1
|
Song J. Molecular mechanisms of phase separation and amyloidosis of ALS/FTD-linked FUS and TDP-43. Aging Dis 2023:AD.2023.1118. [PMID: 38029395 DOI: 10.14336/ad.2023.1118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/18/2023] [Indexed: 12/01/2023] Open
Abstract
FUS and TDP-43, two RNA-binding proteins from the heterogeneous nuclear ribonucleoprotein family, have gained significant attention in the field of neurodegenerative diseases due to their association with amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). They possess folded domains for binding ATP and various nucleic acids including DNA and RNA, as well as substantial intrinsically disordered regions (IDRs) including prion-like domains (PLDs) and RG-/RGG-rich regions. They play vital roles in various cellular processes, including transcription, splicing, microRNA maturation, RNA stability and transport and DNA repair. In particular, they are key components for forming ribonucleoprotein granules and stress granules (SGs) through homotypic or heterotypic liquid-liquid phase separation (LLPS). Strikingly, liquid-like droplets formed by FUS and TDP-43 may undergo aging to transform into less dynamic assemblies such as hydrogels, inclusions, and amyloid fibrils, which are the pathological hallmarks of ALS and FTD. This review aims to synthesize and consolidate the biophysical knowledge of the sequences, structures, stability, dynamics, and inter-domain interactions of FUS and TDP-43 domains, so as to shed light on the molecular mechanisms underlying their liquid-liquid phase separation (LLPS) and amyloidosis. The review further delves into the mechanisms through which ALS-causing mutants of the well-folded hPFN1 disrupt the dynamics of LLPS of FUS prion-like domain, providing key insights into a potential mechanism for misfolding/aggregation-prone proteins to cause neurodegenerative diseases and aging by gain of functions. With better understanding of different biophysical aspects of FUS and TDP-43, the ultimate goal is to develop drugs targeting LLPS and amyloidosis, which could mediate protein homeostasis within cells and lead to new treatments for currently intractable diseases, particularly neurodegenerative diseases such as ALS, FTD and aging. However, the study of membrane-less organelles and condensates is still in its infancy and therefore the review also highlights key questions that require future investigation.
Collapse
|
2
|
Kang S, Kim M, Sun J, Lee M, Min K. Prediction of Protein Aggregation Propensity via Data-Driven Approaches. ACS Biomater Sci Eng 2023; 9:6451-6463. [PMID: 37844262 DOI: 10.1021/acsbiomaterials.3c01001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Protein aggregation occurs when misfolded or unfolded proteins physically bind together and can promote the development of various amyloid diseases. This study aimed to construct surrogate models for predicting protein aggregation via data-driven methods using two types of databases. First, an aggregation propensity score database was constructed by calculating the scores for protein structures in the Protein Data Bank using Aggrescan3D 2.0. Moreover, feature- and graph-based models for predicting protein aggregation have been developed by using this database. The graph-based model outperformed the feature-based model, resulting in an R2 of 0.95, although it intrinsically required protein structures. Second, for the experimental data, a feature-based model was built using the Curated Protein Aggregation Database 2.0 to predict the aggregated intensity curves. In summary, this study suggests approaches that are more effective in predicting protein aggregation, depending on the type of descriptor and the database.
Collapse
Affiliation(s)
- Seungpyo Kang
- School of Mechanical Engineering, Soongsil University, 369 Sangdo-ro, Dongjak-gu 06978, Seoul, Republic of Korea
| | - Minseon Kim
- School of Mechanical Engineering, Soongsil University, 369 Sangdo-ro, Dongjak-gu 06978, Seoul, Republic of Korea
| | - Jiwon Sun
- School of Mechanical Engineering, Soongsil University, 369 Sangdo-ro, Dongjak-gu 06978, Seoul, Republic of Korea
| | - Myeonghun Lee
- School of Systems Biomedical Science, Soongsil University, 369 Sangdo-ro, Dongjak-gu 06978, Seoul, Republic of Korea
| | - Kyoungmin Min
- School of Mechanical Engineering, Soongsil University, 369 Sangdo-ro, Dongjak-gu 06978, Seoul, Republic of Korea
| |
Collapse
|
3
|
Faridi N, Sanjari-Pour M, Wang P, Bathaie SZ. The Effect of Ultrasonication on the Fibrillar/ Oligomeric Structures of Aβ 1-42 at Different Concentrations. Protein J 2023; 42:575-585. [PMID: 37634212 PMCID: PMC10480282 DOI: 10.1007/s10930-023-10138-0] [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] [Accepted: 07/10/2023] [Indexed: 08/29/2023]
Abstract
The number of disease states linked the aberrant regular protein conformations to oligomers and amyloid fibrils. Amyloid beta 1-42 (Aβ1-42) peptide is very hydrophobic and quickly forms the β-rich structure and fibrillar protein aggregates in some solutions and buffer conditions. Ultrasonication pulses can disrupt amyloid fibrils to smaller fragments and produce Aβ1-42 peptides of different sizes and oligomers. Herein, we investigated the effects of buffer and ultrasonication on Aβ1-42 structure at low and high concentrations. After ultrasonication, the Western blot results showed that Aβ1-42 fibrils were disaggregated into different sizes. The transmission electron microscopy results indicated Aβ1-42 at low concentration (25 µM) in Ham's/F12 phenol red-free culture medium formed short-size fragments and oligomers. In comparison, Aβ1-42 at higher concentration (100 µM) formed fibrils that break down into smaller fragments after ultrasonication. However, after regrowth, it formed mature fibrils again. Cell viability assay indicated that Aβ1-42 oligomers formed at a low concentration (25 µM) were more toxic to PC12 cells than other forms. In conclusion, by applying ultrasonication pulses and controlling peptide concentration and buffer condition, we can rich Aβ1-42 aggregates with a particular size and molecular structure.
Collapse
Affiliation(s)
- Nassim Faridi
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box. 14115-133, Tehran, Iran
- Institute for Natural Products and Medicinal Plants, Tarbiat Modares University, Tehran, Iran
| | - Maryam Sanjari-Pour
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box. 14115-133, Tehran, Iran
| | - Ping Wang
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - S Zahra Bathaie
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box. 14115-133, Tehran, Iran.
- Institute for Natural Products and Medicinal Plants, Tarbiat Modares University, Tehran, Iran.
- UCLA-DOE Institute, University of California, Los Angeles, CA, USA.
| |
Collapse
|
4
|
Frese A, Goode C, Zhaliazka K, Holman AP, Dou T, Kurouski D. Length and saturation of fatty acids in phosphatidylserine determine the rate of lysozyme aggregation simultaneously altering the structure and toxicity of amyloid oligomers and fibrils. Protein Sci 2023; 32:e4717. [PMID: 37402649 PMCID: PMC10364468 DOI: 10.1002/pro.4717] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/06/2023]
Abstract
Abrupt aggregation of misfolded proteins is the underlying molecular cause of numerous severe pathologies including Alzheimer's and Parkinson's diseases. Protein aggregation yields small oligomers that can later propagate into amyloid fibrils, β-sheet-rich structures with a variety of topologies. A growing body of evidence suggests that lipids play an important role in abrupt aggregation of misfolded proteins. In this study, we investigate the roles of length and saturation of fatty acids (FAs) in phosphatidylserine (PS), an anionic lipid that is responsible for the recognition of apoptotic cells by macrophages, in lysozyme aggregation. We found that both the length and saturation of FAs in PS contribute to the aggregation rate of insulin. PS with 14-carbon-long FAs (14:0) enabled a much stronger acceleration of protein aggregation compared to PS with 18-carbon-long FAs (18:0). Our results demonstrate that the presence of double bonds in FAs accelerated the rate of insulin aggregation relative to PS with fully saturated FAs. Biophysical methods revealed morphological and structural differences in lysozyme aggregates grown in the presence of PS with varying lengths and FA saturation. We also found that such aggregates exerted diverse cell toxicities. These results demonstrate that the length and saturation of FAs in PS can uniquely alter the stability of misfolded proteins on lipid membranes.
Collapse
Affiliation(s)
- Addison Frese
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTexasUnited States
| | - Cody Goode
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTexasUnited States
| | - Kiryl Zhaliazka
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTexasUnited States
| | - Aidan P. Holman
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTexasUnited States
- Department of EntomologyTexas A&M UniversityCollege StationTexasUnited States
| | - Tianyi Dou
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTexasUnited States
| | - Dmitry Kurouski
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTexasUnited States
- Department of Biomedical EngineeringTexas A&M UniversityCollege StationTexasUnited States
| |
Collapse
|
5
|
Ge WY, Deng X, Shi WP, Lin WJ, Chen LL, Liang H, Wang XT, Zhang TD, Zhao FZ, Guo WH, Yin DC. Amyloid Protein Cross-Seeding Provides a New Perspective on Multiple Diseases In Vivo. Biomacromolecules 2023; 24:1-18. [PMID: 36507729 DOI: 10.1021/acs.biomac.2c01233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Amyloid protein cross-seeding is a peculiar phenomenon of cross-spreading among different diseases. Unlike traditional infectious ones, diseases caused by amyloid protein cross-seeding are spread by misfolded proteins instead of pathogens. As a consequence of the interactions among misfolded heterologous proteins or polypeptides, amyloid protein cross-seeding is considered to be the crucial cause of overlapping pathological transmission between various protein misfolding disorders (PMDs) in multiple tissues and cells. Here, we briefly review the phenomenon of cross-seeding among amyloid proteins. As an interesting example worth mentioning, the potential links between the novel coronavirus pneumonia (COVID-19) and some neurodegenerative diseases might be related to the amyloid protein cross-seeding, thus may cause an undesirable trend in the incidence of PMDs around the world. We then summarize the theoretical models as well as the experimental techniques for studying amyloid protein cross-seeding. Finally, we conclude with an outlook on the challenges and opportunities for basic research in this field. Cross-seeding of amyloid opens up a new perspective in our understanding of the process of amyloidogenesis, which is crucial for the development of new treatments for diseases. It is therefore valuable but still challenging to explore the cross-seeding system of amyloid protein as well as to reveal the structural basis and the intricate processes.
Collapse
Affiliation(s)
- Wan-Yi Ge
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xudong Deng
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Wen-Pu Shi
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Wen-Juan Lin
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Liang-Liang Chen
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Huan Liang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xue-Ting Wang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Tuo-Di Zhang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Feng-Zhu Zhao
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China.,Non-commissioned Officer School, Army Medical University, Shijiazhuang 050081, China
| | - Wei-Hong Guo
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Da-Chuan Yin
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| |
Collapse
|
6
|
Mora M, Board S, Languin-Cattoën O, Masino L, Stirnemann G, Garcia-Manyes S. A Single-Molecule Strategy to Capture Non-native Intramolecular and Intermolecular Protein Disulfide Bridges. NANO LETTERS 2022; 22:3922-3930. [PMID: 35549281 PMCID: PMC9136921 DOI: 10.1021/acs.nanolett.2c00043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/23/2022] [Indexed: 05/04/2023]
Abstract
Non-native disulfide bonds are dynamic covalent bridges that form post-translationally between two cysteines within the same protein (intramolecular) or with a neighboring protein (intermolecular), frequently due to changes in the cellular redox potential. The reversible formation of non-native disulfides is intimately linked to alterations in protein function; while they can provide a mechanism to protect against cysteine overoxidation, they are also involved in the early stages of protein multimerization, a hallmark of several protein aggregation diseases. Yet their identification using current protein chemistry technology remains challenging, mainly because of their fleeting reactivity. Here, we use single-molecule spectroscopy AFM and molecular dynamics simulations to capture both intra- and intermolecular disulfide bonds in γD-crystallin, a cysteine-rich, structural human lens protein involved in age-related eye cataracts. Our approach showcases the power of mechanical force as a conformational probe in dynamically evolving proteins and presents a platform to detect non-native disulfide bridges with single-molecule resolution.
