1
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Dai Z, Ben-Younis A, Vlachaki A, Raleigh D, Thalassinos K. Understanding the structural dynamics of human islet amyloid polypeptide: Advancements in and applications of ion-mobility mass spectrometry. Biophys Chem 2024; 312:107285. [PMID: 38941872 PMCID: PMC11260546 DOI: 10.1016/j.bpc.2024.107285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/30/2024] [Accepted: 06/23/2024] [Indexed: 06/30/2024]
Abstract
Human islet amyloid polypeptide (hIAPP) forms amyloid deposits that contribute to β-cell death in pancreatic islets and are considered a hallmark of Type II diabetes Mellitus (T2DM). Evidence suggests that the early oligomers of hIAPP formed during the aggregation process are the primary pathological agent in islet amyloid induced β-cell death. The self-assembly mechanism of hIAPP, however, remains elusive, largely due to limitations in conventional biophysical techniques for probing the distribution or capturing detailed structures of the early, structurally dynamic oligomers. The advent of Ion-mobility Mass Spectrometry (IM-MS) has enabled the characterisation of hIAPP early oligomers in the gas phase, paving the way towards a deeper understanding of the oligomerisation mechanism and the correlation of structural information with the cytotoxicity of the oligomers. The sensitivity and the rapid structural characterisation provided by IM-MS also show promise in screening hIAPP inhibitors, categorising their modes of inhibition through "spectral fingerprints". This review delves into the application of IM-MS to the dissection of the complex steps of hIAPP oligomerisation, examining the inhibitory influence of metal ions, and exploring the characterisation of hetero-oligomerisation with different hIAPP variants. We highlight the potential of IM-MS as a tool for the high-throughput screening of hIAPP inhibitors, and for providing insights into their modes of action. Finally, we discuss advances afforded by recent advancements in tandem IM-MS and the combination of gas phase spectroscopy with IM-MS, which promise to deliver a more sensitive and higher-resolution structural portrait of hIAPP oligomers. Such information may help facilitate a new era of targeted therapeutic strategies for islet amyloidosis in T2DM.
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Affiliation(s)
- Zijie Dai
- Institute of Structural and Molecular Biology, Division of Bioscience, University College London, London WC1E 6BT, UK
| | - Aisha Ben-Younis
- Institute of Structural and Molecular Biology, Division of Bioscience, University College London, London WC1E 6BT, UK
| | - Anna Vlachaki
- Department of Clinical Neurosciences, John van Geest Centre for Brain Repair, University of Cambridge, Forvie Site, Robinson Way, Cambridge CB2 0PY, UK
| | - Daniel Raleigh
- Institute of Structural and Molecular Biology, Division of Bioscience, University College London, London WC1E 6BT, UK; Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, New York 11794, United States.
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Bioscience, University College London, London WC1E 6BT, UK; Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK.
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2
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Tatulian SA. Analysis of protein-protein and protein-membrane interactions by isotope-edited infrared spectroscopy. Phys Chem Chem Phys 2024; 26:21930-21953. [PMID: 39108200 DOI: 10.1039/d4cp01136h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
The objective of this work is to highlight the power of isotope-edited Fourier transform infrared (FTIR) spectroscopy in resolving important problems encountered in biochemistry, biophysics, and biomedical research, focusing on protein-protein and protein membrane interactions that play key roles in practically all life processes. An overview of the effects of isotope substitutions in (bio)molecules on spectral frequencies and intensities is given. Data are presented demonstrating how isotope-labeled proteins and/or lipids can be used to elucidate enzymatic mechanisms, the mode of membrane binding of peripheral proteins, regulation of membrane protein function, protein aggregation, and local and global structural changes in proteins during functional transitions. The use of polarized attenuated total reflection FTIR spectroscopy to identify the spatial orientation and the secondary structure of a membrane-bound interfacial enzyme and the mode of lipid hydrolysis is described. Methods of production of site-directed, segmental, and domain-specific labeling of proteins by the synthetic, semisynthetic, and recombinant strategies, including advanced protein engineering technologies such as nonsense suppression and frameshift quadruplet codons are overviewed.
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Affiliation(s)
- Suren A Tatulian
- Department of Physics, University of Central Florida, Orlando, FL 32816, USA.
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3
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Liu C, Wang N, Wu D, Wang L, Zhang N, Yu D. Rapid quantitative analysis of soybean protein isolates secondary structure by two-dimensional correlation infrared spectroscopy through pH perturbation. Food Chem 2024; 448:139074. [PMID: 38552460 DOI: 10.1016/j.foodchem.2024.139074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/06/2024] [Accepted: 03/16/2024] [Indexed: 04/24/2024]
Abstract
The infrared spectroscopy (IR) signal of protein is prone to being covered by impurity signals, and the accuracy of the secondary structure content calculated using spectral data is poor. To tackle this challenge, a rapid high-precision quantitative model for protein secondary structure was proposed. Firstly, a two-dimensional correlation calculation was performed based on 60 groups of soybean protein isolates (SPI) infrared spectroscopy data, resulting in a two-dimensional correlation infrared spectroscopy (2DCOS-IR). Subsequently, the optimal characteristic bands of the four secondary structures were extracted from the 2DCOS-IR. Ultimately, partial least squares (PLS), long short-term memory (LSTM), and bidirectional long short-term memory (BILSTM) algorithms were used to model the extracted characteristic bands and predict the content of SPI secondary structure. The findings suggested that BILSTM combined with 2DCOS-IR model (2DCOS-BILSTM) exhibited superior predictive performance. The prediction sets for α-helix, β-sheet, β-turn, and random coil were designated as 0.9257, 0.9077, 0.9476, and 0.8443, respectively, and their corresponding RMSEP values were 0.26, 0.48, 0.20, and 0.15. This strategy enhances the precision of IR and facilitates the rapid identification of secondary structure components within SPI, which is vital for the advancement of protein industrial production.
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Affiliation(s)
- Chang Liu
- College of Food Engineering, Harbin University of Commerce, Harbin 150028, China
| | - Ning Wang
- College of Food Engineering, Harbin University of Commerce, Harbin 150028, China
| | - Dandan Wu
- School of Computer and Information Engineering, Harbin University of Commerce, Harbin 150028, China
| | - Liqi Wang
- College of Food Engineering, Harbin University of Commerce, Harbin 150028, China; School of Computer and Information Engineering, Harbin University of Commerce, Harbin 150028, China.
| | - Na Zhang
- College of Food Engineering, Harbin University of Commerce, Harbin 150028, China
| | - Dianyu Yu
- School of Food Science, Northeast Agricultural University, Harbin 150030, China
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4
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Valli D, Ooi SA, Scattolini G, Chaudhary H, Tietze AA, Maj M. Improving cryo-EM grids for amyloid fibrils using interface-active solutions and spectator proteins. Biophys J 2024; 123:718-729. [PMID: 38368506 PMCID: PMC10995402 DOI: 10.1016/j.bpj.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/28/2024] [Accepted: 02/13/2024] [Indexed: 02/19/2024] Open
Abstract
Preparation of cryoelectron microscopy (cryo-EM) grids for imaging of amyloid fibrils is notoriously challenging. The human islet amyloid polypeptide (hIAPP) serves as a notable example, as the majority of reported structures have relied on the use of nonphysiological pH buffers, N-terminal tags, and seeding. This highlights the need for more efficient, reproducible methodologies that can elucidate amyloid fibril structures formed under diverse conditions. In this work, we demonstrate that the distribution of fibrils on cryo-EM grids is predominantly determined by the solution composition, which is critical for the stability of thin vitreous ice films. We discover that, among physiological pH buffers, HEPES uniquely enhances the distribution of fibrils on cryo-EM grids and improves the stability of ice layers. This improvement is attributed to direct interactions between HEPES molecules and hIAPP, effectively minimizing the tendency of hIAPP to form dense clusters in solutions and preventing ice nucleation. Furthermore, we provide additional support for the idea that denatured protein monolayers forming at the interface are also capable of eliciting a surfactant-like effect, leading to improved particle coverage. This phenomenon is illustrated by the addition of nonamyloidogenic rat IAPP (rIAPP) to a solution of preaggregated hIAPP just before the freezing process. The resultant grids, supplemented with this "spectator protein", exhibit notably enhanced coverage and improved ice quality. Unlike conventional surfactants, rIAPP is additionally capable of disentangling the dense clusters formed by hIAPP. By applying the proposed strategies, we have resolved the structure of the dominant hIAPP polymorph, formed in vitro at pH 7.4, to a final resolution of 4 Å. The advances in grid preparation presented in this work hold significant promise for enabling structural determination of amyloid proteins which are particularly resistant to conventional grid preparation techniques.
