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Kämäräinen T, Nakayama Y, Uchiyama H, Tozuka Y, Kadota K. Amyloid Nanofibril-Assisted Spray Drying of Crumpled Supraparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2309645. [PMID: 38716922 DOI: 10.1002/smll.202309645] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/19/2024] [Indexed: 10/04/2024]
Abstract
Nanofibrils are known to improve the cohesion of supraparticle (SP) assemblies. However, tailoring the morphology of SPs using nanofibrillar additives is not well developed. Herein, β-lactoglobulin amyloid nanofibrils (ANFs) are investigated as means to impart morphological control over the assembly process of spray-dried SPs composed of 10-100 nm silica nanoparticles (SiNPs). Phytoglycogen (PG) and silver nanowires (AgNWs) are used to assess the influence of building block softness and aspect ratio, respectively. The results demonstrate that ANFs promote the onset of structural arrest during the particle consolidation enabling the preparation of corrugated SP morphologies. The critical ANF loading required to induce SP corrugation increases by roughly 1 vol% for every 10-nm increase in SiNP diameter, while the ensuing ANF network density decreases with SiNP volume fraction and increases with SiNP diameter. Results imply that ANF length starts to become influential when it approaches the SiNP diameter. ANFs display a reduced effectiveness in altering soft PG SP morphology compared with hard SiNPs of comparable size. In SiNP-AgNW SPs, ANFs induce a toroid-to-corrugated morphology transformation for sufficiently large SPs and small SiNPs. The results illustrate that ANFs are effective additives for the morphological engineering of spray-dried SPs important for numerous applications.
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Affiliation(s)
- Tero Kämäräinen
- Department of Formulation Design and Pharmaceutical Technology, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Yuzuki Nakayama
- Department of Formulation Design and Pharmaceutical Technology, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Hiromasa Uchiyama
- Department of Formulation Design and Pharmaceutical Technology, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Yuichi Tozuka
- Department of Formulation Design and Pharmaceutical Technology, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Kazunori Kadota
- Department of Formulation Design and Pharmaceutical Technology, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
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2
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Duverger W, Tsaka G, Khodaparast L, Khodaparast L, Louros N, Rousseau F, Schymkowitz J. An end-to-end approach for single-cell infrared absorption spectroscopy of bacterial inclusion bodies: from AFM-IR measurement to data interpretation of large sample sets. J Nanobiotechnology 2024; 22:406. [PMID: 38987828 PMCID: PMC11234752 DOI: 10.1186/s12951-024-02674-3] [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: 03/13/2024] [Accepted: 06/25/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND Inclusion bodies (IBs) are well-known subcellular structures in bacteria where protein aggregates are collected. Various methods have probed their structure, but single-cell spectroscopy remains challenging. Atomic Force Microscopy-based Infrared Spectroscopy (AFM-IR) is a novel technology with high potential for the characterisation of biomaterials such as IBs. RESULTS We present a detailed investigation using AFM-IR, revealing the substructure of IBs and their variation at the single-cell level, including a rigorous optimisation of data collection parameters and addressing issues such as laser power, pulse frequency, and sample drift. An analysis pipeline was developed tailored to AFM-IR image data, allowing high-throughput, label-free imaging of more than 3500 IBs in 12,000 bacterial cells. We examined IBs generated in Escherichia coli under different stress conditions. Dimensionality reduction analysis of the resulting spectra suggested distinct clustering of stress conditions, aligning with the nature and severity of the applied stresses. Correlation analyses revealed intricate relationships between the physical and morphological properties of IBs. CONCLUSIONS Our study highlights the power and limitations of AFM-IR, revealing structural heterogeneity within and between IBs. We show that it is possible to perform quantitative analyses of AFM-IR maps over a large collection of different samples and determine how to control for various technical artefacts.
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Affiliation(s)
- Wouter Duverger
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, Herestraat 49, Leuven, 3000, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, Leuven, 3000, Belgium
| | - Grigoria Tsaka
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, Herestraat 49, Leuven, 3000, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, Leuven, 3000, Belgium
- Laboratory for Neuropathology, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Leuven, 3000, Belgium
- Leuven Brain Institute, KU Leuven, Herestraat 49, Leuven, 3000, Belgium
| | - Ladan Khodaparast
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, Herestraat 49, Leuven, 3000, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, Leuven, 3000, Belgium
| | - Laleh Khodaparast
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, Herestraat 49, Leuven, 3000, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, Leuven, 3000, Belgium
| | - Nikolaos Louros
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, Herestraat 49, Leuven, 3000, Belgium.
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, Leuven, 3000, Belgium.
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, Herestraat 49, Leuven, 3000, Belgium.
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, Leuven, 3000, Belgium.
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3
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Zhao T, Pan Y. Transformation of β-sheets into disordered structures during the fossilization of feathers. Nat Ecol Evol 2024; 8:1233-1235. [PMID: 38867091 DOI: 10.1038/s41559-024-02432-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 05/08/2024] [Indexed: 06/14/2024]
Affiliation(s)
- Tao Zhao
- Institute of Palaeontology, Yunnan Key Laboratory of Earth System Science, Yunnan University, Kunming, China.
| | - Yanhong Pan
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Centre for Research and Education on Biological Evolution and Environment, Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China
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4
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Vazquez-Gutierrez I, Reyes-López MA, Ochoa SA, Cruz-Córdova A, Hernández-Castro R, Orduña-Díaz A, Xicohtencatl-Cortes J. Specific Detection of Uropathogenic Escherichia coli via Fourier Transform Infrared Spectroscopy Using an Optical Biosensor. ACS OMEGA 2024; 9:27528-27536. [PMID: 38947791 PMCID: PMC11209919 DOI: 10.1021/acsomega.4c02794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/12/2024] [Accepted: 05/24/2024] [Indexed: 07/02/2024]
Abstract
Urinary tract infections (UTIs) are caused mainly by uropathogenic Escherichia coli (UPEC), accounting for both uncomplicated (75%) and complicated (65%) UTIs. Detecting UPEC in a specific, rapid, and timely manner is essential for eradication, and optical biosensors may be useful tools for detecting UPEC. Recently, biosensors have been developed for the selective detection of antigen-antibody-specific interactions. In this study, a methodology based on the principle of an optical biosensor was developed to identify specific biomolecules, such as the PapG protein, which is located at the tip of P fimbriae and promotes the interaction of UPEC with the uroepithelium of the human kidney during a UTI. For biosensor construction, recombinant PapG protein was generated and polyclonal anti-PapG antibodies were obtained. The biosensor was fabricated in silicon supports because its surface and anchor biomolecules can be modified through its various properties. The fabrication process was carried out using self-assembled monolayers (SAMs) and an immobilized bioreceptor (anti-PapG) to detect the PapG protein. Each stage of biosensor development was evaluated by Fourier transform infrared (FTIR) spectroscopy. The infrared spectra showed bands corresponding to the C-H, C=O, and amide II bonds, revealing the presence of the PapG protein. Then, the spectra of the second derivative were obtained from 1600 to 1700 cm-1 to specifically determine the interactions that occur in the secondary structures between the biological recognition element (anti-PapG antibodies) and the analyte (PapG protein) complex. The analyzed secondary structure showed β-sheets and β-turns during the detection of the PapG protein. Our data suggest that the PapG protein can be detected through an optical biosensor and that the biosensor exhibited high specificity for the detection of UPEC strains. Furthermore, these studies provide initial support for the development of more specific biosensors that can be applied in the future for the detection of clinical UPEC samples associated with ITUs.
