Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai 600036, India
- Center for Soft and Biological Matter, Indian Institute of Technology Madras, Chennai 600036, India
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11
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Kell DB, Pretorius E. Are fibrinaloid microclots a cause of autoimmunity in Long Covid and other post-infection diseases? Biochem J 2023; 480:1217-1240. [PMID: 37584410 DOI: 10.1042/bcj20230241] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/17/2023]
Abstract
It is now well established that the blood-clotting protein fibrinogen can polymerise into an anomalous form of fibrin that is amyloid in character; the resultant clots and microclots entrap many other molecules, stain with fluorogenic amyloid stains, are rather resistant to fibrinolysis, can block up microcapillaries, are implicated in a variety of diseases including Long COVID, and have been referred to as fibrinaloids. A necessary corollary of this anomalous polymerisation is the generation of novel epitopes in proteins that would normally be seen as 'self', and otherwise immunologically silent. The precise conformation of the resulting fibrinaloid clots (that, as with prions and classical amyloid proteins, can adopt multiple, stable conformations) must depend on the existing small molecules and metal ions that the fibrinogen may (and is some cases is known to) have bound before polymerisation. Any such novel epitopes, however, are likely to lead to the generation of autoantibodies. A convergent phenomenology, including distinct conformations and seeding of the anomalous form for initiation and propagation, is emerging to link knowledge in prions, prionoids, amyloids and now fibrinaloids. We here summarise the evidence for the above reasoning, which has substantial implications for our understanding of the genesis of autoimmunity (and the possible prevention thereof) based on the primary process of fibrinaloid formation.
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Affiliation(s)
- Douglas B Kell
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, U.K
- The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kemitorvet 200, 2800 Kgs Lyngby, Denmark
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Private Bag X1 Matieland, Stellenbosch 7602, South Africa
| | - Etheresia Pretorius
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, U.K
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Private Bag X1 Matieland, Stellenbosch 7602, South Africa
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12
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Schäffler M, Samantray S, Strodel B. Transition Networks Unveil Disorder-to-Order Transformations in A β Caused by Glycosaminoglycans or Lipids. Int J Mol Sci 2023; 24:11238. [PMID: 37510997 PMCID: PMC10380057 DOI: 10.3390/ijms241411238] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/02/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
The aggregation of amyloid-β (Aβ) peptides, particularly of Aβ1-42, has been linked to the pathogenesis of Alzheimer's disease. In this study, we focus on the conformational change of Aβ1-42 in the presence of glycosaminoglycans (GAGs) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipids using molecular dynamics simulations. We analyze the conformational changes that occur in Aβ by extracting the key structural features that are then used to generate transition networks. Using the same three features per network highlights the transitions from intrinsically disordered states ubiquitous in Aβ1-42 in solution to more compact states arising from stable β-hairpin formation when Aβ1-42 is in the vicinity of a GAG molecule, and even more compact states characterized by a α-helix or β-sheet structures when Aβ1-42 interacts with a POPC lipid cluster. We show that the molecular mechanisms underlying these transitions from disorder to order are different for the Aβ1-42/GAG and Aβ1-42/POPC systems. While in the latter the hydrophobicity provided by the lipid tails facilitates the folding of Aβ1-42, in the case of GAG there are hardly any intermolecular Aβ1-42-GAG interactions. Instead, GAG removes sodium ions from the peptide, allowing stronger electrostatic interactions within the peptide that stabilize a β-hairpin. Our results contribute to the growing knowledge of the role of GAGs and lipids in the conformational preferences of the Aβ peptide, which in turn influences its aggregation into toxic oligomers and amyloid fibrils.
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Affiliation(s)
- Moritz Schäffler
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428 Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Suman Samantray
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Birgit Strodel
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428 Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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13
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Li X, Jian H, Han Q, Wang A, Li J, Man N, Li Q, Bai S, Li J. Three-dimensional (3D) bioprinting of medium toughened dipeptide hydrogel scaffolds with Hofmeister effect. J Colloid Interface Sci 2023; 639:1-6. [PMID: 36796110 DOI: 10.1016/j.jcis.2023.02.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023]
Abstract
Short peptide self-assembled hydrogels as 3D bioprinting inks show excellent biocompatibility and diverse functional expansion, and have broad application prospects in cell culture and tissue engineering. However, the preparation of biological hydrogel inks with adjustable mechanical strength and controllable degradation for 3D bioprinting still faces big challenges. Herein, we develop dipeptide bio-inks that can be gelled in-situ based on Hofmeister sequence, and prepare hydrogel scaffold by using a layer-by-layer 3D printing strategy. Excitingly, after the introduction of Dulbecco's Modified Eagle's medium (DMEM), which is necessary for cell culture, the hydrogel scaffolds show an excellent toughening effect, which matches the needs of cell culture. It's notable that in the whole process of preparation and 3D printing of hydrogel scaffolds, no cross-linking agent, ultraviolet (UV), heating or other exogenous factors are involved, ensuring high biosafety and biocompatibility. After two weeks of 3D culture, millimeter-sized cell spheres are obtained. This work provides an opportunity for the development of short peptide hydrogel bioinks without exogenous factors in 3D printing, tissue engineering, tumor simulant reconstruction and other biomedical fields.
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Affiliation(s)
- Xin Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Honglei Jian
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingquan Han
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Anhe Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jieling Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ningyuan Man
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Qi Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Shuo Bai
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences, CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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14
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Seira Curto J, Fernandez MR, Cladera J, Benseny-Cases N, Sanchez de Groot N. Aβ40 Aggregation under Changeable Conditions. Int J Mol Sci 2023; 24:ijms24098408. [PMID: 37176115 PMCID: PMC10179685 DOI: 10.3390/ijms24098408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/28/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Homeostasis is crucial for cell function, and disturbances in homeostasis can lead to health disorders. Under normal conditions, intracellular pH is maintained between 7.35 and 7.45. Altered endosomal and lysosomal pH together with a general drop in brain pH are associated with the aggregation of amyloid-β-peptide (Aβ) and the development of Alzheimer's disease. Under acidic conditions, close to the Aβ isoelectric point, the absence of charges favors the formation of intermolecular contacts and promotes aggregation. Here, we analyzed how pH levels affect the aggregation of Aβ40 considering the variations in brain pH and the coexistence of different aggregated conformations. Our results suggest that different macromolecular conformations can interact with each other and influence the aggregation process. In addition, we showed that neutral pH and physiological salt concentrations favor a slow aggregation, resulting in ordered, stable fibrils, with low cytotoxic effects. Overall, we highlight the complexity of the aggregation processes occurring in different physiological and pathological environments.
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Affiliation(s)
- Jofre Seira Curto
- Unitat de Bioquímica, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Maria Rosario Fernandez
- Unitat de Bioquímica, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Josep Cladera
- Unitat de Biofísica, Departament de Bioquímica i Biologia Molecular, Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Núria Benseny-Cases
- Unitat de Biofísica, Departament de Bioquímica i Biologia Molecular, Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Natalia Sanchez de Groot
- Unitat de Bioquímica, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
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15
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Light, Water, and Melatonin: The Synergistic Regulation of Phase Separation in Dementia. Int J Mol Sci 2023; 24:ijms24065835. [PMID: 36982909 PMCID: PMC10054283 DOI: 10.3390/ijms24065835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/17/2023] [Indexed: 03/22/2023] Open
Abstract
The swift rise in acceptance of molecular principles defining phase separation by a broad array of scientific disciplines is shadowed by increasing discoveries linking phase separation to pathological aggregations associated with numerous neurodegenerative disorders, including Alzheimer’s disease, that contribute to dementia. Phase separation is powered by multivalent macromolecular interactions. Importantly, the release of water molecules from protein hydration shells into bulk creates entropic gains that promote phase separation and the subsequent generation of insoluble cytotoxic aggregates that drive healthy brain cells into diseased states. Higher viscosity in interfacial waters and limited hydration in interiors of biomolecular condensates facilitate phase separation. Light, water, and melatonin constitute an ancient synergy that ensures adequate protein hydration to prevent aberrant phase separation. The 670 nm visible red wavelength found in sunlight and employed in photobiomodulation reduces interfacial and mitochondrial matrix viscosity to enhance ATP production via increasing ATP synthase motor efficiency. Melatonin is a potent antioxidant that lowers viscosity to increase ATP by scavenging excess reactive oxygen species and free radicals. Reduced viscosity by light and melatonin elevates the availability of free water molecules that allow melatonin to adopt favorable conformations that enhance intrinsic features, including binding interactions with adenosine that reinforces the adenosine moiety effect of ATP responsible for preventing water removal that causes hydrophobic collapse and aggregation in phase separation. Precise recalibration of interspecies melatonin dosages that account for differences in metabolic rates and bioavailability will ensure the efficacious reinstatement of the once-powerful ancient synergy between light, water, and melatonin in a modern world.