Collapse
Affiliation(s)
- Marc Mora
- Department
of Physics, Randall Centre for Cell and Molecular Biophysics and London
Centre for Nanotechnology, King’s
College London, Strand, WC2R 2LS London, United Kingdom
- Single
Molecule Mechanobiology Laboratory, The
Francis Crick Institute, 1 Midland Road, London NW1 1AT, London United
Kingdom
| | - Stephanie Board
- Department
of Physics, Randall Centre for Cell and Molecular Biophysics and London
Centre for Nanotechnology, King’s
College London, Strand, WC2R 2LS London, United Kingdom
- Single
Molecule Mechanobiology Laboratory, The
Francis Crick Institute, 1 Midland Road, London NW1 1AT, London United
Kingdom
| | - Olivier Languin-Cattoën
- CNRS
Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Diderot,
Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Laura Masino
- Structural
Biology Science Technology Platform, The
Francis Crick Institute, 1 Midland Road London, NW1 1AT, United Kingdom
| | - Guillaume Stirnemann
- CNRS
Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Diderot,
Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Sergi Garcia-Manyes
- Department
of Physics, Randall Centre for Cell and Molecular Biophysics and London
Centre for Nanotechnology, King’s
College London, Strand, WC2R 2LS London, United Kingdom
- Single
Molecule Mechanobiology Laboratory, The
Francis Crick Institute, 1 Midland Road, London NW1 1AT, London United
Kingdom
| |
Collapse
|
7
|
Balasco N, Diaferia C, Morelli G, Vitagliano L, Accardo A. Amyloid-Like Aggregation in Diseases and Biomaterials: Osmosis of Structural Information. Front Bioeng Biotechnol 2021; 9:641372. [PMID: 33748087 PMCID: PMC7966729 DOI: 10.3389/fbioe.2021.641372] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/05/2021] [Indexed: 11/13/2022] Open
Abstract
The discovery that the polypeptide chain has a remarkable and intrinsic propensity to form amyloid-like aggregates endowed with an extraordinary stability is one of the most relevant breakthroughs of the last decades in both protein/peptide chemistry and structural biology. This observation has fundamental implications, as the formation of these assemblies is systematically associated with the insurgence of severe neurodegenerative diseases. Although the ability of proteins to form aggregates rich in cross-β structure has been highlighted by recent studies of structural biology, the determination of the underlying atomic models has required immense efforts and inventiveness. Interestingly, the progressive molecular and structural characterization of these assemblies has opened new perspectives in apparently unrelated fields. Indeed, the self-assembling through the cross-β structure has been exploited to generate innovative biomaterials endowed with promising mechanical and spectroscopic properties. Therefore, this structural motif has become the fil rouge connecting these diversified research areas. In the present review, we report a chronological recapitulation, also performing a survey of the structural content of the Protein Data Bank, of the milestones achieved over the years in the characterization of cross-β assemblies involved in the insurgence of neurodegenerative diseases. A particular emphasis is given to the very recent successful elucidation of amyloid-like aggregates characterized by remarkable molecular and structural complexities. We also review the state of the art of the structural characterization of cross-β based biomaterials by highlighting the benefits of the osmosis of information between these two research areas. Finally, we underline the new promising perspectives that recent successful characterizations of disease-related amyloid-like assemblies can open in the biomaterial field.
Collapse
Affiliation(s)
- Nicole Balasco
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Carlo Diaferia
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples “Federico II”, Naples, Italy
| | - Giancarlo Morelli
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples “Federico II”, Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Antonella Accardo
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples “Federico II”, Naples, Italy
| |
Collapse
|
8
|
Zhang Y, Tang Y, Zhang D, Liu Y, He J, Chang Y, Zheng J. Amyloid cross-seeding between Aβ and hIAPP in relation to the pathogenesis of Alzheimer and type 2 diabetes. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.09.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
9
|
Zhang W, Fan Y. Preparation of Amyloid Fibrils Using Recombinant Technology. Methods Mol Biol 2021; 2347:113-121. [PMID: 34472060 DOI: 10.1007/978-1-0716-1574-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Amyloid fibrils are widely investigated as they are directly associated with various neurodegenerative diseases. For example, a vast of experimental results have shown that the oligomeric and fibrillar aggregates of the amyloid β-peptide (Aβ) play a critical role in the pathogenesis of Alzheimer's disease (AD). Therefore, the accessibility of certain amounts of pure Aβ peptide is necessary for the studies of the mechanism of neurotoxicity. In this regard, recombinant methods provide the possibility to synthesize the Aβ peptide in vitro and thus promote the investigation of the relationship between peptide structure and pathogenic mechanism. These investigations further provide the fundamental supports for developing potential drugs for AD treatment. In addition to providing support for the study of pathogenic mechanisms, the recombination of Aβ peptides also offers the possibility to utilize these unique protein nanomaterials. For example, Aβ peptides tend to assemble into chiral amyloid fibrils with an ultra-high aspect ratio. These unique nano features, together with the inherent protein characteristics, of amyloid fibrils, allow them to be used in biomedical and environmental fields. Accordingly, herein, we aim to introduce the recombinant protocols for the synthesis of Aβ peptides. The experimental route to assemble these peptides to amyloid fibrils is also summarized in this chapter.
Collapse
Affiliation(s)
- Wenwen Zhang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
| | - Yimin Fan
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China.
| |
Collapse
|
10
|
Li Y, Li D, Zhao P, Nandakumar K, Wang L, Song Y. Microfluidics-Based Systems in Diagnosis of Alzheimer's Disease and Biomimetic Modeling. MICROMACHINES 2020; 11:mi11090787. [PMID: 32825153 PMCID: PMC7569794 DOI: 10.3390/mi11090787] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/13/2020] [Accepted: 08/13/2020] [Indexed: 12/21/2022]
Abstract
Early detection and accurate diagnosis of Alzheimer’s disease (AD) is essential for patient care and disease treatment. Microfluidic technology is emerging as an economical and versatile platform in disease detection and diagnosis. It can be conveniently integrated with nanotechnology and/or biological models for biomedical functional and pre-clinical treatment study. These strengths make it advantageous in disease biomarker detection and functional analysis against a wide range of biological backgrounds. This review highlights the recent developments and trends of microfluidic applications in AD research. The first part looks at the principles and methods for AD diagnostic biomarker detection and profiling. The second part discusses how microfluidic chips, especially organ-on-a-chip platforms, could be used as an independent approach and/or integrated with other technologies in AD biomimetic functional analysis.
Collapse
Affiliation(s)
- Yan Li
- Energy Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China; (Y.L.); (P.Z.); (K.N.)
- School of Energy and Power Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Danni Li
- Department of Neurology, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250013, China;
| | - Pei Zhao
- Energy Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China; (Y.L.); (P.Z.); (K.N.)
- School of Energy and Power Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Krishnaswamy Nandakumar
- Energy Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China; (Y.L.); (P.Z.); (K.N.)
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Liqiu Wang
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong, China
- Correspondence: (L.W.); (Y.S.)
| | - Youqiang Song
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
- State Key Laboratory for Cognitive and Brain Sciences, The University of Hong Kong, Hong Kong, China
- Correspondence: (L.W.); (Y.S.)
| |
Collapse
|
11
|
Espargaró A, Llabrés S, Saupe SJ, Curutchet C, Luque FJ, Sabaté R. On the Binding of Congo Red to Amyloid Fibrils. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916630] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Alba Espargaró
- Department of Pharmacy and Pharmaceutical Technology and Physical-ChemistrySchool of Pharmacy and Food SciencesUniversity of Barcelona Joan XXIII, 27–31 08028 Barcelona Spain
- Institute of Nanoscience and Nanotechnology (IN2UB) Spain
| | - Salomé Llabrés
- School of ChemistryUniversity of Edimburgh David Brewster Road EH9 3FJ Edinburgh UK
| | - Sven J. Saupe
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095CNRSUniversité de Bordeaux 1 rue Camille St Saens 33077 Bordeaux France
| | - Carles Curutchet
- Department of Pharmacy and Pharmaceutical Technology and Physical-ChemistrySchool of Pharmacy and Food SciencesUniversity of Barcelona Joan XXIII, 27–31 08028 Barcelona Spain
- Institute of Theoretical and Computational Chemistry (IQTCUB) Spain
| | - F. Javier Luque
- Institute of Theoretical and Computational Chemistry (IQTCUB) Spain
- Department of Nutrition, Food Sciences, and GastronomySchool of Pharmacy and Food SciencesUniversity of Barcelona Prat de la Riba 171 08921 Santa Coloma de Gramenet Spain
- Institute of Biomedicine (IBUB) Spain
| | - Raimon Sabaté
- Department of Pharmacy and Pharmaceutical Technology and Physical-ChemistrySchool of Pharmacy and Food SciencesUniversity of Barcelona Joan XXIII, 27–31 08028 Barcelona Spain
- Institute of Nanoscience and Nanotechnology (IN2UB) Spain
| |
Collapse
|
12
|
Espargaró A, Llabrés S, Saupe SJ, Curutchet C, Luque FJ, Sabaté R. On the Binding of Congo Red to Amyloid Fibrils. Angew Chem Int Ed Engl 2020; 59:8104-8107. [DOI: 10.1002/anie.201916630] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Indexed: 01/17/2023]
Affiliation(s)
- Alba Espargaró
- Department of Pharmacy and Pharmaceutical Technology and Physical-ChemistrySchool of Pharmacy and Food SciencesUniversity of Barcelona Joan XXIII, 27–31 08028 Barcelona Spain
- Institute of Nanoscience and Nanotechnology (IN2UB) Spain
| | - Salomé Llabrés
- School of ChemistryUniversity of Edimburgh David Brewster Road EH9 3FJ Edinburgh UK
| | - Sven J. Saupe
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095CNRSUniversité de Bordeaux 1 rue Camille St Saens 33077 Bordeaux France
| | - Carles Curutchet
- Department of Pharmacy and Pharmaceutical Technology and Physical-ChemistrySchool of Pharmacy and Food SciencesUniversity of Barcelona Joan XXIII, 27–31 08028 Barcelona Spain
- Institute of Theoretical and Computational Chemistry (IQTCUB) Spain
| | - F. Javier Luque
- Institute of Theoretical and Computational Chemistry (IQTCUB) Spain
- Department of Nutrition, Food Sciences, and GastronomySchool of Pharmacy and Food SciencesUniversity of Barcelona Prat de la Riba 171 08921 Santa Coloma de Gramenet Spain
- Institute of Biomedicine (IBUB) Spain
| | - Raimon Sabaté
- Department of Pharmacy and Pharmaceutical Technology and Physical-ChemistrySchool of Pharmacy and Food SciencesUniversity of Barcelona Joan XXIII, 27–31 08028 Barcelona Spain
- Institute of Nanoscience and Nanotechnology (IN2UB) Spain
| |
Collapse
|
13
|
Shenoy J, El Mammeri N, Dutour A, Berbon M, Saad A, Lends A, Morvan E, Grélard A, Lecomte S, Kauffmann B, Theillet FX, Habenstein B, Loquet A. Structural dissection of amyloid aggregates of TDP-43 and its C-terminal fragments TDP-35 and TDP-16. FEBS J 2019; 287:2449-2467. [PMID: 31782904 DOI: 10.1111/febs.15159] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 10/17/2019] [Accepted: 11/27/2019] [Indexed: 12/12/2022]
Abstract
The TAR DNA-binding protein (TDP-43) self-assembles into prion-like aggregates considered to be the structural hallmark of amyotrophic lateral sclerosis and frontotemporal dementia. Here, we use a combination of electron microscopy, X-ray fiber diffraction, Fourier-transform infrared spectroscopy analysis, and solid-state NMR spectroscopy to investigate the molecular organization of different TDP constructs, namely the full-length TDP-43 (1-414), two C-terminal fragments [TDP-35 (90-414) and TDP-16 (267-414)], and a C-terminal truncated fragment (TDP-43 ∆GaroS2), in their fibrillar state. Although the different protein constructs exhibit similar fibril morphology and a typical cross-β signature by X-ray diffraction, solid-state NMR indicates that TDP-43 and TDP-35 share the same polymorphic molecular structure, while TDP-16 encompasses a well-ordered amyloid core. We identified several residues in the so-called C-terminal GaroS2 (368-414) domain that participates in the rigid core of TDP-16 fibrils, underlining its importance during the aggregation process. Our findings demonstrate that C-terminal fragments can adopt a different molecular conformation in isolation or in the context of the full-length assembly, suggesting that the N-terminal domain and RRM domains play an important role in the TDP-43 amyloid transition.