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Affiliation(s)
- Isabel
G. Vazquez-Gutierrez
- Centro
de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Mexico 90700, Tlaxcala, México
- Centro
de Biotecnología Genómica, Instituto Politécnico Nacional, Mexico 88710, Tamaulipas, México
- Laboratorio
de Investigación en Bacteriología Intestinal, Unidad
de Enfermedades Infecciosas, Hospital Infantil
de México “Federico Gómez”, Mexico 06720, CDMX, México
| | - Miguel A. Reyes-López
- Centro
de Biotecnología Genómica, Instituto Politécnico Nacional, Mexico 88710, Tamaulipas, México
| | - Sara A. Ochoa
- Laboratorio
de Investigación en Bacteriología Intestinal, Unidad
de Enfermedades Infecciosas, Hospital Infantil
de México “Federico Gómez”, Mexico 06720, CDMX, México
| | - Ariadnna Cruz-Córdova
- Laboratorio
de Investigación en Bacteriología Intestinal, Unidad
de Enfermedades Infecciosas, Hospital Infantil
de México “Federico Gómez”, Mexico 06720, CDMX, México
| | - Rigoberto Hernández-Castro
- Departamento
de Ecología de Agentes Patógenos, Hospital General “Dr. Manuel
Gea González”, Mexico 14000, CDMX, México
| | - Abdú Orduña-Díaz
- Centro
de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Mexico 90700, Tlaxcala, México
| | - Juan Xicohtencatl-Cortes
- Laboratorio
de Investigación en Bacteriología Intestinal, Unidad
de Enfermedades Infecciosas, Hospital Infantil
de México “Federico Gómez”, Mexico 06720, CDMX, México
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5
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Freedman H, Tuszynski JA. Study of the Myosin Relay Helix Peptide by Molecular Dynamics Simulations, Pump-Probe and 2D Infrared Spectroscopy. Int J Mol Sci 2024; 25:6406. [PMID: 38928112 PMCID: PMC11203622 DOI: 10.3390/ijms25126406] [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: 03/25/2024] [Revised: 05/07/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
The Davydov model was conjectured to describe how an amide I excitation created during ATP hydrolysis in myosin might be significant in providing energy to drive myosin's chemomechanical cycle. The free energy surfaces of the myosin relay helix peptide dissolved in 2,2,2-trifluoroethanol (TFE), determined by metadynamics simulations, demonstrate local minima differing in free energy by only ~2 kT, corresponding to broken and stabilized hydrogen bonds, respectively. Experimental pump-probe and 2D infrared spectroscopy were performed on the peptide dissolved in TFE. The relative heights of two peaks seen in the pump-probe data and the corresponding relative volumes of diagonal peaks seen in the 2D-IR spectra at time delays between 0.5 ps and 1 ps differ noticeably from what is seen at earlier or later time delays or in the linear spectrum, indicating that a vibrational excitation may influence the conformational state of this helix. Thus, it is possible that the presence of an amide I excitation may be a direct factor in the conformational state taken on by the myosin relay helix following ATP hydrolysis in myosin.
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Affiliation(s)
- Holly Freedman
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, UT 84112, USA
| | - Jack A. Tuszynski
- Department of Physics, University of Alberta, 11335 Saskatchewan Dr NW, Edmonton, AB T6G 2M9, Canada;
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, I-1029 Turin, Italy
- Department of Data Science and Engineering, The Silesian University of Technology, 44-100 Gliwice, Poland
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6
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De Oliveira DH, Gowda V, Sparrman T, Gustafsson L, Sanches Pires R, Riekel C, Barth A, Lendel C, Hedhammar M. Structural conversion of the spidroin C-terminal domain during assembly of spider silk fibers. Nat Commun 2024; 15:4670. [PMID: 38821983 PMCID: PMC11143275 DOI: 10.1038/s41467-024-49111-5] [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: 10/26/2023] [Accepted: 05/24/2024] [Indexed: 06/02/2024] Open
Abstract
The major ampullate Spidroin 1 (MaSp1) is the main protein of the dragline spider silk. The C-terminal (CT) domain of MaSp1 is crucial for the self-assembly into fibers but the details of how it contributes to the fiber formation remain unsolved. Here we exploit the fact that the CT domain can form silk-like fibers by itself to gain knowledge about this transition. Structural investigations of fibers from recombinantly produced CT domain from E. australis MaSp1 reveal an α-helix to β-sheet transition upon fiber formation and highlight the helix No4 segment as most likely to initiate the structural conversion. This prediction is corroborated by the finding that a peptide corresponding to helix No4 has the ability of pH-induced conversion into β-sheets and self-assembly into nanofibrils. Our results provide structural information about the CT domain in fiber form and clues about its role in triggering the structural conversion of spidroins during fiber assembly.
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Affiliation(s)
- Danilo Hirabae De Oliveira
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
- Department of Chemistry, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Vasantha Gowda
- Department of Chemistry, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Linnea Gustafsson
- Spiber Technologies AB, Roslagstullsbacken 15, 114 21, Stockholm, Sweden
| | | | - Christian Riekel
- European Synchrotron Radiation Facility, B.P. 220, F-38043, Grenoble Cedex, France
| | - Andreas Barth
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Christofer Lendel
- Department of Chemistry, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - My Hedhammar
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden.