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Affiliation(s)
- Dylan Valli
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Saik Ann Ooi
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Giorgio Scattolini
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Himanshu Chaudhary
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Alesia A Tietze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Michał Maj
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden.
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5
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Wang Y, Liu J, Liu T, An X, Huang L, Li J, Zhang Y, Xiang Y, Xiao L, Yi W, Qin J, Liu L, Wang C, Yu J. Pyruvate kinase deficiency and PKLR gene mutations: Insights from molecular dynamics simulation analysis. Heliyon 2024; 10:e26368. [PMID: 38434380 PMCID: PMC10904247 DOI: 10.1016/j.heliyon.2024.e26368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 12/25/2023] [Accepted: 02/12/2024] [Indexed: 03/05/2024] Open
Abstract
Pyruvate kinase deficiency is a rare hereditary erythrocyte enzyme disease caused by mutations in the pyruvate kinase liver and red blood cell gene. The clinical presentations of pyruvate kinase deficiency are significantly heterogeneous, ranging from just mild anemia to hemolytic crisis or even death. The proband in our study was a 2-year-old girl for severe skin and scleral icterus with progressive aggravation. We collected the family's data for further analysis. Whole exome genome sequencing of the pedigree revealed a novel compound heterozygous mutation, c.1097del (p.P366Lfs*12) and c.1493G > A (p.R498H), in the pyruvate kinase liver and red blood cell gene. Furthermore, molecular dynamics simulations were employed to uncover differences between the wild type and mutant pyruvate kinase liver and red blood cell proteins, focusing on structural stability, protein flexibility, secondary structure, and overall conformation. The combined bioinformatic tools were also utilised to assess the effects of the missense mutation on protein function. Thereafter, wild type and mutant plasmids were constructed and transfected into 293T cells, and Western blot assay was conducted to validate the impact of the mutations on the expression of pyruvate kinase liver and red blood cell protein. The data presented in our study enriches the genotype database and provides evidence for genetic counseling and molecular diagnosis of pyruvate kinase deficiency.
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Affiliation(s)
- Yang Wang
- Department of Hematology and Oncology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, 136 Zhong shan er lu, Yu zhong district, Chongqing 400014, China
| | - Jiaqi Liu
- Shanghai Cinopath Medical Testing Co Ltd, Shanghai 200000, China
| | - Tao Liu
- Department of Hematology and Oncology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, 136 Zhong shan er lu, Yu zhong district, Chongqing 400014, China
| | - Xizhou An
- Department of Hematology and Oncology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, 136 Zhong shan er lu, Yu zhong district, Chongqing 400014, China
| | - Lan Huang
- Department of Hematology and Oncology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, 136 Zhong shan er lu, Yu zhong district, Chongqing 400014, China
| | - Jiacheng Li
- Department of Hematology and Oncology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, 136 Zhong shan er lu, Yu zhong district, Chongqing 400014, China
| | - Yongjie Zhang
- Department of Hematology and Oncology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, 136 Zhong shan er lu, Yu zhong district, Chongqing 400014, China
| | - Yan Xiang
- Department of Hematology and Oncology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, 136 Zhong shan er lu, Yu zhong district, Chongqing 400014, China
| | - Li Xiao
- Department of Hematology and Oncology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, 136 Zhong shan er lu, Yu zhong district, Chongqing 400014, China
| | - Weijia Yi
- Department of Hematology and Oncology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, 136 Zhong shan er lu, Yu zhong district, Chongqing 400014, China
| | - Jiebin Qin
- Department of Hematology and Oncology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, 136 Zhong shan er lu, Yu zhong district, Chongqing 400014, China
| | - Lili Liu
- Department of Cardiovascular Medicine, Affiliated Hospital of North China University of Science and Technology, Tangshan 063000, China
| | - Cuilan Wang
- Department of Neurology, Affiliated Hospital of North China University of Science and Technology, Tangshan 063000, China
| | - Jie Yu
- Department of Hematology and Oncology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, 136 Zhong shan er lu, Yu zhong district, Chongqing 400014, China
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6
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Hunt NT. Using 2D-IR Spectroscopy to Measure the Structure, Dynamics, and Intermolecular Interactions of Proteins in H 2O. Acc Chem Res 2024; 57:685-692. [PMID: 38364823 PMCID: PMC10918835 DOI: 10.1021/acs.accounts.3c00682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/18/2024]
Abstract
Infrared (IR) spectroscopy probes molecular structure at the level of the chemical bond or functional group. In the case of proteins, the most informative band in the IR spectrum is the amide I band, which arises predominantly from the C═O stretching vibration of the peptide link. The folding of proteins into secondary and tertiary structures leads to vibrational coupling between peptide units, generating specific amide I spectral signatures that provide a fingerprint of the macromolecular conformation. Ultrafast two-dimensional IR (2D-IR) spectroscopy allows the amide I band of a protein to be spread over a second frequency dimension in a way that mirrors 2D-NMR methods. This means that amide I 2D-IR spectroscopy produces a spectral map that is exquisitely sensitive to protein structure and dynamics and so provides detailed insights that cannot be matched by IR absorption spectroscopy. As a result, 2D-IR spectroscopy has emerged as a powerful tool for probing protein structure and dynamics over a broad range of time and length scales in the solution phase at room temperature. However, the protein amide I band coincides with an IR absorption from the bending vibration of water (δHOH), the natural biological solvent. To circumvent this problem, protein IR studies are routinely performed in D2O solutions because H/D substitution shifts the solvent bending mode (δDOD) to a lower frequency, revealing the amide I band. While effective, this method raises fundamental questions regarding the impact of the change in solvent mass on the structural or solvation dynamics of the protein and the removal of the energetic resonance between solvent and solute.In this Account, a series of studies applying 2D-IR to study the spectroscopy and dynamics of proteins in H2O-rich solvents is reviewed. A comparison of IR absorption spectroscopy and 2D-IR spectroscopy of protein-containing fluids is used to demonstrate the basis of the approach before a series of applications is presented. These range from measurements of fundamental protein biophysics to recent applications of machine learning to gain insight into protein-drug binding in complex mixtures. An outlook is presented, considering the potential for 2D-IR measurements to contribute to our understanding of protein behavior under near-physiological conditions, along with an evaluation of the obstacles that still need to be overcome.
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Affiliation(s)
- Neil T. Hunt
- Department of Chemistry and York Biomedical
Research Institute, University of York, Heslington, York, YO10
5DD, U.K.
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7
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Hunt NT. Biomolecular infrared spectroscopy: making time for dynamics. Chem Sci 2024; 15:414-430. [PMID: 38179520 PMCID: PMC10763549 DOI: 10.1039/d3sc05223k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/24/2023] [Indexed: 01/06/2024] Open
Abstract
Time resolved infrared spectroscopy of biological molecules has provided a wealth of information relating to structural dynamics, conformational changes, solvation and intermolecular interactions. Challenges still exist however arising from the wide range of timescales over which biological processes occur, stretching from picoseconds to minutes or hours. Experimental methods are often limited by vibrational lifetimes of probe groups, which are typically on the order of picoseconds, while measuring an evolving system continuously over some 18 orders of magnitude in time presents a raft of technological hurdles. In this Perspective, a series of recent advances which allow biological molecules and processes to be studied over an increasing range of timescales, while maintaining ultrafast time resolution, will be reviewed, showing that the potential for real-time observation of biomolecular function draws ever closer, while offering a new set of challenges to be overcome.
