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Wojciechowski JW, Szczurek W, Szulc N, Szefczyk M, Kotulska M. PACT - Prediction of amyloid cross-interaction by threading. Sci Rep 2023; 13:22268. [PMID: 38097650 PMCID: PMC10721876 DOI: 10.1038/s41598-023-48886-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Amyloid proteins are often associated with the onset of diseases, including Alzheimer's, Parkinson's and many others. However, there is a wide class of functional amyloids that are involved in physiological functions, e.g., formation of microbial biofilms or storage of hormones. Recent studies showed that an amyloid fibril could affect the aggregation of another protein, even from a different species. This may result in amplification or attenuation of the aggregation process. Insight into amyloid cross-interactions may be crucial for better understanding of amyloid diseases and the potential influence of microbial amyloids on human proteins. However, due to the demanding nature of the needed experiments, knowledge of such interactions is still limited. Here, we present PACT (Prediction of Amyloid Cross-interaction by Threading) - the computational method for the prediction of amyloid cross-interactions. The method is based on modeling of a heterogeneous fibril formed by two amyloidogenic peptides. The resulting structure is assessed by the structural statistical potential that approximates its plausibility and energetic stability. PACT was developed and first evaluated mostly on data collected in the AmyloGraph database of interacting amyloids and achieved high values of Area Under ROC (AUC=0.88) and F1 (0.82). Then, we applied our method to study the interactions of CsgA - a bacterial biofilm protein that was not used in our in-reference datasets, which is expressed in several bacterial species that inhabit the human intestines - with two human proteins. The study included alpha-synuclein, a human protein that is involved in Parkinson's disease, and human islet amyloid polypeptide (hIAPP), which is involved in type 2 diabetes. In both cases, PACT predicted the appearance of cross-interactions. Importantly, the method indicated specific regions of the proteins, which were shown to play a central role in both interactions. We experimentally confirmed the novel results of the indicated CsgA fragments interacting with hIAPP based on the kinetic characteristics obtained with the ThT assay. PACT opens the possibility of high-throughput studies of amyloid interactions. Importantly, it can work with fairly long protein fragments, and as a purely physicochemical approach, it relies very little on scarce training data. The tool is available as a web server at https://pact.e-science.pl/pact/ . The local version can be downloaded from https://github.com/KubaWojciechowski/PACT .
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Affiliation(s)
- Jakub W Wojciechowski
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wrocław University of Science and Technology, 50-370, Wrocław, Poland.
| | - Witold Szczurek
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wrocław University of Science and Technology, 50-370, Wrocław, Poland
| | - Natalia Szulc
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wrocław University of Science and Technology, 50-370, Wrocław, Poland
- Department of Physics and Biophysics, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375, Wrocław, Poland
- LPCT, CNRS, Université de Lorraine, F-54000, Nancy, France
| | - Monika Szefczyk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, 50-370, Wrocław, Poland
| | - Malgorzata Kotulska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wrocław University of Science and Technology, 50-370, Wrocław, Poland.
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2
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Rodríguez-Galván A, Contreras-Torres FF. Scanning Tunneling Microscopy of Biological Structures: An Elusive Goal for Many Years. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:3013. [PMID: 36080050 PMCID: PMC9457988 DOI: 10.3390/nano12173013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/29/2022] [Accepted: 04/13/2022] [Indexed: 06/15/2023]
Abstract
Scanning tunneling microscopy (STM) is a technique that can be used to directly observe individual biomolecules at near-molecular scale. Within this framework, STM is of crucial significance because of its role in the structural analysis, the understanding the imaging formation, and the development of relative techniques. Four decades after its invention, it is pertinent to ask how much of the early dream has come true. In this study, we aim to overview different analyses for DNA, lipids, proteins, and carbohydrates. The relevance of STM imaging is exhibited as an opportunity to assist measurements and biomolecular identification in nanobiotechnology, nanomedicine, biosensing, and other cutting-edge applications. We believe STM research is still an entire science research ecosystem for joining several areas of expertise towards a goal settlement that has been elusive for many years.
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Affiliation(s)
- Andrés Rodríguez-Galván
- Carrera de Biología, Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Edo. Mex., Mexico
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3
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Functional Bacterial Amyloids: Understanding Fibrillation, Regulating Biofilm Fibril Formation and Organizing Surface Assemblies. Molecules 2022; 27:molecules27134080. [PMID: 35807329 PMCID: PMC9268375 DOI: 10.3390/molecules27134080] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 02/01/2023] Open
Abstract
Functional amyloid is produced by many organisms but is particularly well understood in bacteria, where proteins such as CsgA (E. coli) and FapC (Pseudomonas) are assembled as functional bacterial amyloid (FuBA) on the cell surface in a carefully optimized process. Besides a host of helper proteins, FuBA formation is aided by multiple imperfect repeats which stabilize amyloid and streamline the aggregation mechanism to a fast-track assembly dominated by primary nucleation. These repeats, which are found in variable numbers in Pseudomonas, are most likely the structural core of the fibrils, though we still lack experimental data to determine whether the repeats give rise to β-helix structures via stacked β-hairpins (highly likely for CsgA) or more complicated arrangements (possibly the case for FapC). The response of FuBA fibrillation to denaturants suggests that nucleation and elongation involve equal amounts of folding, but protein chaperones preferentially target nucleation for effective inhibition. Smart peptides can be designed based on these imperfect repeats and modified with various flanking sequences to divert aggregation to less stable structures, leading to a reduction in biofilm formation. Small molecules such as EGCG can also divert FuBA to less organized structures, such as partially-folded oligomeric species, with the same detrimental effect on biofilm. Finally, the strong tendency of FuBA to self-assemble can lead to the formation of very regular two-dimensional amyloid films on structured surfaces such as graphite, which strongly implies future use in biosensors or other nanobiomaterials. In summary, the properties of functional amyloid are a much-needed corrective to the unfortunate association of amyloid with neurodegenerative disease and a testimony to nature’s ability to get the best out of a protein fold.
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4
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Tran V, Karsai A, Fong MC, Cai W, Fraley JG, Yik JHN, Klineberg E, Haudenschild DR, Liu GY. Direct Visualization of the Binding of Transforming Growth Factor Beta 1 with Cartilage Oligomeric Matrix Protein via High-Resolution Atomic Force Microscopy. J Phys Chem B 2020; 124:9497-9504. [PMID: 33052673 DOI: 10.1021/acs.jpcb.0c07286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This work reports the first direct observations of binding and complex formation between transforming growth factor beta 1 (TGF-β1) and cartilage oligomeric matrix protein (COMP) using high-resolution atomic force microscopy (AFM). Each COMP molecule consists of pentamers whose five identical monomeric units bundle at N-termini. From this central point, the five monomers' flexible arms extend outward with C-terminal domains at the distal ends, forming a bouquet-like structure. In commonly used buffer solutions, TGF-β1 molecules typically form homodimers (majority), double dimers (minority), and aggregates (trace amount). Mixing TGF-β1 and COMP leads to rapid binding and complex formation. The TGF-β1/COMP complexes contain one to three COMP and multiple TGF-β1 molecules. For complexes with one COMP, the structure is more compact and less flexible than that of COMP alone. For complexes with two or more COMP molecules, the conformation varies to a large degree from one complex to another. This is attributed to the presence of double dimers or aggregates of TGF-β1 molecules, whose size and multiple binding sites enable binding to more than one COMP. The number and location of individual TGF-β1 dimers are also clearly visible in all complexes. This molecular-level information provides a new insight into the mechanism of chondrogenesis enhancement by TGF-β1/COMP complexes, i.e., simultaneous and multivalent presentation of growth factors. These presentations help explain the high efficacy in sustained activation of the signaling pathway to augment chondrogenesis.
