1
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Shimanouchi T, Iwamura M, Sano Y, Hayashi K, Noda M, Kimura Y. Classification of binding property of amyloid β to lipid membranes: Membranomic research using quartz crystal microbalance combined with the immobilization of lipid planar membranes. Biochim Biophys Acta Proteins Proteom 2024; 1872:140987. [PMID: 38128808 DOI: 10.1016/j.bbapap.2023.140987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/10/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]
Abstract
A biomembrane-related fibrillogenesis of Amyloid β from Alzheimer' disease (Aβ) is closely related to its accumulation behavior. A binding property of Aβ peptides from Alzheimer' disease to lipid membranes was then classified by a quartz crystal microbalance (QCM) method combined with an immobilization technique using thiol self-assembled membrane. The accumulated amounts of Aβ, Δfmax, was determined from the measurement of the maximal frequency reduction using QCM. The plots of Δfmax to Aβ concentration gave the slope and saturated value of Δfmax, (Δfmax)sat that are the parameters for binding property of Aβ to lipid membranes. Therefore, the Aβ-binding property on lipid membranes was classified by the slope and (Δfmax)sat. The plural lipid system was described as X + Y where X = L1, L1/L2, and L1/L2/L3. The slope and (Δfmax)sat values plotted as a function of mixing ratio of Y to X was classified on a basis of the lever principle (LP). The LP violation observed in both parameters resulted from the formation of the crevice or pothole, as Aβ-specific binding site, generated at the boundary between ld and lo phases. The LP violation observed only in the slope resulted from glycolipid-rich domain acting as Aβ-specific binding site. Furthermore, lipid planar membranes indicating strong LP violation favored strong fibrillogenesis. Especially, lipid planar membranes indicating the LP violation only in the slope induced lateral aggregated and spherulitic fibrillar aggregates. Thus, the classification of Aβ binding property on lipid membranes appeared to be related to the fibrillogenesis with a certain morphology.
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Affiliation(s)
- Toshinori Shimanouchi
- Graduate School of Environment and Life Science, Okayama University, 3-1-1 Tsushimanaka, kita-ku, Okayama 700-8530, Japan.
| | - Miki Iwamura
- Graduate School of Environment and Life Science, Okayama University, 3-1-1 Tsushimanaka, kita-ku, Okayama 700-8530, Japan
| | - Yasuhiro Sano
- Graduate School of Environment and Life Science, Okayama University, 3-1-1 Tsushimanaka, kita-ku, Okayama 700-8530, Japan
| | - Keita Hayashi
- National Institute of Technology, Nara College, 22 Yada-cho, Yamatokoriyama, Nara, Japan
| | - Minoru Noda
- Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Kyoto, Japan
| | - Yukitaka Kimura
- Graduate School of Environment and Life Science, Okayama University, 3-1-1 Tsushimanaka, kita-ku, Okayama 700-8530, Japan
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3
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Strausbaugh Hjelmstad A, Pushie MJ, Ruth K, Escobedo M, Kuter K, Haas KL. Investigating Cu(I) binding to model peptides of N-terminal Aβ isoforms. J Inorg Biochem 2024; 253:112480. [PMID: 38309203 DOI: 10.1016/j.jinorgbio.2024.112480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/10/2023] [Accepted: 01/02/2024] [Indexed: 02/05/2024]
Abstract
Amyloid beta (Aβ) peptides and copper (Cu) ions are each involved in critical biological processes including antimicrobial activity, regulation of synaptic function, angiogenesis, and others. Aβ binds to Cu and may play a role in Cu trafficking. Aβ peptides exist in isoforms that vary at their C-and N-termini; variation at the N-terminal sequence affects Cu binding affinity, structure, and redox activity by providing different sets of coordinating groups to the metal ion. Several N-terminal isoforms have been detected in human brain tissues including Aβ1-40/42, Aβ3-42, pEAβ3-42, Aβ4-42, Aβ11-40 and pEAβ11-40 (where pE denotes an N-terminal pyroglutamic acid). Several previous works have individually investigated the affinity and structure of Cu(I) bound to some of these isoforms' metal binding domains. However, the disparately reported values are apparent constants collected under different sets of conditions, and thus an integrated comparison cannot be made. The work presented here provides the Cu(I) coordination structure and binding affinities of these six biologically relevant Aβ isoforms determined in parallel using model peptides of the Aβ metal binding domains (Aβ1-16, Aβ3-16, pEAβ3-16, Aβ4-16, Aβ11-16 and pEAβ11-16). The binding affinities of Cu(I)-Aβ complexes were measured using solution competition with ferrozine (Fz) and bicinchoninic acid (BCA), two colorimetric Cu(I) indicators in common use. The Cu(I) coordination structures were characterized by X-ray absorption spectroscopy. The data presented here facilitate comparison of the isoforms' Cu-binding interactions and contribute to our understanding of the role of Aβ peptides as copper chelators in healthy and diseased brains.
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Affiliation(s)
| | - M Jake Pushie
- Department of Surgery, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Kaylee Ruth
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Maria Escobedo
- Department of Mathematics and Computer Science, Saint Mary's College, Notre Dame, Indiana 46556, USA
| | - Kristin Kuter
- Department of Mathematics and Computer Science, Saint Mary's College, Notre Dame, Indiana 46556, USA
| | - Kathryn L Haas
- Department of Chemistry, Duke University, Durham, NC 27708, USA.
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4
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Lindberg M, Axell E, Sparr E, Linse S. A label-free high-throughput protein solubility assay and its application to Aβ40. Biophys Chem 2024; 307:107165. [PMID: 38309218 DOI: 10.1016/j.bpc.2023.107165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/18/2023] [Accepted: 12/25/2023] [Indexed: 02/05/2024]
Abstract
A major hallmark of Alzheimer's disease is the accumulation of aggregated amyloid β peptide (Aβ) in the brain. Here we develop a solubility assay for proteins and measure the solubility of Aβ40. In brief, the method utilizes 96-well filter plates to separate monomeric Aβ from aggregated Aβ, and the small species are quantified with the amine reactive dye o-phthalaldehyde (OPA). This procedure ensures that solubility is measured for unlabeled species, and makes the assay high-throughput and inexpensive. We demonstrate that the filter plates successfully separate fibrils from monomer, with negligible monomer adsorption, and that OPA can quantify Aβ peptides in a concentration range from 40 nM to 20 μM. We also show that adding a methionine residue to the N-terminus of Aβ1-40 decreases the solubility by <3-fold. The method will facilitate further solubility studies, and contribute to the understanding of the thermodynamics of amyloid fibril formation.
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Affiliation(s)
- Max Lindberg
- Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Emil Axell
- Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Emma Sparr
- Division of Physical Chemistry, Department of Chemistry, Lund University, Lund, Sweden
| | - Sara Linse
- Biochemistry and Structural Biology, Lund University, Lund, Sweden.
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5
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Dey P, Biswas P. Effect of caffeine on the aggregation of amyloid-β-A 3D RISM study. J Chem Phys 2024; 160:125101. [PMID: 38516974 DOI: 10.1063/5.0202636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/10/2024] [Indexed: 03/23/2024] Open
Abstract
Alzheimer's disease is a detrimental neurological disorder caused by the formation of amyloid fibrils due to the aggregation of amyloid-β peptide. The primary therapeutic approaches for treating Alzheimer's disease are targeted to prevent this amyloid fibril formation using potential inhibitor molecules. The discovery of such inhibitor molecules poses a formidable challenge to the design of anti-amyloid drugs. This study investigates the effect of caffeine on dimer formation of the full-length amyloid-β using a combined approach of all-atom, explicit water molecular dynamics simulations and the three-dimensional reference interaction site model theory. The change in the hydration free energy of amyloid-β dimer, with and without the inhibitor molecules, is calculated with respect to the monomeric amyloid-β, where the hydration free energy is decomposed into energetic and entropic components, respectively. Dimerization is accompanied by a positive change in the partial molar volume. Dimer formation is spontaneous, which implies a decrease in the hydration free energy. However, a reverse trend is observed for the dimer with inhibitor molecules. It is observed that the negatively charged residues primarily contribute for the formation of the amyloid-β dimer. A residue-wise decomposition reveals that hydration/dehydration of the side-chain atoms of the charged amino acid residues primarily contribute to dimerization.
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Affiliation(s)
- Priya Dey
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi 110007, India
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6
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Zhou W, O'Neill CL, Ding T, Zhang O, Rudra JS, Lew MD. Resolving the Nanoscale Structure of β-Sheet Peptide Self-Assemblies Using Single-Molecule Orientation-Localization Microscopy. ACS Nano 2024; 18:8798-8810. [PMID: 38478911 DOI: 10.1021/acsnano.3c11771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Synthetic peptides that self-assemble into cross-β fibrils are versatile building blocks for engineered biomaterials due to their modularity and biocompatibility, but their structural and morphological similarities to amyloid species have been a long-standing concern for their translation. Further, their polymorphs are difficult to characterize by using spectroscopic and imaging techniques that rely on ensemble averaging to achieve high resolution. Here, we utilize Nile red (NR), an amyloidophilic fluorogenic probe, and single-molecule orientation-localization microscopy (SMOLM) to characterize fibrils formed by the designed amphipathic enantiomers KFE8L and KFE8D and the pathological amyloid-beta peptide Aβ42. Importantly, NR SMOLM reveals the helical (bilayer) ribbon structure of both KFE8 and Aβ42 and quantifies the precise tilt of the fibrils' inner and outer backbones in relevant buffer conditions without the need for covalent labeling or sequence mutations. SMOLM also distinguishes polymorphic branched and curved morphologies of KFE8, whose backbones exhibit much more heterogeneity than those of typical straight fibrils. Thus, SMOLM is a powerful tool to interrogate the structural differences and polymorphism between engineered and pathological cross-β-rich fibrils.
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Affiliation(s)
- Weiyan Zhou
- Preston M. Green Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Conor L O'Neill
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tianben Ding
- Preston M. Green Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Oumeng Zhang
- Preston M. Green Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Jai S Rudra
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Matthew D Lew
- Preston M. Green Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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7
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Hsueh SCC, Nijland M, Aina A, Plotkin SS. Cyclization Scaffolding for Improved Vaccine Immunogen Stability: Application to Tau Protein in Alzheimer's Disease. J Chem Inf Model 2024; 64:2035-2044. [PMID: 38427576 DOI: 10.1021/acs.jcim.3c01556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Effective scaffolding of immunogens is crucial for generating conformationally selective antibodies through active immunization, particularly in the treatment of protein misfolding diseases such as Alzheimer's and Parkinson's disease. Previous computational work has revealed that a disorder-prone region of the tau protein, when in a stacked form, is predicted to structurally resemble a small, soluble protofibril, having conformational properties similar to those of experimental in vitro tau oligomers. Such an oligomeric structural mimic has the potential to serve as a vaccine immunogen design for Alzheimer's disease. In this study, we developed a cyclization scaffolding method in Rosetta, in which multiple cyclic peptides are stacked into a protofibril. Cyclization results in significant stabilization of protofibril-like structures by constraining the conformational space. Applying this method to the disorder-prone region of the tau fibril, we evaluated the metastability of the cyclized tau immunogen using molecular dynamics simulations, and we identified sequences of two cyclic constructs having high metastability in the protofibril. We then assessed their thermodynamic stability by computing the free energy required to separate a distal chain from the rest of the stacked structure. Our computational results, based on molecular dynamics simulations and free energy calculations, demonstrate that two cyclized constructs, cyclo-(VKSEKLDFKDRVQSKIFyN) and cyclo-(VKSEKLDFKDRVQSKIYvG) (lowercase letters indicate d-form amino acids), possess significantly increased thermodynamic stability in the protofibril over an uncyclized linear construct VKSEKLDFKDRVQSKI. The cyclization scaffolding approach proposed here holds promise as a means to effectively design immunogens for protein misfolding diseases, particularly those involving liposome-conjugated peptide constructs.
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Affiliation(s)
- Shawn C C Hsueh
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Mark Nijland
- Laboratory of Physical Chemistry, Wageningen University, Wageningen 6708 WG, The Netherlands
| | - Adekunle Aina
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Steven S Plotkin
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
- Genome Science and Technology Program, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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8
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Chia S, Cataldi RL, Ruggeri FS, Limbocker R, Condado-Morales I, Pisani K, Possenti A, Linse S, Knowles TPJ, Habchi J, Mannini B, Vendruscolo M. A Relationship between the Structures and Neurotoxic Effects of Aβ Oligomers Stabilized by Different Metal Ions. ACS Chem Neurosci 2024; 15:1125-1134. [PMID: 38416693 PMCID: PMC10958495 DOI: 10.1021/acschemneuro.3c00718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 03/01/2024] Open
Abstract
Oligomeric assemblies of the amyloid β peptide (Aβ) have been investigated for over two decades as possible neurotoxic agents in Alzheimer's disease. However, due to their heterogeneous and transient nature, it is not yet fully established which of the structural features of these oligomers may generate cellular damage. Here, we study distinct oligomer species formed by Aβ40 (the 40-residue form of Aβ) in the presence of four different metal ions (Al3+, Cu2+, Fe2+, and Zn2+) and show that they differ in their structure and toxicity in human neuroblastoma cells. We then describe a correlation between the size of the oligomers and their neurotoxic activity, which provides a type of structure-toxicity relationship for these Aβ40 oligomer species. These results provide insight into the possible role of metal ions in Alzheimer's disease by the stabilization of Aβ oligomers.