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16
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Moral R, Paul S. Influence of salt and temperature on the self-assembly of cyclic peptides in water: a molecular dynamics study. Phys Chem Chem Phys 2023; 25:5406-5422. [PMID: 36723368 DOI: 10.1039/d2cp05160e] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
It is found in the literature that cyclic peptides (CPs) are able to self-assemble in water to form cyclic peptide nanotubes (CPNTs) and are used extensively in the field of nanotechnology. Several factors influence the formation and stability of these nanotubes in water. However, an extensive study of the contribution of several important factors is still lacking. The purpose of this study is to explore the effect of temperature and salt (NaCl) on the association tendency of CPs. Furthermore, the self-association behavior of CPs in aqueous solutions at various temperatures is also thoroughly discussed. Cyclo-[(Asp-D-Leu-Lys-D-Leu)2] is considered for this study and a series of classical molecular dynamics (MD) simulations at three different temperatures, viz. 280 K, 300 K, and 320 K, both in pure water and in NaCl solutions of different concentrations are carried out. The calculations of radial distribution functions, preferential interaction parameters, cluster formation and hydrogen bonding properties suggest a strong influence of NaCl concentration on the association propensity of CPs. Low NaCl concentration hinders CP association while high NaCl concentration facilitates the association of CPs. Besides this, the association of CPs is found to be enhanced at low temperature. Furthermore, the thermodynamics of CP association is predominantly found to be enthalpy driven in both the presence and absence of salt. No crossover between enthalpy and entropy in CP association is observed. In addition, the MM-GBSA method is used to investigate the binding free energies of the CP rings that self-assembled to form nanotube like structures at all three temperatures.
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Affiliation(s)
- Rimjhim Moral
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam, 781039, India.
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam, 781039, India.
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17
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Multivariate effects of pH, salt, and Zn 2+ ions on Aβ 40 fibrillation. Commun Chem 2022; 5:171. [PMID: 36697708 PMCID: PMC9814776 DOI: 10.1038/s42004-022-00786-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 11/23/2022] [Indexed: 12/15/2022] Open
Abstract
Amyloid-β (Aβ) peptide aggregation plays a central role in the progress of Alzheimer's disease (AD), of which Aβ-deposited extracellular amyloid plaques are a major hallmark. The brain micro-environmental variation in AD patients, like local acidification, increased ionic strength, or changed metal ion levels, cooperatively modulates the aggregation of the Aβ peptides. Here, we investigate the multivariate effects of varied pH, ionic strength and Zn2+ on Aβ40 fibrillation kinetics. Our results reveal that Aβ fibrillation kinetics are strongly affected by pH and ionic strength suggesting the importance of electrostatic interactions in regulating Aβ40 fibrillation. More interestingly, the presence of Zn2+ ions can further alter or even reserve the role of pH and ionic strength on the amyloid fibril kinetics, suggesting the importance of amino acids like Histidine that can interact with Zn2+ ions. Both pH and ionic strength regulate the secondary nucleation processes, however regardless of pH and Zn2+ ions, ionic strength can also modulate the morphology of Aβ40 aggregates. These multivariate effects in bulk solution provide insights into the correlation of pH-, ionic strength- or Zn2+ ions changes with amyloid deposits in AD brain and will deepen our understanding of the molecular pathology in the local brain microenvironment.
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18
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Rahman A, Saikia B, Gogoi CR, Baruah A. Advances in the understanding of protein misfolding and aggregation through molecular dynamics simulation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 175:31-48. [PMID: 36044970 DOI: 10.1016/j.pbiomolbio.2022.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Aberrant protein folding known as protein misfolding is counted as one of the striking factors of neurodegenerative diseases. The extensive range of pathologies caused by protein misfolding, aggregation and subsequent accumulation are mainly classified into either gain of function diseases or loss of function diseases. In order to seek for novel strategies for treatment and diagnosis of neurodegenerative diseases, insights into the mechanism of misfolding and aggregation is essential. A comprehensive knowledge on the factors influencing misfolding and aggregation is required as well. An extensive experimental study on protein aggregation is somewhat challenging due to the insoluble and noncrystalline nature of amyloid fibrils. Thus there has been a growing use of computational approaches including Monte Carlo simulation, docking simulation, molecular dynamics simulation in the study of protein misfolding and aggregation. The review presents a discussion on molecular dynamics simulation alone as to how it has emerged as a promising tool in the understanding of protein misfolding and aggregation in general, detailing upon three different aspects considering four misfold prone proteins in particular. It is noticeable that all four proteins considered in this review i.e prion, superoxide dismutase1, huntingtin and amyloid β are linked to chronic neurodegenerative diseases with debilitating effects. Initially the review elaborates on the factors influencing the misfolding and aggregation. Next, it addresses our current understanding of the amyloid structures and the associated aggregation mechanisms, finally, summarizing the contribution of this computational tool in the search for therapeutic strategies against the respective protein-deposition diseases.
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Affiliation(s)
- Aziza Rahman
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India
| | - Bondeepa Saikia
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India
| | - Chimi Rekha Gogoi
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India
| | - Anupaul Baruah
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India.
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19
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Takekiyo T, Yamada N, Amo T, Nakazawa CT, Asano A, Ichimura T, Kato M, Yoshimura Y. Dissolution of Amyloid Aggregates by Direct Addition of Alkali Halides. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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20
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Antosova A, Gancar M, Bednarikova Z, Marek J, Bystrenova E, Gazova Z. The influence of cations on α-lactalbumin amyloid aggregation. J Biol Inorg Chem 2022; 27:679-689. [PMID: 36151481 PMCID: PMC9569292 DOI: 10.1007/s00775-022-01962-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 09/05/2022] [Indexed: 11/24/2022]
Abstract
There is limited knowledge regarding α-lactalbumin amyloid aggregation and its mechanism. We examined the formation of α-lactalbumin amyloid fibrils (α-LAF) in the presence of cations (Mg2+, Ca2+, Na+, K+, NH4+, and Cs+) in the form of chloride salts at two concentrations. We have shown that studied cations affect the conformation of α-lactalbumin, the kinetics of its amyloid formation, morphology, and secondary structure of α-LAF in a different manner. The higher salts concentration significantly accelerated the aggregation process. Both salt concentrations stabilized α-lactalbumin's secondary structure. However, the presence of divalent cations resulted in shorter fibrils with less β-sheet content. Moreover, strongly hydrated Mg2+ significantly altered α-lactalbumin's tertiary structure, followed by Na+, NH4+, K+, and weakly hydrated Cs+. On the other hand, Ca2+, despite being also strongly hydrated, stabilized the tertiary structure, supposedly due to its high affinity towards α-lactalbumin. Yet, Ca2+ was not able to inhibit α-lactalbumin amyloid aggregation.
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Affiliation(s)
- Andrea Antosova
- Institute of Experimental Physics Slovak Academy of Sciences, Watsonova 47, 040 01, Kosice, Slovakia
| | - Miroslav Gancar
- Institute of Experimental Physics Slovak Academy of Sciences, Watsonova 47, 040 01, Kosice, Slovakia
| | - Zuzana Bednarikova
- Institute of Experimental Physics Slovak Academy of Sciences, Watsonova 47, 040 01, Kosice, Slovakia
| | - Jozef Marek
- Institute of Experimental Physics Slovak Academy of Sciences, Watsonova 47, 040 01, Kosice, Slovakia
| | - Eva Bystrenova
- Consiglio Nazionale Delle Ricerche, Istituto Per Lo Studio Dei Materiali Nanostrutturati (CNR-ISMN), via P. Gobetti 101, 40129, Bologna, Italy.
| | - Zuzana Gazova
- Institute of Experimental Physics Slovak Academy of Sciences, Watsonova 47, 040 01, Kosice, Slovakia.