Collapse
Affiliation(s)
- Jayakrishna Shenoy
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Nadia El Mammeri
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Antoine Dutour
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Mélanie Berbon
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Ahmad Saad
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Alons Lends
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Estelle Morvan
- Université de Bordeaux, CNRS, INSERM, UMS3033, Institut Européen de Chimie et Biologie (IECB), Pessac, France
| | - Axelle Grélard
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Sophie Lecomte
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Brice Kauffmann
- Université de Bordeaux, CNRS, INSERM, UMS3033, Institut Européen de Chimie et Biologie (IECB), Pessac, France
| | - François-Xavier Theillet
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Université Paris Sud, UMR 9198, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Birgit Habenstein
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Antoine Loquet
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| |
Collapse
|
14
|
Ren B, Zhang Y, Zhang M, Liu Y, Zhang D, Gong X, Feng Z, Tang J, Chang Y, Zheng J. Fundamentals of cross-seeding of amyloid proteins: an introduction. J Mater Chem B 2019; 7:7267-7282. [PMID: 31647489 DOI: 10.1039/c9tb01871a] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Misfolded protein aggregates formed by the same (homologous) or different (heterologous/cross) sequences are the pathological hallmarks of many protein misfolding diseases (PMDs) including Alzheimer's disease (AD) and type 2 diabetes (T2D). Different from homologous-amyloid aggregation that is solely associated with a specific PMD, cross-amyloid aggregation (i.e. cross-seeding) of different amyloid proteins is more fundamentally and biologically important for understanding and untangling not only the pathological process of each PMD, but also a potential molecular cross-talk between different PMDs. However, the cross-amyloid aggregation is still a subject poorly explored and little is known about its sequence/structure-dependent aggregation mechanisms, as compared to the widely studied homo-amyloid aggregation. Here, we review the most recent and important findings of amyloid cross-seeding behaviors from in vitro, in vivo, and in silico studies. Some typical cross-seeding phenomena between Aβ/hIAPP, Aβ/tau, Aβ/α-synuclein, and tau/α-synuclein are selected and presented, and the underlying specific or general cross-seeding mechanisms are also discussed to better reveal their sequence-structure-property relationships. The potential use of the cross-seeding concept to design amyloid inhibitors is also proposed. Finally, we offer some personal perspectives on current major challenges and future research directions in this less-studied yet important field, and hopefully this work will stimulate more research to explore all possible fundamental and practical aspects of amyloid cross-seeding.
Collapse
Affiliation(s)
- Baiping Ren
- Department of Chemical and Biomolecular Engineering, The University of Akron, Ohio, USA.
| | - Yanxian Zhang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Ohio, USA.
| | - Mingzhen Zhang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Ohio, USA.
| | - Yonglan Liu
- Department of Chemical and Biomolecular Engineering, The University of Akron, Ohio, USA.
| | - Dong Zhang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Ohio, USA.
| | - Xiong Gong
- Department of Polymer Engineering, The University of Akron, Ohio, USA
| | - Zhangqi Feng
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Jianxin Tang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, China
| | - Yung Chang
- Department of Chemical Engineering, R&D Center for Membrane Technology, Chung Yuan Christian University, Taoyuan, Taiwan
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Ohio, USA.
| |
Collapse
|
15
|
Espargaró A, Pont C, Gamez P, Muñoz-Torrero D, Sabate R. Amyloid Pan-inhibitors: One Family of Compounds To Cope with All Conformational Diseases. ACS Chem Neurosci 2019; 10:1311-1317. [PMID: 30380841 DOI: 10.1021/acschemneuro.8b00398] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Amyloids are ubiquitous protein aggregates sharing common internal structural features; they are present in all organisms, from prokaryotes to eukaryotes, where they play physiological or pathological roles. Importantly, amyloids, which are generated by aggregation of a range of distinct proteins, could be a key factor in a number of major human disorders, the so-called conformational diseases. Because all amyloids exhibit similar cross-β motifs, one may envisage that molecules capable of blocking the formation of β-sheet structures could abolish aggregation of all amyloid proteins, albeit with different efficacies. Herein, two different β-sheet blockers were tested against a selection of amyloidogenic proteins, encompassing all the major types of amyloid-based disorders. Analysis of their blocking efficiency, using a simple but contrasted cell-based screening procedure, unequivocally confirms that they indeed behave as aggregation pan-inhibitors. The significant inhibitory effects observed for these compounds against all tested amyloidogenic proteins could spur a broader biological evaluation of other known and new amyloid aggregation inhibitors to further determine the potential use of this class of compounds for the universal treatment of conformational diseases.
Collapse
Affiliation(s)
- Alba Espargaró
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain
| | - Caterina Pont
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
| | - Patrick Gamez
- Department of Organic and Inorganic Chemistry, Faculty of Chemistry, University of Barcelona, E-08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), E-08010 Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain
| | - Diego Muñoz-Torrero
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
- Institute of Biomedicine (IBUB), University of Barcelona, E-08028 Barcelona, Spain
| | - Raimon Sabate
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain
| |
Collapse
|
16
|
Mudedla SK, Murugan NA, Subramanian V, Agren H. Destabilization of amyloid fibrils on interaction with MoS 2-based nanomaterials. RSC Adv 2019; 9:1613-1624. [PMID: 35518018 PMCID: PMC9059571 DOI: 10.1039/c8ra10184a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 12/18/2018] [Indexed: 12/24/2022] Open
Abstract
The present work is motivated by the established concept that the structure and energetics of biomacromolecules can be modulated by confining their dimensions in the nanoscale. In particular, here we use force-field methods to understand the stability of amyloid fibrils at nanostructured interfaces, which can be useful for the development of new therapeutics for Alzheimer's disease. We explore the binding modes and structural properties of fibrils at the interface of molybdenum disulphide nanotubes and the nanosurface using classical molecular dynamics simulations. We find that in general the MoS2 materials induces disruptions in the structure of the amyloid fibrils where the beta sheet conformation of the fibrils changes to a turned conformation, and it is large in the case of nanotubes in comparison to the nanosurfaces. The intermolecular hydrogen bonds, hydrophilic and hydrophobic contacts between the monomer peptides in the fibril are reduced due to their adsorption onto the MoS2 materials, which results in a destabilization of the fibril. The destabilization of fibril is to some extent compensated for by the van der Waals interactions between the fibril and MoS2. Overall the results indicate that MoS2-based materials can be useful in inhibiting the aggregation of smaller protofibrils to matured fibrils and to bust the already formed fibrils. Therapeutic materials should not exhibit any cross interaction with other off-targets compounds. In order to test whether the MoS2 nanomaterial has any such effect we have studied its interaction with two additional biomacromolecules, the human serum albumin and p53 protein, and we report no significant changes in the secondary structure of these biomolecules. Through molecular docking studies we also established that the drug binding ability of HSA is not altered by its surface binding to MoS2 nanosurface.
Collapse
Affiliation(s)
- Sathish Kumar Mudedla
- Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology S-106 91 Stockholm Sweden
| | - Natarajan Arul Murugan
- Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology S-106 91 Stockholm Sweden
| | | | - Hans Agren
- Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology S-106 91 Stockholm Sweden
- College of Chemistry and Chemical Engineering, Henan University Kaifeng Henan 475004 P. R. China
| |
Collapse
|
17
|
Bakels S, Meijer E, Greuell M, Porskamp SBA, Rouwhorst G, Mahé J, Gaigeot MP, Rijs AM. Interactions of aggregating peptides probed by IR-UV action spectroscopy. Faraday Discuss 2019; 217:322-341. [DOI: 10.1039/c8fd00208h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The interplay between intramolecular and formed inter-sheet hydrogen bonds and the effect of dispersion interactions on the formation of peptide dimers is studied using IR-UV action spectroscopy.
Collapse
Affiliation(s)
- Sjors Bakels
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Eline M. Meijer
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Mart Greuell
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Sebastiaan B. A. Porskamp
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - George Rouwhorst
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Jerôme Mahé
- LAMBE CNRS UMR8587
- Université d’Evry val d’Essonne
- 91025 Evry
- France
| | | | - Anouk M. Rijs
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| |
Collapse
|
18
|
John T, Gladytz A, Kubeil C, Martin LL, Risselada HJ, Abel B. Impact of nanoparticles on amyloid peptide and protein aggregation: a review with a focus on gold nanoparticles. NANOSCALE 2018; 10:20894-20913. [PMID: 30225490 DOI: 10.1039/c8nr04506b] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Society is increasingly exposed to nanoparticles as they are ubiquitous in nature and introduced as man-made air pollutants and as functional ingredients in cosmetic products as well as in nanomedicine. Nanoparticles differ in size, shape and material properties. In addition to their intended function, the side effects on biochemical processes in organisms remain unclear. Nanoparticles can significantly influence the nucleation and aggregation process of peptides. The development of several neurodegenerative diseases, such as Alzheimer's disease, is related to the aggregation of peptides into amyloid fibrils. However, there is no comprehensive or universal mechanism to predict or explain apparent acceleration or inhibition of these aggregation processes. In this work, selected studies and possible mechanisms for amyloid peptide nucleation and aggregation, in the presence of nanoparticles, are highlighted. These studies are discussed in the context of recent data from our group on the role of gold nanoparticles in amyloid peptide aggregation using experimental methods and large-scale molecular dynamics simulations. A complex interplay of the surface properties of the nanoparticles, the properties of the peptides, as well as the resulting forces between both the nanoparticles and the peptides, appear to determine whether amyloid peptide aggregation is influenced, catalysed or inhibited by the presence of nanoparticles.
Collapse
Affiliation(s)
- Torsten John
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany.
| | | | | | | | | | | |
Collapse
|
19
|
Varela AE, Lang JF, Wu Y, Dalphin MD, Stangl AJ, Okuno Y, Cavagnero S. Kinetic Trapping of Folded Proteins Relative to Aggregates under Physiologically Relevant Conditions. J Phys Chem B 2018; 122:7682-7698. [DOI: 10.1021/acs.jpcb.8b05360] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Angela E. Varela
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jonathan F. Lang
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Yufan Wu
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Matthew D. Dalphin
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Andrew J. Stangl
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Yusuke Okuno
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| |
Collapse
|
20
|
Kiran Kumar E, Prasad DK, Prakash Prabhu N. Concentration dependent switch in the kinetic pathway of lysozyme fibrillation: Spectroscopic and microscopic analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 183:187-194. [PMID: 28448956 DOI: 10.1016/j.saa.2017.04.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 03/09/2017] [Accepted: 04/14/2017] [Indexed: 06/07/2023]
Abstract
Formation of amyloid fibrils is found to be a general tendency of many proteins. Investigating the kinetic mechanisms and structural features of the intermediates and the final fibrillar state is essential to understand their role in amyloid diseases. Lysozyme, a notable model protein for amyloidogenic studies, readily formed fibrils in vitro at neutral pH in the presence of urea. It, however, showed two different kinetic pathways under varying urea concentrations when probed with thioflavin T (ThT) fluorescence. In 2M urea, lysozyme followed a nucleation-dependent fibril formation pathway which was not altered by varying the protein concentration from 2mg/ml to 8mg/ml. In 4M urea, the protein exhibited concentration dependent change in the mechanism. At lower protein concentrations, lysozyme formed fibrils without any detectable nuclei (nucleation-independent polymerization pathway). When the concentration of the protein was increased above 3mg/ml, the protein followed nucleation-dependent polymerization pathway as observed in the case of 2M urea condition. This was further verified using microscopic images of the fibrils. The kinetic parameters such as lag time, elongation rate, and fibrillation half-time, which were derived from ThT fluorescence changes, showed linear dependency against the initial protein concentration suggested that under the nucleation-dependent pathway conditions, the protein followed primary-nucleation mechanism without any significant secondary nucleation events. The results also suggested that the differences in the initial protein conformation might alter the mechanism of fibrillation; however, at the higher protein concentrations lysozyme shifted to nucleation-dependent pathway.