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Affiliation(s)
- Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York Heslington York YO10 5DD UK
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8
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Lin R, Tang G, Gao Z, Lei J, Ma B, Mo Y. Molecular Insights into the Self-Assembly of a Full-Length hIAPP Trimer: β-Protofibril Formed by β-Hairpin Lateral or Longitudinal Association. J Phys Chem B 2023. [PMID: 37262327 DOI: 10.1021/acs.jpcb.3c02633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The fibrillar protein deposits of the human islet amyloid polypeptide (hIAPP) in the pancreatic islet of Langerhans are pathological hallmark of type II diabetes. Extensive experimental studies have revealed that the oligomeric formations of the hIAPP are more toxic than the mature fibrils. Exploring the oligomeric conformations in the early aggregation state is valuable for effective therapeutics. In this work, using the all-atom explicit-solvent replica exchange molecular dynamic (REMD) simulations, we investigated the structural features and the assembly mechanisms of the full-length hIAPP trimer in solution. The hIAPP trimer adopted more β-sheets than a-helix conformations, and three types of ordered conformations including open β-barrel, single-layer, and double-layer U-shaped β-sheet structures with five β-strands were captured in our simulations. A representative single-layer β-sheet conformation with a CCS value of 1400 Å2 in our simulations matches exactly the experimentally ESI-IMS-MS-derived hIAPP trimer sample. These five β-strand conformations formed via the β-hairpin lateral and longitudinal association, respectively, showing two β-protofibril formation models. To the best of our knowledge, it is the first time to reveal two routes to β-sheet formation in the hIAPP trimers on the atomic level. The contact probabilities between pairs of the β-stranded residue show that the hydrophobic interactions between the residues F15 ∼ V17 and A25 ∼ L27 are responsible for the inter- and intra-peptide β-hairpin formations. All of these results indicate that the β-sheet formation is the first step in the conformational changes toward pathological aggregation and provides evidence of the β-sheet assembly mechanism into hIAPP aggregation.
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Affiliation(s)
- Rongmei Lin
- College of Physical Science and Technology, Guangxi Normal University, Guilin, Guangxi 541004, People's Republic of China
| | - Guoning Tang
- College of Physical Science and Technology, Guangxi Normal University, Guilin, Guangxi 541004, People's Republic of China
| | - Zhonggui Gao
- College of Physical Science and Technology, Guangxi Normal University, Guilin, Guangxi 541004, People's Republic of China
| | - Jiangtao Lei
- Institute of Space Science and Technology, Nanchang University, Nanchang, Jiangxi 330031, People's Republic of China
| | - Buyong Ma
- Engineering Research Center of Cell & Therapeutic Antibody, School of Pharmacy, Shanghai Jiaotong University, Shanghai 200240, People's Republic of China
| | - Yuxiang Mo
- College of Physical Science and Technology, Guangxi Normal University, Guilin, Guangxi 541004, People's Republic of China
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9
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Webb KR, Hess KA, Shmidt A, Segner KD, Buchanan LE. Probing local changes to α-helical structures with 2D IR spectroscopy and isotope labeling. Biophys J 2023; 122:1491-1502. [PMID: 36906800 PMCID: PMC10147839 DOI: 10.1016/j.bpj.2023.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/13/2022] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
α-Helical secondary structures impart specific mechanical and physiochemical properties to peptides and proteins, enabling them to perform a vast array of molecular tasks ranging from membrane insertion to molecular allostery. Loss of α-helical content in specific regions can inhibit native protein function or induce new, potentially toxic, biological activities. Thus, identifying specific residues that exhibit loss or gain of helicity is critical for understanding the molecular basis of function. Two-dimensional infrared (2D IR) spectroscopy coupled with isotope labeling is capable of capturing detailed structural changes in polypeptides. Yet, questions remain regarding the inherent sensitivity of isotope-labeled modes to local changes in α-helicity, such as terminal fraying; the origin of spectral shifts (hydrogen-bonding versus vibrational coupling); and the ability to definitively detect coupled isotopic signals in the presence of overlapping side chains. Here, we address each of these points individually by characterizing a short, model α-helix (DPAEAAKAAAGR-NH2) with 2D IR and isotope labeling. These results demonstrate that pairs of 13C18O probes placed three residues apart can detect subtle structural changes and variations along the length of the model peptide as the α-helicity is systematically tuned. Comparison of singly and doubly labeled peptides affirm that frequency shifts arise primarily from hydrogen-bonding, while vibrational coupling between paired isotopes leads to increased peak areas that can be clearly differentiated from underlying side-chain modes or uncoupled isotope labels not participating in helical structures. These results demonstrate that 2D IR in tandem with i,i+3 isotope-labeling schemes can capture residue-specific molecular interactions within a single turn of an α-helix.
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Affiliation(s)
| | - Kayla Anne Hess
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Alisa Shmidt
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee
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10
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Fortier M, Côté-Cyr M, Nguyen V, Babych M, Nguyen PT, Gaudreault R, Bourgault S. Contribution of the 12–17 hydrophobic region of islet amyloid polypeptide in self-assembly and cytotoxicity. Front Mol Biosci 2022; 9:1017336. [PMID: 36262476 PMCID: PMC9573943 DOI: 10.3389/fmolb.2022.1017336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022] Open
Abstract
The islet amyloid polypeptide (IAPP) is a 37-residue aggregation-prone peptide hormone whose deposition as insoluble fibrils in the islets of Langerhans is associated with type II diabetes. Therapeutic interventions targeting IAPP amyloidogenesis, which contributes to pancreatic β-cell degeneration, remain elusive owing to the lack of understanding of the self-assembly mechanisms and of the quaternary proteospecies mediating toxicity. While countless studies have investigated the contributions of the 20–29 amyloidogenic core in self-assembly, IAPP central region, i.e. positions 11 to 19, has been less studied, notwithstanding its potential key role in oligomerization. In this context, the present study aimed at investigating the physicochemical and conformational properties driving IAPP self-assembly and associated cytotoxicity. Computational tools and all-atom molecular dynamics simulation suggested that the hydrophobic 12–17 segment promotes IAPP self-recognition and aggregation. Alanine scanning revealed that the hydrophobic side chains of Leu12, Phe15 and Val17 are critical for amyloid fibril formation. Destabilization of the α-helical folding by Pro substitution enhanced self-assembly when the pyrrolidine ring was successively introduced at positions Ala13, Asn14 and Phe15, in comparison to respective Ala-substituted counterparts. Modulating the peptide backbone flexibility at position Leu16 through successive incorporation of Pro, Gly and α-methylalanine, inhibited amyloid formation and reduced cytotoxicity, while the isobutyl side chain of Leu16 was not critical for self-assembly and IAPP-mediated toxicity. These results highlight the importance of the 12–17 hydrophobic region of IAPP for self-recognition, ultimately supporting the development of therapeutic approaches to prevent oligomerization and/or fibrillization.