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21
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Sarkar D, Maity NC, Shome G, Varnava KG, Sarojini V, Vivekanandan S, Sahoo N, Kumar S, Mandal AK, Biswas R, Bhunia A. Mechanistic insight into functionally different human islet polypeptide (hIAPP) amyloid: the intrinsic role of the C-terminal structural motifs. Phys Chem Chem Phys 2022; 24:22250-22262. [PMID: 36098073 DOI: 10.1039/d2cp01650h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Targeting amyloidosis requires high-resolution insight into the underlying mechanisms of amyloid aggregation. The sequence-specific intrinsic properties of a peptide or protein largely govern the amyloidogenic propensity. Thus, it is essential to delineate the structural motifs that define the subsequent downstream amyloidogenic cascade of events. Additionally, it is important to understand the role played by extrinsic factors, such as temperature or sample agitation, in modulating the overall energy barrier that prompts divergent nucleation events. Consequently, these changes can affect the fibrillation kinetics, resulting in structurally and functionally distinct amyloidogenic conformers associated with disease pathogenesis. Here, we have focused on human Islet Polypeptide (hIAPP) amyloidogenesis for the full-length peptide along with its N- and C-terminal fragments, under different temperatures and sample agitation conditions. This helped us to gain a comprehensive understanding of the intrinsic role of specific functional epitopes in the primary structure of the peptide that regulates amyloidogenesis and subsequent cytotoxicity. Intriguingly, our study involving an array of biophysical experiments and ex vivo data suggests a direct influence of external changes on the C-terminal fibrillating sequence. Furthermore, the observations indicate a possible collaborative role of this segment in nucleating hIAPP amyloidogenesis in a physiological scenario, thus making it a potential target for future therapeutic interventions.
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Affiliation(s)
- Dibakar Sarkar
- Department of Biophysics, Bose Institute, EN 80, Sector V, Kolkata 700 091, India.
| | - Narayan Chandra Maity
- Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector-III, Salt Lake, Kolkata 700106, India
| | - Gourav Shome
- Division of Molecular Medicine, Bose Institute, EN 80, Sector V, Kolkata 700 091, India
| | - Kyriakos Gabriel Varnava
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Vijayalekshmi Sarojini
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | | | - Nirakar Sahoo
- Department of Biology, University of Texas Rio Grande Valley, Edinburg, Texas, 78539, USA
| | - Sourav Kumar
- Department of Biophysics, Bose Institute, EN 80, Sector V, Kolkata 700 091, India.
| | - Atin Kumar Mandal
- Division of Molecular Medicine, Bose Institute, EN 80, Sector V, Kolkata 700 091, India
| | - Ranjit Biswas
- Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector-III, Salt Lake, Kolkata 700106, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, EN 80, Sector V, Kolkata 700 091, India.
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22
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Quiñones-Ruiz T, Rosario-Alomar MF, Shanmugasundaram M, Ali MM, Lednev IK. Spontaneous Refolding of Amyloid Fibrils from One Polymorph to Another Caused by Changes in Environmental Hydrophobicity. Biochemistry 2022; 61:1456-1464. [PMID: 35786852 DOI: 10.1021/acs.biochem.2c00143] [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
Here, we report a new phenomenon in which lysozyme fibrils formed in a solution of acetic acid spontaneously refold to a different polymorph through a disassembled intermediate upon the removal of acetic acid. The structural changes were revealed and characterized by deep-UV resonance Raman spectroscopy, nonresonance Raman spectroscopy, intrinsic tryptophan fluorescence spectroscopy, and atomic force microscopy. A PPII-like structure with highly solvent-exposed tryptophan residues predominates the intermediate aggregates before refolding to polymorph II fibrils. Furthermore, the disulfide (SS) bonds undergo significant rearrangements upon the removal of acetic acid from the lysozyme fibril environment. The main SS bond conformation changes from gauche-gauche-trans in polymorph I to gauche-gauche-gauche in polymorph II. Changing the hydrophobicity of the fibril environment was concluded to be the decisive factor causing the spontaneous refolding of lysozyme fibrils from one polymorph to another upon the removal of acetic acid. Potential biological implications of the discovered phenomenon are discussed.
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Affiliation(s)
- Tatiana Quiñones-Ruiz
- Department of Chemistry, University at Albany, SUNY, Albany, New York 12222, United States
| | | | | | - Muhammad M Ali
- Department of Chemistry, University at Albany, SUNY, Albany, New York 12222, United States
| | - Igor K Lednev
- Department of Chemistry, University at Albany, SUNY, Albany, New York 12222, United States
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23
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Rajpoot J, Crooks EJ, Irizarry BA, Amundson A, Van Nostrand WE, Smith SO. Insights into Cerebral Amyloid Angiopathy Type 1 and Type 2 from Comparisons of the Fibrillar Assembly and Stability of the Aβ40-Iowa and Aβ40-Dutch Peptides. Biochemistry 2022; 61:1181-1198. [PMID: 35666749 PMCID: PMC9219409 DOI: 10.1021/acs.biochem.1c00781] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two distinct diseases are associated with the deposition of fibrillar amyloid-β (Aβ) peptides in the human brain in an age-dependent fashion. Alzheimer's disease is primarily associated with parenchymal plaque deposition of Aβ42, while cerebral amyloid angiopathy (CAA) is associated with amyloid formation of predominantly Aβ40 in the cerebral vasculature. In addition, familial mutations at positions 22 and 23 of the Aβ sequence can enhance vascular deposition in the two major subtypes of CAA. The E22Q (Dutch) mutation is associated with CAA type 2, while the D23N (Iowa) mutation is associated with CAA type 1. Here we investigate differences in the formation and structure of fibrils of these mutant Aβ peptides in vitro to gain insights into their biochemical and physiological differences in the brain. Using Fourier transform infrared and nuclear magnetic resonance spectroscopy, we measure the relative propensities of Aβ40-Dutch and Aβ40-Iowa to form antiparallel structure and compare these propensities to those of the wild-type Aβ40 and Aβ42 isoforms. We find that both Aβ40-Dutch and Aβ40-Iowa have strong propensities to form antiparallel β-hairpins in the first step of the fibrillization process. However, there is a marked difference in the ability of these peptides to form elongated antiparallel structures. Importantly, we find marked differences in the stability of the protofibril or fibril states formed by the four Aβ peptides. We discuss these differences with respect to the mechanisms of Aβ fibril formation in CAA.
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Affiliation(s)
- Jitika Rajpoot
- Department of Biochemistry and Cell Biology, Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794-5215, United States
| | - Elliot J Crooks
- Department of Biochemistry and Cell Biology, Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794-5215, United States
| | - Brandon A Irizarry
- Department of Biochemistry and Cell Biology, Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794-5215, United States
| | - Ashley Amundson
- Department of Biochemistry and Cell Biology, Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794-5215, United States
| | | | - Steven O Smith
- Department of Biochemistry and Cell Biology, Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794-5215, United States
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24
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Deol HK, Broom HR, Sienbeneichler B, Lee B, Leonenko Z, Meiering EM. Immature ALS-associated mutant superoxide dismutases form variable aggregate structures through distinct oligomerization processes. Biophys Chem 2022; 288:106844. [DOI: 10.1016/j.bpc.2022.106844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 11/15/2022]
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25
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Chaaban H, Vallooran JJ, van de Weert M, Foderà V. Ion-Mediated Morphological Diversity in Protein Amyloid Systems. J Phys Chem Lett 2022; 13:3586-3593. [PMID: 35426676 DOI: 10.1021/acs.jpclett.2c00182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Salt ions are considered among the major determinants ruling protein folding, stability, and self-assembly in the context of amyloid-related diseases, protein drug development, and functional biomaterials. Here, we report that Hofmeister ions not only determine the rate constants of the aggregation reaction for human insulin and hen egg white lysozyme but also control the generation of a plethora of amyloid-like morphologies ranging from the nanoscale to the microscale. We anticipate that the latter is a result of a balance between colloidal and conformational stability combined with an ion-specific effect and highlight the importance of salt ions in controlling the biological functions of protein aggregates.