Collapse
Affiliation(s)
- E Kiran Kumar
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - Deepak Kumar Prasad
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - N Prakash Prabhu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India.
| |
Collapse
|
21
|
Yousaf M, Huang H, Li P, Wang C, Yang Y. Fluorine Functionalized Graphene Quantum Dots as Inhibitor against hIAPP Amyloid Aggregation. ACS Chem Neurosci 2017; 8:1368-1377. [PMID: 28230965 DOI: 10.1021/acschemneuro.7b00015] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Fibrillar deposits of the human islet amyloid polypeptide (hIAPP) are considered as a root of Type II diabetes mellitus. Fluorinated graphene quantum dots (FGQDs) are new carbon nanomaterials with unique physicochemical properties containing highly electronegative F atoms. Herein we report a single step synthesis method of FGQDs with an inhibitory effect on aggregation and cytotoxicity of hIAPP in vitro. Highly fluorescent and water dispersible FGQDs, less than 3 nm in size, were synthesized by the microwave-assisted hydrothermal method. Efficient inhibition capability of FGQDs to amyloid aggregation was demonstrated. The morphologies of hIAPP aggregates were observed to change from the entangled long fibrils to short thin fibrils and amorphous aggregates in the presence of FGQDs. In thioflavin T fluorescence analysis, inhibited aggregation with prolonged lag time and reduced fluorescence intensity at equilibrium were observed when hIAPP was incubated together with FGQDs. Circular dichroism spectrum results reveal that FGQDs could inhibit conformational transition of the peptide from native structure to β-sheets. FGQDs could also rescue the cytotoxicity of INS-1 cells induced by hIAPP in a dose dependent manner. This study could be beneficial for design and preparation of inhibitors for amyloids, which is important for prevention and treatment of amyloidosis.
Collapse
Affiliation(s)
- Maryam Yousaf
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences , 19 A Yuquan Rd, Shijingshan District, Beijing, P. R. China 100049
| | - Huan Huang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Ping Li
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Chen Wang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences , 19 A Yuquan Rd, Shijingshan District, Beijing, P. R. China 100049
| | - Yanlian Yang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences , 19 A Yuquan Rd, Shijingshan District, Beijing, P. R. China 100049
| |
Collapse
|
22
|
Zhang M, Hu R, Ren B, Chen H, Jiang B, Ma J, Zheng J. Molecular Understanding of Aβ-hIAPP Cross-Seeding Assemblies on Lipid Membranes. ACS Chem Neurosci 2017; 8:524-537. [PMID: 27936589 DOI: 10.1021/acschemneuro.6b00247] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Amyloid-β (Aβ) and human islet polypeptide (hIAPP) are the causative agents responsible for Alzheimer's disease (AD) and type II diabetes (T2D), respectively. While numerous studies have reported the cross-seeding behavior of Aβ and hIAPP in solution, little effort has been made to examine the cross-seeding of Aβ and hIAPP in the presence of cell membranes, which is more biologically relevant to the pathological link between AD and T2D. In this work, we computationally study the cross-seeding and adsorption behaviors of Aβ and hIAPP on zwitterionic POPC and anionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylglycerol (POPG) mixed bilayers using all-atom molecular dynamics (MD) simulations, particularly aiming to the effects of the initial orientation of the Aβ-hIAPP assembly and the lipid composition of cell membranes on mutual structural and interaction changes in both Aβ-hIAPP assembly and lipid bilayers at the atomic level. Aβ-hIAPP cross-seeding assembly always preferred to adopt a specific orientation and interface to associate with both lipid bilayers strongly via the N-terminal strands of Aβ. Such membrane-bound orientation explains experimental observation that hybrid Aβ-hIAPP fibrils on cell membranes showed similar morphologies to pure hIAPP fibrils. Moreover, Aβ-hIAPP assembly, regardless of its initial orientations, interacted more strongly with POPC/POPG bilayer than POPC bilayer, indicating that electrostatic interactions are the major forces governing peptide-lipid interactions. Strong electrostatic interactions were also attributed to the formation of Ca2+ bridges connecting both negatively charged Glu of Aβ and PO4 head groups of lipids, which facilitate the association of Aβ-hIAPP with the POPC/POPG bilayer. It was also found that the strong peptide-lipid binding reduced lipid fluidity. Both facts imply that Aβ-hIAPP assembly may induce cell damage by altering calcium homeostasis and cell membrane phase. This work provides a better fundamental understanding of cross-seeding of Aβ and hIAPP on cell membranes and a potential pathological link between AD and T2D.
Collapse
Affiliation(s)
- Mingzhen Zhang
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Rundong Hu
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Baiping Ren
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Hong Chen
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Binbo Jiang
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
- College
of Chemical and Biological Engineering Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Jie Ma
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
- State
Key Laboratory of Pollution Control and Resource Reuse School of Environmental
Science and Engineering, Tongji University, Shanghai 200092, China
| | - Jie Zheng
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| |
Collapse
|
23
|
Abstract
Amyloids are highly ordered protein aggregates that are associated with both disease (including PrP prion, Alzheimer's, and Parkinson's) and biological function. The amyloid structure is composed of the cross-β-sheet entity, which is an almost indefinitely repeating two-layered intermolecular β-sheet motif. The three-dimensional (3D) structure is unique among protein folds because it folds only upon intermolecular contacts (for a folding to occur, only short sequences of amino acid residues are required), and the structure repeats itself at the atomic level (i.e., every 4.7 Å). As a consequence of this structure, among others, it can grow by recruiting corresponding amyloid peptide/protein and thus has the capacity to be an infectious protein (i.e., a prion). Furthermore, its repetitiveness can translate what would be a nonspecific activity as monomer into a potent one through cooperativity. Because of these and other properties, the activities of amyloids are manifold and include peptide storage, template assistance, loss of function, gain of function, generation of toxicity, membrane binding, infectivity, and more. This review summarizes the structural nature of the cross-β-sheet motif on the basis of a few high-resolution structural studies of amyloids in the context of potential biological activities.
Collapse
Affiliation(s)
- Roland Riek
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
| |
Collapse
|
24
|
Pang X, Jia C, Chen Z, Li L. Structural Characterization of Monomers and Oligomers of D-Amino Acid-Containing Peptides Using T-Wave Ion Mobility Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:110-118. [PMID: 27822705 PMCID: PMC5177490 DOI: 10.1007/s13361-016-1523-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/04/2016] [Accepted: 10/06/2016] [Indexed: 05/03/2023]
Abstract
The D-residues are crucial to biological function of D-amino acid containing peptides (DAACPs). Previous ion mobility mass spectrometry (IM-MS) studies revealing oligomerization patterns of amyloid cascade demonstrated conversion from native soluble unstructured assembly to fibril ß-sheet oligomers, which has been implicated in amyloid diseases, such as Alzheimer's disease and type 2 diabetes. Although neuropeptides are typically present at very low concentrations in circulation, their local concentrations could be much higher in large dense core vesicles, forming dimers or oligomers. We studied the oligomerization of protonated and metal-adducted achatin I and dermorphin peptide isomers with IM-MS. Our results suggested that dimerization, oligomerization, and metal adduction augment the structural differences between D/L peptide isomers compared to protonated monomers. Dimers and oligomers enhanced the structural differences between D/L peptide isomers in both aqueous and organic solvent system. Furthermore, some oligomer forms were only observed for either D- or L-isomers, indicating the importance of chiral center in oligomerization process. The oligomerization patterns of D/L isomers appear to be similar. Potassium adducts were detected to enlarge the structural differences between D/L isomers. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Xueqin Pang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Chenxi Jia
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
- National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Beijing Institute of Radiation Medicine, Beijing, 102206, China
| | - Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- School of Life Sciences, Tianjin University, Tianjin, China.
| |
Collapse
|
25
|
Siddiqi MK, Shahein YE, Hussein N, Khan RH. Effect of surfactants on Ra-sHSPI – A small heat shock protein from the cattle tick Rhipicephalus annulatus. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
26
|
Swiontek M, Rozniakowski K, Fraczyk J, Lipinski W, Galecki K, Wysocki S, R Dupont BG, Kaminski ZJ, Kolesinska B. The quest for the shortest fragments of A (13-19) and B (12-17) responsible for the aggregation of human insulin. Nanomedicine (Lond) 2016; 11:2083-101. [PMID: 27463367 DOI: 10.2217/nnm-2016-0100] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To identify the shortest components of A13-A19, B12-B17 fragments capable for fibrillation and to validate the dependability of aggregation on the presence of hydroxyl group engaged in the 'tyrosine kissing'. MATERIALS & METHODS Fragments A13-A19 and B12-B17 of insulin and all shortened analogues were obtained by using DMT/NMM/TosO(-) as a coupling reagent. The aggregation was studied by three independent tests. RESULTS Studies on the susceptibility to aggregation of truncated analogs of insulin amyloidogenic core show three groups of peptides. CONCLUSION Truncation of A13-A419 fragment shows that fibrous structures are formed by all peptides bearing (13)H-LeuTyr-OH(14). Propensity to aggregation was found for (16)H-TyrLeu-OH(17) B12-B17 fragment. Tyrosine residue modification by incorporation of tert-butyl group on hydroxyl function gave analogues still predisposed to aggregation.
Collapse
Affiliation(s)
- Monika Swiontek
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Kamil Rozniakowski
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Justyna Fraczyk
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Wojciech Lipinski
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Krystian Galecki
- Institute of General Food Chemistry, Faculty of Biotechnology & Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland
| | - Stanislaw Wysocki
- Institute of General Food Chemistry, Faculty of Biotechnology & Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland
| | - Bertrand G R Dupont
- Department of Molecular Physics, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Zbigniew J Kaminski
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Beata Kolesinska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| |
Collapse
|
27
|
Herrera MG, Zamarreño F, Costabel M, Ritacco H, Hütten A, Sewald N, Dodero VI. Circular dichroism and electron microscopy studies in vitro of 33-mer gliadin peptide revealed secondary structure transition and supramolecular organization. Biopolymers 2016; 101:96-106. [PMID: 23703327 DOI: 10.1002/bip.22288] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 05/07/2013] [Accepted: 05/09/2013] [Indexed: 12/17/2022]
Abstract
Gliadin, a protein present in wheat, rye, and barley, undergoes incomplete enzymatic degradation during digestion, producing an immunogenic 33-mer peptide, LQLQPF(PQPQLPY)3 PQPQPF. The special features of 33-mer that provoke a break in its tolerance leading to gliadin sensitivity and celiac disease remains elusive. Herein, it is reported that 33-mer gliadin peptide was not only able to fold into polyproline II secondary structure but also depending on concentration resulted in conformational transition and self-assembly under aqueous condition, pH 7.0. A 33-mer dimer is presented as one initial possible step in the self-assembling process obtained by partial electrostatics charge distribution calculation and molecular dynamics. In addition, electron microscopy experiments revealed supramolecular organization of 33-mer into colloidal nanospheres. In the presence of 1 mM sodium citrate, 1 mM sodium borate, 1 mM sodium phosphate buffer, 15 mM NaCl, the nanospheres were stabilized, whereas in water, a linear organization and formation of fibrils were observed. It is hypothesized that the self-assembling process could be the result of the combination of hydrophobic effect, intramolecular hydrogen bonding, and electrostatic complementarity due to 33-mer's high content of proline and glutamine amino acids and its calculated nonionic amphiphilic character. Although, performed in vitro, these experiments have revealed new features of the 33-mer gliadin peptide that could represent an important and unprecedented event in the early stage of 33-mer interaction with the gut mucosa prior to onset of inflammation. Moreover, these findings may open new perspectives for the understanding and treatment of gliadin intolerance disorders.