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Affiliation(s)
- Sean Chia
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Rodrigo Lessa Cataldi
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Francesco Simone Ruggeri
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Ryan Limbocker
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Itzel Condado-Morales
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Katarina Pisani
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Andrea Possenti
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Sara Linse
- Department
of Biochemistry & Structural Biology, Center for Molecular Protein
Science, Lund University, PO box 124, 221 00 Lund, Sweden
| | - Tuomas P. J. Knowles
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
- Department
of Physics, Cavendish Laboratory, Cambridge CB3 0HE, U.K.
| | - Johnny Habchi
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Benedetta Mannini
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Michele Vendruscolo
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
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9
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Nayak K, Ghosh P, Barman S, Sudhamalla B, Theato P, De P. Amyloid β-Peptide Segment Conjugated Side-Chain Proline-Based Polymers as Potent Inhibitors in Lysozyme Amyloidosis. Bioconjug Chem 2024; 35:312-323. [PMID: 38420925 DOI: 10.1021/acs.bioconjchem.3c00509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Developing effective amyloidosis inhibitors poses a significant challenge due to the dynamic nature of the protein structures, the complex interplay of interfaces in protein-protein interactions, and the irreversible nature of amyloid assembly. The interactions of amyloidogenic polypeptides with other peptides play a pivotal role in modulating amyloidosis and fibril formation. This study presents a novel approach for designing and synthesizing amyloid interaction surfaces using segments derived from the amyloid-promoting sequence of amyloid β-peptide [VF(Aβ(18-19)/FF(Aβ(19-20)/LVF(Aβ(17-19)/LVFF(Aβ(17-20)], where VF, FF, LVF and LVFF stands for valine phenylalanine dipeptide, phenylalanine phenylalanine dipeptide, leucine valine phenylalanine tripeptide and leucine valine phenylalanine phenylalanine tetrapeptide, respectively. These segments are conjugated with side-chain proline-based methacrylate polymers serving as potent lysozyme amyloidosis inhibitors and demonstrating reduced cytotoxicity of amyloid aggregations. Di-, tri-, and tetra-peptide conjugated chain transfer agents (CTAs) were synthesized and used for the reversible addition-fragmentation chain transfer polymerization of tert-butoxycarbonyl (Boc)-proline methacryloyloxyethyl ester (Boc-Pro-HEMA). Deprotection of Boc-groups from the side-chain proline pendants resulted in water-soluble polymers with defined peptide chain ends as peptide-polymer bioconjugates. Among them, the LVFF-conjugated polymer acted as a potent inhibitor with significantly suppressed lysozyme amyloidosis, a finding supported by comprehensive spectroscopic, microscopic, and computational analyses. These results unveil the synergistic effect between the segment-derived amyloid β-peptide and side-chain proline-based polymers, offering new prospects for targeting lysozyme amyloidosis.
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Affiliation(s)
- Kasturee Nayak
- Polymer Research Centre and Centre for Advanced Functional Materials, Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246, India
| | - Pooja Ghosh
- Polymer Research Centre and Centre for Advanced Functional Materials, Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246, India
- Centre for Interdisciplinary Sciences, JIS Institute of Advanced Studies & Research (JISIASR) Kolkata, JIS University, GP Block, Sector-5, Salt Lake, Kolkata, West Bengal 700091, India
| | - Soumen Barman
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246, India
| | - Babu Sudhamalla
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246, India
| | - Patrick Theato
- Karlsruhe Institute of Technology (KIT), Institute for Chemical Technology and Polymer Chemistry (ITCP), Engesserstraße 18, Karlsruhe 76131, Germany
- Karlsruhe Institute of Technology (KIT), Soft Matter Synthesis Laboratory,Institute for Biological Interfaces III (IBG-3), Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany
| | - Priyadarsi De
- Polymer Research Centre and Centre for Advanced Functional Materials, Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246, India
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10
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Khursheed A, Viles JH. Impact of Membrane Phospholipids and Exosomes on the Kinetics of Amyloid-β Fibril Assembly. J Mol Biol 2024; 436:168464. [PMID: 38311235 DOI: 10.1016/j.jmb.2024.168464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/10/2024]
Abstract
Alzheimer's disease (AD) is linked with the self-association of the amyloid-β peptide (Aβ) into oligomers and fibrils. The brain is a lipid rich environment for Aβ to assemble, while the brain membrane composition varies in an age dependent manner, we have therefore monitored the influence of lipid bilayer composition on the kinetics of Aβ40 fibril assembly. Using global-fitting models of fibril formation kinetics, we show that the microscopic rate constant for primary nucleation is influenced by variations in phospholipid composition. Anionic phospholipids and particularly those with smaller headgroups shorten fibril formation lag-times, while zwitterionic phospholipids tend to extend them. Using a physiological vesicle model, we show cellular derived exosomes accelerate Aβ40 and Aβ42 fibril formation. Two distinct effects are observed, the presence of even small amounts of any phospholipid will impact the slope of the fibril growth curve. While subsequent additions of phospholipids only affect primary nucleation with the associated change in lag-times. Heightened anionic phospholipids and cholesterol levels are associated with aging and AD respectively, both these membrane components strongly accelerate primary nucleation during Aβ assembly, making a link between disrupted lipid metabolism and Alzheimer's disease.
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Affiliation(s)
- Anum Khursheed
- School of Biological and Behavioral Science, Queen Mary, University of London, UK
| | - John H Viles
- School of Biological and Behavioral Science, Mile End Road, Queen Mary, University of London, UK, E1 4AS, UK.
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11
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Lefebvre C, Vreulx AC, Dumortier C, Bégard S, Gelle C, Siedlecki-Wullich D, Colin M, Kilinc D, Halliez S. Integration of Microfluidic Devices with Microelectrode Arrays to Functionally Assay Amyloid-β-Induced Synaptotoxicity. ACS Biomater Sci Eng 2024; 10:1856-1868. [PMID: 38385618 DOI: 10.1021/acsbiomaterials.3c00997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease and the most frequent cause of dementia. It is characterized by the accumulation in the brain of two pathological protein aggregates: amyloid-β peptides (Aβ) and abnormally phosphorylated tau. The progressive cognitive decline observed in patients strongly correlates with the synaptic loss. Many lines of evidence suggest that soluble forms of Aβ accumulate into the brain where they cause synapse degeneration. Stopping their spreading and/or targeting the pathophysiological mechanisms leading to synaptic loss would logically be beneficial for the patients. However, we are still far from understanding these processes. Our objective was therefore to develop a versatile model to assay and study Aβ-induced synaptotoxicity. We integrated a microfluidic device that physically isolates synapses from presynaptic and postsynaptic neurons with a microelectrode array. We seeded mouse primary cortical cells in the presynaptic and postsynaptic chambers. After functional synapses have formed in the synaptic chamber, we exposed them to concentrated conditioned media from cell lines overexpressing the wild-type or mutated amyloid precursor protein and thus secreting different levels of Aβ. We recorded the neuronal activity before and after exposition to Aβ and quantified Aβ's effects on the connectivity between presynaptic and postsynaptic neurons. We observed that the application of Aβ on the synapses for 48 h strongly decreased the interchamber connectivity without significantly affecting the neuronal activity in the presynaptic or postsynaptic chambers. Thus, through this model, we are able to functionally assay the impact of Aβ peptides (or other molecules) on synaptic connectivity and to use the latter as a proxy to study Aβ-induced synaptotoxicity. Moreover, since the presynaptic, postsynaptic, and synaptic chambers can be individually targeted, our assay provides a powerful tool to evaluate the involvement of candidate genes in synaptic vulnerability and/or test therapeutic strategies for AD.
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Affiliation(s)
- Camille Lefebvre
- Université de Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, F-59000 Lille, France
| | - Anaïs-Camille Vreulx
- Université de Lille, Institut Pasteur de Lille, CHU Lille, INSERM U1167, LabEx DISTALZ, 59019Lille ,France
| | - Corentin Dumortier
- Université de Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, F-59000 Lille, France
| | - Séverine Bégard
- Université de Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, F-59000 Lille, France
| | - Carla Gelle
- Université de Lille, Institut Pasteur de Lille, CHU Lille, INSERM U1167, LabEx DISTALZ, 59019Lille ,France
| | - Dolores Siedlecki-Wullich
- Université de Lille, Institut Pasteur de Lille, CHU Lille, INSERM U1167, LabEx DISTALZ, 59019Lille ,France
| | - Morvane Colin
- Université de Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, F-59000 Lille, France
| | - Devrim Kilinc
- Université de Lille, Institut Pasteur de Lille, CHU Lille, INSERM U1167, LabEx DISTALZ, 59019Lille ,France
| | - Sophie Halliez
- Université de Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, F-59000 Lille, France
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12
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Roldán-Martín L, Sodupe M, Maréchal JD. Computational Study of Amyloidβ 42 Familial Mutations and Metal Interaction: Impact on Monomers and Aggregates Dynamical Behaviors. Inorg Chem 2024; 63:4725-4737. [PMID: 38408469 PMCID: PMC10934806 DOI: 10.1021/acs.inorgchem.3c04555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 02/28/2024]
Abstract
One of the main hallmarks of Alzheimer's Disease is the formation of β-amyloid plaques, whose formation may be enhanced by metal binding or the appearance of familial mutations. In the present study, the simultaneous effect of familial mutations (E22Q, E22G, E22K, and D23N) and binding to metal ions (Cu(II) or Al(III)) is studied at the Aβ42 monomeric and fibrillar levels. With the application of GaMD and MD simulations, it is observed that the effects of metal binding and mutations differ in the monomeric and fibrillar forms. In the monomeric structures, without metal binding, all mutations reduce the amount of α-helix and increase, in some cases, the β-sheet content. In the presence of Cu(II) and Al(III) metal ions, the peptide becomes less flexible, and the β-sheet content decreases in favor of forming α-helix motifs that stabilize the system through interhelical contacts. Regarding the fibrillar structures, mutations decrease the opening of the fiber in the vertical axis, thereby stabilizing the S-shaped structure of the fiber. This effect is, in general, enhanced upon metal binding. These results may explain the different Aβ42 aggregation patterns observed in familial mutations.
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Affiliation(s)
- Lorena Roldán-Martín
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Vallès, Spain
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Vallès, Spain
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Vallès, Spain
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13
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Dec R, Dzwolak W, Winter R. From a Droplet to a Fibril and from a Fibril to a Droplet: Intertwined Transition Pathways in Highly Dynamic Enzyme-Modulated Peptide-Adenosine Triphosphate Systems. J Am Chem Soc 2024; 146:6045-6052. [PMID: 38394622 DOI: 10.1021/jacs.3c13152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Many cellular coassemblies of proteins and polynucleotides facilitate liquid-liquid phase separation (LLPS) and the subsequent self-assembly of disease-associated amyloid fibrils within the liquid droplets. Here, we explore the dynamics of coupled phase and conformational transitions of model adenosine triphosphate (ATP)-binding peptides, ACC1-13Kn, consisting of the potent amyloidogenic fragment of insulin's A-chain (ACC1-13) merged with oligolysine segments of various lengths (Kn, n = 16, 24, 40). The self-assembly of ATP-stabilized amyloid fibrils is preceded by LLPS for peptides with sufficiently long oligolysine segments. The two-component droplets and fibrils are in dynamic equilibria with free ATP and monomeric peptides, which makes them susceptible to ATP-hydrolyzing apyrase and ACC1-13Kn-digesting proteinase K. Both enzymes are capable of rapid disassembly of amyloid fibrils, producing either monomers of the peptide (apyrase) or free ATP released together with cleaved-off oligolysine segments (proteinase K). In the latter case, the enzyme-sequestered Kn segments form subsequent droplets with the co-released ATP, resulting in an unusual fibril-to-droplet transition. In support of the highly dynamic nature of the aggregate-monomer equilibria, addition of superstoichiometric amounts of free peptide to the ACC1-13Kn-ATP coaggregate causes its disassembly. Our results show that the droplet state is not merely an intermediate phase on the pathway to the amyloid aggregate but may also constitute the final phase of a complex amyloidogenic protein misfolding scenario rich in highly degraded protein fragments incompetent to transition again into fibrils.