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Affiliation(s)
- Hussein Chaaban
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Nano-Science Center, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Jijo J Vallooran
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Marco van de Weert
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Nano-Science Center, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Vito Foderà
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Nano-Science Center, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
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26
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Jalali S, Yang Y, Mahmoudinobar F, Singh SM, Nilsson BL, Dias C. Using all-atom simulations in explicit solvent to study aggregation of amphipathic peptides into amyloid-like fibrils. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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27
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Khan JM, Malik A, Husain FM, Hakeem MJ, Alhomida AS. Sunset Yellow Dye Induces Amorphous Aggregation in β-Lactoglobulin at Acidic pH: A Multi-Techniques Approach. Polymers (Basel) 2022; 14:polym14030395. [PMID: 35160385 PMCID: PMC8839080 DOI: 10.3390/polym14030395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 02/01/2023] Open
Abstract
Protein aggregation is of two types: (i) amorphous and (ii) amyloid fibril. Several extrinsic factors (temperature, pH, and small ligands) stimulate protein aggregation in vitro. In this study, we have examined the role of sunset yellow (SY) on the β-lactoglobulin (BLG) aggregation at pH 2.0. We have used spectroscopic (turbidity, Rayleigh light scattering (RLS), far-UV CD) and microscopic (transmission electron microscopy [TEM]) techniques to describe the effects of SY on BLG aggregation. Our results showed that BLG aggregation is dependent on SY concentrations. Very low concentrations (0.0–0.07 mM) of SY were unable to induce aggregation, while SY in the concentrations range of 0.1–5.0 mM induces aggregation in BLG. The kinetics of SY-stimulated aggregation is very fast and monomeric form of BLG directly converted into polymeric aggregates. The kinetics results also showed SY-induced BLG aggregation disappeared in the presence of NaCl. The far-UV CD and TEM results indicated the amorphous nature of SY-induced BLG aggregates. We believe that our results clearly suggest that SY dye effectively stimulates BLG aggregation.
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Affiliation(s)
- Javed Masood Khan
- Department of Food Science and Nutrition, College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi Arabia; (F.M.H.); (M.J.H.)
- Correspondence:
| | - Ajamaluddin Malik
- Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (A.M.); (A.S.A.)
| | - Fohad Mabood Husain
- Department of Food Science and Nutrition, College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi Arabia; (F.M.H.); (M.J.H.)
| | - Mohammed J. Hakeem
- Department of Food Science and Nutrition, College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi Arabia; (F.M.H.); (M.J.H.)
| | - Abdullah S. Alhomida
- Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (A.M.); (A.S.A.)
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28
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Bagchi D, Maity A, De SK, Chakraborty A. Effect of Metal Ions on the Intrinsic Blue Fluorescence Property and Morphology of Aromatic Amino Acid Self-Assembly. J Phys Chem B 2021; 125:12436-12445. [PMID: 34734524 DOI: 10.1021/acs.jpcb.1c07392] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Metal ions are known to strongly bind with different proteins and peptides, resulting in alteration of their different physicochemical properties. In this work, we investigate the effect of metal ions of different nuclear charges and sizes on the intrinsic blue luminescence of the self-assembled structures formed by aromatic amino acids, namely, phenylalanine and tryptophan, using spectroscopic and imaging techniques. The study reveals that the intrinsic blue fluorescence of amino acid assemblies is influenced by metal ions and the pH of the medium. The metal ions with a higher charge to radius ratio promote clusterization which results in the enhancement of the intrinsic fluorescence, an effect known as "clusteroluminescence" of the amino acids aggregates. The imaging study reveals that metal ions with a higher charge to size ratio inhibit the large fibrillation of aromatic amino acids by promoting the formation of small nonfibrillar aggregates through increased hydrophobicity in the medium. The nanoaggregates are assumed to be responsible for the enhancement in the blue "clusteroluminescence".
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Affiliation(s)
- Debanjan Bagchi
- Indian Institute of Technology Indore, Discipline of Chemistry, Indore 453552, Madhya Pradesh, India
| | - Avijit Maity
- Indian Institute of Technology Indore, Discipline of Chemistry, Indore 453552, Madhya Pradesh, India
| | - Soumya Kanti De
- Indian Institute of Technology Indore, Discipline of Chemistry, Indore 453552, Madhya Pradesh, India
| | - Anjan Chakraborty
- Indian Institute of Technology Indore, Discipline of Chemistry, Indore 453552, Madhya Pradesh, India
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29
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Matuszyk MM, Garwood CJ, Ferraiuolo L, Simpson JE, Staniforth RA, Wharton SB. Biological and methodological complexities of beta-amyloid peptide: Implications for Alzheimer's disease research. J Neurochem 2021; 160:434-453. [PMID: 34767256 DOI: 10.1111/jnc.15538] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/29/2021] [Accepted: 11/09/2021] [Indexed: 01/01/2023]
Abstract
Although controversial, the amyloid cascade hypothesis remains central to the Alzheimer's disease (AD) field and posits amyloid-beta (Aβ) as the central factor initiating disease onset. In recent years, there has been an increase in emphasis on studying the role of low molecular weight aggregates, such as oligomers, which are suggested to be more neurotoxic than fibrillary Aβ. Other Aβ isoforms, such as truncated Aβ, have also been implicated in disease. However, developing a clear understanding of AD pathogenesis has been hampered by the complexity of Aβ biochemistry in vitro and in vivo. This review explores factors contributing to the lack of consistency in experimental approaches taken to model Aβ aggregation and toxicity and provides an overview of the different techniques available to analyse Aβ, such as electron and atomic force microscopy, nuclear magnetic resonance spectroscopy, dye-based assays, size exclusion chromatography, mass spectrometry and SDS-PAGE. The review also explores how different types of Aβ can influence Aβ aggregation and toxicity, leading to variation in experimental outcomes, further highlighting the need for standardisation in Aβ preparations and methods used in current research.
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Affiliation(s)
- Martyna M Matuszyk
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Claire J Garwood
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Laura Ferraiuolo
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Julie E Simpson
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | | | - Stephen B Wharton
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
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30
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Armamentarium of Cryoprotectants in Peptide Vaccines: Mechanistic Insight, Challenges, Opportunities and Future Prospects. Int J Pept Res Ther 2021; 27:2965-2982. [PMID: 34690621 PMCID: PMC8524217 DOI: 10.1007/s10989-021-10303-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2021] [Indexed: 10/30/2022]
Abstract
Vaccines are designed to leverage the immune system and produce long-lasting protection against specific diseases. Peptide vaccines are regarded as safe and effective way of circumventing problems such as mild allergic reactions associated with conventional vaccines. The biggest challenges associated with formulation of peptide vaccines are stability issues and conformational changes which lead to destruction of their activity when exposed to lyophilization process that may act as stressors. Lyophilization process is aimed at removal of water which involves freezing, primary drying and secondary drying. To safeguard the peptide molecules from such stresses, cryoprotectants are used to offer them viability and structural stability. This paper is an attempt to understand the physicochemical properties of peptide vaccines, mechanism of cryoprotection under the shed of water replacement, water substitution theory and cation-pi interaction theory of amino acids which aims at shielding the peptide from external environment by formation of hydrogen bonds, covalent bonds or cation-pi interaction between cryoprotectant and peptide followed by selection criteria of cryoprotectants and their utility in peptide vaccines development along with challenges and opportunities.