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Affiliation(s)
- Victoria Tran
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Arpad Karsai
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Michael C Fong
- Department of Biomedical Engineering, University of California, Davis, California 95616, United States
| | - Weiliang Cai
- Department of Orthopaedic Surgery, University of California-Davis Medical Center, Sacramento, California 95817, United States
| | - J Gabriel Fraley
- Department of Orthopaedic Surgery, University of California-Davis Medical Center, Sacramento, California 95817, United States
| | - Jasper H N Yik
- Department of Orthopaedic Surgery, University of California-Davis Medical Center, Sacramento, California 95817, United States
| | - Eric Klineberg
- Department of Orthopaedic Surgery, University of California-Davis Medical Center, Sacramento, California 95817, United States
| | - Dominik R Haudenschild
- Department of Orthopaedic Surgery, University of California-Davis Medical Center, Sacramento, California 95817, United States
| | - Gang-Yu Liu
- Department of Chemistry, University of California, Davis, California 95616, United States
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5
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Wojciechowski JW, Kotulska M. PATH - Prediction of Amyloidogenicity by Threading and Machine Learning. Sci Rep 2020; 10:7721. [PMID: 32382058 PMCID: PMC7206081 DOI: 10.1038/s41598-020-64270-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/24/2020] [Indexed: 12/18/2022] Open
Abstract
Amyloids are protein aggregates observed in several diseases, for example in Alzheimer's and Parkinson's diseases. An aggregate has a very regular beta structure with a tightly packed core, which spontaneously assumes a steric zipper form. Experimental methods enable studying such peptides, however they are tedious and costly, therefore inappropriate for genomewide studies. Several bioinformatic methods have been proposed to evaluate protein propensity to form an amyloid. However, the knowledge of aggregate structures is usually not taken into account. We propose PATH (Prediction of Amyloidogenicity by THreading) - a novel structure-based method for predicting amyloidogenicity and show that involving available structures of amyloidogenic fragments enhances classification performance. Experimental aggregate structures were used in templatebased modeling to recognize the most stable representative structural class of a query peptide. Several machine learning methods were then applied on the structural models, using their energy terms. Finally, we identified the most important terms in classification of amyloidogenic peptides. The proposed method outperforms most of the currently available methods for predicting amyloidogenicity, with its area under ROC curve equal to 0.876. Furthermore, the method gave insight into significance of selected structural features and the potentially most stable structural class of a peptide fragment if subjected to crystallization.
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Affiliation(s)
- Jakub W Wojciechowski
- Department of Biomedical Engineering, Wroclaw University of Science and Technology, 50-370, Wrocław, Poland
| | - Małgorzata Kotulska
- Department of Biomedical Engineering, Wroclaw University of Science and Technology, 50-370, Wrocław, Poland.
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Tan S, Shi H, Fu L, Ma J, Du X, Song J, Liu Y, Zeng Q, Xu H, Wan J. Superlubricity of Fullerene Derivatives Induced by Host-Guest Assembly. ACS APPLIED MATERIALS & INTERFACES 2020; 12:18924-18933. [PMID: 32227981 DOI: 10.1021/acsami.0c02726] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fullerenes have been recognized as good candidates for solid lubricants. In this study, the microscale superlubricity of fullerene derivatives was accomplished by the construction of regular host-guest assembly structures. Herein, the host-guest assembly structures of fullerene derivatives were successfully constructed on a highly oriented pyrolytic graphite (HOPG) surface by introducing the macrocycles as the templates and were explicitly revealed by scanning tunneling microscopy (STM). Meanwhile, the nanotribological properties of the host-guest assemblies were measured using atomic force microscopy (AFM), revealing ultralow friction coefficients of 0.003-0.008, which could be attributed to the restriction on removal of fullerene molecules after introducing the templates. The interaction energies were calculated by density functional theory (DFT) method, which indicates the correlation between friction coefficients and interaction strength in the host-guest assemblies. The effort on fullerene-related superlubricity could extend the solid superlubrication systems and provide a novel pathway to explore the friction mechanisms at the molecular level.
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Affiliation(s)
- Shanchao Tan
- State Key Laboratory of Tribology, Tsinghua University, Beijing 100084, China
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
| | - Hongyu Shi
- State Key Laboratory of Tribology, Tsinghua University, Beijing 100084, China
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
| | - Lulu Fu
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jing Ma
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xin Du
- College of Chemical Engineering, Jiangsu Key Lab of Biomass-based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing 210037, China
| | - Jian Song
- State Key Laboratory of Tribology, Tsinghua University, Beijing 100084, China
| | - Yuhong Liu
- State Key Laboratory of Tribology, Tsinghua University, Beijing 100084, China
| | - Qingdao Zeng
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
- Center of Materials Science and Optoelectonics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haijun Xu
- College of Chemical Engineering, Jiangsu Key Lab of Biomass-based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing 210037, China
| | - Junhua Wan
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, Hangzhou Normal University, Hangzhou 310012, China
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7
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Zheng Y, Yu L, Zou Y, Yang Y, Wang C. Steric Dependence of Chirality Effect in Surface-Mediated Peptide Assemblies Identified with Scanning Tunneling Microscopy. NANO LETTERS 2019; 19:5403-5409. [PMID: 31265784 DOI: 10.1021/acs.nanolett.9b01904] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Amino acid chirality has been recognized as an important driving force in constructing peptide architectures, via interactions such as chirality-induced stereochemical effect. The introduction of site-specific chiral conversion of l- and d-amino acids in peptide sequences could enable the pursuit of the chirality effects in peptide assembly. In this work, we characterized the assemblies of heptapeptides with various side chain moieties and their chiral variants using STM. Specifically, two pairs of amino acids, Gln (Q) and Asn (N), Glu (E) and Asp (D), having one methylene difference in their side chains, are selected to elucidate the steric dependence of amino acid chiral effects on surface-bound peptide assemblies. The observed heptapeptide assembly structures reveal that chirality switching of a single amino acid is able to destabilize the surface-mediated peptide assemblies, and this disturbance effect can be positively correlated with the steric hindrance of amino acid side chains. Furthermore, the strength of the impact due to chiral conversion on heptapeptide assembly structure is noticeably dependent on the mutation sites, indicative of structural heterogeneity of chiral effects. These results could contribute to the molecular insights of chirality-induced stereochemical interactions in peptide assembly.
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Affiliation(s)
- Yongfang Zheng
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , P. R. China
- Department of Chemistry , Tsinghua University , Beijing 100084 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Lanlan Yu
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Yimin Zou
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Yanlian Yang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Chen Wang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
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8
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Palato LM, Pilcher S, Oakes A, Lamba A, Torres J, Ledesma Monjaraz LI, Munoz C, Njoo E, Rinauro DJ, Menefee KA, Tun A, Jauregui BL, Shapiro S, Nossiff OH, Olivares E, Chang K, Nguyen V, Nogaj LA, Moffet DA. Amyloidogenicity of naturally occurring full-length animal IAPP variants. J Pept Sci 2019; 25:e3199. [PMID: 31231935 DOI: 10.1002/psc.3199] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/28/2019] [Accepted: 05/29/2019] [Indexed: 12/15/2022]
Abstract
The aggregation of the 37-amino acid polypeptide human islet amyloid polypeptide (hIAPP), as either insoluble amyloid or as small oligomers, appears to play a direct role in the death of human pancreatic β-islet cells in type 2 diabetes. hIAPP is considered to be one of the most amyloidogenic proteins known. The quick aggregation of hIAPP leads to the formation of toxic species, such as oligomers and fibers, that damage mammalian cells (both human and rat pancreatic cells). Whether this toxicity is necessary for the progression of type 2 diabetes or merely a side effect of the disease remains unclear. If hIAPP aggregation into toxic amyloid is on-path for developing type 2 diabetes in humans, islet amyloid polypeptide (IAPP) aggregation would likely need to play a similar role within other organisms known to develop the disease. In this work, we compared the aggregation potential and cellular toxicity of full-length IAPP from several diabetic and nondiabetic organisms whose aggregation propensities had not yet been determined for full-length IAPP.
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Affiliation(s)
- Larry M Palato
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, CA
| | - Shannon Pilcher
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, CA
| | - Alissa Oakes
- Department of Biology, Mount Saint Mary's University, Los Angeles, CA
| | - Arleen Lamba
- Department of Biology, Mount Saint Mary's University, Los Angeles, CA
| | - Jaris Torres
- Department of Biology, Mount Saint Mary's University, Los Angeles, CA
| | | | - Crystabel Munoz
- Department of Biology, Mount Saint Mary's University, Los Angeles, CA
| | - Edward Njoo
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, CA
| | - Dillon J Rinauro
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, CA
| | | | - Angela Tun
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, CA
| | - Betssy L Jauregui
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, CA
| | - Sarah Shapiro
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, CA
| | - Olivia H Nossiff
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, CA
| | - Eileen Olivares
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, CA
| | - Kevin Chang
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, CA
| | - Viviane Nguyen
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, CA
| | - Luiza A Nogaj
- Department of Biology, Mount Saint Mary's University, Los Angeles, CA
| | - David A Moffet
- Department of Chemistry and Biochemistry, Loyola Marymount University, Los Angeles, CA
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9
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Shi H, Lu X, Liu Y, Song J, Deng K, Zeng Q, Wang C. Nanotribological Study of Supramolecular Template Networks Induced by Hydrogen Bonds and van der Waals Forces. ACS NANO 2018; 12:8781-8790. [PMID: 30059613 DOI: 10.1021/acsnano.8b05045] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nanotribology has been given increasing attention by researchers in pursuing the nature of friction. In the present work, an approach that combines the supramolecular assembly and nanotribology is introduced. Herein, the nanotribological study was carried out on seven supramolecular template networks [namely, hydrogen bond induced tricarboxylic acids and van der Waals force induced hexaphenylbenzene (HPB) derivatives]. The template networks, as well as the host-guest assemblies of template molecules induced by different forces, were constructed on the highly oriented pyrolytic graphite (HOPG) surface and explicitly characterized using scanning tunneling microscopy (STM). Meanwhile, the nanotribological properties of the template networks were measured using atomic force microscopy (AFM). Together with the theoretical calculation using the density functional theory (DFT) method, it was revealed that the friction coefficients were positively correlated with the interaction strength. The frictional energy dissipation mainly derives from both the intermolecular interaction energy and the interaction energy between molecules and the substrate. The efforts not only help us gain insight into the competitive mechanisms of hydrogen bond and van der Waals force in supramolecular assembly but also shed light on the origin of friction and the relationship between the assembly structures and the nanotribological properties at the molecular level.