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7
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Paul S, Jeništová A, Vosough F, Berntsson E, Mörman C, Jarvet J, Gräslund A, Wärmländer SKTS, Barth A. 13C- and 15N-labeling of amyloid-β and inhibitory peptides to study their interaction via nanoscale infrared spectroscopy. Commun Chem 2023; 6:163. [PMID: 37537303 PMCID: PMC10400569 DOI: 10.1038/s42004-023-00955-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/06/2023] [Indexed: 08/05/2023] Open
Abstract
Interactions between molecules are fundamental in biology. They occur also between amyloidogenic peptides or proteins that are associated with different amyloid diseases, which makes it important to study the mutual influence of two polypeptides on each other's properties in mixed samples. However, addressing this research question with imaging techniques faces the challenge to distinguish different polypeptides without adding artificial probes for detection. Here, we show that nanoscale infrared spectroscopy in combination with 13C, 15N-labeling solves this problem. We studied aggregated amyloid-β peptide (Aβ) and its interaction with an inhibitory peptide (NCAM1-PrP) using scattering-type scanning near-field optical microscopy. Although having similar secondary structure, labeled and unlabeled peptides could be distinguished by comparing optical phase images taken at wavenumbers characteristic for either the labeled or the unlabeled peptide. NCAM1-PrP seems to be able to associate with or to dissolve existing Aβ fibrils because pure Aβ fibrils were not detected after mixing.
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Affiliation(s)
- Suman Paul
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
- attocube systems AG, Haar, Germany
| | - Adéla Jeništová
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Faraz Vosough
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Elina Berntsson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cecilia Mörman
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Jüri Jarvet
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
- National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | | | - Andreas Barth
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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8
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Berntsson E, Vosough F, Noormägi A, Padari K, Asplund F, Gielnik M, Paul S, Jarvet J, Tõugu V, Roos PM, Kozak M, Gräslund A, Barth A, Pooga M, Palumaa P, Wärmländer SKTS. Characterization of Uranyl (UO 22+) Ion Binding to Amyloid Beta (Aβ) Peptides: Effects on Aβ Structure and Aggregation. ACS Chem Neurosci 2023; 14:2618-2633. [PMID: 37487115 PMCID: PMC10401651 DOI: 10.1021/acschemneuro.3c00130] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/06/2023] [Indexed: 07/26/2023] Open
Abstract
Uranium (U) is naturally present in ambient air, water, and soil, and depleted uranium (DU) is released into the environment via industrial and military activities. While the radiological damage from U is rather well understood, less is known about the chemical damage mechanisms, which dominate in DU. Heavy metal exposure is associated with numerous health conditions, including Alzheimer's disease (AD), the most prevalent age-related cause of dementia. The pathological hallmark of AD is the deposition of amyloid plaques, consisting mainly of amyloid-β (Aβ) peptides aggregated into amyloid fibrils in the brain. However, the toxic species in AD are likely oligomeric Aβ aggregates. Exposure to heavy metals such as Cd, Hg, Mn, and Pb is known to increase Aβ production, and these metals bind to Aβ peptides and modulate their aggregation. The possible effects of U in AD pathology have been sparsely studied. Here, we use biophysical techniques to study in vitro interactions between Aβ peptides and uranyl ions, UO22+, of DU. We show for the first time that uranyl ions bind to Aβ peptides with affinities in the micromolar range, induce structural changes in Aβ monomers and oligomers, and inhibit Aβ fibrillization. This suggests a possible link between AD and U exposure, which could be further explored by cell, animal, and epidemiological studies. General toxic mechanisms of uranyl ions could be modulation of protein folding, misfolding, and aggregation.
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Affiliation(s)
- Elina Berntsson
- Chemistry
Section, Arrhenius Laboratories, Stockholm
University, 106 91 Stockholm, Sweden
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology, 19086 Tallinn, Estonia
| | - Faraz Vosough
- Chemistry
Section, Arrhenius Laboratories, Stockholm
University, 106 91 Stockholm, Sweden
| | - Andra Noormägi
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology, 19086 Tallinn, Estonia
| | - Kärt Padari
- Institute
of Molecular and Cell Biology, University
of Tartu, 50090 Tartu, Estonia
| | - Fanny Asplund
- Chemistry
Section, Arrhenius Laboratories, Stockholm
University, 106 91 Stockholm, Sweden
| | - Maciej Gielnik
- Department
of Molecular Biology and Genetics, Aarhus
University, 8000 Aarhus, Denmark
| | - Suman Paul
- Chemistry
Section, Arrhenius Laboratories, Stockholm
University, 106 91 Stockholm, Sweden
| | - Jüri Jarvet
- Chemistry
Section, Arrhenius Laboratories, Stockholm
University, 106 91 Stockholm, Sweden
- CellPept
Sweden AB, Kvarngatan
10B, 118 47 Stockholm, Sweden
| | - Vello Tõugu
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology, 19086 Tallinn, Estonia
| | - Per M. Roos
- Institute
of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
- University
Healthcare Unit of Capio St. Göran Hospital, 112 81 Stockholm, Sweden
| | - Maciej Kozak
- Department
of Biomedical Physics, Institute of Physics, Faculty of Physics, Adam Mickiewicz University, 61-712 Poznań, Poland
- SOLARIS
National Synchrotron Radiation Centre, Jagiellonian
University, 31-007 Kraków, Poland
| | - Astrid Gräslund
- Chemistry
Section, Arrhenius Laboratories, Stockholm
University, 106 91 Stockholm, Sweden
- CellPept
Sweden AB, Kvarngatan
10B, 118 47 Stockholm, Sweden
| | - Andreas Barth
- Chemistry
Section, Arrhenius Laboratories, Stockholm
University, 106 91 Stockholm, Sweden
| | - Margus Pooga
- Institute
of Technology, University of Tartu, 50090 Tartu, Estonia
| | - Peep Palumaa
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology, 19086 Tallinn, Estonia
| | - Sebastian K. T. S. Wärmländer
- Chemistry
Section, Arrhenius Laboratories, Stockholm
University, 106 91 Stockholm, Sweden
- CellPept
Sweden AB, Kvarngatan
10B, 118 47 Stockholm, Sweden
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9
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El Orche A, Cheikh A, Johnson JB, Elhamdaoui O, Jawhari S, El Abbes FM, Cherrah Y, Mbarki M, Bouatia M. A Novel Approach for Therapeutic Drug Monitoring of Valproic Acid Using FT-IR Spectroscopy and Nonlinear Support Vector Regression. J AOAC Int 2023; 106:1070-1076. [PMID: 36367248 DOI: 10.1093/jaoacint/qsac146] [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: 07/03/2022] [Revised: 10/16/2022] [Accepted: 11/06/2022] [Indexed: 07/20/2023]
Abstract
BACKGROUND Recent technological progress has bolstered efforts to bring personalized medicine from theory into clinical practice. However, progress in areas such as therapeutic drug monitoring (TDM) has remained somewhat stagnant. In drugs with well-known dose-response relationships, TDM can enhance patient outcomes and reduce health care costs. Traditional monitoring methods such as chromatography-based or immunoassay techniques are limited by their higher costs and slow turnaround times, making them unsuitable for real-time or onsite analysis. OBJECTIVE In this work, we propose the use of a fast, direct, and simple approach using Fourier transform infrared spectroscopy (FT-IR) combined with chemometric techniques for the therapeutic monitoring of valproic acid (VPA). METHOD In this context, a database of FT-IR spectra was constructed from human plasma samples containing various concentrations of VPA; these samples were characterized by the reference method (immunoassay technique) to determine the VPA contents. The FT-IR spectra were processed by two chemometric regression methods: partial least-squares regression (PLS) and support vector regression (SVR). RESULTS The results provide good evidence for the effectiveness of the combination of FT-IR spectroscopy and SVR modeling for estimating VPA in human plasma. SVR models showed better predictive abilities than PLS models in terms of root-mean-square error of calibration and prediction RMSEC, RMSEP, R2Cal, R2Pred, and residual predictive deviation (RPD). CONCLUSIONS This analytical tool offers potential for real-time TDM in the clinical setting. HIGHLIGHTS FTIR spectroscopy was evaluated for the first time to predict VPA in human plasma for TDM. Two regressions were evaluated to predict VPA in human plasma, and the best-performing model was obtained using nonlinear SVR.
