1
|
Phetsanthad A, Vu NQ, Yu Q, Buchberger AR, Chen Z, Keller C, Li L. Recent advances in mass spectrometry analysis of neuropeptides. MASS SPECTROMETRY REVIEWS 2023; 42:706-750. [PMID: 34558119 PMCID: PMC9067165 DOI: 10.1002/mas.21734] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 08/22/2021] [Accepted: 08/28/2021] [Indexed: 05/08/2023]
Abstract
Due to their involvement in numerous biochemical pathways, neuropeptides have been the focus of many recent research studies. Unfortunately, classic analytical methods, such as western blots and enzyme-linked immunosorbent assays, are extremely limited in terms of global investigations, leading researchers to search for more advanced techniques capable of probing the entire neuropeptidome of an organism. With recent technological advances, mass spectrometry (MS) has provided methodology to gain global knowledge of a neuropeptidome on a spatial, temporal, and quantitative level. This review will cover key considerations for the analysis of neuropeptides by MS, including sample preparation strategies, instrumental advances for identification, structural characterization, and imaging; insightful functional studies; and newly developed absolute and relative quantitation strategies. While many discoveries have been made with MS, the methodology is still in its infancy. Many of the current challenges and areas that need development will also be highlighted in this review.
Collapse
Affiliation(s)
- Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Nhu Q. Vu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Qing Yu
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Amanda R. Buchberger
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Caitlin Keller
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| |
Collapse
|
2
|
Root-Bernstein R, Churchill B. Co-Evolution of Opioid and Adrenergic Ligands and Receptors: Shared, Complementary Modules Explain Evolution of Functional Interactions and Suggest Novel Engineering Possibilities. Life (Basel) 2021; 11:life11111217. [PMID: 34833093 PMCID: PMC8623292 DOI: 10.3390/life11111217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 12/14/2022] Open
Abstract
Cross-talk between opioid and adrenergic receptors is well-characterized and involves second messenger systems, the formation of receptor heterodimers, and the presence of extracellular allosteric binding regions for the complementary ligand; however, the evolutionary origins of these interactions have not been investigated. We propose that opioid and adrenergic ligands and receptors co-evolved from a common set of modular precursors so that they share binding functions. We demonstrate the plausibility of this hypothesis through a review of experimental evidence for molecularly complementary modules and report unexpected homologies between the two receptor types. Briefly, opioids form homodimers also bind adrenergic compounds; opioids bind to conserved extracellular regions of adrenergic receptors while adrenergic compounds bind to conserved extracellular regions of opioid receptors; opioid-like modules appear in both sets of receptors within key ligand-binding regions. Transmembrane regions associated with homodimerization of each class of receptors are also highly conserved across receptor types and implicated in heterodimerization. This conservation of multiple functional modules suggests opioid–adrenergic ligand and receptor co-evolution and provides mechanisms for explaining the evolution of their crosstalk. These modules also suggest the structure of a primordial receptor, providing clues for engineering receptor functions.
Collapse
|
3
|
Cawood EE, Karamanos TK, Wilson AJ, Radford SE. Visualizing and trapping transient oligomers in amyloid assembly pathways. Biophys Chem 2020; 268:106505. [PMID: 33220582 PMCID: PMC8188297 DOI: 10.1016/j.bpc.2020.106505] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 12/31/2022]
Abstract
Oligomers which form during amyloid fibril assembly are considered to be key contributors towards amyloid disease. However, understanding how such intermediates form, their structure, and mechanisms of toxicity presents significant challenges due to their transient and heterogeneous nature. Here, we discuss two different strategies for addressing these challenges: use of (1) methods capable of detecting lowly-populated species within complex mixtures, such as NMR, single particle methods (including fluorescence and force spectroscopy), and mass spectrometry; and (2) chemical and biological tools to bias the amyloid energy landscape towards specific oligomeric states. While the former methods are well suited to following the kinetics of amyloid assembly and obtaining low-resolution structural information, the latter are capable of producing oligomer samples for high-resolution structural studies and inferring structure-toxicity relationships. Together, these different approaches should enable a clearer picture to be gained of the nature and role of oligomeric intermediates in amyloid formation and disease. Methods to study structure, toxicity, and kinetics of transient amyloid oligomers. NMR and single particle methods can characterize lowly-populated oligomers. Chemical tools/antibodies stabilize oligomers for structural and toxicity studies A combination of methods is needed to fully characterize amyloid assembly pathways.