Collapse
Affiliation(s)
- María G Herrera
- Department of Chemistry, INQUISUR, National University of South, CONICET, Av. Alem 1253, 8000 Bahía Blanca, Argentina
| | | | | | | | | | | | | |
Collapse
|
28
|
Kim B, Do TD, Hayden EY, Teplow DB, Bowers MT, Shea JE. Aggregation of Chameleon Peptides: Implications of α-Helicity in Fibril Formation. J Phys Chem B 2016; 120:5874-83. [PMID: 27001160 DOI: 10.1021/acs.jpcb.6b00830] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigate the relationship between the inherent secondary structure and aggregation propensity of peptides containing chameleon sequences (i.e., sequences that can adopt either α or β structure depending on context) using a combination of replica exchange molecular dynamics simulations, ion-mobility mass spectrometry, circular dichroism, and transmission electron microscopy. We focus on an eight-residue long chameleon sequence that can adopt an α-helical structure in the context of the iron-binding protein from Bacillus anthracis (PDB id 1JIG ) and a β-strand in the context of the baculovirus P35 protein (PDB id 1P35 ). We show that the isolated chameleon sequence is intrinsically disordered, interconverting between α-helical and β-rich conformations. The inherent conformational plasticity of the sequence can be constrained by addition of flanking residues with a given secondary structure propensity. Intriguingly, we show that the chameleon sequence with helical flanking residues aggregates rapidly into fibrils, whereas the chameleon sequence with flanking residues that favor β-conformations has weak aggregation propensity. This work sheds new insights into the possible role of α-helical intermediates in fibril formation.
Collapse
Affiliation(s)
| | | | - Eric Y Hayden
- Department of Neurology, David Geffen School of Medicine at UCLA, Mary S. Easton Center for Alzheimer's Disease Research at UCLA, and Brain Research Institute and Molecular Biology Institute, University of California , 635 Charles Young Drive South, Los Angeles, California 90095, United States
| | - David B Teplow
- Department of Neurology, David Geffen School of Medicine at UCLA, Mary S. Easton Center for Alzheimer's Disease Research at UCLA, and Brain Research Institute and Molecular Biology Institute, University of California , 635 Charles Young Drive South, Los Angeles, California 90095, United States
| | | | | |
Collapse
|
29
|
de Almeida NEC, Do TD, Tro M, LaPointe NE, Feinstein SC, Shea JE, Bowers MT. Opposing Effects of Cucurbit[7]uril and 1,2,3,4,6-Penta-O-galloyl-β-d-glucopyranose on Amyloid β25-35 Assembly. ACS Chem Neurosci 2016; 7:218-26. [PMID: 26629788 PMCID: PMC4758880 DOI: 10.1021/acschemneuro.5b00280] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease characterized by extracellular deposits of amyloid β protein (Aβ) in the brain. The conversion of soluble monomers to amyloid Aβ fibrils is a complicated process and involves several transient oligomeric species, which are widely believed to be highly toxic and play a crucial role in the etiology of AD. The development of inhibitors to prevent formation of small and midsized oligomers is a promising strategy for AD treatment. In this work, we employ ion mobility spectrometry (IMS), transmission electron microscopy (TEM), and molecular dynamics (MD) simulations to elucidate the structural modulation promoted by two potential inhibitors of Aβ oligomerization, cucurbit[7]uril (CB[7]) and 1,2,3,4,6-penta-O-galloyl-β-d-glucopyranose (PGG), on early oligomer and fibril formation of the Aβ25-35 fragment. One and two CB[7] molecules bind to Aβ25-35 monomers and dimers, respectively, and suppress aggregation by remodeling early oligomer structures and inhibiting the formation of higher-order oligomers. On the other hand, nonselective binding was observed between PGG and Aβ25-35. The interactions between PGG and Aβ25-35, surprisingly, enhanced the formation of Aβ aggregates by promoting extended Aβ25-35 conformations in both homo- and hetero-oligomers. When both ligands were present, the inhibitory effect of CB[7] overrode the stimulatory effect of PGG on Aβ25-35 aggregation, suppressing the formation of large amyloid oligomers and eliminating the structural conversion from isotropic to β-rich topologies induced by PGG. Our results provide mechanistic insights into CB[7] and PGG action on Aβ oligomerization. They also demonstrate the power of the IMS technique to investigate mechanisms of multiple small-molecule agents on the amyloid formation process.
Collapse
Affiliation(s)
- Natália E. C. de Almeida
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Thanh D. Do
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Michael Tro
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Nichole E. LaPointe
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, United States
| | - Stuart C. Feinstein
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Michael T. Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
- Corresponding author: Michael T. Bowers. Tel: +1-805-893-2673;
| |
Collapse
|
30
|
Do TD, LaPointe NE, Nelson R, Krotee P, Hayden EY, Ulrich B, Quan S, Feinstein SC, Teplow DB, Eisenberg D, Shea JE, Bowers MT. Amyloid β-Protein C-Terminal Fragments: Formation of Cylindrins and β-Barrels. J Am Chem Soc 2016; 138:549-57. [PMID: 26700445 DOI: 10.1021/jacs.5b09536] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In order to evaluate potential therapeutic targets for treatment of amyloidoses such as Alzheimer's disease (AD), it is essential to determine the structures of toxic amyloid oligomers. However, for the amyloid β-protein peptide (Aβ), thought to be the seminal neuropathogenetic agent in AD, its fast aggregation kinetics and the rapid equilibrium dynamics among oligomers of different size pose significant experimental challenges. Here we use ion-mobility mass spectrometry, in combination with electron microscopy, atomic force microscopy, and computational modeling, to test the hypothesis that Aβ peptides can form oligomeric structures resembling cylindrins and β-barrels. These structures are hypothesized to cause neuronal injury and death through perturbation of plasma membrane integrity. We show that hexamers of C-terminal Aβ fragments, including Aβ(24-34), Aβ(25-35) and Aβ(26-36), have collision cross sections similar to those of cylindrins. We also show that linking two identical fragments head-to-tail using diglycine increases the proportion of cylindrin-sized oligomers. In addition, we find that larger oligomers of these fragments may adopt β-barrel structures and that β-barrels can be formed by folding an out-of-register β-sheet, a common type of structure found in amyloid proteins.
Collapse
Affiliation(s)
- Thanh D Do
- Department of Chemistry and Biochemistry and ‡Department of Physics, ¶Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California , Santa Barbara, California 93106, United States.,Departments of Chemistry and Biochemistry and Biological Chemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, and ∥Department of Neurology, David Geffen School of Medicine at UCLA, ∇Mary S. Easton Center for Alzheimer's Disease Research at UCLA, and Brain Research Institute and Molecular Biology Institute, University of California , 635 Charles Young Drive South, Los Angeles, California 90095, United States
| | - Nichole E LaPointe
- Department of Chemistry and Biochemistry and ‡Department of Physics, ¶Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California , Santa Barbara, California 93106, United States.,Departments of Chemistry and Biochemistry and Biological Chemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, and ∥Department of Neurology, David Geffen School of Medicine at UCLA, ∇Mary S. Easton Center for Alzheimer's Disease Research at UCLA, and Brain Research Institute and Molecular Biology Institute, University of California , 635 Charles Young Drive South, Los Angeles, California 90095, United States
| | - Rebecca Nelson
- Department of Chemistry and Biochemistry and ‡Department of Physics, ¶Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California , Santa Barbara, California 93106, United States.,Departments of Chemistry and Biochemistry and Biological Chemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, and ∥Department of Neurology, David Geffen School of Medicine at UCLA, ∇Mary S. Easton Center for Alzheimer's Disease Research at UCLA, and Brain Research Institute and Molecular Biology Institute, University of California , 635 Charles Young Drive South, Los Angeles, California 90095, United States
| | - Pascal Krotee
- Department of Chemistry and Biochemistry and ‡Department of Physics, ¶Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California , Santa Barbara, California 93106, United States.,Departments of Chemistry and Biochemistry and Biological Chemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, and ∥Department of Neurology, David Geffen School of Medicine at UCLA, ∇Mary S. Easton Center for Alzheimer's Disease Research at UCLA, and Brain Research Institute and Molecular Biology Institute, University of California , 635 Charles Young Drive South, Los Angeles, California 90095, United States
| | - Eric Y Hayden
- Department of Chemistry and Biochemistry and ‡Department of Physics, ¶Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California , Santa Barbara, California 93106, United States.,Departments of Chemistry and Biochemistry and Biological Chemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, and ∥Department of Neurology, David Geffen School of Medicine at UCLA, ∇Mary S. Easton Center for Alzheimer's Disease Research at UCLA, and Brain Research Institute and Molecular Biology Institute, University of California , 635 Charles Young Drive South, Los Angeles, California 90095, United States
| | - Brittany Ulrich
- Department of Chemistry and Biochemistry and ‡Department of Physics, ¶Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California , Santa Barbara, California 93106, United States.,Departments of Chemistry and Biochemistry and Biological Chemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, and ∥Department of Neurology, David Geffen School of Medicine at UCLA, ∇Mary S. Easton Center for Alzheimer's Disease Research at UCLA, and Brain Research Institute and Molecular Biology Institute, University of California , 635 Charles Young Drive South, Los Angeles, California 90095, United States
| | - Sarah Quan
- Department of Chemistry and Biochemistry and ‡Department of Physics, ¶Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California , Santa Barbara, California 93106, United States.,Departments of Chemistry and Biochemistry and Biological Chemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, and ∥Department of Neurology, David Geffen School of Medicine at UCLA, ∇Mary S. Easton Center for Alzheimer's Disease Research at UCLA, and Brain Research Institute and Molecular Biology Institute, University of California , 635 Charles Young Drive South, Los Angeles, California 90095, United States
| | - Stuart C Feinstein
- Department of Chemistry and Biochemistry and ‡Department of Physics, ¶Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California , Santa Barbara, California 93106, United States.,Departments of Chemistry and Biochemistry and Biological Chemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, and ∥Department of Neurology, David Geffen School of Medicine at UCLA, ∇Mary S. Easton Center for Alzheimer's Disease Research at UCLA, and Brain Research Institute and Molecular Biology Institute, University of California , 635 Charles Young Drive South, Los Angeles, California 90095, United States
| | - David B Teplow
- Department of Chemistry and Biochemistry and ‡Department of Physics, ¶Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California , Santa Barbara, California 93106, United States.,Departments of Chemistry and Biochemistry and Biological Chemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, and ∥Department of Neurology, David Geffen School of Medicine at UCLA, ∇Mary S. Easton Center for Alzheimer's Disease Research at UCLA, and Brain Research Institute and Molecular Biology Institute, University of California , 635 Charles Young Drive South, Los Angeles, California 90095, United States
| | - David Eisenberg
- Department of Chemistry and Biochemistry and ‡Department of Physics, ¶Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California , Santa Barbara, California 93106, United States.,Departments of Chemistry and Biochemistry and Biological Chemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, and ∥Department of Neurology, David Geffen School of Medicine at UCLA, ∇Mary S. Easton Center for Alzheimer's Disease Research at UCLA, and Brain Research Institute and Molecular Biology Institute, University of California , 635 Charles Young Drive South, Los Angeles, California 90095, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry and ‡Department of Physics, ¶Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California , Santa Barbara, California 93106, United States.,Departments of Chemistry and Biochemistry and Biological Chemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, and ∥Department of Neurology, David Geffen School of Medicine at UCLA, ∇Mary S. Easton Center for Alzheimer's Disease Research at UCLA, and Brain Research Institute and Molecular Biology Institute, University of California , 635 Charles Young Drive South, Los Angeles, California 90095, United States
| | - Michael T Bowers
- Department of Chemistry and Biochemistry and ‡Department of Physics, ¶Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California , Santa Barbara, California 93106, United States.,Departments of Chemistry and Biochemistry and Biological Chemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, and ∥Department of Neurology, David Geffen School of Medicine at UCLA, ∇Mary S. Easton Center for Alzheimer's Disease Research at UCLA, and Brain Research Institute and Molecular Biology Institute, University of California , 635 Charles Young Drive South, Los Angeles, California 90095, United States
| |
Collapse
|
31
|
Kinnunen PKJ, Domanov YA, Mattila JP, Varis T. Formation of lipid/peptide tubules by IAPP and temporin B on supported lipid membranes. SOFT MATTER 2015; 11:9188-9200. [PMID: 26575388 DOI: 10.1039/b925228b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The conversion of various and to is accelerated by , which are also postulated to represent targets mediating the cytotoxicity of protofibrils. Yet, our understanding of the molecular details governing -catalyzed fibrillogenesis of precursors remains limited. To obtain insight into the intricate interplay of and biophysics we have recently introduced supported bilayers (SLBs) with fluorescent analogs as model biomembranes, observed by time-lapse . Here we demonstrate that human islet () induces within minutes of its application on bilayers the expulsion of numerous flexible tubules from the . Intriguingly, these flexible tubules gradually evolve into a network of straight tubes locally attached to the substrate. Two-color imaging of the and the fluorescently labeled revealed to be distributed along the . Similar linear tubules were observed with the antimicrobial temporin B and the non-amyloidogenic rat , revealing that the above mesoscopic perturbations are not related to formation by the human . Micromanipulation experiments revealed that the linearity of the tubules was caused by tension, stretching the tubules between their points of attachment to the substrate. After longer incubation times, for SLBs containing the oxidatively modified 1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine (, bearing a terminal carboxyl at the end of the chain) and human (but not the other ) some of the straight transformed into highly regular helices. This is likely to reflect tension originating from an efficient aggregation of the into parallelly aligned bundles, associated with tubes containing the oxidized , possibly together with a concomitant flow of along the tubules to the immobile aggregates attaching the tubules to the substrate, these two processes cause, upon shortening of the linear scaffold, the attached excess tubule to adopt a helical morphology, coiling around the core. The above studies are in line with the multiphasic kinetics of fibrillation in the presence of oxidized containing liposomes, assessed by fluorescence enhancement. In addition to demonstrating the feasibility of SLBs as biomimetic model system for studying -assisted fibrillation, our results accentuate the role of chemical composition in modulation of different stages of this process and the associated transformation of architecture. Accordingly, changes in the chemical nature of cellular arising from pathophysiological processes such as oxidative stress may participate in the triggering amyloidogenesis as well as amplification of its detrimental effects in vivo.