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Affiliation(s)
- Aimen El Orche
- University of Sultan Moulay Slimane, Faculty of Sciences and Techniques, Beni Mellal 23000, Morocco
| | - Amine Cheikh
- Abulcasis University, Department of Pharmacy, Rabat 10000, Morocco
| | - Joel B Johnson
- Central Queensland University, School of Health, Medical and Applied Sciences, Bruce Hwy, North Rockhampton, Queensland 4701, Australia
| | - Omar Elhamdaoui
- Mohammed V University, Laboratory of Analytical Chemistry, Faculty of Medicine and Pharmacy, Rabat 10100, Morocco
| | - Samira Jawhari
- Abulcasis University, Department of Pharmacy, Rabat 10000, Morocco
| | - Faouzi Moulay El Abbes
- Mohammed University V, Laboratory of Pharmacology and Toxicology, Biopharmaceutical and Toxicological Analysis Research Team, Faculty of Medicine and Pharmacy, Rabat 10100, Morocco
| | - Yahia Cherrah
- Abulcasis University, Department of Pharmacy, Rabat 10000, Morocco
| | - Mohamed Mbarki
- University of Sultan Moulay Slimane, Faculty of Sciences and Techniques, Beni Mellal 23000, Morocco
| | - Mustapha Bouatia
- Mohammed V University, Laboratory of Analytical Chemistry, Faculty of Medicine and Pharmacy, Rabat 10100, Morocco
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10
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Zhao T, Pan Y. An evaluation of the effect of hydrofluoric acid (HF) treatment on keratins. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:377-384. [PMID: 36002950 DOI: 10.1002/jez.b.23173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 06/26/2022] [Accepted: 07/28/2022] [Indexed: 06/09/2023]
Abstract
Hydrofluoric acid (HF) is commonly used in geological and paleontological research to extract organic fossils for morphological and chemical studies. However, during HF treatment, organic matter can also be altered, which raises concerns that HF-treated organic matter may not be representative of the original organic matter. To provide reference data for protein studies on fossils, herein, we use Fourier transform infrared (FTIR) spectroscopy to investigate the effect of HF (21.3 M) treatment on keratins, with treatment durations ranging from 2 to 48 h. Results show that the FTIR spectra of HF-treated samples are overall similar to that of the untreated sample, while curve fitting shows that HF treatment has led to alteration of the secondary structure in all the HF-treated samples and the effect is time-dependent. The 2- and 4-h treatment mainly reduced the content of the random coils, α-helix, and intermolecular β-sheet. From 8h onwards, the content of random coils greatly increased at the expense of other structures. Our results imply that for protein detection in fossils using FTIR spectroscopy, the negative effect of HF treatment is not substantial, as the bands characteristic of proteins, that is, amide A, amide B, amide I, amide II, and amide III, are still present after the 48-h treatment. If the target is a secondary structure, the effect of HF treatment should be considered. When HF treatment is necessary, limiting the treatment duration to less than 4h may be a choice.
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Affiliation(s)
- Tao Zhao
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Centre for Research and Education on Biological Evolution and Environment and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China
| | - Yanhong Pan
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Centre for Research and Education on Biological Evolution and Environment and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China
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11
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Ye J, Liu L, Lan W, Xiong J. Targeted release of soybean peptide from CMC/PVA hydrogels in simulated intestinal fluid and their pharmacokinetics. Carbohydr Polym 2023; 310:120713. [PMID: 36925260 DOI: 10.1016/j.carbpol.2023.120713] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 02/21/2023]
Abstract
Carboxymethyl cellulose (CMC)/polyvinyl alcohol (PVA) hydrogels loaded with soybean peptide (SPE) were fabricated via a freeze-thaw method. These hydrogels conquer barriers in simulated gastric fluid (SGF), and then release SPE in simulated intestinal fluid (SIF). The results of in vitro SPE release from these hydrogels showed that in SGF only a little of the SPE released, but in SIF the SPE was completely released. The released SPE had scavenging rates for DPPH and ABTS free radicals of 41.68 and 31.43 %. The pharmacokinetic model of SPE release from the hydrogels in SIF was studied. When the hydrogels are moved from SGF to SIF, the sorption of the shrinkage hydrogel network is entirely controlled by stress-induced relaxations. There are swollen and shrunken regions during SPE release. For SPE release into the SIF, SPE has to be freed from the weak bonds in the swollen regions by changes in the conformation of CMC and PVA. The release rate of SPE was found to be governed by the diffusion and swelling rate of the shrinkage hydrogel network. The Korsmeyer-Peppas equation diffusion exponents (n) for SPE release from the hydrogels are >2.063, indicating a super case II transport. These data demonstrate CMC/PVA hydrogels have potential applications in oral peptide delivery.
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Affiliation(s)
- Jun Ye
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, China
| | - Luying Liu
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, China
| | - Wu Lan
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, China
| | - Jian Xiong
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China.