Collapse
Affiliation(s)
- Emma E Cawood
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK; Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK.
| |
Collapse
|
4
|
Hu J, Zheng Q. Applications of Mass Spectrometry in the Onset of Amyloid Fibril Formation: Focus on the Analysis of Early-Stage Oligomers. Front Chem 2020; 8:324. [PMID: 32432078 PMCID: PMC7215083 DOI: 10.3389/fchem.2020.00324] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/30/2020] [Indexed: 02/05/2023] Open
Abstract
Amyloid fibril formation is a hallmark of diverse neurodegenerative and metabolic diseases, such as Alzheimer's disease (AD), Parkinson's disease (PD), and type 2 diabetes mellitus (T2DM). Conventional diagnosis is based on the appearance of fibrils or plaques, while neglects the role of early-stage oligomers in the disease progression. Recent studies have uncovered that it is the early-stage oligomer, rather than the mature fibril, that greatly contributes cytotoxicity. The formation of oligomers involves complicate structural conversions and it is essential to investigate their conformational changes for a better understanding of aggregation mechanism. The coexistence of soluble early-stage oligomers, intermediates, and pre-fibril species makes it difficult to be differentiate by morphological methods, and only average structural information is provided as they lack the ability of separation. Therefore, mass spectrometry (MS) becomes an alternative technique that presents new and complementary insights into the onset of amyloid fibrils. This review highlights the hotspots and important achievements by MS in the field of amyloid formation mechanism, including the direct detection and differentiation of soluble oligomers (native MS), unambiguous identification of interacted sites involved in the onset of aggregation [hydrogen/deuterium exchange (HDX) and chemical cross-linking (CX)], and conformational switch that leads to fibrilization [collision cross section (CCS) regularity by ion mobility (IM)].
Collapse
Affiliation(s)
- Jiaojiao Hu
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Qiuling Zheng
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| |
Collapse
|
5
|
Larocca M, Foglia F, Cilibrizzi A. Dihedral Angle Calculations To Elucidate the Folding of Peptides through Its Main Mechanical Forces. Biochemistry 2019; 58:1032-1037. [PMID: 30719916 DOI: 10.1021/acs.biochem.8b01101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study reports a general method to calculate dihedral angles (φ and ψ) of a given amino acid sequence, focusing on potential energy and torque moment concepts. By defining these physical measures in relation to the chemical interactions that occur on each single amino acid residue within a peptide, we analyze the folding process as the result of main mechanical forces (MMFs) exerted in the specific amino acid chain of interest. As a proof of concept, Leu-enkephalin was initially used as a model peptide to carry out the theoretical study. Our data show agreement between calculated Leu-enkephalin backbone dihedral angles and the corresponding experimentally determined X-ray values. Hence, we used calcitonin to validate our MMF-based method on a larger peptide, i.e., 32 amino acid residues forming an α-helix. Through a similar approach (although simplified with regard to electrostatic interactions), the calculations for calcitonin also demonstrate a good agreement with experimental values. This study offers new opportunities to analyze peptides' amino acid sequences and to help in the prediction of how they must fold, assisting in the development of new computational techniques in the field.
Collapse
Affiliation(s)
- Michele Larocca
- Institute of Pharmaceutical Science , King's College London , Stamford Street , London SE1 9NH , U.K
| | - Fabrizia Foglia
- Institute of Pharmaceutical Science , King's College London , Stamford Street , London SE1 9NH , U.K
| | - Agostino Cilibrizzi
- Institute of Pharmaceutical Science , King's College London , Stamford Street , London SE1 9NH , U.K
| |
Collapse
|
6
|
Song R, Wu X, Xue B, Yang Y, Huang W, Zeng G, Wang J, Li W, Cao Y, Wang W, Lu J, Dong H. Principles Governing Catalytic Activity of Self-Assembled Short Peptides. J Am Chem Soc 2018; 141:223-231. [PMID: 30562022 DOI: 10.1021/jacs.8b08893] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Molecular self-assembly provides a chemical strategy for the synthesis of nanostructures by using the principles of nature, and peptides serve as the promising building blocks to construct adaptable molecular architectures. Recently, a series of heptapeptides with alternative hydrophobic and hydrophilic residues were reported to form amyloid-like structures, which are capable of catalyzing acyl ester hydrolysis with remarkable efficiency. However, information remains elusive about the atomic structures of the fibrils. What is the origin of the sequence-dependent catalytic activity? How is the ester hydrolysis catalyzed by the fibrils? In this work, the atomic structures of the aggregates were determined by using molecular modeling and further validated by solid-state NMR experiments, where the fibril with high activity adopts twisted parallel configuration within each layer, and the one with low activity is in flat antiparallel configuration. The polymorphism originates from the interactions between different regions of the building block peptides, where the delicate balance between rigidity and flexibility plays an important role. We further show that the p-nitrophenylacetate ( pNPA) hydrolysis reactions catalyzed by two different fibrils follow a similar mechanism, and the difference in microenvironment at the active site between the natural enzyme and the present self-assembled fibrils should account for the discrepancy in catalytic activities. The present work provides understanding of the structure and function of self-assembled fibrils formed with short peptides at an atomic level and thus sheds new insight on designing aggregates with better functions.