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Affiliation(s)
- Hongyu Shi
- State Key Laboratory of Tribology , Tsinghua University , Beijing 100084 , China
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology (NCNST) , Beijing 100190 , China
| | - Xinchun Lu
- State Key Laboratory of Tribology , Tsinghua University , Beijing 100084 , China
| | - Yuhong Liu
- State Key Laboratory of Tribology , Tsinghua University , Beijing 100084 , China
| | - Jian Song
- State Key Laboratory of Tribology , Tsinghua University , Beijing 100084 , China
| | - Ke Deng
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology (NCNST) , Beijing 100190 , China
| | - Qingdao Zeng
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology (NCNST) , Beijing 100190 , China
| | - Chen Wang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology (NCNST) , Beijing 100190 , China
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10
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Enache TA, Chiorcea-Paquim AM, Oliveira-Brett AM. Amyloid Beta Peptide VHHQ, KLVFF, and IIGLMVGGVV Domains Involved in Fibrilization: AFM and Electrochemical Characterization. Anal Chem 2018; 90:2285-2292. [PMID: 29314823 DOI: 10.1021/acs.analchem.7b04686] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The time-dependent structural modifications and oxidation behavior of specifically chosen five short amyloid beta (Aβ) peptides, Aβ1-16, Aβ1-28, Aβ10-20, Aβ12-28, and Aβ17-42, fragments of the complete human Aβ1-40 peptide, were investigated by atomic force microscopy (AFM) and voltammetry. The objective was to determine the influence of different Aβ domains (VHHQ that contains electroactive histidine H residues, KLVFF that is the peptide hydrophobic aggregation core, and IIGLMVGGVV that is the C-terminus hydrophobic region), and of Aβ peptide hydrophobicity, in the fibrilization mechanism. The short Aβ peptides absence of aggregation or the time-dependent aggregation mechanisms, at room temperature, in free chloride media, within the time window from 0 to 48 h, were established by AFM via changes in their adsorption morphology, and by differential pulse voltammetry, via modifications of the amino acid residues oxidation peak currents. The first oxidation peak was of tyrosine Y residue and the second peak was of histidine H and methionine M residues oxidation. A correlation between the presence of an intact highly hydrophobic KLVFF aggregation core and the time-dependent changes on the Aβ peptides aggregation was found. The hydrophobic C-terminal domain IIGLMVGGVV, present in the Aβ1-40 peptide, also contributed to accelerate the formation of Aβ1-40 peptide aggregates and fibrils.
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Affiliation(s)
- Teodor Adrian Enache
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra , 3004-535, Coimbra, Portugal
| | - Ana-Maria Chiorcea-Paquim
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra , 3004-535, Coimbra, Portugal
| | - Ana Maria Oliveira-Brett
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra , 3004-535, Coimbra, Portugal
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11
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Shi H, Liu Y, Zeng Q, Yang Y, Wang C, Lu X. Interfacial assembly structures and nanotribological properties of saccharic acids. Phys Chem Chem Phys 2017; 19:1236-1243. [DOI: 10.1039/c6cp06759j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The larger friction of the successfully constructed assembly of saccharic acid indicates the higher potential energy barrier at the interface.
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Affiliation(s)
- Hongyu Shi
- State Key Laboratory of Tribology
- Tsinghua University
- Beijing 100084
- China
| | - Yuhong Liu
- State Key Laboratory of Tribology
- Tsinghua University
- Beijing 100084
- China
| | - Qingdao Zeng
- National Center for Nanoscience and Technology
- Beijing 100190
- China
| | - Yanlian Yang
- National Center for Nanoscience and Technology
- Beijing 100190
- China
| | - Chen Wang
- National Center for Nanoscience and Technology
- Beijing 100190
- China
| | - Xinchun Lu
- State Key Laboratory of Tribology
- Tsinghua University
- Beijing 100084
- China
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12
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Haspel N, Zheng J, Aleman C, Zanuy D, Nussinov R. A Protocol for the Design of Protein and Peptide Nanostructure Self-Assemblies Exploiting Synthetic Amino Acids. Methods Mol Biol 2017; 1529:323-352. [PMID: 27914060 PMCID: PMC7900906 DOI: 10.1007/978-1-4939-6637-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
In recent years there has been increasing interest in nanostructure design based on the self-assembly properties of proteins and polymers. Nanodesign requires the ability to predictably manipulate the properties of the self-assembly of autonomous building blocks, which can fold or aggregate into preferred conformational states. The design includes functional synthetic materials and biological macromolecules. Autonomous biological building blocks with available 3D structures provide an extremely rich and useful resource. Structural databases contain large libraries of protein molecules and their building blocks with a range of sizes, shapes, surfaces, and chemical properties. The introduction of engineered synthetic residues or short peptides into these building blocks can greatly expand the available chemical space and enhance the desired properties. Herein, we summarize a protocol for designing nanostructures consisting of self-assembling building blocks, based on our recent works. We focus on the principles of nanostructure design with naturally occurring proteins and synthetic amino acids, as well as hybrid materials made of amyloids and synthetic polymers.
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Affiliation(s)
- Nurit Haspel
- Department of Computer Science, The University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA, 02125, USA.
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Carlos Aleman
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028, Barcelona, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, E-08028, Barcelona, Spain
| | - David Zanuy
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028, Barcelona, Spain
| | - Ruth Nussinov
- Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Inst. of Molecular Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
- Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
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13
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Amyloid-β peptides time-dependent structural modifications: AFM and voltammetric characterization. Anal Chim Acta 2016; 926:36-47. [PMID: 27216391 DOI: 10.1016/j.aca.2016.04.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/14/2016] [Accepted: 04/08/2016] [Indexed: 12/20/2022]
Abstract
The human amyloid beta (Aβ) peptides, Aβ1-40 and Aβ1-42, structural modifications, from soluble monomers to fully formed fibrils through intermediate structures, were investigated, and the results were compared with those obtained for the inverse Aβ40-1 and Aβ42-1, mutant Aβ1-40Phe(10) and Aβ1-40Nle(35), and rat Aβ1-40Rat peptide sequences. The aggregation was followed at a slow rate, in chloride free media and room temperature, and revealed to be a sequence-structure process, dependent on the physicochemical properties of each Aβ peptide isoforms, and occurring at different rates and by different pathways. The fibrilization process was investigated by atomic force microscopy (AFM), via changes in the adsorption morphology from: (i) initially random coiled structures of ∼0.6 nm height, corresponding to the Aβ peptide monomers in random coil or in α-helix conformations, to (ii) aggregates and protofibrils of 1.5-6.0 nm height and (iii) two types of fibrils, corresponding to the Aβ peptide in a β-sheet configuration. The reactivity of the carbon electrode surface was considered. The hydrophobic surface induced rapid changes of the Aβ peptide conformations, and differences between the adsorbed fibrils, formed at the carbon surface (beaded, thin, <2.0 nm height) or in solution (long, smooth, thick, >2.0 nm height), were detected. Differential pulse voltammetry showed that, according to their primary structure, the Aβ peptides undergo oxidation in one or two steps, the first step corresponding to the tyrosine amino acids oxidation, and the second one to the histidine and methionine amino acids oxidation. The fibrilization process was electrochemically detected via the decrease of the Aβ peptide oxidation peak currents that occurred in a time dependent manner.