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12
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Man VH, He X, Nguyen PH, Sagui C, Roland C, Xie XQ, Wang J. Unpolarized laser method for infrared spectrum calculation of amide I CO bonds in proteins using molecular dynamics simulation. Comput Biol Med 2023; 159:106902. [PMID: 37086661 PMCID: PMC10186340 DOI: 10.1016/j.compbiomed.2023.106902] [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: 12/06/2022] [Revised: 03/07/2023] [Accepted: 04/09/2023] [Indexed: 04/24/2023]
Abstract
The investigation of the strong infrared (IR)-active amide I modes of peptides and proteins has received considerable attention because a wealth of detailed information on hydrogen bonding, dipole-dipole interactions, and the conformations of the peptide backbone can be derived from the amide I bands. The interpretation of experimental spectra typically requires substantial theoretical support, such as direct ab-initio molecular dynamics simulation or mixed quantum-classical description. However, considering the difficulties associated with these theoretical methods and their applications are limited in small peptides, it is highly desirable to develop a simple yet efficient approach for simulating the amide I modes of any large proteins in solution. In this work, we proposed a comprehensive computational method that extends the well-established molecular dynamics (MD) simulation method to include an unpolarized IR laser for exciting the CO bonds of proteins. We showed the amide I frequency corresponding to the frequency of the laser pulse which resonated with the CO bond vibration. At this frequency, the protein energy and the CO bond length fluctuation were maximized. Overall, the amide I bands of various single proteins and amyloids agreed well with experimental data. The method has been implemented into the AMBER simulation package, making it widely available to the scientific community. Additionally, the application of the method to simulate the transient amide I bands of amyloid fibrils during the IR laser-induced disassembly process was discussed in details.
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Affiliation(s)
- Viet Hoang Man
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
| | - Xibing He
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Phuong H Nguyen
- CNRS, Université Paris Cité, UPR9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005, Paris, France
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, NC, 27695-8202, USA
| | - Christopher Roland
- Department of Physics, North Carolina State University, Raleigh, NC, 27695-8202, USA
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
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13
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Lebedenko C, Murray ME, Goncalves BG, Perez DS, Lambo DJ, Banerjee IA. Interactions of Nanoscale Self-Assembled Peptide-Based Assemblies with Glioblastoma Cell Models and Spheroids. ACS OMEGA 2023; 8:12124-12143. [PMID: 37033803 PMCID: PMC10077566 DOI: 10.1021/acsomega.2c08049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/03/2023] [Indexed: 06/19/2023]
Abstract
Peptide nanoassemblies have garnered remarkable importance in the development of novel nanoscale biomaterials for drug delivery into tumor cells. Taking advantage of receptor mediated recognition of two known peptides, angiopep-2 (TFFYGGSRGKRNNFKTEEY) and A-COOP-K (ACGLSGLC10 VAK) that bind to the over-expressed receptors low density lipoprotein (LRP-1) and fatty acid binding protein (FABP3) respectively, we have developed new peptide conjugates by combining the anti-inflammatory, antitumor compound azelaic acid with angiopep-2, which efficiently self-assembled into nanofibers. Those nanofibers were then functionalized with the A-COOP-K sequence and formed supramolecular hierarchical structures that were found to entrap the chemotherapeutic drug doxorubicin efficaciously. Furthermore, the nanoassemblies were found to release the drug in a dose-dependent manner and showed a stepwise increase over a period of 2 weeks under acidic conditions. Two cell lines (U-87-MG and U-138-MG) were utilized as models for glioblastoma cells grown in the presence of serum and under serum-free conditions to mimic the growth conditions of natural tumors. The drug entrapped assemblies were found to inhibit the cell proliferation of both U-87 and U-138MG glioblastoma cells. Three dimensional spheroids of different sizes were grown to mimic the tumors and evaluate the efficacy of drug release and internalization. Our results indicated that the nanoassemblies were found to have higher internalization of DOX and were well-spread throughout the spheroids grown, particularly under serum-free conditions. The nanoassemblies also displayed blood-brain barrier penetration when tested with a multicellular in vitro model. Such self-assembled nanostructures with targeting ability may provide a suitable platform for the development of new peptide-based biomaterials that can provide more insights about the mechanistic approach for drug delivery for not only 2D cell cultures but also 3D tumoroids that mimic the tumor microenvironments.
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14
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Shenoy J, Lends A, Berbon M, Bilal M, El Mammeri N, Bertoni M, Saad A, Morvan E, Grélard A, Lecomte S, Theillet FX, Buell AK, Kauffmann B, Habenstein B, Loquet A. Structural polymorphism of the low-complexity C-terminal domain of TDP-43 amyloid aggregates revealed by solid-state NMR. Front Mol Biosci 2023; 10:1148302. [PMID: 37065450 PMCID: PMC10095165 DOI: 10.3389/fmolb.2023.1148302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/17/2023] [Indexed: 03/31/2023] Open
Abstract
Aberrant aggregation of the transactive response DNA-binding protein (TDP-43) is associated with several lethal neurodegenerative diseases, including amyotrophic lateral sclerosis and frontotemporal dementia. Cytoplasmic neuronal inclusions of TDP-43 are enriched in various fragments of the low-complexity C-terminal domain and are associated with different neurotoxicity. Here we dissect the structural basis of TDP-43 polymorphism using magic-angle spinning solid-state NMR spectroscopy in combination with electron microscopy and Fourier-transform infrared spectroscopy. We demonstrate that various low-complexity C-terminal fragments, namely TDP-13 (TDP-43300–414), TDP-11 (TDP-43300–399), and TDP-10 (TDP-43314–414), adopt distinct polymorphic structures in their amyloid fibrillar state. Our work demonstrates that the removal of less than 10% of the low-complexity sequence at N- and C-termini generates amyloid fibrils with comparable macroscopic features but different local structural arrangement. It highlights that the assembly mechanism of TDP-43, in addition to the aggregation of the hydrophobic region, is also driven by complex interactions involving low-complexity aggregation-prone segments that are a potential source of structural polymorphism.