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31
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Mehra S, Gadhe L, Bera R, Sawner AS, Maji SK. Structural and Functional Insights into α-Synuclein Fibril Polymorphism. Biomolecules 2021; 11:1419. [PMID: 34680054 PMCID: PMC8533119 DOI: 10.3390/biom11101419] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 12/21/2022] Open
Abstract
Abnormal accumulation of aggregated α-synuclein (α-Syn) is seen in a variety of neurodegenerative diseases, including Parkinson's disease (PD), multiple system atrophy (MSA), dementia with Lewy body (DLB), Parkinson's disease dementia (PDD), and even subsets of Alzheimer's disease (AD) showing Lewy-body-like pathology. These synucleinopathies exhibit differences in their clinical and pathological representations, reminiscent of prion disorders. Emerging evidence suggests that α-Syn self-assembles and polymerizes into conformationally diverse polymorphs in vitro and in vivo, similar to prions. These α-Syn polymorphs arising from the same precursor protein may exhibit strain-specific biochemical properties and the ability to induce distinct pathological phenotypes upon their inoculation in animal models. In this review, we discuss clinical and pathological variability in synucleinopathies and several aspects of α-Syn fibril polymorphism, including the existence of high-resolution molecular structures and brain-derived strains. The current review sheds light on the recent advances in delineating the structure-pathogenic relationship of α-Syn and how diverse α-Syn molecular polymorphs contribute to the existing clinical heterogeneity in synucleinopathies.
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Affiliation(s)
- Surabhi Mehra
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India; (L.G.); (R.B.); (A.S.S.)
| | | | | | | | - Samir K. Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India; (L.G.); (R.B.); (A.S.S.)
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32
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The curvature of gold nanoparticles influences the exposure of amyloid-β and modulates its aggregation process. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2021; 128:112269. [PMID: 34474828 DOI: 10.1016/j.msec.2021.112269] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 06/09/2021] [Accepted: 06/16/2021] [Indexed: 11/21/2022]
Abstract
Gold nanoparticles (GNP) are tunable nanomaterials that can be used to develop rational therapeutic inhibitors against the formation of pathological aggregates of proteins. In the case of the pathological aggregation of the amyloid-β protein (Aβ), the shape of the GNP can slow down or accelerate its aggregation kinetics. However, there is a lack of elementary knowledge about how the curvature of GNP alters the interaction with the Aβ peptide and how this interaction modifies key molecular steps of fibril formation. In this study, we analysed the effect of flat gold nanoprisms (GNPr) and curved gold nanospheres (GNS) on in vitro Aβ42 fibril formation kinetics by using the thioflavin-based kinetic assay and global fitting analysis, with several models of aggregation. Whereas GNPr accelerate the aggregation process and maintain the molecular mechanism of aggregation, GNS slow down this process and modify the molecular mechanism to one of fragmentation/secondary nucleation, with respect to controls. These results can be explained by a differential interaction between the Aβ peptide and GNP observed by Raman spectroscopy. While flat GNPr expose key hydrophobic residues involved in the Aβ peptide aggregation, curved GNS hide these residues from the solvent. Thus, this study provides mechanistic insights to improve the rational design of GNP nanomaterials for biomedical applications in the field of amyloid-related aggregation.
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33
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Shardlow E, Khan B, Exley C. Monitoring the early aggregatory behaviour and size of Aβ 1-42 in the absence & presence of metal ions using dynamic light scattering. J Trace Elem Med Biol 2021; 67:126766. [PMID: 33964808 DOI: 10.1016/j.jtemb.2021.126766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/19/2021] [Accepted: 04/28/2021] [Indexed: 11/23/2022]
Abstract
BACKGROUND AND AIM Aβ1-42 is an amyloidogenic peptide found within senile plaques extracted from those who died with a diagnosis of Alzheimer's disease. The potent neurotoxicity of this peptide is related to its propensity to form aggregated conformations in vivo, a process that is influenced by the species and concentration of metal ions present within the local environment. This study examines the impact of different metals upon the early aggregatory behaviour and size of Aβ1-42 under simulated physiological conditions. METHODS The size and aggregatory behaviour of Aβ1-42 in the presence and absence of metal ions was monitored during the initial 30 min of fibril formation in real-time using dynamic light scattering. RESULTS Intensity scattering measurements showed a clear tendency towards aggregation with regards to Aβ1-42 only solutions (10 μM). Both equimolar Al3+ & Cu2+ lowered and stabilised the dimensions of Aβ1-42 aggregates; however, a diminutive but significant increase in size was still observed over a 30-min period. While excess Al3+ continued to supress the size of Aβ1-42, a 10-fold increase in the concentration of Cu2+ accelerated peptide aggregation relative to that observed for equimolar metal but not compared to Aβ1-42 alone. CONCLUSION These results infer that Al3+ ions stabilise and aid in the maintenance of smaller, toxic intermediates while excess Cu2+ facilitates the formation of larger, more inert, amorphous species exceeding 1 μm in size. Furthermore, we propose that metal-induced toxicity of Aβ1-42 is reflective of their ability to preserve smaller oligomeric species in vitro.
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Affiliation(s)
- Emma Shardlow
- The Birchall Centre, Lennard-Jones Laboratories, Keele University, Keele, Staffordshire, ST5 5BG, UK.
| | - Bakhtbilland Khan
- The Birchall Centre, Lennard-Jones Laboratories, Keele University, Keele, Staffordshire, ST5 5BG, UK
| | - Christopher Exley
- The Birchall Centre, Lennard-Jones Laboratories, Keele University, Keele, Staffordshire, ST5 5BG, UK
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34
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Khoeini D, Scott TF, Neild A. Microfluidic enhancement of self-assembly systems. LAB ON A CHIP 2021; 21:1661-1675. [PMID: 33949588 DOI: 10.1039/d1lc00038a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Dynamic, kinetically-controlled, self-assembly processes are commonly observed in nature and are capable of creating intricate, functional architectures from simple precursors. However, notably, much of the research into molecular self-assembly has been performed using conventional bulk techniques where the resultant species are dictated by thermodynamic stability to yield relatively simple assemblies. Whereas, the environmental control offered by microfluidic systems offers methods to achieve non-equilibrium reaction conditions capable of increasingly sophisticated self-assembled structures. Alterations to the immediate microenvironment during the assembly of the molecules is possible, providing the basis for kinetically-controlled assembly. This review examines the key mechanism offered by microfluidic systems and the architectures required to access them. The mechanisms include diffusion-led mixing, shear gradient alignment, spatial and temporal confinement, and structural templates in multiphase systems. The works are selected and categorised in terms of the microfluidic approaches taken rather than the chemical constructs which are formed.
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Affiliation(s)
- Davood Khoeini
- Laboratory for Micro Systems, Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia.
| | - Timothy F Scott
- Department of Chemical Engineering, Monash University, Clayton, VIC 3800, Australia and Department of Materials Science and Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Adrian Neild
- Laboratory for Micro Systems, Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia.
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35
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Srivastava A, Mallela KMG, Deorkar N, Brophy G. Manufacturing Challenges and Rational Formulation Development for AAV Viral Vectors. J Pharm Sci 2021; 110:2609-2624. [PMID: 33812887 DOI: 10.1016/j.xphs.2021.03.024] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/19/2021] [Accepted: 03/30/2021] [Indexed: 12/19/2022]
Abstract
Adeno-associated virus (AAV) has emerged as a leading platform for gene delivery for treating various diseases due to its excellent safety profile and efficient transduction to various target tissues. However, the large-scale production and long-term storage of viral vectors is not efficient resulting in lower yields, moderate purity, and shorter shelf-life compared to recombinant protein therapeutics. This review provides a comprehensive analysis of upstream, downstream and formulation unit operation challenges encountered during AAV vector manufacturing, and discusses how desired product quality attributes can be maintained throughout product shelf-life by understanding the degradation mechanisms and formulation strategies. The mechanisms of various physical and chemical instabilities that the viral vector may encounter during its production and shelf-life because of various stressed conditions such as thermal, shear, freeze-thaw, and light exposure are highlighted. The role of buffer, pH, excipients, and impurities on the stability of viral vectors is also discussed. As such, the aim of this review is to outline the tools and a potential roadmap for improving the quality of AAV-based drug products by stressing the need for a mechanistic understanding of the involved processes.