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14
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Marchesan S, Vargiu AV, Styan KE. The Phe-Phe Motif for Peptide Self-Assembly in Nanomedicine. Molecules 2015; 20:19775-88. [PMID: 26540034 PMCID: PMC6332413 DOI: 10.3390/molecules201119658] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 10/25/2015] [Accepted: 10/27/2015] [Indexed: 01/19/2023] Open
Abstract
Since its discovery, the Phe-Phe motif has gained in popularity as a minimalist building block to drive the self-assembly of short peptides and their analogues into nanostructures and hydrogels. Molecules based on the Phe-Phe motif have found a range of applications in nanomedicine, from drug delivery and biomaterials to new therapeutic paradigms. Here we discuss the various production methods for this class of compounds, and the characterization, nanomorphologies, and application of their self-assembled nanostructures. We include the most recent findings on their remarkable properties, which hold substantial promise for the creation of the next generation nanomedicines.
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Affiliation(s)
- Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department, University of Trieste, Via L. Giorgieri 1, Trieste 34127, Italy.
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, Cittadella Universitaria S.P. Monserrato-Sestu Km. 0.700, Monserrato 09042, Italy.
| | - Katie E Styan
- CSIRO Manufacturing, Bayview Ave Clayton, VIC 3168, Australia.
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15
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Tiwari V, Solanki V, Tiwari M. In-vivoandin-vitrotechniques used to investigate Alzheimer's disease. FRONTIERS IN LIFE SCIENCE 2015. [DOI: 10.1080/21553769.2015.1044129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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16
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Sengupta K, Chatterjee S, Pramanik D, Dey SG, Dey A. Self-assembly of stable oligomeric and fibrillar aggregates of Aβ peptides relevant to Alzheimer's disease: morphology dependent Cu/heme toxicity and inhibition of PROS generation. Dalton Trans 2015; 43:13377-83. [PMID: 25076262 DOI: 10.1039/c4dt01991a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Large and small aggregates of Aβ peptides, resembling the morphology and dimensions of fibrillar and oligomeric forms of Aβ respectively, relevant to Alzheimer's disease, are stabilized on electrodes using self-assembly. Both of these forms were found to bind redox active Cu and heme, resulting in active sites having distinctive biophysical properties. The reduced metal bound Aβ active sites of both the oligomeric and fibrillar forms of Aβ produce detrimental partially reduced oxygen species (PROS). While the larger aggregates of heme-Aβ produce more PROS in situ, the smaller aggregates of Cu-Aβ produce more PROS. 8-Hydroxy quinoline and methylene blue are inhibitors of Cu and heme bound Aβ respectively, and are shown to efficiently reduce PROS formation in the oligomeric forms. However, these inhibitors are ineffective in reducing the toxicities of the Cu and heme bound Aβ peptides in the fibrils, making them significantly more lethal than the smaller Aβ aggregates.
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Affiliation(s)
- Kushal Sengupta
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700032, India.
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17
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Caballero L, Mena J, Morales-Alvarez A, Kogan MJ, Melo F. Assessment of the nature interactions of β-amyloid protein by a nanoprobe method. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 31:299-306. [PMID: 25486322 DOI: 10.1021/la502777h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present a method based on atomic force microscopy (AFM) to assess the work of adhesion between the interfaces of gold AFM tips functionalized with three peptides derived from β-sheet breaker LPFFD [CLPFFD-NH2 (i0) and their isomers CDLPFF-NH2 (i1) and CLPDFF-NH2 (i2)], and the beta-amyloid protein (Aβ1-42). β-Amyloid protein was deposited onto a highly oriented graphite (HOPG) surface as protofibrils and fibrils. The presence of the residues Leu (L), Phe (F), and Phe (F), which are also present in the native sequence, confirm that the peptides are able to bind to the aggregates of Aβ1-42 fibrils and protofibrils. Force of adhesion data were directly obtained from the maximum force on retraction, and the work of adhesion was calculated from the Jhonson-Kendall-Roberts model (JKR-Model). Both the polar and dispersive contributions to the surface energy of the peptides i0, i1, and i2, as well as Aβ1-42 fibrils and protofibrils, were determined by means of measuring the contact angle and using the two-fluid method. The macroscopic energies of the functionalized gold surfaces do not differ significantly between isomers, which confirms the similar nature of the peptides i0, i1, and i2 but suggests that the macroscopic measurements are not able to distinguish specific sequences. The nanoprobe reveals a typical adhesion work value associated with the interaction of protofibrils with i0 and i2; this value is three times higher than that of i1. The difference is attributed to the hydrophobic nature of protofibrils, the predominant exposition of hydrophobic residues of the peptides i0 and i2, with respect to i1, and the degree of functionalization. i0 and i2 presented a slight adhesion with Aβ fibrils, which is associated with the exposed hydrophilic groups of these fibrils (onto HOPG) compared to the protofibrils. However, i1 showed interaction with both Aβ fibrils and protofibrils. For this, we propose an explanation based on the fact that the peptide i1 locates itself adjacent to the gold surface of the probe, concealing their hydrophobic groups and therefore decreasing the probability of interaction with Aβ fibrils and protofibrils. The peptide-gold nano probe represents a useful tool to study the nanobiointeractions of functionalized nanoparticles with amyloid aggregates.
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Affiliation(s)
- Leonardo Caballero
- Departamento de Física, Universidad de Santiago , Avenida Ecuador 3493, Casilla 307, Correo 2, Santiago, Chile
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18
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Liu Y, Xu LP, Yu H, Wen Y, Zhang X. Zinc ion induced prefibrillar oligomerization of Aβ peptides: From nanocoin to nanobelt. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.05.085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Tinker-Mill C, Mayes J, Allsop D, Kolosov OV. Ultrasonic force microscopy for nanomechanical characterization of early and late-stage amyloid-β peptide aggregation. Sci Rep 2014; 4:4004. [PMID: 24500006 PMCID: PMC3915309 DOI: 10.1038/srep04004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 01/20/2014] [Indexed: 11/09/2022] Open
Abstract
The aggregation of amyloid-β peptides into protein fibres is one of the main neuropathological features of Alzheimer's disease (AD). While imaging of amyloid-β aggregate morphology in vitro is extremely important for understanding AD pathology and in the development of aggregation inhibitors, unfortunately, potentially highly toxic, early aggregates are difficult to observe by current electron microscopy and atomic force microscopy (AFM) methods, due to low contrast and variability of peptide attachment to the substrate. Here, we use a poly-L-Lysine (PLL) surface that captures all protein components from monomers to fully formed fibres, followed by nanomechanical mapping via ultrasonic force microscopy (UFM), which marries high spatial resolution and nanomechanical contrast with the non-destructive nature of tapping mode AFM. For the main putative AD pathogenic component, Aβ1-42, the PLL-UFM approach reveals the morphology of oligomers, protofibrils and mature fibres, and finds that a fraction of small oligomers is still present at later stages of fibril assembly.
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Affiliation(s)
| | - Jennifer Mayes
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, LA1 4YB, UK
| | - David Allsop
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, LA1 4YB, UK
| | - Oleg V. Kolosov
- Physics Department, Lancaster University, Lancaster, LA1 4YB, UK
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20
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Drolle E, Hane F, Lee B, Leonenko Z. Atomic force microscopy to study molecular mechanisms of amyloid fibril formation and toxicity in Alzheimer's disease. Drug Metab Rev 2014; 46:207-23. [PMID: 24495298 DOI: 10.3109/03602532.2014.882354] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Alzheimer's disease (AD) is a devastating neurodegenerative disease characterized by dementia and memory loss for which no cure or effective prevention is currently available. Neurodegeneration in AD is linked to formation of amyloid plaques found in brain tissues of Alzheimer's patients during post-mortem examination. Amyloid plaques are composed of amyloid fibrils and small oligomers - insoluble protein aggregates. Although amyloid plaques are found on the neuronal cell surfaces, the mechanism of amyloid toxicity is still not well understood. Currently, it is believed that the cytotoxicity is a result of the nonspecific interaction of small soluble amyloid oligomers (rather than longer fibrils) with the plasma membrane. In recent years, nanotechnology has contributed significantly to understanding the structure and function of lipid membranes and to the study of the molecular mechanisms of membrane-associated diseases. We review the current state of research, including applications of the latest nanotechnology approaches, on the interaction of lipid membranes with the amyloid-β (Aβ) peptide in relation to amyloid toxicity. We discuss the interactions of Aβ with model lipid membranes with a focus to demonstrate that composition, charge and phase of the lipid membrane, as well as lipid domains and rafts, affect the binding of Aβ to the membrane and contribute to toxicity. Understanding the role of the lipid membrane in AD at the nanoscale and molecular level will contribute to the understanding of the molecular mechanism of amyloid toxicity and may aid into the development of novel preventive strategies to combat AD.