Collapse
Affiliation(s)
- Paavo K J Kinnunen
- Helsinki Biophysics & Biomembrane Group, Medical Biochemistry/Institute of Biomedicine, University of Helsinki, P.O. Box 63 (Haartmaninkatu 8), FIN-00014, Finland.
| | - Yegor A Domanov
- Helsinki Biophysics & Biomembrane Group, Medical Biochemistry/Institute of Biomedicine, University of Helsinki, P.O. Box 63 (Haartmaninkatu 8), FIN-00014, Finland.
| | - Juha-Pekka Mattila
- Helsinki Biophysics & Biomembrane Group, Medical Biochemistry/Institute of Biomedicine, University of Helsinki, P.O. Box 63 (Haartmaninkatu 8), FIN-00014, Finland.
| | - Teemu Varis
- Helsinki Biophysics & Biomembrane Group, Medical Biochemistry/Institute of Biomedicine, University of Helsinki, P.O. Box 63 (Haartmaninkatu 8), FIN-00014, Finland.
| |
Collapse
|
32
|
Do TD, de Almeida NEC, LaPointe NE, Chamas A, Feinstein SC, Bowers MT. Amino Acid Metaclusters: Implications of Growth Trends on Peptide Self-Assembly and Structure. Anal Chem 2015; 88:868-76. [PMID: 26632663 DOI: 10.1021/acs.analchem.5b03454] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ion-mobility mass spectrometry is utilized to examine the metacluster formation of serine, asparagine, isoleucine, and tryptophan. These amino acids are representative of different classes of noncharged amino acids. We show that they can form relatively large metaclusters in solution that are difficult or impossible to observe by traditional solution techniques. We further demonstrate, as an example, that the formation of Ser metaclusters is not an ESI artifact because large metaclusters can be detected in negative polarity and low concentration with similar cross sections to those measured in positive polarity and higher concentration. The growth trends of tryptophan and isoleucine metaclusters, along with serine, asparagine, and the previously studied phenylalanine, are balanced among various intrinsic properties of individual amino acids (e.g., hydrophobicity, size, and shape). The metacluster cross sections of hydrophilic residues (Ser, Asn, Trp) tend to stay on or fall below the isotropic model trend lines whereas those of hydrophobic amino acids (Ile, Phe) deviate positively from the isotropic trend lines. The growth trends correlate well to the predicted aggregation propensity of individual amino acids. From the metacluster data, we introduce a novel approach to score and predict aggregation propensity of peptides, which can offer a significant improvement over the existing methods in terms of accuracy. Using a set of hexapeptides, we show that the strong negative deviations of Ser metaclusters from the isotropic model leads a prediction of microcrystalline formation for the SFSFSF peptide, whereas the strong positive deviation of Ile leads to prediction or fibril formation for the NININI peptide. Both predictions are confirmed experimentally using ion mobility and TEM measurements. The peptide SISISI is predicted to only weakly aggregate, a prediction confirmed by TEM.
Collapse
Affiliation(s)
- Thanh D Do
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology University of California , Santa Barbara, California 93106, United States
| | - Natália E C de Almeida
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology University of California , Santa Barbara, California 93106, United States
| | - Nichole E LaPointe
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology University of California , Santa Barbara, California 93106, United States
| | - Ali Chamas
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology University of California , Santa Barbara, California 93106, United States
| | - Stuart C Feinstein
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology University of California , Santa Barbara, California 93106, United States
| | - Michael T Bowers
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology University of California , Santa Barbara, California 93106, United States
| |
Collapse
|
33
|
Sharma A, Bruce KL, Chen B, Gyoneva S, Behrens SH, Bommarius AS, Chernoff YO. Contributions of the Prion Protein Sequence, Strain, and Environment to the Species Barrier. J Biol Chem 2015; 291:1277-88. [PMID: 26565023 DOI: 10.1074/jbc.m115.684100] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Indexed: 11/06/2022] Open
Abstract
Amyloid propagation requires high levels of sequence specificity so that only molecules with very high sequence identity can form cross-β-sheet structures of sufficient stringency for incorporation into the amyloid fibril. This sequence specificity presents a barrier to the transmission of prions between two species with divergent sequences, termed a species barrier. Here we study the relative effects of protein sequence, seed conformation, and environment on the species barrier strength and specificity for the yeast prion protein Sup35p from three closely related species of the Saccharomyces sensu stricto group; namely, Saccharomyces cerevisiae, Saccharomyces bayanus, and Saccharomyces paradoxus. Through in vivo plasmid shuffle experiments, we show that the major characteristics of the transmission barrier and conformational fidelity are determined by the protein sequence rather than by the cellular environment. In vitro data confirm that the kinetics and structural preferences of aggregation of the S. paradoxus and S. bayanus proteins are influenced by anions in accordance with their positions in the Hofmeister series, as observed previously for S. cerevisiae. However, the specificity of the species barrier is primarily affected by the sequence and the type of anion present during the formation of the initial seed, whereas anions present during the seeded aggregation process typically influence kinetics rather than the specificity of prion conversion. Therefore, our work shows that the protein sequence and the conformation variant (strain) of the prion seed are the primary determinants of cross-species prion specificity both in vivo and in vitro.
Collapse
Affiliation(s)
- Aditi Sharma
- From the Schools of Chemical & Biomolecular Engineering and
| | - Kathryn L Bruce
- Biology, Georgia Institute of Technology, Atlanta, Georgia 30332 and
| | - Buxin Chen
- Biology, Georgia Institute of Technology, Atlanta, Georgia 30332 and
| | - Stefka Gyoneva
- Biology, Georgia Institute of Technology, Atlanta, Georgia 30332 and
| | - Sven H Behrens
- From the Schools of Chemical & Biomolecular Engineering and
| | | | - Yury O Chernoff
- Biology, Georgia Institute of Technology, Atlanta, Georgia 30332 and the Laboratory of Amyloid Biology and Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
| |
Collapse
|
34
|
Hu R, Zhang M, Chen H, Jiang B, Zheng J. Cross-Seeding Interaction between β-Amyloid and Human Islet Amyloid Polypeptide. ACS Chem Neurosci 2015; 6:1759-68. [PMID: 26255739 DOI: 10.1021/acschemneuro.5b00192] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Alzheimer's disease (AD) and type 2 diabetes (T2D) are two common protein misfolding diseases. Increasing evidence suggests that these two diseases may be correlated with each other via cross-sequence interactions between β-amyloid peptide (Aβ) associated with AD and human islet amyloid polypeptide (hIAPP) associated with T2D. However, little is known about how these two peptides work and how they interact with each other to induce amyloidogenesis. In this work, we study the effect of cross-sequence interactions between Aβ and hIAPP peptides on hybrid amyloid structures, conformational changes, and aggregation kinetics using combined experimental and simulation approaches. Experimental results confirm that Aβ and hIAPP can interact with each other to aggregate into hybrid amyloid fibrils containing β-sheet-rich structures morphologically similar to pure Aβ and hIAPP. The cross-seeding of Aβ and hIAPP leads to the coexistence of both a retarded process at the initial nucleation stage and an accelerated process at the fibrillization stage, in conjunction with a conformational transition from random structures to α-helix to β-sheet. Further molecular dynamics simulations reveal that Aβ and hIAPP oligomers can efficiently cross-seed each other via the association of two highly similar U-shaped β-sheet structures; thus, conformational compatibility between Aβ and hIAPP aggregates appears to play a key role in determining barriers to cross-seeding. The cross-seeding effects in this work may provide new insights into the molecular mechanisms of interactions between AD and T2D.