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Affiliation(s)
- Robert Dec
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, Dortmund 44227, Germany
| | - Wojciech Dzwolak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteur Street 1, Warsaw 02-093, Poland
| | - Roland Winter
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, Dortmund 44227, Germany
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14
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Gou X, Fu Y, Li J, Xiang J, Yang M, Zhang Y. Impact of nanoplastics on Alzheimer 's disease: Enhanced amyloid-β peptide aggregation and augmented neurotoxicity. J Hazard Mater 2024; 465:133518. [PMID: 38228001 DOI: 10.1016/j.jhazmat.2024.133518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/18/2024]
Abstract
Nanoplastics, widely existing in the environment and organisms, have been proven to cross the blood-brain barrier, increasing the incidence of neurodegenerative diseases like Alzheimer's disease (AD). However, current studies mainly focus on the neurotoxicity of nanoplastics themselves, neglecting their synergistic effects with other biomolecules and the resulting neurotoxicity. Amyloid β peptide (Aβ), which triggers neurotoxicity through its self-aggregation, is the paramount pathogenic protein in AD. Here, employing polystyrene nanoparticles (PS) as a model for nanoplastics, we reveal that 100 pM PS nanoparticles significantly accelerate the nucleation rate of two Aβ subtypes (Aβ40 and Aβ42) at low concentrations, promoting the formation of more Aβ oligomers and leading to evident neurotoxicity. The hydrophobic surface of PS facilitates the interaction of hydrophobic fragments between Aβ monomers, responsible for the augmented neurotoxicity. This work provides consequential insights into the modulatory impact of low-dose PS on Aβ aggregation and the ensuing neurotoxicity, presenting a valuable foundation for future research on the intricate interplay between environmental toxins and brain diseases.
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Affiliation(s)
- Xiaoli Gou
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Yongchun Fu
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Juan Li
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Juan Xiang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China.
| | - Minghui Yang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China.
| | - Yi Zhang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China.
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15
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Zhang D, Zhang J, Ma Z, Wu Q, Liu M, Fan T, Ding L, Ren D, Wen A, Wang J. Luteoloside inhibits Aβ1-42 fibrillogenesis, disintegrates preformed fibrils, and alleviates amyloid-induced cytotoxicity. Biophys Chem 2024; 306:107171. [PMID: 38194817 DOI: 10.1016/j.bpc.2023.107171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/17/2023] [Accepted: 12/30/2023] [Indexed: 01/11/2024]
Abstract
Abnormal aggregation and fibrillogenesis of amyloid-β protein (Aβ) can cause Alzheimer's disease (AD). Thus, the discovery of effective drugs that inhibit Aβ fibrillogenesis in the brain is crucial for the treatment of AD. Luteoloside, as one of the polyphenolic compounds, is found to have a certain therapeutic effect on nervous system diseases. However, it remains unknown whether luteoloside is a potential drug for treating AD by modulating Aβ aggregation pathway. In this study, we performed diverse biophysical and biochemical methods to explore the inhibition of luteoloside on Aβ1-42 which is linked to AD. The results demonstrated that luteoloside efficiently prevented amyloid oligomerization and cross-β-sheet formation, reduced the rate of amyloid growth and the length of amyloid fibrils in a dose-dependent manner. Moreover, luteoloside was able to influence aggregation and conformation of Aβ1-42 during different fiber-forming phases, and it could disintegrate already preformed fibrils of Aβ1-42 and convert them into nontoxic aggregates. Furthermore, luteoloside protected cells from amyloid-induced cytotoxicity and hemolysis, and attenuated the level of reactive oxygen species (ROS). The molecular docking study showed that luteoloside interacted with Aβ1-42 mainly via Conventional Hydrogen Bond, Carbon Hydrogen Bond, Pi-Pi T-shaped, Pi-Alkyl and Pi-Anion, thereby possibly preventing it from forming the aggregates. These observations indicate that luteoloside, a natural anti-oxidant molecule, may be applicable as an effective inhibitor of Aβ, and promote further exploration of the therapeutic strategy against AD.
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Affiliation(s)
- Di Zhang
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Juanli Zhang
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Zhongying Ma
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Qianwen Wu
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Meiyou Liu
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Tingting Fan
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Likun Ding
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Danjun Ren
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Aidong Wen
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China.
| | - Jingwen Wang
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China.
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16
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Vicente-Zurdo D, Rosales-Conrado N, León-González ME. Unravelling the in vitro and in vivo potential of selenium nanoparticles in Alzheimer's disease: A bioanalytical review. Talanta 2024; 269:125519. [PMID: 38086100 DOI: 10.1016/j.talanta.2023.125519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 11/30/2023] [Accepted: 12/03/2023] [Indexed: 01/05/2024]
Abstract
Alzheimer's disease (AD) is a devastating neurodegenerative disorder characterized by progressive cognitive decline and the accumulation of beta-amyloid plaques and tau tangles in the brain. Current therapies have limited efficacy, prompting the search for novel treatments. Selenium nanoparticles (SeNPs) have emerged as promising candidates for AD therapy due to their unique physicochemical properties and potential therapeutic effects. This review provides an overview of SeNPs and their potential application in AD treatment, as well as the main bioanalytical techniques applied in this field. SeNPs possess antioxidant and anti-inflammatory properties, making them potential candidates to combat the oxidative stress and neuroinflammation associated with AD. Moreover, SeNPs have shown the ability to cross the blood-brain barrier (BBB), allowing them to target brain regions affected by AD pathology. Various methods for synthesizing SeNPs are explored, including chemical, physical and biological synthesis approaches. Based on the employment of algae, yeast, fungi, and plants, green methods offer a promising and biocompatible alternative for SeNPs production. In vitro studies have demonstrated the potential of SeNPs in reducing beta-amyloid aggregation and inhibiting tau hyperphosphorylation, providing evidence of their neuroprotective effects on neuronal cells. In vivo studies using transgenic mouse models and AD-induced symptoms have shown promising results, with SeNPs treatment leading to cognitive improvements and reduced amyloid plaque burden in the hippocampus. Looking ahead, future trends in SeNPs research involve developing innovative brain delivery strategies to enhance their therapeutic potential, exploring alternative animal models to complement traditional mouse studies, and investigating multi-targeted SeNPs formulations to address multiple aspects of AD pathology. Overall, SeNPs represent a promising avenue for AD treatment, and further research in this field may pave the way for effective and much-needed therapeutic interventions for individuals affected by this debilitating disease.
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Affiliation(s)
- David Vicente-Zurdo
- Dpto. Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain; Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, Madrid, Spain.
| | - Noelia Rosales-Conrado
- Dpto. Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - María Eugenia León-González
- Dpto. Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain.
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17
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Grazioli G, Tao A, Bhatia I, Regan P. Genetic Algorithm for Automated Parameterization of Network Hamiltonian Models of Amyloid Fibril Formation. J Phys Chem B 2024; 128:1854-1865. [PMID: 38359362 PMCID: PMC10910512 DOI: 10.1021/acs.jpcb.3c07322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 01/07/2024] [Accepted: 02/05/2024] [Indexed: 02/17/2024]
Abstract
The time scales of long-time atomistic molecular dynamics simulations are typically reported in microseconds, while the time scales for experiments studying the kinetics of amyloid fibril formation are typically reported in minutes or hours. This time scale deficit of roughly 9 orders of magnitude presents a major challenge in the design of computer simulation methods for studying protein aggregation events. Coarse-grained molecular simulations offer a computationally tractable path forward for exploring the molecular mechanism driving the formation of these structures, which are implicated in diseases such as Alzheimer's, Parkinson's, and type-II diabetes. Network Hamiltonian models of aggregation are centered around a Hamiltonian function that returns the total energy of a system of aggregating proteins, given the graph structure of the system as an input. In the graph, or network, representation of the system, each protein molecule is represented as a node, and noncovalent bonds between proteins are represented as edges. The parameter, i.e., a set of coefficients that determine the degree to which each topological degree of freedom is favored or disfavored, must be determined for each network Hamiltonian model, and is a well-known technical challenge. The methodology is first demonstrated by beginning with an initial set of randomly parametrized models of low fibril fraction (<5% fibrillar), and evolving to subsequent generations of models, ultimately leading to high fibril fraction models (>70% fibrillar). The methodology is also demonstrated by applying it to optimizing previously published network Hamiltonian models for the 5 key amyloid fibril topologies that have been reported in the Protein Data Bank (PDB). The models generated by the AI produced fibril fractions that surpass previously published fibril fractions in 3 of 5 cases, including the most naturally abundant amyloid fibril topology, the 1,2 2-ribbon, which features a steric zipper. The authors also aim to encourage more widespread use of the network Hamiltonian methodology for fitting a wide variety of self-assembling systems by releasing a free open-source implementation of the genetic algorithm introduced here.
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Affiliation(s)
- Gianmarc Grazioli
- Department of Chemistry, San
José State University, San Jose, California 95192, United States
| | - Andy Tao
- Department of Chemistry, San
José State University, San Jose, California 95192, United States
| | - Inika Bhatia
- Department of Chemistry, San
José State University, San Jose, California 95192, United States
| | - Patrick Regan
- Department of Chemistry, San
José State University, San Jose, California 95192, United States
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18
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Li X, Zhang Y, Wang Y, Zhang S, Zhang L. Molecular Insights into the Inhibition and Disaggregation Effects of EGCG on Aβ40 and Aβ42 Cofibrillation. J Phys Chem B 2024; 128:1843-1853. [PMID: 38359305 DOI: 10.1021/acs.jpcb.3c07232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
The misfolding and aggregation of amyloid-β (Aβ) peptides play a pivotal role in the pathogenesis of Alzheimer's disease (AD). Aβ40 and Aβ42, the two primary isoforms of Aβ, can not only self-aggregate into homogeneous aggregates but also coaggregate to form mixed fibrils. Epigallocatechin-3-gallate (EGCG), a prominent tea polyphenol, has shown the capability to prevent the self-aggregation of Aβ40 and Aβ42 peptides and disaggregate their homogeneous fibrils. However, its effects on the cofibrillation of Aβ40 and Aβ42 have not yet been explored. Here, we employed molecular dynamic simulations to investigate the effects of EGCG on the coaggregation of Aβ40 and Aβ42, as well as on their mixed fibril. Our findings indicated that EGCG effectively inhibits the codimerization of Aβ40 and Aβ42 primarily by impeding the interchain interaction between the two isoforms. The key binding sites for EGCG on Aβ40 and Aβ42 are the polar residues and aromatic residues, engaging in hydrogen-bond , π-π, and cation-π interactions with EGCG. Additionally, EGCG disaggregates the Aβ40-Aβ42 mixed fibril by reducing its long-range interaction through similar binding sites and interactions as those between EGCG and Aβ40-Aβ42 heterodimers. Our research reveals the comprehensive inhibition and disaggregation effects of EGCG on the cofibrillation of Aβ isoforms, which provides further support for the development of EGCG as an effective antiaggregation agent for AD.
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Affiliation(s)
- Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, 28 West Xianning Road, Xi'an 710049, China
- State Key Laboratory of Surface Physics, Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Yu Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, 28 West Xianning Road, Xi'an 710049, China
| | - Yuetian Wang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, 28 West Xianning Road, Xi'an 710049, China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, 28 West Xianning Road, Xi'an 710049, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, 28 West Xianning Road, Xi'an 710049, China
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19
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Andrikopoulos N, Tang H, Wang Y, Liang X, Li Y, Davis TP, Ke PC. Exploring Peptido-Nanocomposites in the Context of Amyloid Diseases. Angew Chem Int Ed Engl 2024; 63:e202309958. [PMID: 37943171 DOI: 10.1002/anie.202309958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 11/10/2023]
Abstract
Therapeutic peptides are a major class of pharmaceutical drugs owing to their target-binding specificity as well as their versatility in inhibiting aberrant protein-protein interactions associated with human pathologies. Within the realm of amyloid diseases, the use of peptides and peptidomimetics tailor-designed to overcome amyloidogenesis has been an active research endeavor since the late 90s. In more recent years, incorporating nanoparticles for enhancing the biocirculation and delivery of peptide drugs has emerged as a frontier in nanomedicine, and nanoparticles have further demonstrated a potency against amyloid aggregation and cellular inflammation to rival strategies employing small molecules, peptides, and antibodies. Despite these efforts, however, a fundamental understanding of the chemistry, characteristics and function of peptido-nanocomposites is lacking, and a systematic analysis of such strategy for combating a range of amyloid pathogeneses is missing. Here we review the history, principles and evolving chemistry of constructing peptido-nanocomposites from bottom up and discuss their future application against amyloid diseases that debilitate a significant portion of the global population.