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Affiliation(s)
- Elizabeth Drolle
- Department of Biology, University of Waterloo , Waterloo, ON , Canada
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21
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Li C, Mezzenga R. The interplay between carbon nanomaterials and amyloid fibrils in bio-nanotechnology. NANOSCALE 2013; 5:6207-6218. [PMID: 23744243 DOI: 10.1039/c3nr01644g] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Recent advances in bio-nanotechnology have not only rapidly broadened the applications and scope of hybrid nanomaterials in biological fields, but also greatly enriched the examples of ordered materials based on supramolecular self-assembly. Among eminent examples of functional nanostructured materials of undisputed impact in nanotechnology and biological environments, carbon nanomaterials (such as fullerenes, carbon nanotubes and graphene) and amyloid fibrils have attracted great attention because of their unique architectures and exceptional physical properties. Nonetheless, combination of these two classes of nanomaterials into functional hybrids is far from trivial. For example, the presence of carbon nanomaterials can offer either an inhibitory effect or promotion of amyloid fibrillation, depending on the structural architectures of carbon nanomaterials and the starting amyloid proteins/peptides considered. To date, numerous studies have been devoted to evaluating both the biological toxicity of carbon nanomaterials and their use in developing therapies for amyloidosis. At the same time, hybridization of these two classes of nanomaterials offers new possibilities for combining some of their desirable properties into nanocomposites of possible use in electronics, actuators, sensing, biomedicine and structural materials. This review describes recent developments in the hybridization of carbon nanomaterials and amyloid fibrils and discusses the current state of the art on the application of carbon nanomaterial-amyloid fibril hybrids in bio-nanotechnology.
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Affiliation(s)
- Chaoxu Li
- ETH Zurich, Food & Soft Materials, Department of Health Science & Technology, Zurich, Switzerland
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22
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Forman CJ, Wang N, Yang ZY, Mowat CG, Jarvis S, Durkan C, Barker PD. Probing the location of displayed cytochrome b562 on amyloid by scanning tunnelling microscopy. NANOTECHNOLOGY 2013; 24:175102. [PMID: 23571459 DOI: 10.1088/0957-4484/24/17/175102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Amyloid fibres displaying cytochrome b562 were probed using scanning tunnelling microscopy (STM) in vacuo. The cytochromes are electron transfer proteins containing a haem cofactor and could, in principle, mediate electron transfer between the tip and the gold substrate. If the core fibres were insulating and electron transfer within the 3D haem network was detected, then the electron transport properties of the fibre could be controlled by genetic engineering. Three kinds of STM images were obtained. At a low bias (<1.5 V) the fibres appeared as regions of low conductivity with no evidence of cytochrome mediated electron transfer. At a high bias, stable peaks in tunnelling current were observed for all three fibre species containing haem and one species of fibre that did not contain haem. In images of this kind, some of the current peaks were collinear and spaced around 10 nm apart over ranges longer than 100 nm, but background monomers complicate interpretation. Images of the third kind were rare (1 in 150 fibres); in these, fully conducting structures with the approximate dimensions of fibres were observed, suggesting the possibility of an intermittent conduction mechanism, for which a precedent exists in DNA. To test the conductivity, some fibres were immobilized with sputtered gold, and no evidence of conduction between the grains of gold was seen. In control experiments, a variation of monomeric cytochrome b562 was not detected by STM, which was attributed to low adhesion, whereas a monomeric multi-haem protein, GSU1996, was readily imaged. We conclude that the fibre superstructure may be intermittently conducting, that the cytochromes have been seen within the fibres and that they are too far apart for detectable current flow between sites to occur. We predict that GSU1996, being 10 nm long, is more likely to mediate successful electron transfer along the fibre as well as being more readily detectable when displayed from amyloid.
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Affiliation(s)
- C J Forman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.
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23
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Mahmoudi M, Kalhor HR, Laurent S, Lynch I. Protein fibrillation and nanoparticle interactions: opportunities and challenges. NANOSCALE 2013; 5:2570-88. [PMID: 23463168 DOI: 10.1039/c3nr33193h] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Due to their ultra-small size, nanoparticles (NPs) have distinct properties compared with the bulk form of the same materials. These properties are rapidly revolutionizing many areas of medicine and technology. NPs are recognized as promising and powerful tools to fight against the human brain diseases such as multiple sclerosis or Alzheimer's disease. In this review, after an introductory part on the nature of protein fibrillation and the existing approaches for its investigations, the effects of NPs on the fibrillation process have been considered. More specifically, the role of biophysicochemical properties of NPs, which define their affinity for protein monomers, unfolded monomers, oligomers, critical nuclei, and other prefibrillar states, together with their influence on protein fibrillation kinetics has been described in detail. In addition, current and possible-future strategies for controlling the desired effect of NPs and their corresponding effects on the conformational changes of the proteins, which have significant roles in the fibrillation process, have been presented.
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Affiliation(s)
- Morteza Mahmoudi
- Department of Nanotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
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24
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Zhai J, Lee TH, Small DH, Aguilar MI. Characterization of Early Stage Intermediates in the Nucleation Phase of Aβ Aggregation. Biochemistry 2012; 51:1070-8. [DOI: 10.1021/bi201871r] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jiali Zhai
- Department of Biochemistry and
Molecular Biology, Monash University, Clayton,
Victoria 3800, Australia
| | - Tzong-Hsien Lee
- Department of Biochemistry and
Molecular Biology, Monash University, Clayton,
Victoria 3800, Australia
| | - David H. Small
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Marie-Isabel Aguilar
- Department of Biochemistry and
Molecular Biology, Monash University, Clayton,
Victoria 3800, Australia
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25
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Vlad C, Lindner K, Karreman C, Schildknecht S, Leist M, Tomczyk N, Rontree J, Langridge J, Danzer K, Ciossek T, Petre A, Gross ML, Hengerer B, Przybylski M. Autoproteolytic fragments are intermediates in the oligomerization/aggregation of the Parkinson's disease protein alpha-synuclein as revealed by ion mobility mass spectrometry. Chembiochem 2011; 12:2740-4. [PMID: 22162214 DOI: 10.1002/cbic.201100569] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Indexed: 12/29/2022]
Abstract
Gas-phase protein separation by ion mobility: With its ability to separate the Parkinson's disease protein α-synuclein and its autoproteolytic products-despite the small concentrations of the latter-ion-mobility MS has enabled the characterization of intermediate fragments in in vitro oligomerization-aggregation. In particular, a possible key fragment, the highly aggregating C-terminal fragment, αSyn(72-140), has been revealed.
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Affiliation(s)
- Camelia Vlad
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
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26
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Abstract
There has been a growing recognition of a wide variety of diseases commonly referred to as conformational diseases, which share the feature of specific disease-related proteins adopting nonnative conformation that promote their ordered aggregation and deposition on surfaces. Due to the nanoscale dimensions and the varied morphology of such aggregates, atomic force microscopy (AFM) has emerged as an ideal tool for distinguishing structural features of the numerous potential aggregate forms, ranging from small globular oligomers to large mature amyloid fibrils. Beyond the ability to morphologically distinguish aggregate forms, AFM also can dynamically track the aggregation process due to its unique ability to be operated not only in air (ex situ), but also in solution (in situ). This feature provides for tracking the fate of individual aggregates over time. This chapter describes the use of AFM in characterizing the aggregation of the amyloid-β peptide (Aβ), which is hypothesized to play a key role in Alzheimer's disease (AD), a late-onset neurodegenerative conformational disease.
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Affiliation(s)
- Justin Legleiter
- The C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
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27
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Komatsu H, Feingold-Link E, Sharp KA, Rastogi T, Axelsen PH. Intrinsic linear heterogeneity of amyloid β protein fibrils revealed by higher resolution mass-per-length determinations. J Biol Chem 2010; 285:41843-51. [PMID: 20940298 PMCID: PMC3009912 DOI: 10.1074/jbc.m110.165068] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 10/01/2010] [Indexed: 11/06/2022] Open
Abstract
Amyloid β proteins spontaneously form fibrils in vitro that vary in their thermodynamic stability and in morphological characteristics such as length, width, shape, longitudinal twist, and the number of component filaments. It is vitally important to determine which variant best represents the type of fibril that accumulates in Alzheimer disease. In the present study, the nature of morphological variation was examined by dark-field and transmission electron microscopy in a preparation of seeded amyloid β protein fibrils that formed at relatively low protein concentrations and exhibited remarkably high thermodynamic stability. The number of filaments comprising these fibrils changed frequently from two to six along their length, and these changes only became apparent when mass-per-length (MPL) determinations are made with sufficient resolution. The MPL results could be reproduced by a simple stochastic model with a single adjustable parameter. The presence of more than two primary filaments could not be discerned by transmission electron microscopy, and they had no apparent relationship to the longitudinal twist of the fibrils. However, the pitch of the twist was strongly affected by the pH of the negative stain. We conclude that highly stable amyloid fibrils may form in which a surprising amount of intrinsic linear heterogeneity may be obscured by MPL measurements of insufficient resolution, and by the negative stains used for imaging fibrils by electron microscopy.