Collapse
Affiliation(s)
- Ruiheng Song
- Kuang Yaming Honors School , Nanjing University , Nanjing 210023 , China
| | - Xialian Wu
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Bin Xue
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics , Nanjing University , Nanjing 210093 , China
| | - Yuqin Yang
- Kuang Yaming Honors School , Nanjing University , Nanjing 210023 , China
| | - Wenmao Huang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics , Nanjing University , Nanjing 210093 , China
| | - Guixiang Zeng
- Kuang Yaming Honors School , Nanjing University , Nanjing 210023 , China.,Institute for Brain Sciences , Nanjing University , Nanjing 210023 , China
| | - Jian Wang
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Wenfei Li
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics , Nanjing University , Nanjing 210093 , China.,Institute for Brain Sciences , Nanjing University , Nanjing 210023 , China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics , Nanjing University , Nanjing 210093 , China.,Institute for Brain Sciences , Nanjing University , Nanjing 210023 , China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics , Nanjing University , Nanjing 210093 , China.,Institute for Brain Sciences , Nanjing University , Nanjing 210023 , China
| | - Junxia Lu
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Hao Dong
- Kuang Yaming Honors School , Nanjing University , Nanjing 210023 , China.,Institute for Brain Sciences , Nanjing University , Nanjing 210023 , China
| |
Collapse
|
7
|
Rydzewski J, Jakubowski R, Nicosia G, Nowak W. Conformational Sampling of a Biomolecular Rugged Energy Landscape. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:732-739. [PMID: 27913358 DOI: 10.1109/tcbb.2016.2634008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The protein structure refinement using conformational sampling is important in hitherto protein studies. In this paper, we examined the protein structure refinement by means of potential energy minimization using immune computing as a method of sampling conformations. The method was tested on the x-ray structure and 30 decoys of the mutant of [Leu]Enkephalin, a paradigmatic example of the biomolecular multiple-minima problem. In order to score the refined conformations, we used a standard potential energy function with the OPLSAA force field. The effectiveness of the search was assessed using a variety of methods. The robustness of sampling was checked by the energy yield function which measures quantitatively the number of the peptide decoys residing in an energetic funnel. Furthermore, the potential energy-dependent Pareto fronts were calculated to elucidate dissimilarities between peptide conformations and the native state as observed by x-ray crystallography. Our results showed that the probed potential energy landscape of [Leu]Enkephalin is self-similar on different metric scales and that the local potential energy minima of the peptide decoys are metastable, thus they can be refined to conformations whose potential energy is decreased by approximately 250 kJ/mol.
Collapse
|
8
|
Di Natale G, Bellia F, Sciacca MF, Campagna T, Pappalardo G. Tau-peptide fragments and their copper(II) complexes: Effects on Amyloid-β aggregation. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.09.061] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
9
|
Do TD, Sangwan S, de Almeida NEC, Ilitchev AI, Giammona M, Sawaya MR, Buratto SK, Eisenberg DS, Bowers MT. Distal amyloid β-protein fragments template amyloid assembly. Protein Sci 2018; 27:1181-1190. [PMID: 29349888 DOI: 10.1002/pro.3375] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/16/2018] [Accepted: 01/16/2018] [Indexed: 01/06/2023]
Abstract
Amyloid formation is associated with devastating diseases such as Alzheimer's, Parkinson's and Type-2 diabetes. The large amyloid deposits found in patients suffering from these diseases have remained difficult to probe by structural means. Recent NMR models also predict heterotypic interactions from distinct peptide fragments but limited evidence of heterotypic packed sheets is observed in solution. Here we characterize two segments of the protein amyloid β (Aβ) known to form fibrils in Alzheimer's disease patients. We designed two variants of Aβ(19-24) and Aβ(27-32), IFAEDV (I6V) and NKGAIF (N6F) to lower the aggregation propensity of individual peptides while maintaining the similar interactions between the two segments in their native forms. We found that the variants do not form significant amyloid fibrils individually but a 1:1 mixture forms abundant fibrils. Using ion mobility-mass spectrometry (IM-MS), hetero-oligomers up to decamers were found in the mixture while the individual peptides formed primarily dimers and some tetramers consistent with a strong heterotypic interaction between the two segments. We showed by X-ray crystallography that I6V formed a Class 7 zipper with a weakly packed pair of β-sheets and no segregated dry interface, while N6F formed a more stable Class 1 zipper. In a mixture of equimolar N6F:I6V, I6V forms a more stable zipper than in I6V alone while no N6F or hetero-typic zippers are observed. These data are consistent with a mechanism where N6F catalyzes assembly of I6V into a stable zipper and perhaps into stable, pure I6V fibrils that are observed in AFM measurements.