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Affiliation(s)
- Mathilde Fortier
- Department of Chemistry, Succursale Centre-Ville, Université du Québec à Montréal, Montreal, QC, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Montreal, QC, Canada
| | - Mélanie Côté-Cyr
- Department of Chemistry, Succursale Centre-Ville, Université du Québec à Montréal, Montreal, QC, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Montreal, QC, Canada
| | - Vy Nguyen
- Department of Chemistry, Succursale Centre-Ville, Université du Québec à Montréal, Montreal, QC, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Montreal, QC, Canada
| | - Margaryta Babych
- Department of Chemistry, Succursale Centre-Ville, Université du Québec à Montréal, Montreal, QC, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Montreal, QC, Canada
| | - Phuong Trang Nguyen
- Department of Chemistry, Succursale Centre-Ville, Université du Québec à Montréal, Montreal, QC, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Montreal, QC, Canada
| | - Roger Gaudreault
- Department of Chemistry, Succursale Centre-Ville, Université du Québec à Montréal, Montreal, QC, Canada
- Department of Physics, Université de Montréal, Succursale Centre-ville, Montreal, QC, Canada
- *Correspondence: Roger Gaudreault, ; Steve Bourgault,
| | - Steve Bourgault
- Department of Chemistry, Succursale Centre-Ville, Université du Québec à Montréal, Montreal, QC, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Montreal, QC, Canada
- *Correspondence: Roger Gaudreault, ; Steve Bourgault,
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11
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Dicke SS, Maj M, Fields CR, Zanni MT. Metastable intermediate during hIAPP aggregation catalyzed by membranes as detected with 2D IR spectroscopy. RSC Chem Biol 2022; 3:931-940. [PMID: 35866164 PMCID: PMC9257649 DOI: 10.1039/d2cb00028h] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/24/2022] [Indexed: 11/26/2022] Open
Abstract
The aggregation of human islet amyloid polypeptide (hIAPP) into amyloid fibrils involves formation of oligomeric intermediates that are thought to be the cytotoxic species responsible for β-cell dysfunction in type 2 diabetes. hIAPP oligomers permeating or disrupting the cellular membrane may be one mechanism of toxicity and so measuring the structural kinetics of aggregation in the presence of membranes is of much interest. In this study, we use 2D IR spectroscopy and 13C18O isotope labeling to study the secondary structure of the oligomeric intermediates formed in solution and in the presence of phospholipid vesicles at sites L12A13, L16V17, G24A25 and V32G33. Pairs of labels monitor the couplings between associated polypeptides and the dihedral angles between adjacent residues. In solution, the L12A13 residues form an oligomeric β-sheet in addition to an α-helix whereas with the phospholipid vesicles they are α-helical throughout the aggregation process. In both solution and with DOPC vesicles, L16V17 and V32G33 have disordered structures until fibrils are formed. Similarly, under both conditions, G24A25 exhibits 3-state kinetics, created by an oligomeric intermediate with a well-defined β-sheet structure. Amyloid fibril formation is often thought to involve intermediates with exceedingly low populations that are difficult to detect experimentally. These experiments establish that amyloid fibril formation of hIAPP when catalyzed by membranes includes a metastable intermediate and that this intermediate has a similar structure at G24A25 in the FGAIL region as the corresponding intermediate in solution, thought to be the toxic species. 2D IR and 13C18O isotope labeling establish that amyloid formation of hIAPP catalyzed by membranes includes a metastable intermediate with a similar structure at G24A25 in the FGAIL region as the corresponding intermediate in solution.![]()
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Affiliation(s)
- Sidney S Dicke
- Department of Chemistry, University of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA
| | - Michał Maj
- Department of Chemistry, University of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA .,Formally at Department of Chemistry, University of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA
| | - Caitlyn R Fields
- Department of Chemistry, University of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA
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12
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Tang H, Sun Y, Ding F. Hydrophobic/Hydrophilic Ratio of Amphiphilic Helix Mimetics Determines the Effects on Islet Amyloid Polypeptide Aggregation. J Chem Inf Model 2022; 62:1760-1770. [PMID: 35311274 PMCID: PMC9123946 DOI: 10.1021/acs.jcim.1c01566] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Amyloid depositions of human islet amyloid polypeptides (hIAPP) are associated with type II diabetes (T2D) impacting millions of people globally. Accordingly, strategies against hIAPP aggregation are essential for the prevention and eventual treatment of the disease. Helix mimetics, which modulate the protein-protein interaction by mimicking the side chain residues of a natural α-helix, were found to be a promising strategy for inhibiting hIAPP aggregation. Here, we applied molecular dynamics simulations to investigate two helix mimetics reported to have opposite effects on hIAPP aggregation in solution, the oligopyridylamide-based scaffold 1e promoted, whereas naphthalimide-appended oligopyridylamide scaffold DM 1 inhibited the aggregation of hIAPP in solution. We found that 1e promoted hIAPP aggregation because of the recruiting effects through binding with the N-termini of hIAPP peptides. In contrast, DM 1 with a higher hydrophobic/hydrophilic ratio effectively inhibited hIAPP aggregation by strongly binding with the C-termini of hIAPP peptides, which competed for the interpeptide contacts between amyloidogenic regions in the C-termini and impaired the fibrillization of hIAPP. Structural analyses revealed that DM 1 formed the core of hIAPP-DM 1 complexes and stabilized the off-pathway oligomers, whereas 1e formed the corona outside the hIAPP-1e complexes and remained active in recruiting free hIAPP peptides. The distinct interaction mechanisms of DM 1 and 1e, together with other reported potent antagonists in the literature, emphasized the effective small molecule-based amyloid inhibitors by disrupting peptide interactions that should reach a balanced hydrophobic/hydrophilic ratio, providing a viable and generic strategy for the rational design of novel anti-amyloid nanomedicine.
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Affiliation(s)
- Huayuan Tang
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
| | - Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States.,Department of Physics, Ningbo University, Ningbo 315211, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
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13
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Tumbic GW, Hossan MY, Thielges MC. Protein Dynamics by Two-Dimensional Infrared Spectroscopy. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:299-321. [PMID: 34314221 PMCID: PMC8713465 DOI: 10.1146/annurev-anchem-091520-091009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Proteins function as ensembles of interconverting structures. The motions span from picosecond bond rotations to millisecond and longer subunit displacements. Characterization of functional dynamics on all spatial and temporal scales remains challenging experimentally. Two-dimensional infrared spectroscopy (2D IR) is maturing as a powerful approach for investigating proteins and their dynamics. We outline the advantages of IR spectroscopy, describe 2D IR and the information it provides, and introduce vibrational groups for protein analysis. We highlight example studies that illustrate the power and versatility of 2D IR for characterizing protein dynamics and conclude with a brief discussion of the outlook for biomolecular 2D IR.
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Affiliation(s)
- Goran W Tumbic
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA;
| | - Md Yeathad Hossan
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA;
| | - Megan C Thielges
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA;
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14
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Watson MD, Lee JC. Coupling chemical biology and vibrational spectroscopy for studies of amyloids in vitro and in cells. Curr Opin Chem Biol 2021; 64:90-97. [PMID: 34186291 DOI: 10.1016/j.cbpa.2021.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/04/2021] [Accepted: 05/18/2021] [Indexed: 01/21/2023]
Abstract
Amyloid diseases are characterized by the aggregation of various proteins to form insoluble β-sheet-rich fibrils leading to cell death. Vibrational spectroscopies have emerged as attractive methods to study this process because of the rich structural information that can be extracted without large, perturbative probes. Importantly, specific vibrations such as the amide-I band directly report on secondary structure changes, which are key features of amyloid formation. Beyond intrinsic vibrations, the incorporation of unnatural vibrational probes can improve sensitivity for secondary structure determination (e.g. isotopic labeling), can provide residue-specific information of the surrounding polarity (e.g. unnatural amino acid), and are translatable into cellular studies. Here, we review the latest studies that have leveraged tools from chemical biology for the incorporation of novel vibrational probes into amyloidogenic proteins for both mechanistic and cellular studies.