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Affiliation(s)
| | | | | | | | - Paul H. Axelsen
- From the Departments of Pharmacology
- Biochemistry and Biophysics, and
- Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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28
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Wang Q, Zhao C, Zhao J, Wang J, Yang JC, Yu X, Zheng J. Comparative molecular dynamics study of Abeta adsorption on the self-assembled monolayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:3308-3316. [PMID: 19928820 DOI: 10.1021/la903070y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The adsorption and aggregation of the amyloid-beta (Abeta) peptides on the cell membrane plays a causal role in the pathogenesis of Alzheimer's disease. Here, we report all-atom molecular dynamics (MD) simulations to study the interactions of Abeta oligomer with self-assembled monolayers (SAMs) terminated with hydrophobic CH(3) and hydrophilic OH functional groups, with particular interests in how surface chemistry and Abeta orientation affect the adsorption behavior of Abeta. Simulation results show that the CH(3)-SAM has a stronger binding affinity to Abeta than the OH-SAM does, although both surfaces can induce Abeta adsorption. Regardless of the characteristics of the surface, the hydrophobic C-terminal region is more likely to be adsorbed on the SAMs, indicating a preferential orientation and interface for Abeta adsorption. Structural and energetic comparison among six Abeta-SAM systems further reveals that Abeta orientation, SAM surface hydrophobicity, and interfacial waters all determine Abeta adsorption behavior on the surface, highlighting the importance of hydrophobic interactions at the interface. This work may provide parallel insights into the interactions of Abeta with lipid bilayers.
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Affiliation(s)
- Qiuming Wang
- Department of Chemical and Biomolecular Engineering University of Akron, Akron, Ohio 44325, USA
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29
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Chaudhary N, Singh S, Nagaraj R. Morphology of self-assembled structures formed by short peptides from the amyloidogenic protein tau depends on the solvent in which the peptides are dissolved. J Pept Sci 2009; 15:675-84. [DOI: 10.1002/psc.1172] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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30
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Amyloid beta (1-42) folding multiplicity and single-molecule binding behavior studied with STM. J Mol Biol 2009; 388:894-901. [PMID: 19328210 DOI: 10.1016/j.jmb.2009.03.054] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Revised: 01/21/2009] [Accepted: 03/15/2009] [Indexed: 01/08/2023]
Abstract
The fine folding and assembling characteristics of amyloid beta (Abeta) peptides are important to pharmaceutical studies of drug molecules and to the pathological analysis of neurodegenerative disorders such as Alzheimer's disease at the molecular level. Here we present observations of the multiple folding characteristics of amyloid peptide Abeta(42) lamellae using scanning tunneling microscopy. Molecularly resolved core regions of Abeta(42) hairpins and unfolded peptide assembly structures are identified. The parallel assembling characteristics of Abeta(42) hairpins can be confirmed in the study. In addition, single-molecule binding characteristics of Congo red and thioflavin T have been shown to bind at the groove regions of peptide assemblies. This study demonstrates a complementary venue for studying molecular heterogeneity of peptide assemblies, as well as the binding characteristics of molecular modulators.
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31
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Interprotofilament interactions between Alzheimer's Abeta1-42 peptides in amyloid fibrils revealed by cryoEM. Proc Natl Acad Sci U S A 2009; 106:4653-8. [PMID: 19264960 DOI: 10.1073/pnas.0901085106] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Alzheimer's disease is a neurodegenerative disorder characterized by the accumulation of amyloid plaques in the brain. This amyloid primarily contains amyloid-beta (Abeta), a 39- to 43-aa peptide derived from the proteolytic cleavage of the endogenous amyloid precursor protein. The 42-residue-length Abeta peptide (Abeta(1-42)), the most abundant Abeta peptide found in plaques, has a much greater propensity to self-aggregate into fibrils than the other peptides and is believed to be more pathogenic. Synthetic human Abeta(1-42) peptides self-aggregate into stable but poorly-ordered helical filaments. We determined their structure to approximately 10-A resolution by using cryoEM and the iterative real-space reconstruction method. This structure reveals 2 protofilaments winding around a hollow core. Previous hairpin-like NMR models for Abeta(17-42) fit well in the cryoEM density map and reveal that the juxtaposed protofilaments are joined via the N terminus of the peptide from 1 protofilament connecting to the loop region of the peptide in the opposite protofilament. This model of mature Abeta(1-42) fibrils is markedly different from previous cryoEM models of Abeta(1-40) fibrils. In our model, the C terminus of Abeta forms the inside wall of the hollow core, which is supported by partial proteolysis analysis.
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Chaudhary N, Singh S, Nagaraj R. Organic solvent mediated self-association of an amyloid forming peptide from β2-microglobulin: An atomic force microscopy study. Biopolymers 2008; 90:783-91. [DOI: 10.1002/bip.21087] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Rahimi F, Shanmugam A, Bitan G. Structure-function relationships of pre-fibrillar protein assemblies in Alzheimer's disease and related disorders. Curr Alzheimer Res 2008; 5:319-41. [PMID: 18537546 DOI: 10.2174/156720508784533358] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Several neurodegenerative diseases, including Alzheimer's, Parkinson's, Huntington's and prion diseases, are characterized pathognomonically by the presence of intra- and/or extracellular lesions containing proteinaceous aggregates, and by extensive neuronal loss in selective brain regions. Related non-neuropathic systemic diseases, e.g., light-chain and senile systemic amyloidoses, and other organ-specific diseases, such as dialysis-related amyloidosis and type-2 diabetes mellitus, also are characterized by deposition of aberrantly folded, insoluble proteins. It is debated whether the hallmark pathologic lesions are causative. Substantial evidence suggests that these aggregates are the end state of aberrant protein folding whereas the actual culprits likely are transient, pre-fibrillar assemblies preceding the aggregates. In the context of neurodegenerative amyloidoses, the proteinaceous aggregates may eventuate as potentially neuroprotective sinks for the neurotoxic, oligomeric protein assemblies. The pre-fibrillar, oligomeric assemblies are believed to initiate the pathogenic mechanisms that lead to synaptic dysfunction, neuronal loss, and disease-specific regional brain atrophy. The amyloid beta-protein (Abeta), which is believed to cause Alzheimer's disease (AD), is considered an archetypal amyloidogenic protein. Intense studies have led to nominal, functional, and structural descriptions of oligomeric Abeta assemblies. However, the dynamic and metastable nature of Abeta oligomers renders their study difficult. Different results generated using different methodologies under different experimental settings further complicate this complex area of research and identification of the exact pathogenic assemblies in vivo seems daunting. Here we review structural, functional, and biological experiments used to produce and study pre-fibrillar Abeta assemblies, and highlight similar studies of proteins involved in related diseases. We discuss challenges that contemporary researchers are facing and future research prospects in this demanding yet highly important field.
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Affiliation(s)
- F Rahimi
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095-7334, USA
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Rubin N, Perugia E, Goldschmidt M, Fridkin M, Addadi L. Chirality of Amyloid Suprastructures. J Am Chem Soc 2008; 130:4602-3. [DOI: 10.1021/ja800328y] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Noa Rubin
- Department of Structural Biology and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel 76100
| | - Emanuel Perugia
- Department of Structural Biology and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel 76100
| | - Michal Goldschmidt
- Department of Structural Biology and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel 76100
| | - Mati Fridkin
- Department of Structural Biology and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel 76100
| | - Lia Addadi
- Department of Structural Biology and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel 76100
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35
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Kellermayer MSZ, Karsai A, Benke M, Soós K, Penke B. Stepwise dynamics of epitaxially growing single amyloid fibrils. Proc Natl Acad Sci U S A 2008; 105:141-4. [PMID: 18162558 PMCID: PMC2224175 DOI: 10.1073/pnas.0704305105] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Indexed: 11/18/2022] Open
Abstract
The assembly mechanisms of amyloid fibrils, tissue deposits in a variety of degenerative diseases, is poorly understood. With a simply modified application of the atomic force microscope, we monitored the growth, on mica surface, of individual fibrils of the amyloid beta25-35 peptide with near-subunit spatial and subsecond temporal resolution. Fibril assembly was polarized and discontinuous. Bursts of rapid (up to 300-nm(-1)) growth phases that extended the fibril by approximately 7 nm or its integer multiples were interrupted with pauses. Stepwise dynamics were also observed for amyloid beta1-42 fibrils growing on graphite, suggesting that the discontinuous assembly mechanisms may be a general feature of epitaxial amyloid growth. Amyloid assembly may thus involve fluctuation between a fast-growing and a blocked state in which the fibril is kinetically trapped because of intrinsic structural features. The used scanning-force kymography method may be adapted to analyze the assembly dynamics of a wide range of linear biopolymers.