Collapse
Affiliation(s)
- Thanh D Do
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Smriti Sangwan
- Departments of Chemistry and Biochemistry and Biological Chemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, University of California, 611 Charles Young Drive East, Los Angeles, California
| | - Natália E C de Almeida
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Alexandre I Ilitchev
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Maxwell Giammona
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Michael R Sawaya
- Departments of Chemistry and Biochemistry and Biological Chemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, University of California, 611 Charles Young Drive East, Los Angeles, California
| | - Steven K Buratto
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - David S Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, University of California, 611 Charles Young Drive East, Los Angeles, California
| | - Michael T Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| |
Collapse
|
10
|
Bleiholder C, Bowers MT. The Solution Assembly of Biological Molecules Using Ion Mobility Methods: From Amino Acids to Amyloid β-Protein. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:365-386. [PMID: 28375705 PMCID: PMC6287953 DOI: 10.1146/annurev-anchem-071114-040304] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Ion mobility spectrometry-mass spectrometry (IMS-MS) methods are increasingly used to study noncovalent assemblies of peptides and proteins. This review focuses on the noncovalent self-assembly of amino acids and peptides, systems at the heart of the amyloid process that play a central role in a number of devastating diseases. Three different systems are discussed in detail: the 42-residue peptide amyloid-β42 implicated in the etiology of Alzheimer's disease, several amyloid-forming peptides with 6-11 residues, and the assembly of individual amino acids. We also discuss from a more fundamental perspective the processes that determine how quickly proteins and their assemblies denature when the analyte ion has been stripped of its solvent in an IMS-MS measurement and how to soften the measurement so that biologically meaningful data can be recorded.
Collapse
Affiliation(s)
- Christian Bleiholder
- Department of Chemistry and Biochemistry, Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306;
| | - Michael T Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| |
Collapse
|
11
|
Shen C, Xue M, Qiu H, Guo W. Insertion of Neurotransmitters into a Lipid Bilayer Membrane and Its Implication on Membrane Stability: A Molecular Dynamics Study. Chemphyschem 2017; 18:626-633. [PMID: 28054433 DOI: 10.1002/cphc.201601184] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 12/13/2016] [Indexed: 12/29/2022]
Abstract
The signaling molecules in neurons, called neurotransmitters, play an essential role in the transportation of neural signals, during which the neurotransmitters interact with not only specific receptors, but also cytomembranes, such as synaptic vesicle membranes and postsynaptic membranes. Through extensive molecular dynamics simulations, the atomic-scale insertion dynamics of typical neurotransmitters, including methionine enkephalin (ME), leucine enkephalin (LE), dopamine (DA), acetylcholine (ACh), and aspartic acid (ASP), into lipid bilayers is investigated. The results show that the first three neurotransmitters (ME, LE, and DA) are able to diffuse freely into both 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) membranes, and are guided by the aromatic residues Tyr and Phe. Only a limited number of these neurotransmitters are allowed to penetrate into the membrane, which suggests an intrinsic mechanism by which the membrane is protected from being destroyed by excessive inserted neurotransmitters. After spontaneous insertion, the neurotransmitters disturb the surrounding phospholipids in the membrane, as indicated by the altered distribution of components in lipid leaflets and the disordered lipid tails. In contrast, the last two neurotransmitters (ACh and ASP) cannot enter the membrane, but instead always diffuse freely in solution. These findings provide an understanding at the atomic level of how neurotransmitters interact with the surrounding cytomembrane, as well as their impact on membrane behavior.