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Affiliation(s)
- Matthew D Watson
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jennifer C Lee
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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15
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El Khoury Y, Le Breton G, Cunha AV, Jansen TLC, van Wilderen LJGW, Bredenbeck J. Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome c. J Chem Phys 2021; 154:124201. [PMID: 33810651 DOI: 10.1063/5.0039969] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Amide I difference spectroscopy is widely used to investigate protein function and structure changes. In this article, we show that the common approach of assigning features in amide I difference signals to distinct secondary structure elements in many cases may not be justified. Evidence comes from Fourier transform infrared (FTIR) and 2D-IR spectroelectrochemistry of the protein cytochrome c in the amide I range, in combination with computational spectroscopy based on molecular dynamics (MD) simulations. This combination reveals that each secondary structure unit, such as an alpha-helix or a beta-sheet, exhibits broad overlapping contributions, usually spanning a large part of the amide I region, which in the case of difference absorption experiments (such as in FTIR spectroelectrochemistry) may lead to intensity-compensating and even sign-changing contributions. We use cytochrome c as the test case, as this small electron-transferring redox-active protein contains different kinds of secondary structure units. Upon switching its redox-state, the protein exhibits a different charge distribution while largely retaining its structural scaffold. Our theoretical analysis suggests that the change in charge distribution contributes to the spectral changes and that structural changes are small. However, in order to confidently interpret FTIR amide I difference signals in cytochrome c and proteins in general, MD simulations in combination with additional experimental approaches such as isotope labeling, the insertion of infrared labels to selectively probe local structural elements will be required. In case these data are not available, a critical assessment of previous interpretations of protein amide I 1D- and 2D-IR difference spectroscopy data is warranted.
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Affiliation(s)
- Youssef El Khoury
- Institut für Biophysik, Johann-Wolfgang-Goethe-Universität, Max-von-Laue-Strasse. 1, 60438 Frankfurt am Main, Germany
| | - Guillaume Le Breton
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ana V Cunha
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Luuk J G W van Wilderen
- Institut für Biophysik, Johann-Wolfgang-Goethe-Universität, Max-von-Laue-Strasse. 1, 60438 Frankfurt am Main, Germany
| | - Jens Bredenbeck
- Institut für Biophysik, Johann-Wolfgang-Goethe-Universität, Max-von-Laue-Strasse. 1, 60438 Frankfurt am Main, Germany
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16
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Devitt G, Crisford A, Rice W, Weismiller HA, Fan Z, Commins C, Hyman BT, Margittai M, Mahajan S, Mudher A. Conformational fingerprinting of tau variants and strains by Raman spectroscopy. RSC Adv 2021; 11:8899-8915. [PMID: 34381596 PMCID: PMC8330415 DOI: 10.1039/d1ra00870f] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 02/18/2021] [Indexed: 12/11/2022] Open
Abstract
Tauopathies are a group of disorders in which the deposition of abnormally folded tau protein accompanies neurodegeneration. The development of methods for detection and classification of pathological changes in protein conformation are desirable for understanding the factors that influence the structural polymorphism of aggregates in tauopathies. We have previously demonstrated the utility of Raman spectroscopy for the characterization and discrimination of different protein aggregates, including tau, based on their unique conformational signatures. Building on this, in the present study, we assess the utility of Raman spectroscopy for characterizing and distinguishing different conformers of the same protein which in the case of tau are unique tau strains generated in vitro. We now investigate the impact of aggregation environment, cofactors, post-translational modification and primary sequence on the Raman fingerprint of tau fibrils. Using quantitative conformational fingerprinting and multivariate statistical analysis, we found that the aggregation of tau in different buffer conditions resulted in the formation of distinct fibril strains. Unique spectral markers were identified for tau fibrils generated using heparin or RNA cofactors, as well as for phosphorylated tau. We also determined that the primary sequence of the tau monomer influenced the conformational signature of the resulting tau fibril, including 2N4R, 0N3R, K18 and P301S tau variants. These results highlight the conformational polymorphism of tau fibrils, which is reflected in the wide range of associated neurological disorders. Furthermore, the analyses presented in this study provide a benchmark for the Raman spectroscopic characterization of tau strains, which may shed light on how the aggregation environment, cofactors and post-translational modifications influence tau conformation in vivo in future studies.
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Affiliation(s)
- George Devitt
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton Highfield Southampton SO17 1BJ UK .,School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton Highfield Southampton SO17 1BJ UK.,Institute for Life Sciences, University of Southampton Highfield Southampton SO17 1BJ UK
| | - Anna Crisford
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton Highfield Southampton SO17 1BJ UK .,School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton Highfield Southampton SO17 1BJ UK
| | - William Rice
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton Highfield Southampton SO17 1BJ UK
| | - Hilary A Weismiller
- Department of Chemistry and Biochemistry, University of Denver 2190 E. Iliff Ave. Denver CO 80208 USA
| | - Zhanyun Fan
- Department of Neurology, Harvard Medical School, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital Charlestown MA 02129 USA
| | - Caitlin Commins
- Department of Neurology, Harvard Medical School, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital Charlestown MA 02129 USA
| | - Bradley T Hyman
- Department of Neurology, Harvard Medical School, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital Charlestown MA 02129 USA
| | - Martin Margittai
- Department of Chemistry and Biochemistry, University of Denver 2190 E. Iliff Ave. Denver CO 80208 USA
| | - Sumeet Mahajan
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton Highfield Southampton SO17 1BJ UK.,Institute for Life Sciences, University of Southampton Highfield Southampton SO17 1BJ UK
| | - Amrit Mudher
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton Highfield Southampton SO17 1BJ UK .,Institute for Life Sciences, University of Southampton Highfield Southampton SO17 1BJ UK
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17
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Milardi D, Gazit E, Radford SE, Xu Y, Gallardo RU, Caflisch A, Westermark GT, Westermark P, Rosa CL, Ramamoorthy A. Proteostasis of Islet Amyloid Polypeptide: A Molecular Perspective of Risk Factors and Protective Strategies for Type II Diabetes. Chem Rev 2021; 121:1845-1893. [PMID: 33427465 DOI: 10.1021/acs.chemrev.0c00981] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The possible link between hIAPP accumulation and β-cell death in diabetic patients has inspired numerous studies focusing on amyloid structures and aggregation pathways of this hormone. Recent studies have reported on the importance of early oligomeric intermediates, the many roles of their interactions with lipid membrane, pH, insulin, and zinc on the mechanism of aggregation of hIAPP. The challenges posed by the transient nature of amyloid oligomers, their structural heterogeneity, and the complex nature of their interaction with lipid membranes have resulted in the development of a wide range of biophysical and chemical approaches to characterize the aggregation process. While the cellular processes and factors activating hIAPP-mediated cytotoxicity are still not clear, it has recently been suggested that its impaired turnover and cellular processing by proteasome and autophagy may contribute significantly toward toxic hIAPP accumulation and, eventually, β-cell death. Therefore, studies focusing on the restoration of hIAPP proteostasis may represent a promising arena for the design of effective therapies. In this review we discuss the current knowledge of the structures and pathology associated with hIAPP self-assembly and point out the opportunities for therapy that a detailed biochemical, biophysical, and cellular understanding of its aggregation may unveil.
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Affiliation(s)
- Danilo Milardi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via P. Gaifami 18, 95126 Catania, Italy
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Yong Xu
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Rodrigo U Gallardo
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
| | - Gunilla T Westermark
- Department of Medical Cell Biology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Per Westermark
- Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Carmelo La Rosa
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Ayyalusamy Ramamoorthy
- Biophysics, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 41809-1055, United States
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18
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Fields CR, Dicke SS, Petti MK, Zanni MT, Lomont JP. A Different hIAPP Polymorph Is Observed in Human Serum Than in Aqueous Buffer: Demonstration of a New Method for Studying Amyloid Fibril Structure Using Infrared Spectroscopy. J Phys Chem Lett 2020; 11:6382-6388. [PMID: 32706257 PMCID: PMC7968077 DOI: 10.1021/acs.jpclett.0c01345] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
There is enormous interest in measuring amyloid fibril structures, but most structural studies measure fibril formation in vitro using aqueous buffer. Ideally, one would like to measure fibril structure and mechanism under more physiological conditions. Toward this end, we have developed a method for studying amyloid fibril structure in human serum. Our approach uses isotope labeling, antibody depletion of the most abundant proteins (albumin and IgG), and infrared spectroscopy to measure aggregation in human serum with reduced protein content. Reducing the nonamyloid protein content enables the measurements by decreasing background signals but retains the full composition of salts, sugars, metal ions, etc. that are naturally present but usually missing from in vitro studies. We demonstrate the method by measuring the two-dimensional infrared (2D IR) spectra of isotopically labeled human islet amyloid polypeptide (hIAPP or amylin). We find that the fibril structure of hIAPP formed in serum differs from that formed via aggregation in aqueous buffer at residues Gly24 and Ala25, which reside in the putative "amyloidogenic core" or FGAIL region of the sequence. The spectra are consistent with extended parallel stacks of strands consistent with β-sheet-like structure, rather than a partially disordered loop that forms in aqueous buffer. These experiments provide a new method for using infrared spectroscopy to monitor the structure of proteins under physiological conditions and reveal the formation of a significantly different polymorph structure in the most important region of hIAPP.