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Affiliation(s)
- Nicholas Andrikopoulos
- Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Huayuan Tang
- College of Mechanics and Materials, Hohai University, Nanjing, 211100, China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Yue Wang
- Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou 510006, China
| | - Xiufang Liang
- Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou 510006, China
| | - Yuhuan Li
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, 200032, China
| | - Thomas P Davis
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Pu Chun Ke
- Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
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20
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Iorio A, Melchionna S, Derreumaux P, Sterpone F. Dynamics and Structures of Amyloid Aggregates under Fluid Flows. J Phys Chem Lett 2024; 15:1943-1949. [PMID: 38346112 DOI: 10.1021/acs.jpclett.3c03084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
In this work, we investigate how fluid flows impact the aggregation mechanisms of Aβ40 proteins and Aβ16-22 peptides and mechanically perturb their (pre)fibrillar aggregates. We exploit the OPEP coarse-grained model for proteins and the Lattice Boltzmann Molecular Dynamics technique. We show that beyond a critical shear rate, amyloid aggregation speeds up in Couette flow because of the shorter collisions times between aggregates, following a transition from diffusion limited to advection dominated dynamics. We also characterize the mechanical deformation of (pre)fibrillar states due to the fluid flows (Couette and Poiseuille), confirming the capability of (pre)fibrils to form pathological loop-like structures as detected in experiments. Our findings can be of relevance for microfluidic applications and for understanding aggregation in the interstitial brain space.
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Affiliation(s)
- Antonio Iorio
- Laboratoire de Biochimie Théorique (UPR9080), CNRS, Université Paris-Cité, Paris 75005, France
- Institut de Biologie Physico-Chimique, Fondation Edmond Rothschild, Paris 75005, France
| | - Simone Melchionna
- IAC CNR, 00185 Rome, Italy
- Lexma Technology, Arlington, Massachusetts 02476, United States
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique (UPR9080), CNRS, Université Paris-Cité, Paris 75005, France
- Institut de Biologie Physico-Chimique, Fondation Edmond Rothschild, Paris 75005, France
- Institut Universitaire de France, 75005 Paris, France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique (UPR9080), CNRS, Université Paris-Cité, Paris 75005, France
- Institut de Biologie Physico-Chimique, Fondation Edmond Rothschild, Paris 75005, France
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21
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Scheidt HA, Korn A, Schwarze B, Krueger M, Huster D. Conformation of Pyroglutamated Amyloid β (3-40) and (11-40) Fibrils - Extended or Hairpin? J Phys Chem B 2024; 128:1647-1655. [PMID: 38334278 PMCID: PMC10895672 DOI: 10.1021/acs.jpcb.3c07285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/04/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
Amyloid β (Aβ) is a hallmark protein of Alzheimer's disease. One physiologically important Aβ variant is formed by initial N-terminal truncation at a glutamic acid position (either E3 or E11), which is subsequently cyclized to a pyroglutamate (either pE3 or pE11). Both forms have been found in high concentrations in the core of amyloid plaques and are likely of high importance in the pathology of Alzheimer's disease. However, the molecular structure of the fibrils of these variants is not entirely clear. Solid-state NMR spectroscopy studies have reported a molecular contact between Gly25 and Ile31, which would disagree with the conventional hairpin model of wildtype (WT-)Aβ1-40 fibrils, most often described in the literature. We investigated the conformation of the monomeric unit of pE3-Aβ3-40 and pE11-Aβ11-40 (and for comparison also wildtype (WT)-Aβ1-40) fibrils to find out whether the hairpin or a newly suggested extended structure dominates the structure of the Aβ monomers in these fibrils. To this end, solid-state NMR spectroscopy was applied probing the inter-residual contacts between Phe19/Leu34, Ala21/Leu34, and especially Gly25/Ile31 using suitable isotopic labeling schemes. In the second part, the flexible turn of the Aβ40 peptides was replaced by a (3-(3-aminomethyl)phenylazo)phenylacetic acid (AMPP)-based photoswitch, which can predefine the peptide conformation to either an extended (trans) or hairpin (cis) conformation. This enables simultaneous spectroscopic assessment of the conformation of the AMPP-photoswitch, allowing in situ structural investigations during fibrillation in contrast to structural techniques such as NMR spectroscopy or cryo-EM, which can only be applied to stable conformers. Both methods confirm an extended structure for the peptidic monomers in fibrils of all investigated Aβ variants. Especially the Gly25/Ile31 contact is a decisive indicator for the extended structure along with the characteristic absorption spectra of trans-AMPP-Aβ.
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Affiliation(s)
- Holger A. Scheidt
- Institute
for Medical Physics and Biophysics, Leipzig
University Härtelstr. 16/18, D-04107 Leipzig, Germany
| | - Alexander Korn
- Institute
for Medical Physics and Biophysics, Leipzig
University Härtelstr. 16/18, D-04107 Leipzig, Germany
| | - Benedikt Schwarze
- Institute
for Medical Physics and Biophysics, Leipzig
University Härtelstr. 16/18, D-04107 Leipzig, Germany
| | - Martin Krueger
- Institute
of Anatomy, Leipzig University, Liebigstr. 13, 04103 Leipzig, Germany
| | - Daniel Huster
- Institute
for Medical Physics and Biophysics, Leipzig
University Härtelstr. 16/18, D-04107 Leipzig, Germany
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22
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Thurber KR, Yau WM, Tycko R. Structure of Amyloid Peptide Ribbons Characterized by Electron Microscopy, Atomic Force Microscopy, and Solid-State Nuclear Magnetic Resonance. J Phys Chem B 2024; 128:1711-1723. [PMID: 38348474 DOI: 10.1021/acs.jpcb.3c07867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Polypeptides often self-assemble to form amyloid fibrils, which contain cross-β structural motifs and are typically 5-15 nm in width and micrometers in length. In many cases, short segments of longer amyloid-forming protein or peptide sequences also form cross-β assemblies but with distinctive ribbon-like morphologies that are characterized by a well-defined thickness (on the order of 5 nm) in one lateral dimension and a variable width (typically 10-100 nm) in the other. Here, we use a novel combination of data from solid-state nuclear magnetic resonance (ssNMR), dark-field transmission electron microscopy (TEM), atomic force microscopy (AFM), and cryogenic electron microscopy (cryoEM) to investigate the structures within amyloid ribbons formed by residues 14-23 and residues 11-25 of the Alzheimer's disease-associated amyloid-β peptide (Aβ14-23 and Aβ11-25). The ssNMR data indicate antiparallel β-sheets with specific registries of intermolecular hydrogen bonds. Mass-per-area values are derived from dark-field TEM data. The ribbon thickness is determined from AFM images. For Aβ14-23 ribbons, averaged cryoEM images show a periodic spacing of β-sheets. The combined data support structures in which the amyloid ribbon growth direction is the direction of intermolecular hydrogen bonds between β-strands, the ribbon thickness corresponds to the width of one β-sheet (i.e., approximately the length of one molecule), and the variable ribbon width is a variable multiple of the thickness of one β-sheet (i.e., a multiple of the repeat distance in a stack of β-sheets). This architecture for a cross-β assembly may generally exist within amyloid ribbons.
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Affiliation(s)
- Kent R Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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23
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Gardon L, Becker N, Gremer L, Heise H. Structural Impact of N-terminal Pyroglutamate in an Amyloid-β(3-42) Fibril Probed by Solid-State NMR Spectroscopy. Chemistry 2024; 30:e202303007. [PMID: 38100216 DOI: 10.1002/chem.202303007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Indexed: 12/31/2023]
Abstract
Extracellular amyloid-β (Aβ) plaques, primarily formed by Aβ(1-40) and Aβ(1-42) fibrils, are a hallmark of Alzheimer's disease. The Aβ peptide can undergo a high variety of different post-translational modifications including formation of a pyroglutamate (pGlu, pE) at N-terminal Glu3 or Glu11 of truncated Aβ(3-x) or Aβ(11-x), respectively. Here we studied structural similarities and differences between pEAβ(3-42) and LS-shaped Aβ(1-42) fibrils grown under identical conditions (pH 2) using solid-state NMR spectroscopy. We show that the central region of pEAβ(3-42) fibrils including the turn region around V24 is almost identical to Aβ(1-42) showing similar β-strands also at the N-terminus. The missing N-terminal residues D1-A2 along with pE3 formation in pEAβ(3-42) preclude a salt bridge between K28-D1' as in Aβ(1-42) fibrils. G37 and G38 act as highly sensitive internal sensors for the modified N-terminus, which remains rigid over ~five pH units.
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Affiliation(s)
- Luis Gardon
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf, Germany
| | - Nina Becker
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf, Germany
| | - Lothar Gremer
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf, Germany
| | - Henrike Heise
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf, Germany
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24
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Vugmeyster L, Ostrovsky D, Rodgers A, Gwin K, Smirnov SL, McKnight CJ, Fu R. Persistence of Methionine Side Chain Mobility at Low Temperatures in a Nine-Residue Low Complexity Peptide, as Probed by 2 H Solid-State NMR. Chemphyschem 2024; 25:e202300565. [PMID: 38175858 PMCID: PMC10922872 DOI: 10.1002/cphc.202300565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/01/2023] [Indexed: 01/06/2024]
Abstract
Methionine side chains are flexible entities which play important roles in defining hydrophobic interfaces. We utilize deuterium static solid-state NMR to assess rotameric inter-conversions and other dynamic modes of the methionine in the context of a nine-residue random-coil peptide (RC9) with the low-complexity sequence GGKGMGFGL. The measurements in the temperature range of 313 to 161 K demonstrate that the rotameric interconversions in the hydrated solid powder state persist to temperatures below 200 K. Removal of solvation significantly reduces the rate of the rotameric motions. We employed 2 H NMR line shape analysis, longitudinal and rotation frame relaxation, and chemical exchange saturation transfer methods and found that the combination of multiple techniques creates a significantly more refined model in comparison with a single technique. Further, we compare the most essential features of the dynamics in RC9 to two different methionine-containing systems, characterized previously. Namely, the M35 of hydrated amyloid-β1-40 in the three-fold symmetric polymorph as well as Fluorenylmethyloxycarbonyl (FMOC)-methionine amino acid with the bulky hydrophobic group. The comparison suggests that the driving force for the enhanced methionine side chain mobility in RC9 is the thermodynamic factor stemming from distributions of rotameric populations, rather than the increase in the rate constant.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver CO USA 80204
| | - Aryana Rodgers
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Kirsten Gwin
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Serge L. Smirnov
- Department of Chemistry, Western Washington University, Bellingham, WA 98225
| | - C. James McKnight
- Department of Pharmacology, Physiology and Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, 02118
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, FL USA 32310
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25
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Pfeiffer PB, Ugrina M, Schwierz N, Sigurdson CJ, Schmidt M, Fändrich M. Cryo-EM Analysis of the Effect of Seeding with Brain-derived Aβ Amyloid Fibrils. J Mol Biol 2024; 436:168422. [PMID: 38158175 DOI: 10.1016/j.jmb.2023.168422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/05/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
Aβ amyloid fibrils from Alzheimer's brain tissue are polymorphic and structurally different from typical in vitro formed Aβ fibrils. Here, we show that brain-derived (ex vivo) fibril structures can be proliferated by seeding in vitro. The proliferation reaction is only efficient for one of the three abundant ex vivo Aβ fibril morphologies, which consists of two peptide stacks, while the inefficiently proliferated fibril morphologies contain four or six peptide stacks. In addition to the seeded fibril structures, we find that de novo nucleated fibril structures can emerge in seeded samples if the seeding reaction is continued over multiple generations. These data imply a competition between de novo nucleation and seed extension and suggest further that seeding favours the outgrowth of fibril morphologies that contain fewer peptide stacks.
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Affiliation(s)
| | - Marijana Ugrina
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
| | - Nadine Schwierz
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
| | - Christina J Sigurdson
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0612, USA
| | - Matthias Schmidt
- Institute of Protein Biochemistry, Ulm University, Helmholtzstraße 8/1, 89081 Ulm, Germany
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, Helmholtzstraße 8/1, 89081 Ulm, Germany
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26
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Song Y, Wu M, Wang C, Fang H, Lei X. Zn 2+ Binding Increases Parallel Structure in the Aβ(16-22) Oligomer by Disrupting Salt Bridge in Antiparallel Structure. J Phys Chem B 2024; 128:1385-1393. [PMID: 38294417 DOI: 10.1021/acs.jpcb.3c06925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The aggregation of monomeric amyloid β protein (Aβ) into oligomers and amyloid plaque in the brain is associated with Alzheimer's disease. The hydrophobic central core Aβ16-22 has been widely studied due to its essential role in the fibrillization of full-length Aβ peptides. Compared to the homogeneous antiparallel structure of Aβ16-22 at the late stage, the early-stage prefibrillar aggregates contain varying proportions of different β structures. In this work, we studied the appearance probabilities of various self-assembly structures of Aβ16-22 and the effects of Zn2+ on these probabilities by replica exchange molecular dynamics simulations. It was found that at room temperature, Aβ16-22 can readily form assembled β-sheet structures in pure water, where a typical antiparallel arrangement dominates (24.8% of all sampled trimer structures). The addition of Zn2+ to the Aβ16-22 solution will dramatically decrease the appearance probability of antiparallel trimer structures to 12.5% by disrupting the formation of the Lys16-Glu22 salt bridge. Meanwhile, the probabilities of hybrid antiparallel/parallel structures increase. Our simulation results not only reveal the competition between antiparallel and parallel structures in the Aβ16-22 oligomers but also show that Zn2+ can affect the oligomer structures. The results also provide insights into the role of metal ions in the self-assembly of short peptides.