Collapse
Affiliation(s)
- Chun Shen
- State Key Laboratory of Mechanics and Control of Mechanical Structure and Key Laboratory for Intelligent Nano Materials and Devices of the, Ministry of Education, and Institute of Nanoscience, Nanjing University of Aeronautics and Astronautics, 29 Yudao Street, Nanjing, P.R. China
| | - Minmin Xue
- State Key Laboratory of Mechanics and Control of Mechanical Structure and Key Laboratory for Intelligent Nano Materials and Devices of the, Ministry of Education, and Institute of Nanoscience, Nanjing University of Aeronautics and Astronautics, 29 Yudao Street, Nanjing, P.R. China
| | - Hu Qiu
- State Key Laboratory of Mechanics and Control of Mechanical Structure and Key Laboratory for Intelligent Nano Materials and Devices of the, Ministry of Education, and Institute of Nanoscience, Nanjing University of Aeronautics and Astronautics, 29 Yudao Street, Nanjing, P.R. China
| | - Wanlin Guo
- State Key Laboratory of Mechanics and Control of Mechanical Structure and Key Laboratory for Intelligent Nano Materials and Devices of the, Ministry of Education, and Institute of Nanoscience, Nanjing University of Aeronautics and Astronautics, 29 Yudao Street, Nanjing, P.R. China
| |
Collapse
|
12
|
Seo J, Hoffmann W, Warnke S, Huang X, Gewinner S, Schöllkopf W, Bowers MT, von Helden G, Pagel K. An infrared spectroscopy approach to follow β-sheet formation in peptide amyloid assemblies. Nat Chem 2016; 9:39-44. [PMID: 27995915 DOI: 10.1038/nchem.2615] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 08/10/2016] [Indexed: 12/18/2022]
Abstract
Amyloidogenic peptides and proteins play a crucial role in a variety of neurodegenerative disorders such as Alzheimer's and Parkinson's disease. These proteins undergo a spontaneous transition from a soluble, often partially folded form, into insoluble amyloid fibrils that are rich in β-sheets. Increasing evidence suggests that highly dynamic, polydisperse folding intermediates, which occur during fibril formation, are the toxic species in the amyloid-related diseases. Traditional condensed-phase methods are of limited use for characterizing these states because they typically only provide ensemble averages rather than information about individual oligomers. Here we report the first direct secondary-structure analysis of individual amyloid intermediates using a combination of ion mobility spectrometry-mass spectrometry and gas-phase infrared spectroscopy. Our data reveal that oligomers of the fibril-forming peptide segments VEALYL and YVEALL, which consist of 4-9 peptide strands, can contain a significant amount of β-sheet. In addition, our data show that the more-extended variants of each oligomer generally exhibit increased β-sheet content.
Collapse
Affiliation(s)
- Jongcheol Seo
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, Berlin 14195, Germany
| | - Waldemar Hoffmann
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, Berlin 14195, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, Berlin 14195, Germany
| | - Stephan Warnke
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, Berlin 14195, Germany
| | - Xing Huang
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, Berlin 14195, Germany
| | - Sandy Gewinner
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, Berlin 14195, Germany
| | - Wieland Schöllkopf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, Berlin 14195, Germany
| | - Michael T Bowers
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, Berlin 14195, Germany
| | - Kevin Pagel
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, Berlin 14195, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, Berlin 14195, Germany
| |
Collapse
|
13
|
Matthes D, Gapsys V, Brennecke JT, de Groot BL. An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase. Sci Rep 2016; 6:33156. [PMID: 27616019 PMCID: PMC5018807 DOI: 10.1038/srep33156] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/22/2016] [Indexed: 01/01/2023] Open
Abstract
The formation of well-defined filamentous amyloid structures involves a polydisperse collection of oligomeric states for which relatively little is known in terms of structural organization. Here we use extensive, unbiased explicit solvent molecular dynamics (MD) simulations to investigate the structural and dynamical features of oligomeric aggregates formed by a number of highly amyloidogenic peptides at atomistic resolution on the μs time scale. A consensus approach has been adopted to analyse the simulations in multiple force fields, yielding an in-depth characterization of pre-fibrillar oligomers and their global and local structure properties. A collision cross section analysis revealed structurally heterogeneous aggregate ensembles for the individual oligomeric states that lack a single defined quaternary structure during the pre-nucleation phase. To gain insight into the conformational space sampled in early aggregates, we probed their substructure and found emerging β-sheet subunit layers and a multitude of ordered intermolecular β-structure motifs with growing aggregate size. Among those, anti-parallel out-of-register β-strands compatible with toxic β-barrel oligomers were particularly prevalent already in smaller aggregates and formed prior to ordered fibrillar structure elements. Notably, also distinct fibril-like conformations emerged in the oligomeric state and underscore the notion that pre-nucleated oligomers serve as a critical intermediate step on-pathway to fibrils.