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Affiliation(s)
- Arvind Srivastava
- Biopharma Production, Avantor, Inc., 1013 US Highway, 202/206, Bridgewater, NJ, United States.
| | - Krishna M G Mallela
- Center for Pharmaceutical Biotechnology, Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 East Montview Boulevard, MS C238-V20, Aurora, CO 80045, United States.
| | - Nandkumar Deorkar
- Biopharma Production, Avantor, Inc., 1013 US Highway, 202/206, Bridgewater, NJ, United States
| | - Ger Brophy
- Biopharma Production, Avantor, Inc., 1013 US Highway, 202/206, Bridgewater, NJ, United States
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36
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Wang Y, Guo Z, Tan T, Ji Y, Hu J, Zhang Y. The effects of nanobubbles on the assembly of glucagon amyloid fibrils. SOFT MATTER 2021; 17:3486-3493. [PMID: 33657201 DOI: 10.1039/d0sm02279a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Some recent studies have shown that the surface and interface play an important role in the assembly and aggregation of amyloid proteins. However, it is unclear how the gas-liquid interface affects the protein assembly at the nanometer scale although the presence of gas-liquid interfaces is very common in in vitro experiments. Nanobubbles have a large specific surface area, which provides a stage for interactions with various proteins and peptides on the nanometer scale. In this work, nanobubbles produced in solution were employed for studying the effects of the gas-liquid interface on the assembly of glucagon proteins. Atomic force microscopy (AFM) studies showed that nanobubble-treated glucagon solution formed fibrils with an apparent height of 4.02 ± 0.71 nm, in contrast to the fibrils formed with a height of 2.14 ± 0.53 nm in the control. Transmission electron microscopy (TEM) results also showed that nanobubbles promoted the assembly of glucagon to form more fibrils. Thioflavin T (ThT) fluorescence and Fourier transform infrared (FTIR) analyses indicated that the nanobubbles induced the change of the glucagon conformation to a β-sheet structure. A mechanism that explains how nanobubbles affect the assembly of glucagon amyloid fibrils was proposed based on the above-mentioned experimental results. Given the fact that there are a considerable amount of nanobubbles existing in protein solutions, our results indicate that nanobubbles should be considered for fully understanding the protein aggregation events in vitro.
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Affiliation(s)
- Yujiao Wang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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37
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Gaudreault R, Hervé V, van de Ven TGM, Mousseau N, Ramassamy C. Polyphenol-Peptide Interactions in Mitigation of Alzheimer's Disease: Role of Biosurface-Induced Aggregation. J Alzheimers Dis 2021; 81:33-55. [PMID: 33749653 DOI: 10.3233/jad-201549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Alzheimer's disease (AD) is the most common age-related neurodegenerative disorder, responsible for nearly two-thirds of all dementia cases. In this review, we report the potential AD treatment strategies focusing on natural polyphenol molecules (green chemistry) and more specifically on the inhibition of polyphenol-induced amyloid aggregation/disaggregation pathways: in bulk and on biosurfaces. We discuss how these pathways can potentially alter the structure at the early stages of AD, hence delaying the aggregation of amyloid-β (Aβ) and tau. We also discuss multidisciplinary approaches, combining experimental and modelling methods, that can better characterize the biochemical and biophysical interactions between proteins and phenolic ligands. In addition to the surface-induced aggregation, which can occur on surfaces where protein can interact with other proteins and polyphenols, we suggest a new concept referred as "confinement stability". Here, on the contrary, the adsorption of Aβ and tau on biosurfaces other than Aβ- and tau-fibrils, e.g., red blood cells, can lead to confinement stability that minimizes the aggregation of Aβ and tau. Overall, these mechanisms may participate directly or indirectly in mitigating neurodegenerative diseases, by preventing protein self-association, slowing down the aggregation processes, and delaying the progression of AD.
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Affiliation(s)
- Roger Gaudreault
- Department of Physics, Université de Montréal, Montreal, QC, Canada
| | - Vincent Hervé
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, QC, Canada
| | | | - Normand Mousseau
- Department of Physics, Université de Montréal, Montreal, QC, Canada
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38
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Mahmoudinobar F, Nilsson BL, Dias CL. Effects of Ions and Small Compounds on the Structure of Aβ 42 Monomers. J Phys Chem B 2021; 125:1085-1097. [PMID: 33481611 DOI: 10.1021/acs.jpcb.0c09617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aggregation of amyloid-β (Aβ) proteins in the brain is a hallmark of Alzheimer's disease. This phenomenon can be promoted or inhibited by adding small molecules to the solution where Aβ is embedded. These molecules affect the ensemble of conformations sampled by Aβ monomers even before aggregation starts. Here, we perform extensive all-atom replica exchange molecular dynamics (REMD) simulations to provide a comparative study of the ensemble of conformations sampled by Aβ42 monomers in solutions that promote (i.e., aqueous solution containing NaCl) and inhibit (i.e., aqueous solutions containing scyllo-inositol or 4-aminophenol) aggregation. Simulations performed in pure water are used as our reference. We find that secondary-structure content is only affected in an antagonistic manner by promoters and inhibitors at the C-terminus and the central hydrophilic core. Moreover, the end of the C-terminus binds more favorably to the central hydrophobic core region of Aβ42 in NaCl adopting a type of strand-loop-strand structure that is disfavored by inhibitors. Nonpolar residues that form the dry core of larger aggregates of Aβ42 (e.g., PDB ID 2BEG) are found at close proximity in these strand-loop-strand structures, suggesting that their formation could play an important role in initiating nucleation. In the presence of inhibitors, the C-terminus binds the central hydrophilic core with a higher probability than in our reference simulation. This sensitivity of the C-terminus, which is affected in an antagonistic manner by inhibitors and promoters, provides evidence for its critical role in accounting for aggregation.
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Affiliation(s)
- Farbod Mahmoudinobar
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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39
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Söldner CA, Sticht H, Horn AH. Molecular Simulations and Alzheimer׳s Disease. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11541-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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40
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Ramis R, Ortega-Castro J, Vilanova B, Adrover M, Frau J. Unraveling the NaCl Concentration Effect on the First Stages of α-Synuclein Aggregation. Biomacromolecules 2020; 21:5200-5212. [PMID: 33140640 DOI: 10.1021/acs.biomac.0c01292] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intraneuronal aggregation of the intrinsically disordered protein α-synuclein is at the core of Parkinson's disease and related neurodegenerative disorders. Several reports show that the concentration of salts in the medium heavily affects its aggregation rate and fibril morphology, but a characterization of the individual monomeric conformations underlying these effects is still lacking. In this work, we have applied our α-synuclein-optimized coarse-grained molecular dynamics approach to decipher the structural features of the protein monomer under a range of NaCl concentrations (0.0-1.0 M). The results show that key intramolecular contacts between the terminal domains are lost at intermediate concentrations (leading to extended conformations likely to fibrillate), but recovered at high concentrations (leading to compact conformations likely to evolve toward amorphous aggregates). The pattern of direct interactions of the terminal α-synuclein domains with Na+ and Cl- ions plays a key role in explaining this effect. Our results are consistent with a recent study reporting a fibrillation enhancement at moderate NaCl concentrations but an inhibition at higher concentrations. The present work will contribute to improving our understanding of the structural features of monomeric α-synuclein, determining its NaCl-induced fibrillation propensity and the molecular basis of synucleinopathies, necessary for the future development of disease-halting therapies.