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Affiliation(s)
- Caitlyn R Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Sidney S Dicke
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Megan K Petti
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Justin P Lomont
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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19
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Donaldson PM. Photon echoes and two dimensional spectra of the amide I band of proteins measured by femtosecond IR - Raman spectroscopy. Chem Sci 2020; 11:8862-8874. [PMID: 34123140 PMCID: PMC8163424 DOI: 10.1039/d0sc02978e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Infrared (IR) and Raman spectroscopy are fundamental techniques in chemistry, allowing the convenient determination of bond specific chemical composition and structure. Over the last decades, ultrafast multidimensional IR approaches using sequences of femtosecond IR pulses have begun to provide a new means of gaining additional information on molecular vibrational couplings, distributions of molecular structures and ultrafast molecular structural dynamics. In this contribution, new approaches to measuring multidimensional spectra involving IR and Raman processes are presented and applied to the study of the amide I band of proteins. Rephasing of the amide I band is observed using dispersed IR-Raman photon echoes and frequency domain 2D-IR-Raman spectra are measured by use of a mid-IR pulse shaper or over a broader spectral range using a tuneable picosecond laser. A simple pulse shaping approach to performing heterodyned time-domain Fourier Transform 2D-IR-Raman spectroscopy is introduced, revealing that the 2D-IR-Raman spectra distinguish homogeneous and inhomogeneous broadening in the same way as the well-established methods of 2D-IR spectroscopy. Across all datasets, the unique dependence of the amide I data on the IR and Raman strengths, vibrational anharmonicities and inhomogeneous broadening provides a fascinating spectroscopic view of the amide I band. New ultrafast 2D-IR-Raman photon echo spectroscopy techniques are introduced and applied to the structural analysis of proteins.![]()
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Affiliation(s)
- Paul M Donaldson
- Central Laser Facility, RCaH, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus Didcot OX11 0QX UK
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20
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Ostrander JS, Lomont JP, Rich KL, Saraswat V, Feingold BR, Petti MK, Birdsall ER, Arnold MS, Zanni MT. Monolayer Sensitivity Enables a 2D IR Spectroscopic Immuno-biosensor for Studying Protein Structures: Application to Amyloid Polymorphs. J Phys Chem Lett 2019; 10:3836-3842. [PMID: 31246039 PMCID: PMC6823637 DOI: 10.1021/acs.jpclett.9b01267] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Immunosensors use antibodies to detect and quantify biomarkers of disease, though the sensors often lack structural information. We create a surface-sensitive two-dimensional infrared (2D IR) spectroscopic immunosensor for studying protein structures. We tether antibodies to a plasmonic surface, flow over a solution of amyloid proteins, and measure the 2D IR spectra. The 2D IR spectra provide a global assessment of antigen structure, and isotopically labeled proteins give residue-specific structural information. We report the 2D IR spectra of fibrils and monomers using a polyclonal antibody that targets human islet amyloid polypeptide (hIAPP). We observe two fibrillar polymorphs differing in their structure at the G24 residue, which supports the hypothesis that hIAPP polymorphs form from a common oligomeric intermediate. This work provides insight into the structure of hIAPP, establishes a new method for studying protein structures using 2D IR spectroscopy, and creates a spectroscopic immunoassay applicable for studying a wide range of biomarkers.
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Affiliation(s)
- Joshua S. Ostrander
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Justin P. Lomont
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Kacie L. Rich
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Vivek Saraswat
- Department of Materials Science and Engineering, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Benjamin R. Feingold
- Department of Materials Science and Engineering, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Megan K. Petti
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Erin R. Birdsall
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Michael S. Arnold
- Department of Materials Science and Engineering, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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21
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Zheng X, Yu P, Wang J. Ultrafast intramolecular vibrational energy transfer in carbon nitride hydrocolloid examined by femtosecond two-dimensional infrared spectroscopy. J Chem Phys 2019; 150:194703. [PMID: 31117771 DOI: 10.1063/1.5093542] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In this work, ultrafast vibrational and structural processes in a graphitic carbon nitride hydrocolloid system were studied using a combination of linear infrared and nonlinear two-dimensional infrared (2D IR) spectroscopies. The experimentally observed three IR line shapes in the C=N stretching vibration frequency region were analyzed and attributed to the rigid and conjugated molecular frame of the prepared g-CN molecular species, which is believed to be a dimeric tris-s-triazine, as well as attributed to insignificant solvent influence on the delocalized C=N vibrations. Vibrational transition density cubes were also computed for the proposed g-CN dimer, confirming the heterocyclic C=N stretching nature of the three IR absorption peaks. Intramolecular vibrational energy transfer dynamics and spectral diffusion of the g-CN system were characterized by examining a series of time-dependent 2D IR spectra. A picosecond intramolecular vibrational energy redistribution process was found to occur among these delocalized C=N stretching modes, acting as an efficient vibrational energy transfer channel. This work reasonably connects the experimentally observed IR signature to a specific g-CN structure and also provides the first report on the ultrafast intramolecular processes of such carbon nitride systems. The obtained results are fundamentally important for understanding the molecular mechanisms of such carbon-nitride based functional materials.
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Affiliation(s)
- Xuan Zheng
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Pengyun Yu
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
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22
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Sun Y, Kakinen A, Xing Y, Faridi P, Nandakumar A, Purcell AW, Davis TP, Ke PC, Ding F. Amyloid Self-Assembly of hIAPP8-20 via the Accumulation of Helical Oligomers, α-Helix to β-Sheet Transition, and Formation of β-Barrel Intermediates. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805166. [PMID: 30908844 PMCID: PMC6499678 DOI: 10.1002/smll.201805166] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/21/2019] [Indexed: 05/19/2023]
Abstract
The self-assembly of human islet amyloid polypeptide (hIAPP) into β-sheet-rich nanofibrils is associated with the pathogeny of type 2 diabetes. Soluble hIAPP is intrinsically disordered with N-terminal residues 8-17 as α-helices. To understand the contribution of the N-terminal helix to the aggregation of full-length hIAPP, here the oligomerization dynamics of the hIAPP fragment 8-20 (hIAPP8-20) are investigated with combined computational and experimental approaches. hIAPP8-20 forms cross-β nanofibrils in silico from isolated helical monomers via the helical oligomers and α-helices to β-sheets transition, as confirmed by transmission electron microscopy, atomic force microscopy, circular dichroism spectroscopy, Fourier transform infrared spectroscopy, and reversed-phase high performance liquid chromatography. The computational results also suggest that the critical nucleus of aggregation corresponds to hexamers, consistent with a recent mass-spectroscopy study of hIAPP8-20 aggregation. hIAPP8-20 oligomers smaller than hexamers are helical and unstable, while the α-to-β transition starts from the hexamers. Converted β-sheet-rich oligomers first form β-barrel structures as intermediates before aggregating into cross-β nanofibrils. This study uncovers a complete picture of hIAPP8-20 peptide oligomerization, aggregation nucleation via conformational conversion, formation of β-barrel intermediates, and assembly of cross-β protofibrils, thereby shedding light on the aggregation of full-length hIAPP, a hallmark of pancreatic beta-cell degeneration.