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Affiliation(s)
- Jayakrishna Shenoy
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Alons Lends
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Mélanie Berbon
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Muhammed Bilal
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Nadia El Mammeri
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Mathilde Bertoni
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Ahmad Saad
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Estelle Morvan
- University Bordeaux, CNRS, INSERM, IECB, UAR 3033, Pessac, France
| | - Axelle Grélard
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Sophie Lecomte
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - François-Xavier Theillet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-surYvette Cedex, France
| | - Alexander K. Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Brice Kauffmann
- University Bordeaux, CNRS, INSERM, IECB, UAR 3033, Pessac, France
| | - Birgit Habenstein
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
- *Correspondence: Birgit Habenstein, ; Antoine Loquet,
| | - Antoine Loquet
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
- *Correspondence: Birgit Habenstein, ; Antoine Loquet,
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15
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Berntsson E, Vosough F, Svantesson T, Pansieri J, Iashchishyn IA, Ostojić L, Dong X, Paul S, Jarvet J, Roos PM, Barth A, Morozova-Roche LA, Gräslund A, Wärmländer SKTS. Residue-specific binding of Ni(II) ions influences the structure and aggregation of amyloid beta (Aβ) peptides. Sci Rep 2023; 13:3341. [PMID: 36849796 PMCID: PMC9971182 DOI: 10.1038/s41598-023-29901-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/13/2023] [Indexed: 03/01/2023] Open
Abstract
Alzheimer's disease (AD) is the most common cause of dementia worldwide. AD brains display deposits of insoluble amyloid plaques consisting mainly of aggregated amyloid-β (Aβ) peptides, and Aβ oligomers are likely a toxic species in AD pathology. AD patients display altered metal homeostasis, and AD plaques show elevated concentrations of metals such as Cu, Fe, and Zn. Yet, the metal chemistry in AD pathology remains unclear. Ni(II) ions are known to interact with Aβ peptides, but the nature and effects of such interactions are unknown. Here, we use numerous biophysical methods-mainly spectroscopy and imaging techniques-to characterize Aβ/Ni(II) interactions in vitro, for different Aβ variants: Aβ(1-40), Aβ(1-40)(H6A, H13A, H14A), Aβ(4-40), and Aβ(1-42). We show for the first time that Ni(II) ions display specific binding to the N-terminal segment of full-length Aβ monomers. Equimolar amounts of Ni(II) ions retard Aβ aggregation and direct it towards non-structured aggregates. The His6, His13, and His14 residues are implicated as binding ligands, and the Ni(II)·Aβ binding affinity is in the low µM range. The redox-active Ni(II) ions induce formation of dityrosine cross-links via redox chemistry, thereby creating covalent Aβ dimers. In aqueous buffer Ni(II) ions promote formation of beta sheet structure in Aβ monomers, while in a membrane-mimicking environment (SDS micelles) coil-coil helix interactions appear to be induced. For SDS-stabilized Aβ oligomers, Ni(II) ions direct the oligomers towards larger sizes and more diverse (heterogeneous) populations. All of these structural rearrangements may be relevant for the Aβ aggregation processes that are involved in AD brain pathology.
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Affiliation(s)
- Elina Berntsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden.
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia.
| | - Faraz Vosough
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden
| | - Teodor Svantesson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden
| | - Jonathan Pansieri
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden
| | - Igor A Iashchishyn
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden
| | - Lucija Ostojić
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden
| | - Xiaolin Dong
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden
| | - Suman Paul
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden
| | - Jüri Jarvet
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden
- The National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - Per M Roos
- Institute of Environmental Medicine, Karolinska Institutet, Nobels Väg 13, 171 77, Stockholm, Sweden
- Department of Clinical Physiology, Capio St. Göran Hospital, St. Göransplan 1, 112 19, Stockholm, Sweden
| | - Andreas Barth
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden
| | | | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden
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16
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Vorob’ev MM, Açıkgöz BD, Güler G, Golovanov AV, Sinitsyna OV. Proteolysis of Micellar β-Casein by Trypsin: Secondary Structure Characterization and Kinetic Modeling at Different Enzyme Concentrations. Int J Mol Sci 2023; 24:ijms24043874. [PMID: 36835285 PMCID: PMC9960058 DOI: 10.3390/ijms24043874] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
Tryptic proteolysis of protein micelles was studied using β-casein (β-CN) as an example. Hydrolysis of specific peptide bonds in β-CN leads to the degradation and rearrangement of the original micelles and the formation of new nanoparticles from their fragments. Samples of these nanoparticles dried on a mica surface were characterized by atomic force microscopy (AFM) when the proteolytic reaction had been stopped by tryptic inhibitor or by heating. The changes in the content of β-sheets, α-helices, and hydrolysis products during proteolysis were estimated by using Fourier-transform infrared (FTIR) spectroscopy. In the current study, a simple kinetic model with three successive stages is proposed to predict the rearrangement of nanoparticles and the formation of proteolysis products, as well as changes in the secondary structure during proteolysis at various enzyme concentrations. The model determines for which steps the rate constants are proportional to the enzyme concentration, and in which intermediate nano-components the protein secondary structure is retained and in which it is reduced. The model predictions were in agreement with the FTIR results for tryptic hydrolysis of β-CN at different concentrations of the enzyme.
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Affiliation(s)
- Mikhail M. Vorob’ev
- A.N. Nesmeyanov Institute of Organoelement Compounds, RAS, 28 ul. Vavilova, 119991 Moscow, Russia
- Correspondence:
| | - Burçin Dersu Açıkgöz
- Division of Bioengineering, Graduate School, Izmir University of Economics, Izmir 35330, Turkey
| | - Günnur Güler
- Biophysics Laboratory, Department of Physics, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
- Biomedical Bioengineering, Izmir University of Economics, Sakarya Cad., Izmir 35330, Turkey
| | - Andrey V. Golovanov
- A.N. Nesmeyanov Institute of Organoelement Compounds, RAS, 28 ul. Vavilova, 119991 Moscow, Russia
| | - Olga V. Sinitsyna
- A.N. Nesmeyanov Institute of Organoelement Compounds, RAS, 28 ul. Vavilova, 119991 Moscow, Russia
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17
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Waeytens J, De Meutter J, Goormaghtigh E, Dazzi A, Raussens V. Determination of Secondary Structure of Proteins by Nanoinfrared Spectroscopy. Anal Chem 2023; 95:621-627. [PMID: 36598929 PMCID: PMC9851152 DOI: 10.1021/acs.analchem.2c01431] [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: 04/01/2022] [Accepted: 10/21/2022] [Indexed: 01/05/2023]
Abstract
Nanoscale infrared spectroscopy (AFMIR) is becoming an important tool for the analysis of biological sample, in particular protein assemblies, at the nanoscale level. While the amide I band is usually used to determine the secondary structure of proteins in Fourier transform infrared spectroscopy, no tool has been developed so far for AFMIR. The paper introduces a method for the study of secondary structure of protein based on a protein library of 38 well-characterized proteins. Ascending stepwise linear regression (ASLR) and partial least square (PLS) regression were used to correlate spectrum characteristic bands with the major secondary structures (α-helixes and β-sheets). ASLR appears to provide better results than PLS. The secondary structure predictions are characterized by a root mean square standard error in a cross validation of 6.39% for α-helixes and 6.23% for β-sheets.