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Affiliation(s)
- Rafael Ramis
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain.,Institut d'Investigació Sanitària Illes Balears (IdISBa), 07020 Palma de Mallorca, Spain
| | - Joaquín Ortega-Castro
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain.,Institut d'Investigació Sanitària Illes Balears (IdISBa), 07020 Palma de Mallorca, Spain
| | - Bartolomé Vilanova
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain.,Institut d'Investigació Sanitària Illes Balears (IdISBa), 07020 Palma de Mallorca, Spain
| | - Miquel Adrover
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain.,Institut d'Investigació Sanitària Illes Balears (IdISBa), 07020 Palma de Mallorca, Spain
| | - Juan Frau
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain.,Institut d'Investigació Sanitària Illes Balears (IdISBa), 07020 Palma de Mallorca, Spain
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41
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Stephens AD, Lu M, Fernandez-Villegas A, Kaminski Schierle GS. Fast Purification of Recombinant Monomeric Amyloid-β from E. coli and Amyloid-β-mCherry Aggregates from Mammalian Cells. ACS Chem Neurosci 2020; 11:3204-3213. [PMID: 32960567 PMCID: PMC7581289 DOI: 10.1021/acschemneuro.0c00300] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Alzheimer's disease related peptide, Amyloid-beta (Aβ)1-40 and 1-42, has proven difficult to be purified as a recombinant monomeric protein due its expression in E. coli leading to the formation of insoluble inclusion bodies and its tendency to quickly form insoluble aggregates. A vast array of methods have been used so far, yet many have pitfalls, such as the use of tags for ease of Aβ isolation, the formation of Aβ multimers within the time frame of extraction, or the need to reconstitute Aβ from a freeze-dried state. Here, we present a rapid protocol to produce highly pure and monomeric recombinant Aβ using a one-step ion exchange purification method and to label the peptide using a maleimide dye. The washing, solubilization, and purification steps take only 3 h. We also present a protocol for the isolation of Aβ-mCherry from mammalian cells.
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Affiliation(s)
- Amberley D. Stephens
- Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, United Kingdom
| | - Meng Lu
- Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, United Kingdom
| | - Ana Fernandez-Villegas
- Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, United Kingdom
| | - Gabriele S. Kaminski Schierle
- Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, United Kingdom
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42
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Hofmeister Ions Modulate the Autocatalytic Amyloidogenesis of an Intrinsically Disordered Functional Amyloid Domain via Unusual Biphasic Kinetics. J Mol Biol 2020; 432:6173-6186. [PMID: 33068637 DOI: 10.1016/j.jmb.2020.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/01/2020] [Accepted: 10/11/2020] [Indexed: 02/06/2023]
Abstract
Hofmeister ions are thought to play fundamentally important roles in protein solubility, folding, stability, and function. Salt ions profoundly influence the course of protein misfolding, aggregation, and amyloid formation associated with devastating human diseases. However, the molecular origin of the salt-effect in protein aggregation remains elusive. Here, we report an unusual biphasic amyloidogenesis of a pH-responsive, intrinsically disordered, oligopeptide repeat domain of a melanosomal protein, Pmel17, that regulates the amyloid-assisted melanin synthesis in mammals via functional amyloid formation. We demonstrate that a symphony of molecular events involving charge-peptide interactions and hydration, in conjunction with secondary phenomena, critically governs the course of this biphasic amyloid assembly. We show that at mildly acidic pH, typical of melanosomes, highly amyloidogenic oligomeric units assemble into metastable, dendritic, fractal networks following the forward Hofmeister series. However, the subsequent condensation of fractal networks via conformational maturation into amyloid fibrils follows an inverse Hofmeister series due to fragmentation events coupled with secondary nucleation processes. Our results indicate that ions exert a strong influence on the aggregation kinetics as well as on the nanoscale morphology and also modulate the autocatalytic amplification processes during amyloid assembly via an intriguing dual Hofmeister effect. This unique interplay of molecular drivers will be of prime importance in delineating the aggregation pathways of a multitude of intrinsically disordered proteins involved in physiology and disease.
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43
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Kim HY, Lee H, Lee JK, Kim HV, Kim KS, Kim Y. Bicine promotes rapid formation of β-sheet-rich amyloid-β fibrils. PLoS One 2020; 15:e0240608. [PMID: 33048999 PMCID: PMC7553346 DOI: 10.1371/journal.pone.0240608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/29/2020] [Indexed: 12/27/2022] Open
Abstract
Fibrillar aggregates of amyloid-β (Aβ) are the main component of plaques lining the cerebrovasculature in cerebral amyloid angiopathy. As the predominant Aβ isoform in vascular deposits, Aβ40 is a valuable target in cerebral amyloid angiopathy research. However, the slow process of Aβ40 aggregation in vitro is a bottleneck in the search for Aβ-targeting molecules. In this study, we sought a method to accelerate the aggregation of Aβ40in vitro, to improve experimental screening procedures. We evaluated the aggregating ability of bicine, a biological buffer, using various in vitro methods. Our data suggest that bicine promotes the aggregation of Aβ40 with high speed and reproducibility, yielding a mixture of aggregates with significant β-sheet-rich fibril formation and toxicity.
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Affiliation(s)
- Hye Yun Kim
- Department of Pharmacy, Yonsei University, Incheon, Republic of Korea
- Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea
| | - HeeYang Lee
- Department of Pharmacy, Yonsei University, Incheon, Republic of Korea
- Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea
- Integrated Science and Engineering Division, Yonsei University, Incheon, Republic of Korea
| | - Jong Kook Lee
- Brain Science Institute, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Hyunjin Vincent Kim
- Brain Science Institute, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Key-Sun Kim
- Brain Science Institute, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - YoungSoo Kim
- Department of Pharmacy, Yonsei University, Incheon, Republic of Korea
- Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea
- Integrated Science and Engineering Division, Yonsei University, Incheon, Republic of Korea
- * E-mail:
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44
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Moons R, Konijnenberg A, Mensch C, Van Elzen R, Johannessen C, Maudsley S, Lambeir AM, Sobott F. Metal ions shape α-synuclein. Sci Rep 2020; 10:16293. [PMID: 33004902 PMCID: PMC7529799 DOI: 10.1038/s41598-020-73207-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/27/2020] [Indexed: 12/24/2022] Open
Abstract
α-Synuclein is an intrinsically disordered protein that can self-aggregate and plays a major role in Parkinson's disease (PD). Elevated levels of certain metal ions are found in protein aggregates in neurons of people suffering from PD, and environmental exposure has also been linked with neurodegeneration. Importantly, cellular interactions with metal ions, particularly Ca2+, have recently been reported as key for α-synuclein's physiological function at the pre-synapse. Here we study effects of metal ion interaction with α-synuclein at the molecular level, observing changes in the conformational behaviour of monomers, with a possible link to aggregation pathways and toxicity. Using native nano-electrospray ionisation ion mobility-mass spectrometry (nESI-IM-MS), we characterize the heterogeneous interactions of alkali, alkaline earth, transition and other metal ions and their global structural effects on α-synuclein. Different binding stoichiometries found upon titration with metal ions correlate with their specific binding affinity and capacity. Subtle conformational effects seen for singly charged metals differ profoundly from binding of multiply charged ions, often leading to overall compaction of the protein depending on the preferred binding sites. This study illustrates specific effects of metal coordination, and the associated electrostatic charge patterns, on the complex structural space of the intrinsically disordered protein α-synuclein.
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Affiliation(s)
- Rani Moons
- Biomolecular and Analytical Mass Spectrometry Group, University of Antwerp, Antwerp, Belgium.,Receptor Biology Laboratory, University of Antwerp, Antwerp, Belgium
| | - Albert Konijnenberg
- Biomolecular and Analytical Mass Spectrometry Group, University of Antwerp, Antwerp, Belgium
| | - Carl Mensch
- Molecular Spectroscopy Group, University of Antwerp, Antwerp, Belgium.,Flemish Supercomputer Centre, Antwerp, Belgium
| | - Roos Van Elzen
- Laboratory of Medical Biochemistry, University of Antwerp, Antwerp, Belgium
| | | | - Stuart Maudsley
- Receptor Biology Laboratory, University of Antwerp, Antwerp, Belgium
| | - Anne-Marie Lambeir
- Laboratory of Medical Biochemistry, University of Antwerp, Antwerp, Belgium
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, University of Antwerp, Antwerp, Belgium. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK. .,School of Molecular and Cellular Biology, University of Leeds, Leeds, UK.