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Affiliation(s)
- Yunxiang Sun
- Department of Physics, Faculty of Science, Ningbo University, Ningbo 315211, China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Aleksandr Kakinen
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Yanting Xing
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Pouya Faridi
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Aparna Nandakumar
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Anthony W. Purcell
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Thomas P. Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Pu Chun Ke
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
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23
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Godin E, Nguyen PT, Zottig X, Bourgault S. Identification of a hinge residue controlling islet amyloid polypeptide self-assembly and cytotoxicity. J Biol Chem 2019; 294:8452-8463. [PMID: 30975901 DOI: 10.1074/jbc.ra118.006454] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 04/04/2019] [Indexed: 11/06/2022] Open
Abstract
The islet amyloid polypeptide (IAPP) is a 37-residue peptide hormone whose deposition as amyloid fibrils in the pancreatic islets is associated with type 2 diabetes. Previous studies have suggested that residue Asn-21 plays a critical role in the in vitro self-assembly of IAPP. Herein, we studied structure-self-assembly relationships focusing on position 21 to gain detailed insights into the molecular mechanisms of IAPP self-assembly and to probe the conformational nature of the toxic assemblies associated with β-cell death. Thioflavin T (ThT) fluorescence, CD spectroscopy, and transmission EM analysis revealed that the Asn-21 amide side chain is not required for IAPP nucleation and amyloid elongation, as N21A and N21G variants assembled into prototypical fibrils. In contrast, Asn-21 substitution with the conformationally constrained and turn-inducing residue Pro accelerated IAPP self-assembly. Successive substitutions with hydrophobic residues led to the formation of ThT-negative β-sheet-rich aggregates having high surface hydrophobicity. Cell-based assays revealed no direct correlation between the in vitro amyloidogenicity of these variants and their toxicity. In contrast, leakage of anionic lipid vesicles disclosed that membrane disruption is closely associated with cytotoxicity. We observed that the N21F variant self-assembles into worm-like aggregates, causing loss of lipid membrane structural integrity and inducing β-cell apoptosis. These results indicate that specific intra- and intermolecular interactions involving Asn-21 promote IAPP primary nucleation events by modulating the conformational conversion of the oligomeric intermediates into amyloid fibrils. Our study identifies position 21 as a hinge residue that modulates IAPP amyloidogenicity and cytotoxicity.
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Affiliation(s)
- Elizabeth Godin
- Department of Chemistry, Pharmaqam, Université du Québec à Montréal, Montreal, Quebec H3C 3P8, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Quebec G1V 0A6, Canada
| | - Phuong Trang Nguyen
- Department of Chemistry, Pharmaqam, Université du Québec à Montréal, Montreal, Quebec H3C 3P8, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Quebec G1V 0A6, Canada
| | - Ximena Zottig
- Department of Chemistry, Pharmaqam, Université du Québec à Montréal, Montreal, Quebec H3C 3P8, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Quebec G1V 0A6, Canada
| | - Steve Bourgault
- Department of Chemistry, Pharmaqam, Université du Québec à Montréal, Montreal, Quebec H3C 3P8, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Quebec G1V 0A6, Canada.
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24
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Li J, Chen R, Zhang S, Ma Z, Luo Z, Gao G. Chiral Effect at Nano-Bio Interface: A Model of Chiral Gold Nanoparticle on Amylin Fibrillation. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E412. [PMID: 30862041 PMCID: PMC6474006 DOI: 10.3390/nano9030412] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 02/25/2019] [Accepted: 03/05/2019] [Indexed: 02/07/2023]
Abstract
Protein/Peptide amyloidosis is the main cause of several diseases, such as neurodegenerative diseases. It has been widely acknowledged that the unnatural fibrillation of protein/peptides in vivo is significantly affected by the physical and chemical properties of multiscale biological membranes. For example, previous studies have proved that molecule chirality could greatly influence the misfolding, fibrillation and assembly of β-Amyloid peptides at the flat liquid-solid surface. However, how the nanoscale chirality influences this process remains unclear. Here we used gold nanoparticles (AuNPs, d = 4 ± 1 nm)-modified with N-isobutyl-L(D)-cysteine (L(D)-NIBC) enantiomers-as a model to illustrate the chiral effect on the amylin fibrillation at nano-bio interface. We reported that both two chiral AuNPs could inhibit amylin fibrillation in a dosage-dependent manner but the inhibitory effect of L-NIBC-AuNPs was more effective than that of D-NIBC-AuNPs. In-situ real time circular dichroism (CD) spectra showed that L-NIBC-AuNPs could inhibit the conformation transition process of amylin from random coils to α-helix, while D-NIBC-AuNPs could only delay but not prevent the formation of α-helix; however, they could inhibit the further conformation transition process of amylin from α-helix to β-sheet. These results not only provide interesting insight for reconsidering the mechanism of peptides amyloidosis at the chiral interfaces provided by biological nanostructures in vivo but also would help us design therapeutic inhibitors for anti-amyloidosis targeting diverse neurodegenerative diseases.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, No.122 Luoshi Road, Wuhan 430070, China.
| | - Rui Chen
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, No.122 Luoshi Road, Wuhan 430070, China.
| | - Shasha Zhang
- School of Arts and Media, Wuhan Vocational College of Software and Engineering, No. 117 Guanggu Road, Wuhan 430205, China.
| | - Zhongjie Ma
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, No.122 Luoshi Road, Wuhan 430070, China.
| | - Zhuoying Luo
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, No.122 Luoshi Road, Wuhan 430070, China.
| | - Guanbin Gao
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, No.122 Luoshi Road, Wuhan 430070, China.
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25
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Synthesis and identification of novel pyridazinylpyrazolone based diazo compounds as inhibitors of human islet amyloid polypeptide aggregation. Bioorg Chem 2019; 84:339-346. [DOI: 10.1016/j.bioorg.2018.11.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 11/17/2018] [Accepted: 11/24/2018] [Indexed: 02/06/2023]
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26
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Vibrational Approach to the Dynamics and Structure of Protein Amyloids. Molecules 2019; 24:molecules24010186. [PMID: 30621325 PMCID: PMC6337179 DOI: 10.3390/molecules24010186] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023] Open
Abstract
Amyloid diseases, including neurodegenerative diseases such as Alzheimer’s and Parkinson’s, are linked to a poorly understood progression of protein misfolding and aggregation events that culminate in tissue-selective deposition and human pathology. Elucidation of the mechanistic details of protein aggregation and the structural features of the aggregates is critical for a comprehensive understanding of the mechanisms of protein oligomerization and fibrillization. Vibrational spectroscopies, such as Fourier transform infrared (FTIR) and Raman, are powerful tools that are sensitive to the secondary structure of proteins and have been widely used to investigate protein misfolding and aggregation. We address the application of the vibrational approaches in recent studies of conformational dynamics and structural characteristics of protein oligomers and amyloid fibrils. In particular, introduction of isotope labelled carbonyl into a peptide backbone, and incorporation of the extrinsic unnatural amino acids with vibrational moieties on the side chain, have greatly expanded the ability of vibrational spectroscopy to obtain site-specific structural and dynamic information. The applications of these methods in recent studies of protein aggregation are also reviewed.