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Affiliation(s)
- Yongshun Song
- School of Physics, East China University of Science and Technology, Shanghai 200237, China
| | - Mengjiao Wu
- School of Physics, East China University of Science and Technology, Shanghai 200237, China
| | - Changying Wang
- School of Sciences, Changzhou Institute of Technology, Changzhou 213032, China
| | - Haiping Fang
- School of Physics, East China University of Science and Technology, Shanghai 200237, China
- Department of Physics, Zhejiang Normal University, Jinhua 321004, China
| | - Xiaoling Lei
- School of Physics, East China University of Science and Technology, Shanghai 200237, China
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27
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Sun S, Ma Q, Sheng Q, Huang S, Wu C, Liu J, Xu J. Amyloid-β Oligomer-Induced Electrophysiological Mechanisms and Electrical Impedance Changes in Neurons. Sensors (Basel) 2024; 24:1211. [PMID: 38400369 PMCID: PMC10892449 DOI: 10.3390/s24041211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/04/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024]
Abstract
Amyloid plays a critical role in the pathogenesis of Alzheimer's disease (AD) and can aggregate to form oligomers and fibrils in the brain. There is increasing evidence that highly toxic amyloid-β oligomers (AβOs) lead to tau protein aggregation, hyperphosphorylation, neuroinflammation, neuronal loss, synaptic loss, and dysfunction. Although the effects of AβOs on neurons have been investigated using conventional biochemical experiments, there are no established criteria for electrical evaluation. To this end, we explored electrophysiological changes in mouse hippocampal neurons (HT22) following exposure to AβOs and/or naringenin (Nar, a flavonoid compound) using electrical impedance spectroscopy (EIS). AβO-induced HT22 showed a decreased impedance amplitude and increased phase angle, and the addition of Nar reversed these changes. The characteristic frequency was markedly increased with AβO exposure, which was also reversed by Nar. The AβOs decreased intranuclear and cytoplasmic resistance and increased nucleus resistance and extracellular capacitance. Overall, the innovative construction of the eight-element CPE-equivalent circuit model further reflects that the pseudo-capacitance of the cell membrane and cell nucleus was increased in the AβO-induced group. This study conclusively revealed that AβOs induce cytotoxic effects by disrupting the resistance characteristics of unit membranes. The results further support that EIS is an effective technique for evaluating AβO-induced neuronal damage and microscopic electrical distinctions in the sub-microscopic structure of reactive cells.
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Affiliation(s)
- Shimeng Sun
- Department of Physiology and Pharmacology, Health Science Center, Ningbo University, Ningbo 315211, China; (S.S.); (Q.M.); (Q.S.); (S.H.); (C.W.)
| | - Qing Ma
- Department of Physiology and Pharmacology, Health Science Center, Ningbo University, Ningbo 315211, China; (S.S.); (Q.M.); (Q.S.); (S.H.); (C.W.)
| | - Qiyu Sheng
- Department of Physiology and Pharmacology, Health Science Center, Ningbo University, Ningbo 315211, China; (S.S.); (Q.M.); (Q.S.); (S.H.); (C.W.)
| | - Shangwei Huang
- Department of Physiology and Pharmacology, Health Science Center, Ningbo University, Ningbo 315211, China; (S.S.); (Q.M.); (Q.S.); (S.H.); (C.W.)
| | - Chenxia Wu
- Department of Physiology and Pharmacology, Health Science Center, Ningbo University, Ningbo 315211, China; (S.S.); (Q.M.); (Q.S.); (S.H.); (C.W.)
| | - Junsong Liu
- State Key Laboratory of Superhard Materials, College of Physics, Jilin University, Changchun 130012, China
| | - Jia Xu
- Department of Physiology and Pharmacology, Health Science Center, Ningbo University, Ningbo 315211, China; (S.S.); (Q.M.); (Q.S.); (S.H.); (C.W.)
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28
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Curk S, Krausser J, Meisl G, Frenkel D, Linse S, Michaels TCT, Knowles TPJ, Šarić A. Self-replication of A β42 aggregates occurs on small and isolated fibril sites. Proc Natl Acad Sci U S A 2024; 121:e2220075121. [PMID: 38335256 PMCID: PMC10873593 DOI: 10.1073/pnas.2220075121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 11/17/2023] [Indexed: 02/12/2024] Open
Abstract
Self-replication of amyloid fibrils via secondary nucleation is an intriguing physicochemical phenomenon in which existing fibrils catalyze the formation of their own copies. The molecular events behind this fibril surface-mediated process remain largely inaccessible to current structural and imaging techniques. Using statistical mechanics, computer modeling, and chemical kinetics, we show that the catalytic structure of the fibril surface can be inferred from the aggregation behavior in the presence and absence of a fibril-binding inhibitor. We apply our approach to the case of Alzheimer's A[Formula: see text] amyloid fibrils formed in the presence of proSP-C Brichos inhibitors. We find that self-replication of A[Formula: see text] fibrils occurs on small catalytic sites on the fibril surface, which are far apart from each other, and each of which can be covered by a single Brichos inhibitor.
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Affiliation(s)
- Samo Curk
- Institute of Science and Technology Austria, Klosterneuburg3400, Austria
- Department of Physics and Astronomy, Laboratory for Molecular Cell Biology, University College London, LondonWC1E 6BT, United Kingdom
| | - Johannes Krausser
- Department of Physics and Astronomy, Laboratory for Molecular Cell Biology, University College London, LondonWC1E 6BT, United Kingdom
| | - Georg Meisl
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Daan Frenkel
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, Lund22100, Sweden
| | - Thomas C. T. Michaels
- Department of Physics and Astronomy, Laboratory for Molecular Cell Biology, University College London, LondonWC1E 6BT, United Kingdom
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich8093, Switzerland
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Anđela Šarić
- Institute of Science and Technology Austria, Klosterneuburg3400, Austria
- Department of Physics and Astronomy, Laboratory for Molecular Cell Biology, University College London, LondonWC1E 6BT, United Kingdom
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29
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Roy M, Dey A, Dey SG. Rapid autoxidation of ferrous heme-Aβ complexes relevant to Alzheimer's disease. Chem Commun (Camb) 2024; 60:1940-1943. [PMID: 38273797 DOI: 10.1039/d3cc05025d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Heme bound Aβ peptides have been reported to reduce O2 by 2e- to H2O2 which may result in oxidative stress commonly encountered in Alzheimer's disease. In this study we report the first instance of rapid freeze quench trapping and characterizing the heme(III)-O2˙- intermediate involved in the heme-Aβ induced formation of partially reduced oxygen species (PROS) in physiologically relevant aqueous medium using absorption and resonance Raman spectroscopy. The kinetics of this process indicates a key role of the Tyr10 residue, unique to human Aβ, in the generation of H2O2 from O2.
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Affiliation(s)
- Madhuparna Roy
- Indian Association for the Cultivation of Science, School of Chemical Sciences, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India.
| | - Abhishek Dey
- Indian Association for the Cultivation of Science, School of Chemical Sciences, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India.
| | - Somdatta Ghosh Dey
- Indian Association for the Cultivation of Science, School of Chemical Sciences, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India.
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30
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Tolstova AP, Makarov AA, Adzhubei AA. Structure Comparison of Beta Amyloid Peptide Aβ 1-42 Isoforms. Molecular Dynamics Modeling. J Chem Inf Model 2024; 64:918-932. [PMID: 38241093 DOI: 10.1021/acs.jcim.3c01624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
Beta amyloid peptide Aβ 1-42 (Aβ42) has a unique dual role in the human organism, as both the peptide with an important physiological function and one of the most toxic biological compounds provoking Alzheimer's disease (AD). There are several known Aβ42 isoforms that we discuss here that are highly neurotoxic and lead to the early onset of AD. Aβ42 is an intrinsically disordered protein with no experimentally solved structure under physiological conditions. The objective of this research was to establish the appropriate molecular dynamics (MD) methodology and model a uniform set of structures for the Aβ42 isoforms that form the core of this study. For that purpose, force field selection and verification including convergence testing for MD simulations was made. Replica exchange MD and conventional MD modeling of several Aβ42 and Aβ16 isoforms that have neurotoxic and amyloidogenic effects impacting the severity of Alzheimer's disease were carried out with the optimal force field and solvent parameters. A standardized ensemble of structures for the Aβ42 and Aβ16 isoforms covering 30-50% of the conformational ensembles extracted from the free energy minima was calculated from MD trajectories. The resulting data set of modeled structures includes Aβ42 wild type, isoD7, pS8, D7H, and H6R-Aβ42 and Aβ16 wild type, isoD7, pS8, D7H, and H6R-Aβ16. The representative structures are given in the Supporting Information; they are open for public access. In the study, we also evaluated the differences between the structures of Aβ42 isoforms and speculate on their possible relevance to the known functions. Utilizing several representative structures for a single disordered protein for docking, with their subsequent averaging by conformations, would markedly increase the reliability of docking results.
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Affiliation(s)
- Anna P Tolstova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexei A Adzhubei
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Washington University School of Medicine and Health Sciences, Washington 20052, D.C., United States
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31
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Dinda S, Ghosh D, Govindaraju T. Cooperative dissolution of peptidomimetic vesicles and amyloid β fibrils. Nanoscale 2024; 16:2993-3005. [PMID: 38259156 DOI: 10.1039/d3nr04847k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The aggregation of amyloid proteins in the brain is a significant neurotoxic event that contributes to neurodegenerative disorders. The aggregation of amyloid beta (Aβ), particularly Aβ42 monomers, into various forms such as oligomers, protofibrils, fibrils, and amyloid plaques is a key pathological feature in Alzheimer's disease. As a result, Aβ42 is a primary target and the development of molecular strategies for the dissolution of Aβ42 aggregates is considered a promising approach to mitigating Alzheimer's disease pathology. A set of pyrene-conjugated peptidomimetics derived from Aβ14-23 (AkdcPy, AkdmPy, and AkdnPy) by incorporating an unnatural amino acid [kd: cyclo(Lys-Asp)] were studied for their ability to modulate Aβ42 aggregation. AkdcPy and AkdmPy formed vesicular structures in aqueous media. The vesicles of AkdmPy loaded with the neuroprotective compound berberine (Ber), dissipated mutually in the presence of preformed Aβ42 fibrils. During this process, the active drug Ber was released. This work is expected to inspire the development of drug-loaded peptidomimetic-based therapeutic formulations to modulate disorders associated with amyloid toxicity.
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Affiliation(s)
- Soumik Dinda
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur P.O., Bengaluru 560064, Karnataka, India.
| | - Debasis Ghosh
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur P.O., Bengaluru 560064, Karnataka, India.
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur P.O., Bengaluru 560064, Karnataka, India.
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32
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Jain M, Sahoo A, Matysiak S. Modulation of Aβ 16-22 aggregation by glucose. Phys Chem Chem Phys 2024; 26:5038-5044. [PMID: 38258497 DOI: 10.1039/d3cp04494g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The self-assembly of amyloid-beta (Aβ) peptides into fibrillar structures in the brain is a signature of Alzheimer's disease. Recent studies have reported correlations between Alzheimer's disease and type-2 diabetes. Structurally, hyperglycemia induces covalent protein crosslinkings by advanced glycation end products (AGE), which can affect the stability of Aβ oligomers. In this work, we leverage physics-based coarse-grained molecular simulations to probe alternate thermodynamic pathways that affect peptide aggregation propensities at varying concentrations of glucose molecules. Similar to previous experimental reports, our simulations show a glucose concentration-dependent increase in Aβ aggregation rates, without changes in the overall secondary structure content. We discovered that glucose molecules prefer partitioning onto the aggregate-water interface at a specific orientation, resulting in a loss of molecular rotational entropy. This effectively hastens the aggregation rates, as peptide self-assembly can reduce the available surface area for peptide-glucose interactions. This work introduces a new thermodynamic-driven pathway, beyond chemical cross-linking, that can modulate Aβ aggregation.