Collapse
Affiliation(s)
- Dirk Matthes
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Vytautas Gapsys
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Julian T Brennecke
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| |
Collapse
|
14
|
Tabatabaei Ghomi H, Topp EM, Lill MA. Fibpredictor: a computational method for rapid prediction of amyloid fibril structures. J Mol Model 2016; 22:206. [PMID: 27502172 DOI: 10.1007/s00894-016-3066-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/03/2016] [Indexed: 12/13/2022]
Abstract
Amyloid fibrils are important in diseases such as Alzheimer's disease and Parkinson's disease, and are also a common instability in peptide and protein drug products. Despite their importance, experimental structures of amyloid fibrils in atomistic detail are rare. To address this limitation, we have developed a novel, rapid computational method to predict amyloid fibril structures (Fibpredictor). The method combines β-sheet model building, β-sheet replication, and symmetry operations with side-chain prediction and statistical scoring functions. When applied to nine amyloid fibrils with experimentally determined structures, the method predicted the correct structures of amyloid fibrils and enriched those among the top-ranked structures. These models can be used as the initial heuristic structures for more complicated computational studies. Fibpredictor is available at http://nanohub.org/resources/fibpredictor .
Collapse
Affiliation(s)
- Hamed Tabatabaei Ghomi
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Elizabeth M Topp
- Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Markus A Lill
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA.
| |
Collapse
|
15
|
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
|
16
|
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
|
17
|
Guo K, Guo Z, Ludlow JM, Xie T, Liao S, Newkome GR, Wesdemiotis C. Characterization of Metallosupramolecular Polymers by Top-Down Multidimensional Mass Spectrometry Methods. Macromol Rapid Commun 2015; 36:1539-52. [PMID: 26248126 DOI: 10.1002/marc.201500084] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 05/15/2015] [Indexed: 11/07/2022]
Abstract
Top-down multidimensional mass spectrometry, interfacing electrospray ionization (ESI) with ion mobility mass spectrometry (IM-MS), and energy resolved (gradient) tandem mass spectrometry (gMS(2) ) are employed to characterize the stoichiometries, architectures, and intrinsic stabilities of coordinatively bound supramolecular polymers containing terpyridine functionalized ligands. As a soft ionization method, ESI prevents or minimizes unwanted assembly destruction. The IM dimension affords separation of the supramolecular ions by charge and collision cross-section (a function of size and shape). The mobility separated ions are subsequently identified by their mass-to-charge-ratios and isotope patterns in the orthogonal MS dimension. Finally, the gMS(2) dimension reveals bond breaking proclivities and disintegration pathways of the assemblies. The described methodology does not require high sample purity due to the dispersive nature of the IM and MS steps. Its utility is demonstrated with the comprehensive analysis of bisterpyridine-based metallomacrocycle mixtures and a tristerpyridine based complex with 3-D nanosphere-like architecture.
Collapse
Affiliation(s)
- Kai Guo
- Department of Polymer Science, The University of Akron, Akron, OH, 44325, USA
| | - Zaihong Guo
- Department of Chemistry, The University of Akron, Akron, OH, 44325, USA
| | - James M Ludlow
- Department of Polymer Science, The University of Akron, Akron, OH, 44325, USA
| | - Tingzheng Xie
- Department of Polymer Science, The University of Akron, Akron, OH, 44325, USA
| | - Shengyun Liao
- Department of Polymer Science, The University of Akron, Akron, OH, 44325, USA
| | - George R Newkome
- Departments of Chemistry and Polymer Science, The University of Akron, Akron, OH, 44325, USA
| | - Chrys Wesdemiotis
- Departments of Chemistry and Polymer Science, The University of Akron, Akron, OH, 44325, USA
| |
Collapse
|
18
|
Lyubchenko YL. Amyloid misfolding, aggregation, and the early onset of protein deposition diseases: insights from AFM experiments and computational analyses. AIMS MOLECULAR SCIENCE 2015; 2:190-210. [PMID: 27830177 PMCID: PMC5098429 DOI: 10.3934/molsci.2015.3.190] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The development of Alzheimer's disease is believed to be caused by the assembly of amyloid β proteins into aggregates and the formation of extracellular senile plaques. Similar models suggest that structural misfolding and aggregation of proteins are associated with the early onset of diseases such as Parkinson's, Huntington's, and other protein deposition diseases. Initially, the aggregates were structurally characterized by traditional techniques such as x-ray crystallography, NMR, electron microscopy, and AFM. However, data regarding the structures formed during the early stages of the aggregation process were unknown. Experimental models of protein deposition diseases have demonstrated that the small oligomeric species have significant neurotoxicity. This highlights the urgent need to discover the properties of these species, to enable the development of efficient diagnostic and therapeutic strategies. The oligomers exist transiently, making it impossible to use traditional structural techniques to study their characteristics. The recent implementation of single-molecule imaging and probing techniques that are capable of probing transient states have enabled the properties of these oligomers to be characterized. Additionally, powerful computational techniques capable of structurally analyzing oligomers at the atomic level advanced our understanding of the amyloid aggregation problem. This review outlines the progress in AFM experimental studies and computational analyses with a primary focus on understanding the very first stage of the aggregation process. Experimental approaches can aid in the development of novel sensitive diagnostic and preventive strategies for protein deposition diseases, and several examples of these approaches will be discussed.