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Affiliation(s)
- Jehan Waeytens
- Center
for Structural Biology and Bioinformatics, Laboratory for the Structure
and Function of Biological Membranes, Université
libre de Bruxelles, 1050Brussels, Belgium
- Institut
de Chimie Physique d’Orsay, CNRS
UMR8000, Université Paris-Saclay, 91400Orsay, France
| | - Joëlle De Meutter
- Center
for Structural Biology and Bioinformatics, Laboratory for the Structure
and Function of Biological Membranes, Université
libre de Bruxelles, 1050Brussels, Belgium
| | - Erik Goormaghtigh
- Center
for Structural Biology and Bioinformatics, Laboratory for the Structure
and Function of Biological Membranes, Université
libre de Bruxelles, 1050Brussels, Belgium
| | - Alexandre Dazzi
- Institut
de Chimie Physique d’Orsay, CNRS
UMR8000, Université Paris-Saclay, 91400Orsay, France
| | - Vincent Raussens
- Center
for Structural Biology and Bioinformatics, Laboratory for the Structure
and Function of Biological Membranes, Université
libre de Bruxelles, 1050Brussels, Belgium
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18
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Li Y, Yu Y, Ma G. Modulation Effects of Fe 3+, Zn 2+, and Cu 2+ Ions on the Amyloid Fibrillation of α-Synuclein: Insights from a FTIR Investigation. Molecules 2022; 27:molecules27238383. [PMID: 36500474 PMCID: PMC9740228 DOI: 10.3390/molecules27238383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/17/2022] [Accepted: 11/24/2022] [Indexed: 12/02/2022] Open
Abstract
Amyloid fibrillation of α-synuclein is implicated in the pathogenesis of Parkinson's disease and heavy metal ions such as Fe3+, Zn2+, and Cu2+ are known to be involved in the process. In this work, we explored the use of FTIR spectroscopy to look into the modulation effects of Fe3+, Zn2+, and Cu2+ on the amyloid fibrillation of α-synuclein. We performed a curve-fitting analysis on the FTIR amide I bands of these α-synuclein fibril systems, namely, the pristine fibril and the fibrils prepared in the presence of Fe3+, Zn2+, and Cu2+. We found that the α-synuclein fibrils under the influences of metal ions all possessed a parallel β-sheet structure, turn structure, and disordered structure, similar to that of pristine α-synuclein fibril. We also observed metal-induced increases in the proportions of the β-sheet secondary structure within the α-synuclein fibrils, with Fe3+ being the most effective inducer. We performed second derivative analysis of the side chain carboxylic groups of α-synuclein fibrils and found that the side chain microenvironment of the α-synuclein fibrils was more influenced by Fe3+ than Zn2+, and Cu2+. In addition, our atomic force microscopic study revealed that the morphologies of α-synuclein fibrils under the influence of Fe3+ was quite different from that of the Zn2+ and Cu2+ systems. Our FTIR results suggested that the modulation effects of Fe3+, Zn2+, and Cu2+ on α-synuclein fibrillation occurred at both secondary and quaternary structural levels. At last, we proposed a mechanistic hypothesis to interpret how metal ions could affect the morphology of α-synuclein amyloid fibril based on the conformational plasticity properties of intrinsically disordered proteins.
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19
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Molecularly Imprinted Ligand-Free Nanogels for Recognizing Bee Venom-Originated Phospholipase A2 Enzyme. Polymers (Basel) 2022; 14:polym14194200. [PMID: 36236149 PMCID: PMC9571764 DOI: 10.3390/polym14194200] [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: 09/19/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022] Open
Abstract
In this study, ligand-free nanogels (LFNGs) as potential antivenom mimics were developed with the aim of preventing hypersensitivity and other side effects following massive bee attacks. For this purpose, poly (ethylene glycol) diacrylate was chosen as a main synthetic biocompatible matrix to prepare the experimental LFNGs. The overall concept uses inverse mini-emulsion polymerization as the main route to deliver nanogel caps with complementary cavities for phospholipase A2 (PLA2) from bee venom, created artificially with the use of molecular imprinting (MI) technologies. The morphology and the hydrodynamic features of the nanogels were confirmed by transmission electron microscopy (TEM) and dynamic light scattering (DLS) analysis. The following rebinding experiments evidenced the specificity of molecularly imprinted LFNG for PLA2, with rebinding capacities up to 8-fold higher compared to the reference non-imprinted nanogel, while the in vitro binding assays of PLA2 from commercial bee venom indicated that such synthetic nanogels are able to recognize and retain the targeted PLA2 enzyme. The results were finally collaborated with in vitro cell-viability experiments and resulted in a strong belief that such LFNG may actually be used for future therapies against bee envenomation.
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20
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Koshy RR, Reghunadhan A, Mary SK, Sadanandan S, Jose S, Thomas S, Pothen LA. AgNP anchored carbon dots and chitin nanowhisker embedded soy protein isolate films with freshness preservation for active packaging. Food Packag Shelf Life 2022. [DOI: 10.1016/j.fpsl.2022.100876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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Di Meo V, Moccia M, Sanità G, Crescitelli A, Lamberti A, Galdi V, Rendina I, Esposito E. Probing Denaturation of Protein A via Surface-Enhanced Infrared Absorption Spectroscopy. BIOSENSORS 2022; 12:bios12070530. [PMID: 35884333 PMCID: PMC9313297 DOI: 10.3390/bios12070530] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 12/22/2022]
Abstract
We apply surface-enhanced infrared absorption (SEIRA) spectroscopy to monitor the denaturation process of a surface-bound protein A monolayer. Our proposed platform relies on a plasmonic metasurface comprising different spatial subregions (“pixels”) that are engineered to exhibit different resonances covering the infrared region of the electromagnetic spectrum that is matched to the vibrational modes of the Amide groups. Specifically, we are able to determine changes in the Amide I and Amide II vibration coupled modes, by comparing the SEIRA reflectance spectra pertaining to the native state and a denatured state induced by a pH variation. In particular, we observe some evident red-shifts in the principal Amide I mode and the Amide II vibration coupled modes (attributable to the breaking of hydrogen bonds), which result in insurmountable barriers for refolding. Thanks to the strong field localization, and consequent enhancement of the light-matter interactions, our proposed sensing platform can operate with extremely small amounts of an analyte, with an estimated detection limit of about 3 femtomoles of molecules.