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Affiliation(s)
- Meenal Jain
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Abhilash Sahoo
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
- Center for Computational Mathematics, Flatiron Institute, New York, NY, USA
| | - Silvina Matysiak
- Biophysics Program, Institute of Physical Science and Technology, University of Maryland, College Park, MD, USA.
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
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Wang K, Cai W. Aggregation, structure and water permeability of membrane-embedded helical Aβ oligomers. Phys Chem Chem Phys 2024; 26:5128-5140. [PMID: 38259193 DOI: 10.1039/d3cp05317b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
It is widely recognized that membranes can facilitate the aggregation of amyloid-β (Aβ) peptides, while Aβ can in turn cause membrane damage. Many studies focus on the peptide-membrane interactions of Aβ oligomers with β-rich structures. However, the exact aggregation and toxicity mechanism of the membrane-embedded helical Aβ oligomers remain ambiguous. Herein, the molecular dynamics simulations were performed on membrane-embedded helical Aβ42 peptides. Initiated by eight Aβ42 monomers embedded in a lipid bilayer, the monomers aggregate into oligomers with stable transmembrane helix structures. With the aggregation of peptides, the membrane perturbations caused by Aβ aggregates decrease. The molecular architectures of oligomers were characterized and a helix-rich octamer stabilized by an annular network of hydrogen bonds was observed. The oligomers demonstrate the capability to assist transmembrane water transport. Our study may provide new insights for the investigation of transmembrane Aβ oligomers.
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Affiliation(s)
- Ke Wang
- Research Center for Analytical Sciences, College of Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, China.
| | - Wensheng Cai
- Research Center for Analytical Sciences, College of Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, China.
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Vugmeyster L, Au DF, Frazier B, Qiang W, Ostrovsky D. Rigidifying of the internal dynamics of amyloid-beta fibrils generated in the presence of synaptic plasma vesicles. Phys Chem Chem Phys 2024; 26:5466-5478. [PMID: 38277177 PMCID: PMC10956644 DOI: 10.1039/d3cp04824a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
We investigated the changes in internal flexibility of amyloid-β1-40 (Aβ) fibrils grown in the presence of rat synaptic plasma vesicles. The fibrils are produced using a modified seeded growth protocol, in which the Aβ concentration is progressively increased at the expense of the decreased lipid to protein ratio. The morphologies of each generation are carefully assessed at several fibrils' growth time points using transmission electron microscopy. The side-chain dynamics in the fibrils is investigated using deuterium solid-state NMR measurements, with techniques spanning line shapes analysis and several NMR relaxation rates measurements. The dynamics is probed in the site-specific fashion in the hydrophobic C-terminal domain and the disordered N-terminal domain. An overall strong rigidifying effect is observed in comparison with the wild-type fibrils generated in the absence of the membranes. In particular, the overall large-scale fluctuations of the N-terminal domain are significantly reduced, and the activation energies of rotameric inter-conversion in methyl-bearing side-chains of the core (L17, L34, M35, V36), as well as the ring-flipping motions of F19 are increased, indicating a restricted core environment. Membrane-induced flexibility changes in Aβ aggregates can be important for the re-alignment of protein aggregates within the membrane, which in turn would act as a disruption pathway of the bilayers' integrity.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver, CO, USA, 80204.
| | - Dan Fai Au
- Department of Chemistry, University of Colorado Denver, Denver, CO, USA, 80204.
| | - Bailey Frazier
- Department of Chemistry, University of Colorado Denver, Denver, CO, USA, 80204.
| | - Wei Qiang
- Department of Chemistry, Binghamton University, Binghamton, New York, USA, 13902
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver, CO, USA, 80204
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Manzoor S, Gabr MT, Nafie MS, Raza MK, Khan A, Nayeem SM, Arafa RK, Hoda N. Discovery of Quinolinone Hybrids as Dual Inhibitors of Acetylcholinesterase and Aβ Aggregation for Alzheimer's Disease Therapy. ACS Chem Neurosci 2024; 15:539-559. [PMID: 38149821 DOI: 10.1021/acschemneuro.3c00588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023] Open
Abstract
The development of multitargeted therapeutics has evolved as a promising strategy to identify efficient therapeutics for neurological disorders. We report herein new quinolinone hybrids as dual inhibitors of acetylcholinesterase (AChE) and Aβ aggregation that function as multitargeted ligands for Alzheimer's disease. The quinoline hybrids (AM1-AM16) were screened for their ability to inhibit AChE, BACE1, amyloid fibrillation, α-syn aggregation, and tau aggregation. Among the tested compounds, AM5 and AM10 inhibited AChE activity by more than 80% at single-dose screening and possessed a remarkable ability to inhibit the fibrillation of Aβ42 oligomers at 10 μM. In addition, dose-dependent screening of AM5 and AM10 was performed, giving half-maximal AChE inhibitory concentration (IC50) values of 1.29 ± 0.13 and 1.72 ± 0.18 μM, respectively. In addition, AM5 and AM10 demonstrated concentration-dependent inhibitory profiles for the aggregation of Aβ42 oligomers with estimated IC50 values of 4.93 ± 0.8 and 1.42 ± 0.3 μM, respectively. Moreover, the neuroprotective properties of the lead compounds AM5 and AM10 were determined in SH-SY5Y cells incubated with Aβ oligomers. This work would enable future research efforts aiming at the structural optimization of AM5 and AM10 to develop potent dual inhibitors of AChE and amyloid aggregation. Furthermore, the in vivo assay confirmed the antioxidant activity of compounds AM5 and AM10 through increasing GSH, CAT, and SOD activities that are responsible for scavenging the ROS and restoring its normal level. Blood investigation illustrated the protective activity of the two compounds against lead-induced neurotoxicity through retaining hematological and liver enzymes near normal levels. Finally, immunohistochemistry investigation revealed the inhibitory activity of β-amyloid (Aβ) aggregation.
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Affiliation(s)
- Shoaib Manzoor
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi 110025, India
- Department of Pharmacy and Pharmacology, University of Bath, Bath BA2 7AY, U.K
| | - Moustafa T Gabr
- Molecular Imaging Innovations Institute, Department of Radiology, Weill Cornell Medicine, New York, New York10021, United States
| | - Mohamed S Nafie
- Department of Chemistry, College of Sciences, University of Sharjah, Sharjah (P.O. Box 27272), United Arab Emirates
- Chemistry Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
| | - Md Kausar Raza
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Ashma Khan
- Department of Chemistry, Aligarh Muslim University, Aligarh, UP 202002, India
| | - Shahid M Nayeem
- Department of Chemistry, Aligarh Muslim University, Aligarh, UP 202002, India
| | - Reem K Arafa
- Drug Design and Discovery Lab, Helmy Institute for Medical Sciences, Zewail City of Science, Technology and Innovation, Giza 12578, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science, Technology and Innovation, Giza12578,Egypt
| | - Nasimul Hoda
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi 110025, India
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Rulmont C, Stigliani JL, Hureau C, Esmieu C. Rationally Designed Cu(I) Ligand to Prevent CuAβ-Generated ROS Production in the Alzheimer's Disease Context. Inorg Chem 2024; 63:2340-2351. [PMID: 38243896 DOI: 10.1021/acs.inorgchem.3c02693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2024]
Abstract
In the context of Alzheimer's disease, copper (Cu) can be loosely bound to the amyloid-β (Aβ) peptide, leading to the formation of CuAβ, which can catalytically generate reactive oxygen species that contribute to oxidative stress. To fight against this phenomenon, the chelation therapy approach has been developed and consists of using a ligand able to remove Cu from Aβ and to redox-silence it, thus stopping the reactive oxygen species (ROS) production. A large number of Cu(II) chelators has been studied, allowing us to define and refine the properties required to design a "good" ligand, but without strong therapeutic outcomes to date. Those chelators targeted the Cu(II) redox state. Herein, we explore a parallel and relevant alternative pathway by designing a chelator able to target the Cu(I) redox state. To that end, we designed LH2 ([1N3S] binding set) and demonstrated that (i) it is perfectly able to extract Cu(I) from Cu(I)Aβ even in the presence of an excess of Zn(II) and (ii) it redox-silences the Cu, preventing the formation of ROS. We showed that LH2 that is sensitive to oxidation can efficiently replace the [Zn(II)L] complex without losing its excellent ability to stop the ROS production while increasing its resistance to oxidation.
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Affiliation(s)
- Clément Rulmont
- LCC-CNRS, Université de Toulouse, CNRS, Toulouse 31077, France
| | | | | | - Charlène Esmieu
- LCC-CNRS, Université de Toulouse, CNRS, Toulouse 31077, France
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Grcic L, Leech G, Kwan K, Storr T. Targeting misfolding and aggregation of the amyloid-β peptide and mutant p53 protein using multifunctional molecules. Chem Commun (Camb) 2024; 60:1372-1388. [PMID: 38204416 DOI: 10.1039/d3cc05834d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Biomolecule misfolding and aggregation play a major role in human disease, spanning from neurodegeneration to cancer. Inhibition of these processes is of considerable interest, and due to the multifactorial nature of these diseases, the development of drugs that act on multiple pathways simultaneously is a promising approach. This Feature Article focuses on the development of multifunctional molecules designed to inhibit the misfolding and aggregation of the amyloid-β (Aβ) peptide in Alzheimer's disease (AD), and the mutant p53 protein in cancer. While for the former, the goal is to accelerate the removal of the Aβ peptide and associated aggregates, for the latter, the goal is reactivation via stabilization of the active folded form of mutant p53 protein and/or aggregation inhibition. Due to the similar aggregation pathway of the Aβ peptide and mutant p53 protein, a common therapeutic approach may be applicable.
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Affiliation(s)
- Lauryn Grcic
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
| | - Grace Leech
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
| | - Kalvin Kwan
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
| | - Tim Storr
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
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Ragonis-Bachar P, Axel G, Blau S, Ben-Tal N, Kolodny R, Landau M. What can AlphaFold do for antimicrobial amyloids? Proteins 2024; 92:265-281. [PMID: 37855235 DOI: 10.1002/prot.26618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/05/2023] [Accepted: 10/05/2023] [Indexed: 10/20/2023]
Abstract
Amyloids, protein, and peptide assemblies in various organisms are crucial in physiological and pathological processes. Their intricate structures, however, present significant challenges, limiting our understanding of their functions, regulatory mechanisms, and potential applications in biomedicine and technology. This study evaluated the AlphaFold2 ColabFold method's structure predictions for antimicrobial amyloids, using eight antimicrobial peptides (AMPs), including those with experimentally determined structures and AMPs known for their distinct amyloidogenic morphological features. Additionally, two well-known human amyloids, amyloid-β and islet amyloid polypeptide, were included in the analysis due to their disease relevance, short sequences, and antimicrobial properties. Amyloids typically exhibit tightly mated β-strand sheets forming a cross-β configuration. However, certain amphipathic α-helical subunits can also form amyloid fibrils adopting a cross-α structure. Some AMPs in the study exhibited a combination of cross-α and cross-β amyloid fibrils, adding complexity to structure prediction. The results showed that the AlphaFold2 ColabFold models favored α-helical structures in the tested amyloids, successfully predicting the presence of α-helical mated sheets and a hydrophobic core resembling the cross-α configuration. This implies that the AI-based algorithms prefer assemblies of the monomeric state, which was frequently predicted as helical, or capture an α-helical membrane-active form of toxic peptides, which is triggered upon interaction with lipid membranes.