Collapse
Affiliation(s)
- Rundong Hu
- Department
of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Mingzhen Zhang
- Department
of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Hong Chen
- Department
of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Binbo Jiang
- Department
of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
- College
of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Jie Zheng
- Department
of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| |
Collapse
|
35
|
Sablón-Carrazana M, Fernández I, Bencomo A, Lara-Martínez R, Rivera-Marrero S, Domínguez G, Pérez-Perera R, Jiménez-García LF, Altamirano-Bustamante NF, Diaz-Delgado M, Vedrenne F, Rivillas-Acevedo L, Pasten-Hidalgo K, Segura-Valdez MDL, Islas-Andrade S, Garrido-Magaña E, Perera-Pintado A, Prats-Capote A, Rodríguez-Tanty C, Altamirano-Bustamante MM. Drug Development in Conformational Diseases: A Novel Family of Chemical Chaperones that Bind and Stabilise Several Polymorphic Amyloid Structures. PLoS One 2015; 10:e0135292. [PMID: 26327208 PMCID: PMC4556714 DOI: 10.1371/journal.pone.0135292] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/20/2015] [Indexed: 11/18/2022] Open
Abstract
The increasing prevalence of conformational diseases, including Alzheimer's disease, type 2 Diabetes Mellitus and Cancer, poses a global challenge at many different levels. It has devastating effects on the sufferers as well as a tremendous economic impact on families and the health system. In this work, we apply a cross-functional approach that combines ideas, concepts and technologies from several disciplines in order to study, in silico and in vitro, the role of a novel chemical chaperones family (NCHCHF) in processes of protein aggregation in conformational diseases. Given that Serum Albumin (SA) is the most abundant protein in the blood of mammals, and Bovine Serum Albumin (BSA) is an off-the-shelf protein available in most labs around the world, we compared the ligandability of BSA:NCHCHF with the interaction sites in the Human Islet Amyloid Polypeptide (hIAPP):NCHCHF, and in the amyloid pharmacophore fragments (Aβ17-42 and Aβ16-21):NCHCHF. We posit that the merging of this interaction sites is a meta-structure of pharmacophore which allows the development of chaperones that can prevent protein aggregation at various states from: stabilizing the native state to destabilizing oligomeric state and protofilament. Furthermore to stabilize fibrillar structures, thus decreasing the amount of toxic oligomers in solution, as is the case with the NCHCHF. The paper demonstrates how a set of NCHCHF can be used for studying and potentially treating the various physiopathological stages of a conformational disease. For instance, when dealing with an acute phase of cytotoxicity, what is needed is the recruitment of cytotoxic oligomers, thus chaperone F, which accelerates fiber formation, would be very useful; whereas in a chronic stage it is better to have chaperones A, B, C, and D, which stabilize the native and fibril structures halting self-catalysis and the creation of cytotoxic oligomers as a consequence of fiber formation. Furthermore, all the chaperones are able to protect and recondition the cerebellar granule cells (CGC) from the cytotoxicity produced by the hIAPP20-29 fragment or by a low potassium medium, regardless of their capacity for accelerating or inhibiting in vitro formation of fibers. In vivo animal experiments are required to study the impact of chemical chaperones in cognitive and metabolic syndromes.
Collapse
Affiliation(s)
- Marquiza Sablón-Carrazana
- Dpto. Neurodiagnóstico, Centro de Neurociencias de Cuba, Cubanacán, Playa, La Habana, Cuba
- Unidad de Investigación Médica en Enfermedades Metabólicas, Hospital de Cardiología, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, México D.F., México
| | - Isaac Fernández
- Unidad de Investigación Médica en Enfermedades Metabólicas, Hospital de Cardiología, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, México D.F., México
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D.F., México
| | - Alberto Bencomo
- Dpto. Neurodiagnóstico, Centro de Neurociencias de Cuba, Cubanacán, Playa, La Habana, Cuba
- Unidad de Investigación Médica en Enfermedades Metabólicas, Hospital de Cardiología, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, México D.F., México
| | - Reyna Lara-Martínez
- Laboratorio de Nanobiología Celular, Departamento de Biología Celular, Facultad de Ciencias, UNAM, México D.F., México
| | | | | | - Rafaela Pérez-Perera
- Dpto. Neurodiagnóstico, Centro de Neurociencias de Cuba, Cubanacán, Playa, La Habana, Cuba
| | - Luis Felipe Jiménez-García
- Laboratorio de Nanobiología Celular, Departamento de Biología Celular, Facultad de Ciencias, UNAM, México D.F., México
| | | | - Massiel Diaz-Delgado
- Dpto. Neurodiagnóstico, Centro de Neurociencias de Cuba, Cubanacán, Playa, La Habana, Cuba
| | - Fernand Vedrenne
- Unidad de Investigación Médica en Enfermedades Metabólicas, Hospital de Cardiología, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, México D.F., México
| | - Lina Rivillas-Acevedo
- Unidad de Investigación Médica en Enfermedades Metabólicas, Hospital de Cardiología, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, México D.F., México
| | - Karina Pasten-Hidalgo
- Servicio de Endocrinología, Instituto Nacional de Pediatría, SS, México D.F., México
- Cátedra Conacyt, México D.F., México
| | | | - Sergio Islas-Andrade
- Unidad de Investigación Médica en Enfermedades Metabólicas, Hospital de Cardiología, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, México D.F., México
| | | | | | | | - Chryslaine Rodríguez-Tanty
- Dpto. Neurodiagnóstico, Centro de Neurociencias de Cuba, Cubanacán, Playa, La Habana, Cuba
- * E-mail: (CR-T); (MMA-B)
| | - Myriam M. Altamirano-Bustamante
- Unidad de Investigación Médica en Enfermedades Metabólicas, Hospital de Cardiología, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, México D.F., México
- * E-mail: (CR-T); (MMA-B)
| |
Collapse
|
36
|
Gladytz A, Lugovoy E, Charvat A, Häupl T, Siefermann KR, Abel B. Intermediates caught in the act: tracing insulin amyloid fibril formation in time by combined optical spectroscopy, light scattering, mass spectrometry and microscopy. Phys Chem Chem Phys 2015; 17:918-27. [DOI: 10.1039/c4cp03072a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Insulin under acidic conditions. PDB-Databank structure visualized with VMD.
Collapse
Affiliation(s)
- A. Gladytz
- Leibniz-Institute of Surface Modification (IOM)
- 04318 Leipzig
- Germany
| | - E. Lugovoy
- Leibniz-Institute of Surface Modification (IOM)
- 04318 Leipzig
- Germany
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie
- Universität Leipzig
| | - A. Charvat
- Leibniz-Institute of Surface Modification (IOM)
- 04318 Leipzig
- Germany
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie
- Universität Leipzig
| | - T. Häupl
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie
- Universität Leipzig
- 04103 Leipzig
- Germany
| | - K. R. Siefermann
- Leibniz-Institute of Surface Modification (IOM)
- 04318 Leipzig
- Germany
| | - B. Abel
- Leibniz-Institute of Surface Modification (IOM)
- 04318 Leipzig
- Germany
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie
- Universität Leipzig
| |
Collapse
|
37
|
Stringfellow HM, Jones MR, Green MC, Wilson AK, Francisco JS. Selectivity in ROS-Induced Peptide Backbone Bond Cleavage. J Phys Chem A 2014; 118:11399-404. [DOI: 10.1021/jp508877m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Hannah M. Stringfellow
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Michael R. Jones
- Department
of Chemistry and Center for Advanced Scientific Computing and Modeling
(CASCaM), University of North Texas, Denton, Texas 76203-5017, United States
| | - Mandy C. Green
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Angela K. Wilson
- Department
of Chemistry and Center for Advanced Scientific Computing and Modeling
(CASCaM), University of North Texas, Denton, Texas 76203-5017, United States
| | - Joseph S. Francisco
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588-0304, United States
| |
Collapse
|
38
|
Bowers MT. Ion mobility spectrometry: A personal view of its development at UCSB. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2014; 370:75-95. [PMID: 25147478 PMCID: PMC4135396 DOI: 10.1016/j.ijms.2014.06.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Ion mobility is not a newly discovered phenomenon. It has roots going back to Langevin at the beginning of the 20th century. Our group initially got involved by accident around 1990 and this paper is a brief account of what has transpired here at UCSB the past 25 years in response to this happy accident. We started small, literally, with transition metal atomic ions and transitioned to carbon clusters, synthetic polymers, most types of biological molecules and eventually peptide and protein oligomeric assembly. Along the way we designed and built several generations of instruments, a process that is still ongoing. And perhaps most importantly we have incorporated theory with experiment from the beginning; a necessary wedding that allows an atomistic face to be put on the otherwise interesting but not fully informative cross section measurements.
Collapse
|
39
|
Greiner ER, Kelly JW, Palhano FL. Immunoprecipitation of amyloid fibrils by the use of an antibody that recognizes a generic epitope common to amyloid fibrils. PLoS One 2014; 9:e105433. [PMID: 25144803 PMCID: PMC4140755 DOI: 10.1371/journal.pone.0105433] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 07/17/2014] [Indexed: 11/30/2022] Open
Abstract
Amyloid fibrils are associated with many maladies, including Alzheimer's disease (AD). The isolation of amyloids from natural materials is very challenging because the extreme structural stability of amyloid fibrils makes it difficult to apply conventional protein science protocols to their purification. A protocol to isolate and detect amyloids is desired for the diagnosis of amyloid diseases and for the identification of new functional amyloids. Our aim was to develop a protocol to purify amyloid from organisms, based on the particular characteristics of the amyloid fold, such as its resistance to proteolysis and its capacity to be recognized by specific conformational antibodies. We used a two-step strategy with proteolytic digestion as the first step followed by immunoprecipitation using the amyloid conformational antibody LOC. We tested the efficacy of this method using as models amyloid fibrils produced in vitro, tissue extracts from C. elegans that overexpress Aβ peptide, and cerebrospinal fluid (CSF) from patients diagnosed with AD. We were able to immunoprecipitate Aβ(1-40) amyloid fibrils, produced in vitro and then added to complex biological extracts, but not α-synuclein and gelsolin fibrils. This method was useful for isolating amyloid fibrils from tissue homogenates from a C. elegans AD model, especially from aged worms. Although we were able to capture picogram quantities of Aβ(1-40) amyloid fibrils produced in vitro when added to complex biological solutions, we could not detect any Aβ amyloid aggregates in CSF from AD patients. Our results show that although immunoprecipitation using the LOC antibody is useful for isolating Aβ(1-40) amyloid fibrils, it fails to capture fibrils of other amyloidogenic proteins, such as α-synuclein and gelsolin. Additional research might be needed to improve the affinity of these amyloid conformational antibodies for an array of amyloid fibrils without compromising their selectivity before application of this protocol to the isolation of amyloids.
Collapse
Affiliation(s)
- Erin R. Greiner
- Departments of Chemistry and Molecular and Experimental Medicine and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jeffery W. Kelly
- Departments of Chemistry and Molecular and Experimental Medicine and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Fernando L. Palhano
- Departments of Chemistry and Molecular and Experimental Medicine and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
40
|
Do TD, LaPointe NE, Sangwan S, Teplow DB, Feinstein SC, Sawaya MR, Eisenberg DS, Bowers MT. Factors that drive peptide assembly from native to amyloid structures: experimental and theoretical analysis of [leu-5]-enkephalin mutants. J Phys Chem B 2014; 118:7247-56. [PMID: 24915112 PMCID: PMC4084844 DOI: 10.1021/jp502473s] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Five different mutants of [Leu-5]
Enkephalin YGGFL peptide have been investigated for fibril formation
propensities. The early oligomer structures have been probed with
a combination of ion-mobility mass spectrometry and computational
modeling. The two peptides YVIFL and YVVFL form oligomers and amyloid-like
fibrils. YVVFV shows an early stage oligomer distribution similar
to those of the previous two, but amyloid-like aggregates are less
abundant. Atomic resolution X-ray structures of YVVFV show two different
modes of interactions at the dry interface between steric zippers
and pairs of antiparallel β-sheets, but both are less favorable
than the packing motif found in YVVFL. Both YVVFV and YVVFL can form
a Class 6 steric zipper. However, in YVVFV, the strands between mating
sheets are parallel to each other and in YVVFL they are antiparallel.
The overall data highlight the importance of structurally characterizing
high order oligomers within oligomerization pathways in studies of
nanostructure assembly.