Collapse
Affiliation(s)
- Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| |
Collapse
|
19
|
Yuan Z, Yang L, Chen B, Zhu T, Hassan MF, Yin X, Zhou X, Zhao D. Protein misfolding cyclic amplification induces the conversion of recombinant prion protein to PrP oligomers causing neuronal apoptosis. J Neurochem 2015; 133:722-9. [DOI: 10.1111/jnc.13098] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 03/12/2015] [Accepted: 03/15/2015] [Indexed: 12/29/2022]
Affiliation(s)
- Zhen Yuan
- State Key Laboratories for Agrobiotechnology; Key Lab of Animal Epidemiology and Zoonosis; Ministry of Agriculture; National Animal Transmissible Spongiform Encephalopathy Laboratory; College of Veterinary Medicine; China Agricultural University; Beijing China
| | - Lifeng Yang
- State Key Laboratories for Agrobiotechnology; Key Lab of Animal Epidemiology and Zoonosis; Ministry of Agriculture; National Animal Transmissible Spongiform Encephalopathy Laboratory; College of Veterinary Medicine; China Agricultural University; Beijing China
| | - Baian Chen
- Department of Laboratory Animal Science; School of Basic Medical Science; Capital Medical University; Beijing China
| | - Ting Zhu
- State Key Laboratories for Agrobiotechnology; Key Lab of Animal Epidemiology and Zoonosis; Ministry of Agriculture; National Animal Transmissible Spongiform Encephalopathy Laboratory; College of Veterinary Medicine; China Agricultural University; Beijing China
| | - Mohammad Farooque Hassan
- State Key Laboratories for Agrobiotechnology; Key Lab of Animal Epidemiology and Zoonosis; Ministry of Agriculture; National Animal Transmissible Spongiform Encephalopathy Laboratory; College of Veterinary Medicine; China Agricultural University; Beijing China
| | - Xiaomin Yin
- State Key Laboratories for Agrobiotechnology; Key Lab of Animal Epidemiology and Zoonosis; Ministry of Agriculture; National Animal Transmissible Spongiform Encephalopathy Laboratory; College of Veterinary Medicine; China Agricultural University; Beijing China
| | - Xiangmei Zhou
- State Key Laboratories for Agrobiotechnology; Key Lab of Animal Epidemiology and Zoonosis; Ministry of Agriculture; National Animal Transmissible Spongiform Encephalopathy Laboratory; College of Veterinary Medicine; China Agricultural University; Beijing China
| | - Deming Zhao
- State Key Laboratories for Agrobiotechnology; Key Lab of Animal Epidemiology and Zoonosis; Ministry of Agriculture; National Animal Transmissible Spongiform Encephalopathy Laboratory; College of Veterinary Medicine; China Agricultural University; Beijing China
| |
Collapse
|
20
|
Do TD, Bowers MT. Diphenylalanine self assembly: novel ion mobility methods showing the essential role of water. Anal Chem 2015; 87:4245-52. [PMID: 25785477 DOI: 10.1021/ac5046774] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The mechanism and driving forces behind the formation of diphenylalanine (FF) nanotubes have attracted much attention in the past decades. The hollow structure of the nanotubes suggests a role for water during the self-assembly process. Here, we use novel ion-mobility mass spectrometry methods to probe the early oligomers formed by diphenylalanine peptides. Interestingly, water-bound oligomers are observed in nano-electrospray ionization (ESI) mass spectra in the absence of bulk solvent. In addition, ligated water clusters transit the ion mobility cell but (often) dissociate before detection. These water molecules are shown to be essential for the formation of diphenylalanine oligomers larger than the dimer. The ligated water molecules exist in the solvent free environment either as neutral water or as protonated water clusters, depending on the composition of solvent from which they are sprayed. Water adduction helps stabilize conformers that are otherwise energetically unstable ultimately leading to the assembly of FF nanotubes.