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Affiliation(s)
| | - Gabriel Axel
- George S. Wise Faculty of Life Sciences, Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel
| | - Shahar Blau
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Nir Ben-Tal
- George S. Wise Faculty of Life Sciences, Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel
| | - Rachel Kolodny
- Department of Computer Science, University of Haifa, Haifa, Israel
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- The Center for Experimental Medicine, Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany
- European Molecular Biology Laboratory (EMBL), Hamburg, Germany
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Malhis M, Funke SA. Mirror-Image Phage Display for the Selection of D-Amino Acid Peptide Ligands as Potential Therapeutics. Curr Protoc 2024; 4:e957. [PMID: 38372457 DOI: 10.1002/cpz1.957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
In neurodegenerative diseases like Alzheimer's disease (AD), endogenous proteins or peptides aggregate with themselves. These proteins may lose their function or aggregates and/or oligomers can obtain toxicity, causing injury or death to cells. Aggregation of two major proteins characterizes AD. Amyloid-β peptide (Aβ) is deposited in amyloid plaques within the extracellular space of the brain and Tau in so-called neurofibrillary tangles in neurons. Finding peptide ligands to halt protein aggregation is a promising therapeutical approach. Using mirror-image phage display with a commercially available, randomized 12-mer peptide library, we have selected D-amino acid peptides, which bind to the Tau protein and modulate its aggregation in vitro. Peptides can bind specifically and selectively to a target molecule, but natural L-amino acid peptides may have crucial disadvantages for in vivo applications, as they are sensitive to protease degradation and may elicit immune responses. One strategy to circumvent these disadvantages is the use of non-naturally occurring D-amino acid peptides as they exhibit increased protease resistance and generally do not activate the immune system. To perform mirror-image phage display, the target protein needs to be synthesized as D-amino acid version. If the target protein sequence is too long to be synthesized properly, smaller peptides derived from the full length protein can be used for the selection process. This also offers the possibility to influence the binding region of the selected D-peptides in the full-length target protein. Here we provide the protocols for mirror-image phage display selection on the PHF6* peptide of Tau, based on the commercially available Ph.D.™-12 Phage Display Peptide Library Kit, leading to D-peptides that also bind the full length Tau protein (Tau441), next to PHF6*. In addition, we provide protocols and data for the first characterization of those D-peptides that inhibit Tau aggregation in vitro. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Mirror image phage display selection against D-PHF6* fibrils Support Protocol 1: Single phage ELISA Basic Protocol 2: Sequencing and D-peptide generation Basic Protocol 3: Thioflavin-T (ThT) test to control inhibition of Tau aggregation Support Protocol 2: Purification of full-length Tau protein Basic Protocol 4: ELISA to demonstrate the binding of the generated D-peptides to PHF6* and full-length Tau fibrils.
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Affiliation(s)
- Marwa Malhis
- Institut für Bioanalytik, Hochschule für Angewandte Wissenschaften, Coburg, Germany
| | - Susanne Aileen Funke
- Institut für Bioanalytik, Hochschule für Angewandte Wissenschaften, Coburg, Germany
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40
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Ullah A, Lee GJ, Kwon HT, Lim SI. Covalent immobilization of human serum albumin on cellulose acetate membrane for scavenging amyloid beta - A stepping extracorporeal strategy for ameliorating Alzheimer's disease. Colloids Surf B Biointerfaces 2024; 234:113753. [PMID: 38241888 DOI: 10.1016/j.colsurfb.2024.113753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/21/2024]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by interrupted neurocognitive functions and impaired mental development presumably caused by the accumulation of amyloid beta (Aβ) in the form of plaques. Targeting Aβ has been considered a promising approach for treating AD. In the current study, human serum albumin (HSA), a natural Aβ binder, is covalently immobilized onto the surface of a cellulose acetate (CA) membrane to devise an extracorporeal Aβ sequester. The immobilization of HSA at 3.06 ± 0.22 μg/mm2 of the CA membrane was found to be active functionally, as evidenced by the esterase-like activity converting p-nitrophenyl acetate into p-nitrophenol. The green fluorescent protein-Aβ (GFP-Aβ) fusion protein, recombinantly produced as a model ligand, exhibited characteristics of native Aβ. These features include the propensity to form aggregates or fibrils and an affinity for HSA with a dissociation constant (KD) of 0.91 μM. The HSA on the CA membrane showed concentration-dependent sequestration of GFP-Aβ in the 1-10-μM range. Moreover, it had a greater binding capacity than HSA immobilized on a commercial amine-binding plate. Results suggest that the covalent immobilization of HSA on the CA surface can be used as a potential platform for sequestering Aβ to alleviate AD.
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Affiliation(s)
- Aziz Ullah
- Department of Chemical Engineering, Pukyong National University, Busan 48513, Republic of Korea; Gomal Centre of Pharmaceutical Sciences, Faculty of Pharmacy, Gomal University, Dera Ismail Khan 29050, Khyber Pakhtunkhwa, Pakistan
| | - Gyu-Jin Lee
- Department of Chemical Engineering, Pukyong National University, Busan 48513, Republic of Korea
| | - Hyuk Taek Kwon
- Department of Chemical Engineering, Pukyong National University, Busan 48513, Republic of Korea.
| | - Sung In Lim
- Department of Chemical Engineering, Pukyong National University, Busan 48513, Republic of Korea.
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Cournut A, Moustiez P, Coffinier Y, Enjalbal C, Bich C. Innovative SALDI mass spectrometry analysis for Alzheimer's disease synthetic peptides detection. Talanta 2024; 268:125357. [PMID: 37951181 DOI: 10.1016/j.talanta.2023.125357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/12/2023] [Accepted: 10/26/2023] [Indexed: 11/13/2023]
Abstract
Alzheimer's disease (AD) is nowadays the prominent cause of senile dementia. This pathology is characterized by aggregation of neurofibrillary tangles in cells and by the accumulation of amyloid plaques in the brain. Noteworthy, a phosphorylated protein (tau protein) and a peptide presenting two overlapping sequences of 40 or 42 residues named β-amyloid peptides 1-40 (Aβ 1-40) and 1-42 (Aβ 1-42), respectively, were related to such deleterious phenomena. Singularly, the neurotoxicity was primarily attributed to the amyloid peptide Aβ 1-42 form due to its capacity to fold into beta-sheets rendering it insoluble thus causing subsequent aggregation and accumulation in vivo. Regarding AD diagnosis relying on mass spectrometry, Aβ 1-42 and/or Aβ 1-40 were considered as relevant biomarkers being measured in cerebrospinal fluids (CSF), blood and urine. Under that context, we aimed at implementing an innovative method to evidence the depletion of circulating Aβ 1-42 amyloid peptide compared to the shorter Aβ 1-40 form indicating a pathologic state. We investigated Surface-Assisted Laser Desorption/Ionization Mass Spectrometry (SALDI-MS) in order to monitor the Aβ 1-42/Aβ 1-40 ratio without any prior sample treatment or enrichment. Taking into account that β-amyloid peptide and 1-42 can aggregate into beta-sheets depending on the experimental conditions, specific attention was devoted to sample integrity monitoring performed by circular dichroism experiments during SALDI-MS method development.
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Affiliation(s)
- Aline Cournut
- Univ Montpellier, IBMM, CNRS, ENSCM, Montpellier, France
| | - Paul Moustiez
- Univ Lille, IEMN, UMR CNRS 8520, Villeneuve d'Ascq, France
| | | | | | - Claudia Bich
- Univ Montpellier, IBMM, CNRS, ENSCM, Montpellier, France.
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He YJ, Liu JS, Zhang L, Yan JW. A quinolinium-based dual-functional NIR fluorescent probe for the imaging of Aβ aggregation and mitochondrial pH. Talanta 2024; 268:125362. [PMID: 37918242 DOI: 10.1016/j.talanta.2023.125362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 10/18/2023] [Accepted: 10/26/2023] [Indexed: 11/04/2023]
Abstract
Mitochondria are the most important energy supply centers in the cell, the changes in function and structure are implicated in many diseases. Among them, Aβ peptide, one of the targets of Alzheimer's disease, is closely related to mitochondrial autophagy, during the process of mitochondrial autophagy, the mitochondrial matrix will undergo acidification and the pH will be obviously reduced. Herein, a quinolinium-based NIR fluorescent probe QM12 was rationally designed and synthesized for the simultaneous imaging of Aβ aggregates and mitochondrial pH with different emission readout. The probe QM12 exhibited excellent selective toward Aβ aggregates, and can also trace the real-time changes of mitochondrial pH, which could serve as a promising tool for the pathological study of Alzheimer's disease, especially the cross talk between different biomarkers of Alzheimer's disease.
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Affiliation(s)
- Yi-Jiao He
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, PR China
| | - Jin-Sheng Liu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, PR China
| | - Lei Zhang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, PR China.
| | - Jin-Wu Yan
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, PR China.
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Kuhn AJ, Chan K, Sajimon M, Yoo S, Balasco Serrão VH, Lee J, Abrams B, Nowick JS, Uversky VN, Wheeler C, Raskatov JA. Amyloid-α Peptide Formed through Alternative Processing of the Amyloid Precursor Protein Attenuates Alzheimer's Amyloid-β Toxicity via Cross-Chaperoning. J Am Chem Soc 2024; 146:2634-2645. [PMID: 38236059 DOI: 10.1021/jacs.3c11511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Amyloid aggregation is a key feature of Alzheimer's disease (AD) and a primary target for past and present therapeutic efforts. Recent research is making it increasingly clear that the heterogeneity of amyloid deposits, extending past the commonly targeted amyloid-β (Aβ), must be considered for successful therapy. We recently demonstrated that amyloid-α (Aα or p3), a C-terminal peptidic fragment of Aβ, aggregates rapidly to form amyloids and can expedite the aggregation of Aβ through seeding. Here, we advance the understanding of Aα biophysics and biology in several important ways. We report the first cryogenic electron microscopy (cryo-EM) structure of an Aα amyloid fibril, proving unambiguously that the peptide is fibrillogenic. We demonstrate that Aα induces Aβ to form amyloid aggregates that are less toxic than pure Aβ aggregates and use nuclear magnetic resonance spectroscopy (NMR) to provide insights into specific interactions between Aα and Aβ in solution. This is the first evidence that Aα can coassemble with Aβ and alter its biological effects at relatively low concentrations. Based on the above, we urge researchers in the field to re-examine the significance of Aα in AD.
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Affiliation(s)
- Ariel J Kuhn
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064, United States
| | - Ka Chan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064, United States
| | - Maria Sajimon
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064, United States
| | - Stan Yoo
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Vitor Hugo Balasco Serrão
- Biomolecular Cryoelectron Microscopy Facility, University of California, Santa Cruz, Santa Cruz, California 95064, United States
| | - Jack Lee
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064, United States
| | - Benjamin Abrams
- Department of Biomolecular Engineering, Life Sciences Microscopy Center, University of California, Santa Cruz, Santa Cruz, California 95064, United States
| | - James S Nowick
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, MDC07, Tampa, Florida 33612, United States
| | - Christopher Wheeler
- World Brain Mapping Foundation, Society for Brain Mapping & Therapeutics, 860 Via De La Paz, Suite E-1, Pacific Palisades, California 90272-3668, United States
- StemVax Therapeutics (Subsidiary of NovAccess Global), 8584 E. Washington Street #127, Chagrin Falls, Ohio 44023, United States
- StemVax Therapeutics (Subsidiary of NovAccess Global), 2265 E. Foothill Boulevard, Pasadena, California 91107, United States
- T-Neuro Pharma, 1451 Innovation Parkway SE, Suite 600, Albuquerque, New Mexico 87123, United States
- T-Neuro Pharma, P.O. Box 781, Aptos, California 95003, United States
| | - Jevgenij A Raskatov
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064, United States
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Zhang Y, Borch LA, Fischer NH, Meldal M. Hydrodynamic Control of Alzheimer Aβ Fibrillation with Glucosaminic Acid Containing Click-Cyclized β-Bodies. J Am Chem Soc 2024; 146:2654-2662. [PMID: 38126710 DOI: 10.1021/jacs.3c12118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
It is well established that the dynamic hydration shell plays a vital role in macromolecular functions such as protein-ligand, protein-protein, protein-DNA, and protein-lipid interactions. Here we investigate how the water modality affects conformational changes, solubility, and motion of fibrillar proteins. The hypothesis is that the introduction of a poly hydroxyl amino acid would increase solvation of the fibril forming peptides, preventing their misfolding and aggregation. For the amyloid β (Aβ) peptide, which is considered to be connected with nervous system diseases, including dementia and cognitive decline in Alzheimer's disease, the formation of β-sheet fibrils always occurs with a conformational change and a decrease in the dynamic hydration shell around Aβ(1-42). We present novel cyclic d-amino acid peptides that effectively inhibit fibrillation through affecting the dynamic hydration shell of Aβ(1-42) in vitro. Using de novo design within the software Molecular Operating Environment (MOE), five different peptides that recognize Alzheimer's fibrils were designed and synthesized. Three of them were cyclic all-d-amino acid peptides incorporating the same polyhydroxy building block derived from d-glucosaminic acid (GA). One peptide was the parent cyclic all d-amino acid inhibitor with no GA incorporated, and another was an all l-amino acid linear fibrillation inhibitor. The GA-containing peptides were found to show significantly improved inhibition of Aβ(1-42) aggregation. The inhibition was dramatically improved by the synergistic application of two GA peptides targeting each end of the growing fibril. The present study may facilitate future developments of intervention strategies for Alzheimer's disease and similar neurodegenerative diseases.