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Affiliation(s)
- Miklós S Z Kellermayer
- Department of Biophysics, Faculty of Medicine, University of Pécs, Szigeti út 12, H-7624, Pécs, Hungary.
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36
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Long X, Zhang C, Cheng J, Bi S. A novel method for study of the aggregation of protein induced by metal ion aluminum(III) using resonance Rayleigh scattering technique. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2008; 69:71-7. [PMID: 17434334 DOI: 10.1016/j.saa.2007.03.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2006] [Revised: 03/09/2007] [Accepted: 03/13/2007] [Indexed: 05/14/2023]
Abstract
We present a novel method for the study of the aggregation of protein induced by metal ion aluminum(III) using resonance Rayleigh scattering (RRS) technique. In neutral Tris-HCl medium, the effect of this aggregation of protein results in the enhancement of RRS intensity and the relationship between the enhancement of the RRS signal and the Al concentration is nonlinear. On this basis, we established a new method for the determination of the critical induced-aggregation concentrations (C(CIAC)) of metal ion Al(III) inducing the protein aggregation. Our results show that many factors, such as, pH value, anions, salts, temperature and solvents have obvious effects. We also studied the extent of aggregation and structural changes using ultra-violet spectrometry, protein intrinsic fluorescence and circular dichroism to further understand the exact mechanisms of the aggregation characteristics of proteins induced by metal ion Al(III) at the molecular level, to help us to develop effective methods to investigate the toxicity of metal ion Al, and to provide theoretical and quantitative evidences for the development of appropriate treatments for neurodementia such as Parkinson's disease, Alzheimer's disease and dementia related to dialysis.
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Affiliation(s)
- Xiufen Long
- School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210093, China
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37
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Abstract
Protein misfolding and the subsequent assembly of protein molecules into aggregates of various morphologies represent common mechanisms that link a number of important human diseases, known as protein-misfolding diseases. The current list of these disorders includes (but is not limited to) numerous neurodegenerative diseases, cataracts, arthritis, medullary carcinoma of the thyroid, late-onset diabetes mellitus, symptomatic (hemodialysis-related) beta(2)-microglobulin amyloidosis, arthritis and many other systemic, localized and familial amyloidoses. Progress in understanding protein-misfolding pathologies and in potential rational drug design aimed at the inhibition or reversal of protein aggregation depends on our ability to study the details of the misfolding process, to follow the aggregation process and to see and analyze the structure and mechanical properties of the aggregated particles. Nanoimaging provides a method to monitor the aggregation process, visualize protein aggregates and analyze their properties and provides fundamental knowledge of key factors that lead to protein misfolding and self-assembly in various protein-misfolding pathologies, therefore advancing medicine dramatically.
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Affiliation(s)
- Vladimir N Uversky
- Indiana University School of Medicine, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, IN, USA.
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38
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Charge transport and intrinsic fluorescence in amyloid-like fibrils. Proc Natl Acad Sci U S A 2007; 104:18019-24. [PMID: 17984067 DOI: 10.1073/pnas.0702843104] [Citation(s) in RCA: 150] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The self-assembly of polypeptides into stable, conductive, and intrinsically fluorescent biomolecular nanowires is reported. We have studied the morphology and electrical conduction of fibrils made of an elastin-related polypeptide, poly(ValGlyGlyLeuGly). These amyloid-like nanofibrils, with a diameter ranging from 20 to 250 nm, result from self-assembly in aqueous solution at neutral pH. Their morphological properties and conductivity have been investigated by atomic force microscopy, scanning tunneling microscopy, and two-terminal transport experiments at the micro- and nanoscales. We demonstrate that the nanofibrils can sustain significant electrical conduction in the solid state at ambient conditions and have remarkable stability. We also show intrinsic blue-green fluorescence of the nanofibrils by confocal microscopy analyses. These results indicate that direct (label-free) excitation can be used to investigate the aggregation state or the polymorphism of amyloid-like fibrils (and possibly of other proteinaceous material) and open up interesting perspectives for the use of peptide-based nanowire structures, with tunable physical and chemical properties, for a wide range of nanobiotechnological and bioelectronic applications.
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39
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Hepler RW, Grimm KM, Nahas DD, Breese R, Dodson EC, Acton P, Keller PM, Yeager M, Wang H, Shughrue P, Kinney G, Joyce JG. Solution state characterization of amyloid beta-derived diffusible ligands. Biochemistry 2006; 45:15157-67. [PMID: 17176037 DOI: 10.1021/bi061850f] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A growing body of evidence suggests that soluble oligomeric forms of the amyloid beta peptide known as amyloid-derived diffusible ligands (ADDLs) are the toxic species responsible for neurodegeneration associated with Alzheimer's disease. Accurate biophysical characterization of ADDL preparations is hampered by the peptide's strong tendency to self-associate and the effect of factors such as ionic strength, temperature, and pH on its behavior. In addition, amyloid peptides are known to interact with common laboratory excipients, specifically detergents, further complicating the results from standard analytical methods such as denaturing polyacrylamide gel electrophoresis. We have studied the solution behavior of various amyloid peptide preparations using analytical ultracentrifugation and size exclusion chromatography coupled with multiangle laser light scattering. Our results indicate that ADDL preparations exist in solution primarily as a binary mixture of a monomeric peptide and high-molecular mass oligomers. We relate our findings to previously described characterizations utilizing atomic force microscopy and electrophoretic methods and demonstrate that low-molecular mass oligomers identified by gel electrophoresis likely represent artifacts induced by the peptide's interaction with detergent, while atomic force microscopy results are likely skewed by differential binding of monomeric and oligomeric peptide species. Finally, we confirm that only the high-molecular mass oligomeric components of an ADDL preparation are capable of binding to subpopulations of primary hippocampal neurons in vitro.
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Affiliation(s)
- Robert W Hepler
- Department of Vaccine & Biologics Research, Merck Research Laboratories, West Point, Pennsylvania 19486, USA.
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40
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Mastrangelo IA, Ahmed M, Sato T, Liu W, Wang C, Hough P, Smith SO. High-resolution Atomic Force Microscopy of Soluble Aβ42 Oligomers. J Mol Biol 2006; 358:106-19. [PMID: 16499926 DOI: 10.1016/j.jmb.2006.01.042] [Citation(s) in RCA: 179] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Revised: 12/12/2005] [Accepted: 01/09/2006] [Indexed: 11/25/2022]
Abstract
Soluble oligomers and protofibrils are widely thought to be the toxic forms of the Abeta42 peptide associated with Alzheimer's disease. We have investigated the structure and formation of these assemblies using a new approach in atomic force microscopy (AFM) that yields high-resolution images of hydrated proteins and allows the structure of the smallest molecular weight (MW) oligomers to be observed and characterized. AFM images of monomers, dimers and other low MW oligomers at early incubation times (< 1h) are consistent with a hairpin structure for the monomeric Abeta42 peptide. The low MW oligomers are relatively compact and have significant order. The most constant dimension of these oligomers is their height (approximately 1-3 nm) above the mica surface; their lateral dimensions (width and length) vary between 5 nm and 10nm. Flat nascent protofibrils with lengths of over 40 nm are observed at short incubation times (< or = 3h); their lateral dimensions of 6-8 nm are consistent with a mass-per-length of 9 kDa/nm previously predicted for the elementary fibril subunit. High MW oligomers with lateral dimensions of 15-25 nm and heights ranging from 2-8 nm are common at high concentrations of Abeta. We show that an inhibitor designed to block the sheet-to-sheet packing in Abeta fibrils is able to cap the heights of these oligomers at approximately 4 nm. The observation of fine structure in the high MW oligomers suggests that they are able to nucleate fibril formation. AFM images obtained as a function of incubation time reveal a sequence of assembly from monomers to soluble oligomers and protofibrils.