Collapse
Affiliation(s)
- Thanh D Do
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Michael T Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| |
Collapse
|
21
|
Ghosh A, Pithadia AS, Bhat J, Bera S, Midya A, Fierke CA, Ramamoorthy A, Bhunia A. Self-assembly of a nine-residue amyloid-forming peptide fragment of SARS corona virus E-protein: mechanism of self aggregation and amyloid-inhibition of hIAPP. Biochemistry 2015; 54:2249-2261. [PMID: 25785896 DOI: 10.1021/acs.biochem.5b00061] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular self-assembly, a phenomenon widely observed in nature, has been exploited through organic molecules, proteins, DNA, and peptides to study complex biological systems. These self-assembly systems may also be used in understanding the molecular and structural biology which can inspire the design and synthesis of increasingly complex biomaterials. Specifically, use of these building blocks to investigate protein folding and misfolding has been of particular value since it can provide tremendous insights into peptide aggregation related to a variety of protein misfolding diseases, or amyloid diseases (e.g., Alzheimer's disease, Parkinson's disease, type-II diabetes). Herein, the self-assembly of TK9, a nine-residue peptide of the extra membrane C-terminal tail of the SARS corona virus envelope, and its variants were characterized through biophysical, spectroscopic, and simulated studies, and it was confirmed that the structure of these peptides influences their aggregation propensity, hence, mimicking amyloid proteins. TK9, which forms a beta-sheet rich fibril, contains a key sequence motif that may be critical for beta-sheet formation, thus making it an interesting system to study amyloid fibrillation. TK9 aggregates were further examined through simulations to evaluate the possible intra- and interpeptide interactions at the molecular level. These self-assembly peptides can also serve as amyloid inhibitors through hydrophobic and electrophilic recognition interactions. Our results show that TK9 inhibits the fibrillation of hIAPP, a 37 amino acid peptide implicated in the pathology of type-II diabetes. Thus, biophysical and NMR experimental results have revealed a molecular level understanding of peptide folding events, as well as the inhibition of amyloid-protein aggregation are reported.
Collapse
Affiliation(s)
- Anirban Ghosh
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700 054, India
| | - Amit S Pithadia
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109-1055, USA
| | - Jyotsna Bhat
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700 054, India
| | - Supriyo Bera
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700 054, India
| | - Anupam Midya
- School of Nanoscience and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Carol A Fierke
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109-1055, USA.,Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109-1055, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109-1055, USA.,Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109-1055, USA
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700 054, India.,Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109-1055, USA.,Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109-1055, USA
| |
Collapse
|
22
|
Do TD, Economou NJ, Chamas A, Buratto SK, Shea JE, Bowers MT. Interactions between amyloid-β and Tau fragments promote aberrant aggregates: implications for amyloid toxicity. J Phys Chem B 2014; 118:11220-30. [PMID: 25153942 PMCID: PMC4174992 DOI: 10.1021/jp506258g] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
We have investigated at the oligomeric
level interactions between
Aβ(25–35) and Tau(273–284), two important fragments
of the amyloid-β and Tau proteins, implicated in Alzheimer’s
disease. We are able to directly observe the coaggregation of these
two peptides by probing the conformations of early heteroligomers
and the macroscopic morphologies of the aggregates. Ion-mobility experiment
and theoretical modeling indicate that the interactions of the two
fragments affect the self-assembly processes of both peptides. Tau(273–284)
shows a high affinity to form heteroligomers with existing Aβ(25–35)
monomer and oligomers in solution. The configurations and characteristics
of the heteroligomers are determined by whether the population of
Aβ(25–35) or Tau(273–284) is dominant. As a result,
two types of aggregates are observed in the mixture with distinct
morphologies and dimensions from those of pure Aβ(25–35)
fibrils. The incorporation of some Tau into β-rich Aβ(25–35)
oligomers reduces the aggregation propensity of Aβ(25–35)
but does not fully abolish fibril formation. On the other hand, by
forming complexes with Aβ(25–35), Tau monomers and dimers
can advance to larger oligomers and form granular aggregates. These
heteroligomers may contribute to toxicity through loss of normal function
of Tau or inherent toxicity of the aggregates themselves.
Collapse
Affiliation(s)
- Thanh D Do
- Department of Chemistry and Biochemistry and ‡Department of Physics, University of California , Santa Barbara, California 93106, United States
| | | | | | | | | | | |
Collapse
|