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Affiliation(s)
- Yuan Zhang
- Center for Evolutionary Chemical Biology, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Line A Borch
- Center for Evolutionary Chemical Biology, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Niklas H Fischer
- Center for Evolutionary Chemical Biology, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Morten Meldal
- Center for Evolutionary Chemical Biology, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
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45
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Nandi S, Sarkar N. Interactions between Lipid Vesicle Membranes and Single Amino Acid Fibrils: Probable Origin of Specific Neurological Disorders. Langmuir 2024; 40:1971-1987. [PMID: 38240221 DOI: 10.1021/acs.langmuir.3c02429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Amyloid fibrils are known to be responsible for several neurological disorders, like Alzheimer's disease (AD), Parkinson's disease (PD), etc. For decades, mostly proteins and peptide-based amyloid fibrils have been focused on, and the topic has acknowledged the rise, development, understanding of, and controversy, as well. However, the single amino acid based amyloid fibrils, responsible for several disorders, such as phenylketonuria, tyrosenimia type II, hypermethioninemia, etc., have gotten scientific attention lately. To understand the molecular level pathogenesis of such disorders originated due to the accumulation of single amino acid-based amyloid fibrils, interaction of these fibrils with phospholipid vesicle membranes is found to be an excellent cell-free in vitro setup. Based on such an in vitro setup, these fibrils show a generic mechanism of membrane insertion driven by electrostatic and hydrophobic effects inside the membrane that reduces the integral rigidity of the membrane. Alteration of such fundamental properties of the membrane, therefore, might be referred to as one of the prime pathological factors for the development of these neurological disorders. Hence, such interactions must be investigated in cellular and intracellular compartments to design suitable therapeutic modulators against fibrils.
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Affiliation(s)
- Sourav Nandi
- Yale School of Medicine, Yale University, New Haven, Connecticut 06510, United States
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology, Kharagpur, 721302, West Bengal, India
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46
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Wu R, Svingou D, Metternich JB, Benzenberg LR, Zenobi R. Transition Metal Ion FRET-Based Probe to Study Cu(II)-Mediated Amyloid- β Ligand Binding. J Am Chem Soc 2024; 146:2102-2112. [PMID: 38225538 DOI: 10.1021/jacs.3c11533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Recent therapeutic strategies suggest that small peptides can act as aggregation inhibitors of monomeric amyloid-β (Αβ) by inducing structural rearrangements upon complexation. However, characterizing the binding events in such dynamic and transient noncovalent complexes, especially in the presence of natively occurring metal ions, remains a challenge. Here, we deploy a combined transition metal ion Förster resonance energy transfer (tmFRET) and native ion mobility-mass spectrometry (IM-MS) approach to characterize the structure of mass- and charge-selected Aβ complexes with Cu(II) ions (a quencher) and a potential aggregation inhibitor, a small neuropeptide named leucine enkephalin (LE). We show conformational changes of monomeric Αβ species upon Cu(II)-binding, indicating an uncoiled N-terminus and a close interaction between the C-terminus and the central hydrophobic region. Furthermore, we introduce LE labeled at the N-terminus with a metal-chelating agent, nitrilotriacetic acid (NTA). This allows us to employ tmFRET to probe the binding even in low-abundance and transient Aβ-inhibitor-metal ion complexes. Complementary intramolecular distance and global shape information from tmFRET and native IM-MS, respectively, confirmed Cu(II) displacement toward the N-terminus of Αβ, which discloses the binding region and the inhibitor's orientation.
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Affiliation(s)
- Ri Wu
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Despoina Svingou
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Jonas B Metternich
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Lukas R Benzenberg
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Renato Zenobi
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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47
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Yokoyama K, Barbour E, Hirschkind R, Martinez Hernandez B, Hausrath K, Lam T. Protein Corona Formation and Aggregation of Amyloid β 1-40-Coated Gold Nanocolloids. Langmuir 2024; 40:1728-1746. [PMID: 38194428 DOI: 10.1021/acs.langmuir.3c02923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Amyloid fibrillogenesis is a pathogenic protein aggregation process that occurs through a highly ordered process of protein-protein interactions. To better understand the protein-protein interactions involved in amyloid fibril formation, we formed nanogold colloid aggregates by stepwise additions of ∼2 nmol of amyloid β 1-40 peptide (Aβ1-40) at pH ∼3.7 and ∼25 °C. The processes of protein corona formation and building of gold colloid [diameters (d) of 20 and 80 nm] aggregates were confirmed by a red-shift of the surface plasmon resonance (SPR) band, λpeak, as the number of Aβ1-40 peptides [N(Aβ1-40)] increased. The normalized red-shift of λpeak, Δλ, was correlated with the degree of protein aggregation, and this process was approximated as the adsorption isotherm explained by the Langmuir-Freundlich model. As the coverage fraction (θ) was analyzed as a function of ϕ, which is the N(Aβ1-40) per total surface area of nanogold colloids available for adsorption, the parameters for explaining the Langmuir-Freundlich model were in good agreement for both 20 and 80 nm gold, indicating that ϕ could define the stage of the aggregation process. Surface-enhanced Raman scattering (SERS) imaging was conducted at designated values of ϕ and suggested that a protein-gold surface interaction during the initial adsorption stage may be dependent on the nanosize. The 20 nm gold case seems to prefer a relatively smaller contacting section, such as a -C-N or C═C bond, but a plane of the benzene ring may play a significant role for 80 nm gold. Regardless of the size of the particles, the β-sheet and random coil conformations were considered to be used to form gold colloid aggregates. The methodology developed in this study allows for new insights into protein-protein interactions at distinct stages of aggregation.
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Affiliation(s)
- Kazushige Yokoyama
- Department of Chemistry, The State University of New York Geneseo College, 1 College Circle, Geneseo, New York 14454, United States
| | - Eli Barbour
- Department of Chemistry, The State University of New York Geneseo College, 1 College Circle, Geneseo, New York 14454, United States
| | - Rachel Hirschkind
- Department of Chemistry, The State University of New York Geneseo College, 1 College Circle, Geneseo, New York 14454, United States
| | - Bryan Martinez Hernandez
- Department of Chemistry, The State University of New York Geneseo College, 1 College Circle, Geneseo, New York 14454, United States
| | - Kaylee Hausrath
- Department of Chemistry, The State University of New York Geneseo College, 1 College Circle, Geneseo, New York 14454, United States
| | - Theresa Lam
- Department of Chemistry, The State University of New York Geneseo College, 1 College Circle, Geneseo, New York 14454, United States
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48
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Huang F, Fan X, Wang Y, Zou Y, Lian J, Wang C, Ding F, Sun Y. Computational insights into the cross-talk between medin and Aβ: implications for age-related vascular risk factors in Alzheimer's disease. Brief Bioinform 2024; 25:bbad526. [PMID: 38271485 PMCID: PMC10810335 DOI: 10.1093/bib/bbad526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/07/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
The aggregation of medin forming aortic medial amyloid is linked to arterial wall degeneration and cerebrovascular dysfunction. Elevated levels of arteriolar medin are correlated with an increased presence of vascular amyloid-β (Aβ) aggregates, a hallmark of Alzheimer's disease (AD) and vascular dementia. The cross-interaction between medin and Aβ results in the formation of heterologous fibrils through co-aggregation and cross-seeding processes both in vitro and in vivo. However, a comprehensive molecular understanding of the cross-interaction between medin and Aβ-two intrinsically disordered proteins-is critically lacking. Here, we employed atomistic discrete molecular dynamics simulations to systematically investigate the self-association, co-aggregation and also the phenomenon of cross-seeding between these two proteins. Our results demonstrated that both Aβ and medin were aggregation prone and their mixture tended to form β-sheet-rich hetero-aggregates. The formation of Aβ-medin hetero-aggregates did not hinder Aβ and medin from recruiting additional Aβ and medin peptides to grow into larger β-sheet-rich aggregates. The β-barrel oligomer intermediates observed in the self-aggregations of Aβ and medin were also present during their co-aggregation. In cross-seeding simulations, preformed Aβ fibrils could recruit isolated medin monomers to form elongated β-sheets. Overall, our comprehensive simulations suggested that the cross-interaction between Aβ and medin may contribute to their pathological aggregation, given the inherent amyloidogenic tendencies of both medin and Aβ. Targeting medin, therefore, could offer a novel therapeutic approach to preserving brain function during aging and AD by improving vascular health.
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Affiliation(s)
- Fengjuan Huang
- Ningbo Institute of Innovation for Combined Medicine and Engineering, Lihuili Hospital Affiliated to Ningbo University, Ningbo University, Ningbo 315211, China
| | - Xinjie Fan
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Ying Wang
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Yu Zou
- Department of Sport and Exercise Science, Zhejiang University, Hangzhou 310058, China
| | - Jiangfang Lian
- Ningbo Institute of Innovation for Combined Medicine and Engineering, Lihuili Hospital Affiliated to Ningbo University, Ningbo University, Ningbo 315211, China
| | - Chuang Wang
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Yunxiang Sun
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
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49
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Ruttenberg S, Kreutzer AG, Truex NL, Nowick JS. β-Hairpin Alignment Alters Oligomer Formation in Aβ-Derived Peptides. Biochemistry 2024; 63:212-218. [PMID: 38163326 PMCID: PMC10795187 DOI: 10.1021/acs.biochem.3c00526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/14/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
Amyloid-β (Aβ) forms heterogeneous oligomers, which are implicated in the pathogenesis of Alzheimer's disease (AD). Many Aβ oligomers consist of β-hairpin building blocks─Aβ peptides in β-hairpin conformations. β-Hairpins of Aβ can adopt a variety of alignments, but the role that β-hairpin alignment plays in the formation and heterogeneity of Aβ oligomers is poorly understood. To explore the effect of β-hairpin alignment on the oligomerization of Aβ peptides, we designed and studied two model peptides with two different β-hairpin alignments. Peptides Aβm17-36 and Aβm17-35 mimic two different β-hairpins that Aβ can form, the Aβ17-36 and Aβ17-35 β-hairpins, respectively. These hairpins are similar in composition but differ in hairpin alignment, altering the facial arrangements of the side chains of the residues that they contain. X-ray crystallography and SDS-PAGE demonstrate that the difference in facial arrangement between these peptides leads to distinct oligomer formation. In the crystal state, Aβm17-36 forms triangular trimers that further assemble to form hexamers, while Aβm17-35 forms tetrameric β-barrels. In SDS-PAGE, Aβm17-36 assembles to form a ladder of oligomers, while Aβm17-35 either assembles to form a dimer or does not assemble at all. The differences in the behavior of Aβm17-36 and Aβm17-35 suggest β-hairpin alignment as a source of the observed heterogeneity of Aβ oligomers.
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Affiliation(s)
- Sarah
M. Ruttenberg
- Department of Chemistry, University of California, Irvine Irvine, California 92697-2025, United
States
| | - Adam G. Kreutzer
- Department of Chemistry, University of California, Irvine Irvine, California 92697-2025, United
States
| | - Nicholas L. Truex
- Department of Chemistry, University of California, Irvine Irvine, California 92697-2025, United
States
| | - James S. Nowick
- Department of Chemistry, University of California, Irvine Irvine, California 92697-2025, United
States
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50
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de Oliveira AP, Chase W, Confer MP, Walker S, Baghel D, Ghosh A. Colocalization of β-Sheets and Carotenoids in Aβ Plaques Revealed with Multimodal Spatially Resolved Vibrational Spectroscopy. J Phys Chem B 2024; 128:33-44. [PMID: 38124262 PMCID: PMC10851346 DOI: 10.1021/acs.jpcb.3c04782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The aggregation of amyloid β(Aβ) peptides is at the heart of Alzheimer's disease development and progression. As a result, amyloid aggregates have been studied extensively in vitro, and detailed structural information on fibrillar amyloid aggregates is available. However, forwarding these structural models to amyloid plaques in the human brain is still a major challenge. The chemistry of amyloid plaques, particularly in terms of the protein secondary structure and associated chemical moieties, remains poorly understood. In this report, we use Raman microspectroscopy to identify the presence of carotenoids in amyloid plaques and demonstrate that the abundance of carotenoids is correlated with the overall protein secondary structure of plaques, specifically to the population of β-sheets. While the association of carotenoids with plaques has been previously identified, their correlation with the β structure has never been identified. To further validate these findings, we have used optical photothermal infrared (O-PTIR) spectroscopy, which is a spatially resolved technique that yields complementary infrared contrast to Raman. O-PTIR unequivocally demonstrates the presence of elevated β-sheets in carotenoid-containing plaques and the lack of β structure in noncarotenoid plaques. Our findings underscore the potential link between anti-inflammatory species as carotenoids to specific secondary structural motifs within Aβ plaques and highlight the possible role of chemically distinct plaques in neuroinflammation, which can uncover new mechanistic insights and lead to new therapeutic strategies for AD.
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Affiliation(s)
| | - William Chase
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, AL 35401, USA
| | - Matthew P. Confer
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana Champaign, Urbana, Illinois 61801, USA
| | - Savannah Walker
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, AL 35401, USA
| | - Divya Baghel
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, AL 35401, USA
| | - Ayanjeet Ghosh
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, AL 35401, USA
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