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41
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Losic D, Martin LL, Mechler A, Aguilar MI, Small DH. High resolution scanning tunnelling microscopy of the beta-amyloid protein (Abeta1-40) of Alzheimer's disease suggests a novel mechanism of oligomer assembly. J Struct Biol 2006; 155:104-10. [PMID: 16650774 DOI: 10.1016/j.jsb.2006.02.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2005] [Revised: 02/21/2006] [Accepted: 02/24/2006] [Indexed: 10/24/2022]
Abstract
The aggregation of the beta-amyloid protein (Abeta) is an important step in the pathogenesis of Alzheimer's disease. There is increasing evidence that lower molecular weight oligomeric forms of Abeta may be the most toxic species in vivo. However, little is known about the structure of Abeta oligomers. In this study, scanning tunnelling microscopy (STM) was used to examine the structure of Abeta monomers, dimers and oligomers. Abeta1-40 was visualised by STM on a surface of atomically flat gold. At low concentrations (0.5 microM) small globular structures were observed. High resolution STM of these structures revealed them to be monomers of Abeta. The monomers measured approximately 3-4 nm in diameter. Internal structure was seen in many of the monomers consistent with a conformation in which the polypeptide chain is folded into 3 or 4 domains. Oligomers were seen after ageing the Abeta solution for 24 h. The oligomers were also 3-4 nm in width and appeared to be formed by the end-to-end association of monomers with the polypeptide chain oriented at 90 degrees to the axis of the oligomer. The results suggest that the oligomer formation can proceed through a mechanism involving the linear association of monomers.
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Affiliation(s)
- Dusan Losic
- Department of Biochemistry and Molecular Biology, Monash University, Vic. 3800, Australia
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42
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Arimon M, Díez-Pérez I, Kogan MJ, Durany N, Giralt E, Sanz F, Fernàndez-Busquets X. Fine structure study of Abeta1-42 fibrillogenesis with atomic force microscopy. FASEB J 2005; 19:1344-6. [PMID: 15919759 DOI: 10.1096/fj.04-3137fje] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
One of the hallmarks of Alzheimer's disease is the self-aggregation of the amyloid beta peptide (Abeta) in extracellular amyloid fibrils. Among the different forms of Abeta, the 42-residue fragment (Abeta1-42) readily self-associates and forms nucleation centers from where fibrils can quickly grow. The strong tendency of Abeta1-42 to aggregate is one of the reasons for the scarcity of data on its fibril formation process. We have used atomic force microscopy (AFM) to visualize in liquid environment the fibrillogenesis of synthetic Abeta1-42 on hydrophilic and hydrophobic surfaces. The results presented provide nanometric resolution of the main structures characteristic of the several steps from monomeric Abeta1-42 to mature fibrils in vitro. Oligomeric globular aggregates of Abeta1-42 precede the appearance of protofibrils, the first fibrillar species, although we have not obtained direct evidence of oligomer-protofibril interconversion. The protofibril dimensions deduced from our AFM images are consistent with a model that postulates the stacking of the peptide in a hairpin conformation perpendicular to the long axis of the protofibril, forming single beta-sheets ribbon-shaped. The most abundant form of Abeta1-42 fibril exhibits a nodular structure with a ~100-nm periodicity. This length is very similar 1) to the length of protofibril bundles that are the dominant feature at earlier stages in the aggregation process, 2) to the period of helical structures that have been observed in the core of fibrils, and 3) to the distance between regularly spaced, structurally weak fibril points. Taken together, these data are consistent with the existence of a ~100-nm long basic protofibril unit that is a key fibril building block.
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Affiliation(s)
- Muriel Arimon
- Laboratori de Recerca en Nanobioenginyeria, Parc Científic de Barcelona (PCB), Universitat de Barcelona (UB), Spain
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43
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Tiribilli B, Bani D, Quercioli F, Ghirelli A, Vassalli M. Atomic force microscopy of histological sections using a chemical etching method. Ultramicroscopy 2005; 102:227-32. [PMID: 15639354 DOI: 10.1016/j.ultramic.2004.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2004] [Revised: 10/05/2004] [Accepted: 10/12/2004] [Indexed: 11/30/2022]
Abstract
Physiology and pathology have a big deal on tissue morphology, and the intrinsic spatial resolution of an atomic force microscope (AFM) is able to observe ultrastructural details. In order to investigate cellular and subcellular structures in histological sections with the AFM, we used a new simple method for sample preparation, i.e. chemical etching of semithin sections from epoxy resin-embedded specimens: such treatment appears to melt the upper layers of the embedding resin; thus, removing the superficial roughness caused by the edge of the microtome knife and bringing into high relief the biological structures hidden in the bulk. Consecutive ultrathin sections embedded in epoxy resin were observed with a transmission electron microscope (TEM) to compare the different imaging properties on the same specimen sample. In this paper we report, as an example, our AFM and TEM images of two different tissue specimens, rat pancreas and skeletal muscle fibres, showing that most of the inner details are visible with the AFM. These results suggest that chemical etching of histological sections may be a simple, fast and cost-effective method for AFM imaging with ultrastructural resolution.
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Affiliation(s)
- B Tiribilli
- Biophotonics Laboratory, National Institute of Applied Optics, Florence, Italy.
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44
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Abstract
Although the structures of Thioflavin T and another benzothiazole, BTA-1, are similar, they bind to A beta non-competitively, probably to different sites on the A beta(1-40) fibrils. The amyloid fibril-induced fluorescence of ThT that corresponds to a fraction of total ThT binding is not displaced by high concentrations of (S)-naproxen or (R)-ibuprofen, which are reported to potently block high affinity binding of the radiolabeled malononitrile FDDNP and derivatives. The binding of the benzothiazole ligands is significantly substoichiometric with respect to A beta(1-40) monomer peptide, unlike Congo Red, which binds to A beta(1-40) fibrils on a 1:1 basis with monomer peptide. These results indicate that there are multiple domains for ligand binding to amyloid fibrils and suggest that it may be possible to design ligands that bind selectively to particular forms of fibrils that are connected with the pathogenesis of Alzheimer's disease and potentially other protein misfolding diseases.
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Affiliation(s)
- Harry LeVine
- Department of Molecular and Cellular Biochemistry, Chandler School of Medicine and the Center on Aging, University of Kentucky, USA.
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45
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Harris JR. The contribution of microscopy to the study of Alzheimer's disease, amyloid plaques and Abeta fibrillogenesis. Subcell Biochem 2005; 38:1-44. [PMID: 15709471 DOI: 10.1007/0-387-23226-5_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
A broad survey is presented in this chapter, dealing with the impact that microscopy has made to the study of Alzheimer's disease, amyloid plaques and amyloid-beta fibrillogenesis. This includes classical light microscopy and the modem immunolabelling and confocal microscopies, together with the contribution of transmission electron microscopy and atomic force microscopy. Whilst usefully standing alone, the individual microscopies often contribute most effectively when they are integrated with cellular, biophysical and molecular approaches.
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Affiliation(s)
- J Robin Harris
- Institute of Zoology, University of Mainz, D-55099 Mainz, Germany
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46
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Gruden MA, Davudova TB, Malisauskas M, Zamotin VV, Sewell RDE, Voskresenskaya NI, Kostanyan IA, Sherstnev VV, Morozova-Roche LA. Autoimmune responses to amyloid structures of Abeta(25-35) peptide and human lysozyme in the serum of patients with progressive Alzheimer's disease. Dement Geriatr Cogn Disord 2005; 18:165-71. [PMID: 15211072 DOI: 10.1159/000079197] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/30/2004] [Indexed: 01/10/2023] Open
Abstract
We have found an increased level of serum antibodies to the prefibrillar structures of both Abeta(25-35) peptide and human lysozyme in Alzheimer's disease (AD) patients compared to age-matched controls, indicating that autoimmunity is implicated in AD. In the serum of AD patients with a long-term duration (>15 years) the titer of serum antibodies to aggregates of Abeta(25-35) peptide increased by approximately 5-fold, whilst the antibody titer to lysozyme protofilaments decreased by approximately 8-fold compared to patients with AD duration of <5 years. The content of immunoglobulins of the A, G and M types declined, particularly in AD duration of >15 years. An increase in the concentration of immune complexes and higher lysozyme activity was detected in the serum of all patients and this was suggestive of an inflammatory reaction. We propose that the autoimmune response to different amyloid structures in AD can be viewed as a clearance pathway targeting amyloid development. Autoimmune response can be exploited as a marker of ongoing protein aggregation and hence be used as a diagnostic feature of AD.
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Affiliation(s)
- M A Gruden
- P.K. Anokhin Institute of Normal Physiology, RAS, Moscow, Russia
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