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27
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Sun Y, Kakinen A, Xing Y, Pilkington EH, Davis TP, Ke PC, Ding F. Nucleation of β-rich oligomers and β-barrels in the early aggregation of human islet amyloid polypeptide. Biochim Biophys Acta Mol Basis Dis 2018; 1865:434-444. [PMID: 30502402 DOI: 10.1016/j.bbadis.2018.11.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/10/2018] [Accepted: 11/26/2018] [Indexed: 10/27/2022]
Abstract
The self-assembly of human islet amyloid polypeptide (hIAPP) into β-sheet rich amyloid aggregates is associated with pancreatic β-cell death in type 2 diabetes (T2D). Prior experimental studies of hIAPP aggregation reported the early accumulation of α-helical intermediates before the rapid conversion into β-sheet rich amyloid fibrils, as also corroborated by our experimental characterizations with transmission electron microscopy and Fourier transform infrared spectroscopy. Although increasing evidence suggests that small oligomers populating early hIAPP aggregation play crucial roles in cytotoxicity, structures of these oligomer intermediates and their conformational conversions remain unknown, hindering our understanding of T2D disease mechanism and therapeutic design targeting these early aggregation species. We further applied large-scale discrete molecule dynamics simulations to investigate the oligomerization of full-length hIAPP, employing multiple molecular systems of increasing number of peptides. We found that the oligomerization process was dynamic, involving frequent inter-oligomeric exchanges. On average, oligomers had more α-helices than β-sheets, consistent with ensemble-based experimental measurements. However, in ~4-6% independent simulations, β-rich oligomers expected as the fibrillization intermediates were observed, especially in the pentamer and hexamer simulations. These β-rich oligomers could adopt β-barrel conformations, recently postulated to be the toxic oligomer species but only observed computationally in the aggregates of short amyloid protein fragments. Free-energy analysis revealed high energies of these β-rich oligomers, supporting the nucleated conformational changes of oligomers in amyloid aggregation. β-barrel oligomers of full-length hIAPP with well-defined three-dimensional structures may play an important pathological role in T2D etiology and may be a therapeutic target for the disease.
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Affiliation(s)
- Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Aleksandr Kakinen
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Yanting Xing
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Emily H Pilkington
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia; Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Thomas P Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia; Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Pu Chun Ke
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia.
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
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28
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Buchanan LE, Maj M, Dunkelberger EB, Cheng PN, Nowick JS, Zanni MT. Structural Polymorphs Suggest Competing Pathways for the Formation of Amyloid Fibrils That Diverge from a Common Intermediate Species. Biochemistry 2018; 57:6470-6478. [PMID: 30375231 DOI: 10.1021/acs.biochem.8b00997] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
It is now recognized that many amyloid-forming proteins can associate into multiple fibril structures. Here, we use two-dimensional infrared spectroscopy to study two fibril polymorphs formed by human islet amyloid polypeptide (hIAPP or amylin), which is associated with type 2 diabetes. The polymorphs exhibit different degrees of structural organization near the loop region of hIAPP fibrils. The relative populations of these polymorphs are systematically altered by the presence of macrocyclic peptides which template β-sheet formation at specific sections of the hIAPP sequence. These experiments are consistent with polymorphs that result from competing pathways for fibril formation and that the macrocycles bias hIAPP aggregation toward one pathway or the other. Another macrocyclic peptide that matches the loop region but extends the lag time leaves the relative populations of the polymorphs unaltered, suggesting that the branching point for structural divergence occurs after the lag phase, when the oligomers convert into seeds that template fibril formation. Thus, we conclude that the structures of the polymorphs stem from restricting oligomers along diverging folding pathways, which has implications for drug inhibition, cytotoxicity, and the free energy landscape of hIAPP aggregation.
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Affiliation(s)
- Lauren E Buchanan
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , United States
| | - Michał Maj
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , United States
| | - Emily B Dunkelberger
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , United States
| | - Pin-Nan Cheng
- Department of Chemistry , University of California-Irvine , Irvine , California 92697-2025 , United States
| | - James S Nowick
- Department of Chemistry , University of California-Irvine , Irvine , California 92697-2025 , United States
| | - Martin T Zanni
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , United States
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29
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Wang M, Sun Y, Cao X, Peng G, Javed I, Kakinen A, Davis TP, Lin S, Liu J, Ding F, Ke PC. Graphene quantum dots against human IAPP aggregation and toxicity in vivo. NANOSCALE 2018; 10:19995-20006. [PMID: 30350837 PMCID: PMC6212334 DOI: 10.1039/c8nr07180b] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The development of biocompatible nanomaterials has become a new frontier in the detection, treatment and prevention of human amyloid diseases. Here we demonstrated the use of graphene quantum dots (GQDs) as a potent inhibitor against the in vivo aggregation and toxicity of human islet amyloid polypeptide (IAPP), a hallmark of type 2 diabetes. GQDs initiated contact with IAPP through electrostatic and hydrophobic interactions as well as hydrogen bonding, which subsequently drove the peptide fibrillization off-pathway to eliminate the toxic intermediates. Such interactions, probed in vitro by a thioflavin T kinetic assay, fluorescence quenching, circular dichroism spectroscopy, a cell viability assay and in silico by discrete molecular dynamics simulations, translated to a significant recovery of embryonic zebrafish from the damage elicited by IAPP in vivo, as indicated by improved hatching as well as alleviated reactive oxygen species production, abnormality and mortality of the organism. This study points to the potential of using zero-dimensional nanomaterials for in vivo mitigation of a range of amyloidosis.
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Affiliation(s)
- Miaoyi Wang
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- College of Environmental Science and Engineering, Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, Shanghai Institute of Pollution Control and Ecological Security, Key Laboratory of Yangtze River Water Environment, Ministry of Education, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Xueying Cao
- College of Materials Science and Engineering, Institute for Graphene Applied Technology Innovation, Qingdao University, Qingdao 266071, China
| | - Guotao Peng
- College of Environmental Science and Engineering, Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, Shanghai Institute of Pollution Control and Ecological Security, Key Laboratory of Yangtze River Water Environment, Ministry of Education, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Ibrahim Javed
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Aleksandr Kakinen
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Thomas P. Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Sijie Lin
- College of Environmental Science and Engineering, Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, Shanghai Institute of Pollution Control and Ecological Security, Key Laboratory of Yangtze River Water Environment, Ministry of Education, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Jingquan Liu
- College of Materials Science and Engineering, Institute for Graphene Applied Technology Innovation, Qingdao University, Qingdao 266071, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Pu Chun Ke
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
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30
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Guo AZ, Fluitt AM, de Pablo JJ. Early-stage human islet amyloid polypeptide aggregation: Mechanisms behind dimer formation. J Chem Phys 2018; 149:025101. [DOI: 10.1063/1.5033458] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Ashley Z. Guo
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Aaron M. Fluitt
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Juan J. de Pablo
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
- Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
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31
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Introduction to State-of-the-Art Multidimensional Time-Resolved Spectroscopy Methods. Top Curr Chem (Cham) 2018; 376:28. [DOI: 10.1007/s41061-018-0206-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/13/2018] [Indexed: 10/28/2022]
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32
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Petti MK, Lomont JP, Maj M, Zanni MT. Two-Dimensional Spectroscopy Is Being Used to Address Core Scientific Questions in Biology and Materials Science. J Phys Chem B 2018; 122:1771-1780. [PMID: 29346730 DOI: 10.1021/acs.jpcb.7b11370] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two-dimensional spectroscopy is a powerful tool for extracting structural and dynamic information from a wide range of chemical systems. We provide a brief overview of the ways in which two-dimensional visible and infrared spectroscopies are being applied to elucidate fundamental details of important processes in biological and materials science. The topics covered include amyloid proteins, photosynthetic complexes, ion channels, photovoltaics, batteries, as well as a variety of promising new methods in two-dimensional spectroscopy.
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Affiliation(s)
- Megan K Petti
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Justin P Lomont
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Michał Maj
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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33
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Ho JJ, Ghosh A, Zhang TO, Zanni MT. Heterogeneous Amyloid β-Sheet Polymorphs Identified on Hydrogen Bond Promoting Surfaces Using 2D SFG Spectroscopy. J Phys Chem A 2018; 122:1270-1282. [DOI: 10.1021/acs.jpca.7b11934] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jia-Jung Ho
- University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Ayanjeet Ghosh
- University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Tianqi O. Zhang
- University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Martin T. Zanni
- University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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