Collapse
Affiliation(s)
- Thanh D Do
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California , Santa Barbara, California 93106, United States
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Fanghänel S, Wadhwani P, Strandberg E, Verdurmen WPR, Bürck J, Ehni S, Mykhailiuk PK, Afonin S, Gerthsen D, Komarov IV, Brock R, Ulrich AS. Structure analysis and conformational transitions of the cell penetrating peptide transportan 10 in the membrane-bound state. PLoS One 2014; 9:e99653. [PMID: 24937132 PMCID: PMC4061077 DOI: 10.1371/journal.pone.0099653] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 05/18/2014] [Indexed: 11/18/2022] Open
Abstract
Structure analysis of the cell-penetrating peptide transportan 10 (TP10) revealed an exemplary range of different conformations in the membrane-bound state. The bipartite peptide (derived N-terminally from galanin and C-terminally from mastoparan) was found to exhibit prominent characteristics of (i) amphiphilic α-helices, (ii) intrinsically disordered peptides, as well as (iii) β-pleated amyloid fibrils, and these conformational states become interconverted as a function of concentration. We used a complementary approach of solid-state (19)F-NMR and circular dichroism in oriented membrane samples to characterize the structural and dynamical behaviour of TP10 in its monomeric and aggregated forms. Nine different positions in the peptide were selectively substituted with either the L- or D-enantiomer of 3-(trifluoromethyl)-bicyclopent-[1.1.1]-1-ylglycine (CF3-Bpg) as a reporter group for (19)F-NMR. Using the L-epimeric analogs, a comprehensive three-dimensional structure analysis was carried out in lipid bilayers at low peptide concentration, where TP10 is monomeric. While the N-terminal region is flexible and intrinsically unstructured within the plane of the lipid bilayer, the C-terminal α-helix is embedded in the membrane with an oblique tilt angle of ∼ 55° and in accordance with its amphiphilic profile. Incorporation of the sterically obstructive D-CF3-Bpg reporter group into the helical region leads to a local unfolding of the membrane-bound peptide. At high concentration, these helix-destabilizing C-terminal substitutions promote aggregation into immobile β-sheets, which resemble amyloid fibrils. On the other hand, the obstructive D-CF3-Bpg substitutions can be accommodated in the flexible N-terminus of TP10 where they do not promote aggregation at high concentration. The cross-talk between the two regions of TP10 thus exerts a delicate balance on its conformational switch, as the presence of the α-helix counteracts the tendency of the unfolded N-terminus to self-assemble into β-pleated fibrils.
Collapse
Affiliation(s)
- Susanne Fanghänel
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry and DFG-Center for Functional Nanostructures (CFN), Karlsruhe, Germany
| | - Parvesh Wadhwani
- KIT, Institute of Biological Interfaces (IBG2), Karlsruhe, Germany
| | - Erik Strandberg
- KIT, Institute of Biological Interfaces (IBG2), Karlsruhe, Germany
| | - Wouter P. R. Verdurmen
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Jochen Bürck
- KIT, Institute of Biological Interfaces (IBG2), Karlsruhe, Germany
| | - Sebastian Ehni
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry and DFG-Center for Functional Nanostructures (CFN), Karlsruhe, Germany
| | - Pavel K. Mykhailiuk
- Taras Shevchenko National University of Kyiv, Chemistry Department, Kyiv, Ukraine and Enamine Ltd., Kyiv, Ukraine
| | - Sergii Afonin
- KIT, Institute of Biological Interfaces (IBG2), Karlsruhe, Germany
| | | | - Igor V. Komarov
- Taras Shevchenko National University of Kyiv, Institute of High Technologies, Kyiv, Ukraine
| | - Roland Brock
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Anne S. Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry and DFG-Center for Functional Nanostructures (CFN), Karlsruhe, Germany
- KIT, Institute of Biological Interfaces (IBG2), Karlsruhe, Germany
| |
Collapse
|
42
|
Palmal S, Maity AR, Singh BK, Basu S, Jana NR, Jana NR. Inhibition of amyloid fibril growth and dissolution of amyloid fibrils by curcumin-gold nanoparticles. Chemistry 2014; 20:6184-91. [PMID: 24691975 DOI: 10.1002/chem.201400079] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Indexed: 12/20/2022]
Abstract
Inhibition of amyloid fibrillation and clearance of amyloid fibrils/plaques are essential for the prevention and treatment of various neurodegenerative disorders involving protein aggregation. Herein, we report curcumin-functionalized gold nanoparticles (Au-curcumin) of hydrodynamic diameter 10-25 nm, which serve to inhibit amyloid fibrillation and disintegrate/dissolve amyloid fibrils. In nanoparticle form, curcumin is water-soluble and can efficiently interact with amyloid protein/peptide, offering enhanced performance in inhibiting amyloid fibrillation and dissolving amyloid fibrils. Our results imply that nanoparticle-based artificial molecular chaperones may offer a promising therapeutic approach to combat neurodegenerative disease.
Collapse
Affiliation(s)
- Sharbari Palmal
- Centre for Advanced Materials, Indian Association for the Cultivation of Science, Kolkata-700032 (India)
| | | | | | | | | | | |
Collapse
|
43
|
Thangakani AM, Kumar S, Nagarajan R, Velmurugan D, Gromiha MM. GAP: towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies. Bioinformatics 2014; 30:1983-90. [DOI: 10.1093/bioinformatics/btu167] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
|
44
|
Competing aggregation pathways for monoclonal antibodies. FEBS Lett 2014; 588:936-41. [PMID: 24530501 DOI: 10.1016/j.febslet.2014.01.051] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/30/2013] [Accepted: 01/24/2014] [Indexed: 11/22/2022]
Abstract
Aggregation is mediated by local unfolding to allow aggregation "hot spot(s)" to become solvent exposed and available to associate with a hot spot on another partially unfolded protein. Historically, the unfolding of either the crystallizable fragment (Fc) or the antigen binding fragment (Fab) regions of a given monoclonal antibody (MAb) has been implicated in aggregation, with differing results across different proteins. The present work focuses on separately quantifying the aggregation kinetics of isolated Fc, isolated Fab, and intact MAb as a function of pH under accelerated (high temperature) conditions. The results show that both Fab and Fc are aggregation prone and compete within the same MAb.
Collapse
|
45
|
Volpatti LR, Knowles TPJ. Polymer physics inspired approaches for the study of the mechanical properties of amyloid fibrils. ACTA ACUST UNITED AC 2013. [DOI: 10.1002/polb.23428] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Lisa R. Volpatti
- Department of Chemistry; University of Cambridge; Lensfield Road, CB2 1EW United Kingdom
| | - Tuomas P. J. Knowles
- Department of Chemistry; University of Cambridge; Lensfield Road, CB2 1EW United Kingdom
| |
Collapse
|
46
|
Maurer RW, Hunter AK, Wang X, Wang WK, Robinson AS, Roberts CJ. Folding and aggregation of a multi-domain engineered immunotoxin. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2013.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
47
|
Weiss WF, Zhang A, Ivanova MI, Sahin E, Jordan JL, Fernandez EJ, Roberts CJ. Reduction of the C191-C220 disulfide of α-chymotrypsinogen A reduces nucleation barriers for aggregation. Biophys Chem 2013; 185:79-87. [PMID: 24374388 DOI: 10.1016/j.bpc.2013.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 11/05/2013] [Accepted: 11/14/2013] [Indexed: 10/26/2022]
Abstract
Proper disulfide formation can be essential for the conformational stability of natively folded proteins. For proteins that must unfold in order to aggregate, disruption of native disulfides may therefore promote aggregation. This study characterizes differences in the aggregation process for wild-type (WT) α-chymostrypsinogen A (aCgn) and the same molecule with one of its native disulfides (C191-C220) reduced to free thiols (aCgnSH) at acidic pH, where WT aCgn forms semi-flexible amyloid polymers. Loss of the disulfide leads to no discernable differences in folded monomer secondary or tertiary structure based on circular dichroism (CD) or intrinsic fluorescence (FL), and causes a small decrease in the free energy change upon unfolding. After unfolding-mediated aggregation, the resulting amyloid morphology and structure are similar or indistinguishable for aCgn and aCgnSH by CD, FL, ThT binding, multi-angle laser light scattering, and transmission electron microscopy. Aggregates of aCgn and aCgnSH are also able to cross-seed with monomers of the other species. However, aggregates of aCgnSH are more resistive than aCgn aggregates to urea-mediated dissociation, suggesting some degree of structural differences in the aggregated species that was not resolvable in detail without higher resolution methods. Mechanistic analyses of aggregation kinetics indicate that the initiation or nucleation of new aggregates from aCgnSH involves a mono-molecular rate limiting step, possibly the unfolding step. In contrast, that for aCgn involves an oligomeric intermediate, suggesting native disulfide linkages help to hinder non-native protein aggregation by providing conformational barriers to key nucleation event(s).
Collapse
Affiliation(s)
- William F Weiss
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States
| | - Aming Zhang
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA 22904, United States
| | - Magdalena I Ivanova
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, United States
| | - Erinc Sahin
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States
| | - Jacob L Jordan
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA 22904, United States
| | - Erik J Fernandez
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA 22904, United States
| | - Christopher J Roberts
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States.
| |
Collapse
|
48
|
Maurer RW, Hunter AK, Robinson AS, Roberts CJ. Aggregates of α-chymotrypsinogen anneal to access more stable states. Biotechnol Bioeng 2013; 111:782-91. [PMID: 24122552 DOI: 10.1002/bit.25129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 09/19/2013] [Accepted: 10/02/2013] [Indexed: 11/11/2022]
Abstract
Non-native protein aggregates present a variety of problems in fundamental and applied biochemistry and biotechnology, from quality and safety issues in pharmaceutical development to their association with a number of chronic diseases. The aggregated, often amyloid, protein state is often considered to be more thermodynamically and kinetically stable than (partially) unfolded or folded monomers except under highly denaturing conditions. However, evolution of the structure and stability of aggregated states has received much less attention. Here it is shown that under mildly-denaturing conditions (elevated temperature or [urea]), where the native monomer (N) is slightly favored compared to the unfolded state (U), α-chymotrypsinogen A (aCgn) non-native aggregates undergo a structural relaxation or annealing process to reach even more stable states. The annealed aggregates are more resistant to dissociation than aggregates that do not undergo this relaxation process. Aggregates without annealing dissociate via linear chain depolymerization, and annealing is accelerated under conditions that promote slow dissociation (partially denaturing conditions). This is consistent with a free energy landscape with multiple barriers and local minima that allows for a kinetic competition between aggregate dissociation and structural relaxation to more stable aggregate states. This highlights added complexities for protein refolding or aggregate dissociation processes, and may explain why it is often difficult to completely recover monomeric protein from aggregates.
Collapse
Affiliation(s)
- Ronald W Maurer
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, 19716
| | | | | | | |
Collapse
|
49
|
Chaplins of Streptomyces coelicolor self-assemble into two distinct functional amyloids. J Struct Biol 2013; 184:301-9. [DOI: 10.1016/j.jsb.2013.08.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 08/23/2013] [Accepted: 08/27/2013] [Indexed: 11/18/2022]
|
50
|
Petkau-Milroy K, Sonntag MH, Colditz A, Brunsveld L. Multivalent protein assembly using monovalent self-assembling building blocks. Int J Mol Sci 2013; 14:21189-201. [PMID: 24152447 PMCID: PMC3821665 DOI: 10.3390/ijms141021189] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 09/13/2013] [Accepted: 10/08/2013] [Indexed: 11/17/2022] Open
Abstract
Discotic molecules, which self-assemble in water into columnar supramolecular polymers, emerged as an alternative platform for the organization of proteins. Here, a monovalent discotic decorated with one single biotin was synthesized to study the self-assembling multivalency of this system in regard to streptavidin. Next to tetravalent streptavidin, monovalent streptavidin was used to study the protein assembly along the supramolecular polymer in detail without the interference of cross-linking. Upon self-assembly of the monovalent biotinylated discotics, multivalent proteins can be assembled along the supramolecular polymer. The concentration of discotics, which influences the length of the final polymers at the same time dictates the amount of assembled proteins.
Collapse
Affiliation(s)
- Katja Petkau-Milroy
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, Eindhoven 5612AZ, The Netherlands; E-Mails: (K.P.-M.); (M.H.S.); (A.C.)
| | - Michael H. Sonntag
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, Eindhoven 5612AZ, The Netherlands; E-Mails: (K.P.-M.); (M.H.S.); (A.C.)
| | - Alexander Colditz
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, Eindhoven 5612AZ, The Netherlands; E-Mails: (K.P.-M.); (M.H.S.); (A.C.)
| | - Luc Brunsveld
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, Eindhoven 5612AZ, The Netherlands; E-Mails: (K.P.-M.); (M.H.S.); (A.C.)
| |
Collapse
|