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45
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Lucas MJ, Pan HS, Verbeke EJ, Webb LJ, Taylor DW, Keitz BK. Functionalized Mesoporous Silicas Direct Structural Polymorphism of Amyloid-β Fibrils. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:7345-7355. [PMID: 32482072 DOI: 10.1021/acs.langmuir.0c00827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The aggregation of amyloid-β (Aβ) is associated with the onset of Alzheimer's disease (AD) and involves a complex kinetic pathway as monomers self-assemble into fibrils. A central feature of amyloid fibrils is the existence of multiple structural polymorphs, which complicates the development of disease-relevant structure-function relationships. Developing these relationships requires new methods to control fibril structure. In this work, we evaluated the effect that mesoporous silicas (SBA-15) functionalized with hydrophobic (SBA-PFDTS) and hydrophilic groups (SBA-PEG) have on the aggregation kinetics and resulting structure of Aβ1-40 fibrils. The hydrophilic SBA-PEG had little effect on amyloid kinetics, while as-synthesized and hydrophobic SBA-PFDTS accelerated aggregation kinetics. Subsequently, we quantified the relative population of fibril structures formed in the presence of each material using electron microscopy. Fibrils formed from Aβ1-40 exposed to SBA-PEG were structurally similar to control fibrils. In contrast, Aβ1-40 incubated with SBA-15 or SBA-PFDTS formed fibrils with shorter crossover distances that were more structurally representative of fibrils found in AD patient derived samples. Overall, our results suggest that mesoporous silicas and other exogenous materials are promising scaffolds for the de novo production of specific fibril polymorphs of Aβ1-40 and other amyloidogenic proteins.
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Affiliation(s)
- Michael J Lucas
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Henry S Pan
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Eric J Verbeke
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lauren J Webb
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - David W Taylor
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
- LIVESTRONG Cancer Institutes, Dell Medical School, Austin, Texas 78712, United States
| | - Benjamin K Keitz
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
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46
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Sasanian N, Bernson D, Horvath I, Wittung-Stafshede P, Esbjörner EK. Redox-Dependent Copper Ion Modulation of Amyloid-β (1-42) Aggregation In Vitro. Biomolecules 2020; 10:E924. [PMID: 32570820 PMCID: PMC7355640 DOI: 10.3390/biom10060924] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/12/2020] [Accepted: 06/16/2020] [Indexed: 12/20/2022] Open
Abstract
Plaque deposits composed of amyloid-β (Aβ) fibrils are pathological hallmarks of Alzheimer's disease (AD). Although copper ion dyshomeostasis is apparent in AD brains and copper ions are found co-deposited with Aβ peptides in patients' plaques, the molecular effects of copper ion interactions and redox-state dependence on Aβ aggregation remain elusive. By combining biophysical and theoretical approaches, we here show that Cu2+ (oxidized) and Cu+ (reduced) ions have opposite effects on the assembly kinetics of recombinant Aβ(1-42) into amyloid fibrils in vitro. Cu2+ inhibits both the unseeded and seeded aggregation of Aβ(1-42) at pH 8.0. Using mathematical models to fit the kinetic data, we find that Cu2+ prevents fibril elongation. The Cu2+-mediated inhibition of Aβ aggregation shows the largest effect around pH 6.0 but is lost at pH 5.0, which corresponds to the pH in lysosomes. In contrast to Cu2+, Cu+ ion binding mildly catalyzes the Aβ(1-42) aggregation via a mechanism that accelerates primary nucleation, possibly via the formation of Cu+-bridged Aβ(1-42) dimers. Taken together, our study emphasizes redox-dependent copper ion effects on Aβ(1-42) aggregation and thereby provides further knowledge of putative copper-dependent mechanisms resulting in AD.
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Affiliation(s)
| | | | | | | | - Elin K. Esbjörner
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden; (N.S.); (D.B.); (I.H.); (P.W.-S.)
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47
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Exploration of Insulin Amyloid Polymorphism Using Raman Spectroscopy and Imaging. Biophys J 2020; 118:2997-3007. [PMID: 32428440 DOI: 10.1016/j.bpj.2020.04.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/10/2020] [Accepted: 04/27/2020] [Indexed: 11/20/2022] Open
Abstract
We aimed to investigate insulin amyloid fibril polymorphism caused by salt effects and heating temperature and to visualize the structural differences of the polymorphisms in situ using Raman imaging without labeling. The time course monitoring for amyloid formation was carried out in an acidic condition without any salts and with two species of salts (NaCl and Na2SO4) by heating at 60, 70, 80, and 90°C. The intensity ratio of two Raman bands at 1672 and 1657 cm-1 due to antiparallel β-sheet and α-helix structures, respectively, was revealed to be an indicator of amyloid fibril formation, and the relative proportion of the β-sheet structure was higher in the case with salts, especially at a higher temperature with Na2SO4. In conjunction with the secondary structural changes of proteins, the S-S stretching vibrational mode of a disulfide bond (∼514 cm-1) and the ratio of the tyrosine doublet I850/I826 were also found to be markers distinguishing polymorphisms of insulin amyloid fibrils by principal component analysis. Especially, amyloid fibrils with Na2SO4 media formed the gauche-gauche-gauche conformation of disulfide bond at a higher rate, but without any salts, the gauche-gauche-gauche conformation was partially transformed into the gauche-gauche-trans conformation at higher temperatures. The different environments of the hydroxyl groups of the tyrosine residue were assumed to be caused by fibril polymorphism. Raman imaging using these marker bands also successfully visualized the two- and three- dimensional structural differences of amyloid polymorphisms. These results demonstrate the potential of Raman imaging as a diagnostic tool for polymorphisms in tissues of amyloid-related diseases.
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48
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Horváth D, Menyhárd DK, Perczel A. Protein Aggregation in a Nutshell: The Splendid Molecular Architecture of the Dreaded Amyloid Fibrils. Curr Protein Pept Sci 2020; 20:1077-1088. [PMID: 31553291 DOI: 10.2174/1389203720666190925102832] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 04/04/2019] [Accepted: 04/07/2019] [Indexed: 11/22/2022]
Abstract
The recent high-resolution structures of amyloid fibrils show that the organization of peptide segments into amyloid aggregate architecture is a general process, though the morphology is more complex and intricate than suspected previously. The amyloid fibrils are often cytotoxic, accumulating as intracellular inclusions or extracellular plaques and have the ability to interfere with cellular physiology causing various cellular malfunctions. At the same time, the highly ordered amyloid structures also present an opportunity for nature to store and protect peptide chains under extreme conditions - something that might be used for designing storage, formulation, and delivery of protein medications or for contriving bio-similar materials of great resistance or structure-ordering capacity. Here we summarize amyloid characteristics; discussing the basic morphologies, sequential requirements and 3D-structure that are required for the understanding of this newly (re)discovered protein structure - a prerequisite for developing either inhibitors or promoters of amyloid-forming processes.
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Affiliation(s)
- Dániel Horváth
- Laboratory of Structural Chemistry & Biology and MTA-ELTE Protein Modeling Research Group at the Institute of Chemistry, Eotvos Lorand University, H-1518, 112, PO Box 32, Budapest, Hungary
| | - Dóra K Menyhárd
- Laboratory of Structural Chemistry & Biology and MTA-ELTE Protein Modeling Research Group at the Institute of Chemistry, Eotvos Lorand University, H-1518, 112, PO Box 32, Budapest, Hungary
| | - András Perczel
- Laboratory of Structural Chemistry & Biology and MTA-ELTE Protein Modeling Research Group at the Institute of Chemistry, Eotvos Lorand University, H-1518, 112, PO Box 32, Budapest, Hungary
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49
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Khan JM, Malik A, Ahmad Khan M, Sharma P, Sen P. Pre-micellar concentrations of sodium dodecylbenzene sulphonate induce amyloid-like fibril formation in myoglobin at pH 4.5. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2019.124240] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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50
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Hosseinpour S, Roeters SJ, Bonn M, Peukert W, Woutersen S, Weidner T. Structure and Dynamics of Interfacial Peptides and Proteins from Vibrational Sum-Frequency Generation Spectroscopy. Chem Rev 2020; 120:3420-3465. [DOI: 10.1021/acs.chemrev.9b00410] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Saman Hosseinpour
- Institute of Particle Technology (LFG), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | | | - Mischa Bonn
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Wolfgang Peukert
- Institute of Particle Technology (LFG), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Sander Woutersen
- Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 EP Amsterdam, The Netherlands
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
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