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Affiliation(s)
- Valentina Di Meo
- Institute of Applied Sciences and Intelligent Systems—Unit of Naples, National Research Council, 80131 Naples, Italy; (V.D.M.); (G.S.); (A.C.); (I.R.)
| | - Massimo Moccia
- Fields & Waves Lab, Department of Engineering, University of Sannio, 82100 Benevento, Italy; (M.M.); (V.G.)
| | - Gennaro Sanità
- Institute of Applied Sciences and Intelligent Systems—Unit of Naples, National Research Council, 80131 Naples, Italy; (V.D.M.); (G.S.); (A.C.); (I.R.)
| | - Alessio Crescitelli
- Institute of Applied Sciences and Intelligent Systems—Unit of Naples, National Research Council, 80131 Naples, Italy; (V.D.M.); (G.S.); (A.C.); (I.R.)
| | - Annalisa Lamberti
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy;
| | - Vincenzo Galdi
- Fields & Waves Lab, Department of Engineering, University of Sannio, 82100 Benevento, Italy; (M.M.); (V.G.)
| | - Ivo Rendina
- Institute of Applied Sciences and Intelligent Systems—Unit of Naples, National Research Council, 80131 Naples, Italy; (V.D.M.); (G.S.); (A.C.); (I.R.)
| | - Emanuela Esposito
- Institute of Applied Sciences and Intelligent Systems—Unit of Naples, National Research Council, 80131 Naples, Italy; (V.D.M.); (G.S.); (A.C.); (I.R.)
- Correspondence:
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22
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Deol HK, Broom HR, Sienbeneichler B, Lee B, Leonenko Z, Meiering EM. Immature ALS-associated mutant superoxide dismutases form variable aggregate structures through distinct oligomerization processes. Biophys Chem 2022; 288:106844. [DOI: 10.1016/j.bpc.2022.106844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 11/15/2022]
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23
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Khemtemourian L, Fatafta H, Davion B, Lecomte S, Castano S, Strodel B. Structural Dissection of the First Events Following Membrane Binding of the Islet Amyloid Polypeptide. Front Mol Biosci 2022; 9:849979. [PMID: 35372496 PMCID: PMC8965455 DOI: 10.3389/fmolb.2022.849979] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/18/2022] [Indexed: 11/13/2022] Open
Abstract
The islet amyloid polypeptide (IAPP) is the main constituent of the amyloid fibrils found in the pancreas of type 2 diabetes patients. The aggregation of IAPP is known to cause cell death, where the cell membrane plays a dual role: being a catalyst of IAPP aggregation and being the target of IAPP toxicity. Using ATR-FTIR spectroscopy, transmission electron microscopy, and molecular dynamics simulations we investigate the very first molecular steps following IAPP binding to a lipid membrane. In particular, we assess the combined effects of the charge state of amino-acid residue 18 and the IAPP-membrane interactions on the structures of monomeric and aggregated IAPP. Distinct IAPP-membrane interaction modes for the various IAPP variants are revealed. Membrane binding causes IAPP to fold into an amphipathic α-helix, which in the case of H18K-, and H18R-IAPP readily moves beyond the headgroup region. For all IAPP variants but H18E-IAPP, the membrane-bound helix is an intermediate on the way to amyloid aggregation, while H18E-IAPP remains in a stable helical conformation. The fibrillar aggregates of wild-type IAPP and H18K-IAPP are dominated by an antiparallel β-sheet conformation, while H18R- and H18A-IAPP exhibit both antiparallel and parallel β-sheets as well as amorphous aggregates. Our results emphasize the decisive role of residue 18 for the structure and membrane interaction of IAPP. This residue is thus a good therapeutic target for destabilizing membrane-bound IAPP fibrils to inhibit their toxic actions.
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Affiliation(s)
- Lucie Khemtemourian
- Université de Bordeaux, CNRS, Bordeaux IMP, CBMN, Pessac, France
- *Correspondence: Lucie Khemtemourian, ; Birgit Strodel,
| | - Hebah Fatafta
- Institute of Biological Information Processing, Structural Biochemistry, Jülich, Germany
- JuStruct, Jülich Center for Structural Biology, Jülich, Germany
| | - Benoit Davion
- Université de Bordeaux, CNRS, Bordeaux IMP, CBMN, Pessac, France
| | - Sophie Lecomte
- Université de Bordeaux, CNRS, Bordeaux IMP, CBMN, Pessac, France
| | - Sabine Castano
- Université de Bordeaux, CNRS, Bordeaux IMP, CBMN, Pessac, France
| | - Birgit Strodel
- Institute of Biological Information Processing, Structural Biochemistry, Jülich, Germany
- JuStruct, Jülich Center for Structural Biology, Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- *Correspondence: Lucie Khemtemourian, ; Birgit Strodel,
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24
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Ren S, Rodriguez-Saona L, Giusti MM. Analyzing the Interaction between Anthocyanins and Native or Heat-Treated Whey Proteins Using Infrared Spectroscopy. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27051538. [PMID: 35268638 PMCID: PMC8911780 DOI: 10.3390/molecules27051538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 11/24/2022]
Abstract
The color stability of anthocyanins (ACN) has been shown to be improved by interaction with whey proteins (WP). In this study, we explore the ACN–WP interaction using Fourier transform infrared spectroscopy (IR). ACN from purple corn, grape, and black carrot (50 μM) were evaluated. IR spectra (4000–700 cm−1) were collected for native and preheated (40–80 °C) WP (5 mg/mL) and ACN–WP mixtures at pH 7.4. Soft independent modeling of class analogy was used to analyze the IR data. The WP secondary structure changed after heat treatments and after interaction with ACN. As expected, the WP α-helices decreased, and β-sheet increased after heat treatment. The intensities of the WP amide I and II bands decreased after ACN addition, revealing a decrease in the WP α-helix content. Higher preheating temperatures (70–80 °C) resulted in a more disordered WP structure that favored stronger WP–ACN interactions related to amide III changes. Addition of ACN stabilized WP structure due to heat denaturation, but different ACN structures had different binding affinities with WP. WP structure had less change after interaction with ACN with simpler structures. These results increase our understanding of ACN–WP interactions, providing a potential strategy to extend anthocyanin color stability by WP addition.
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25
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Benzitoune N, kadri N, Adouane M, Berkani F, Abbou A, Dahmoune F, Remini H, Bensmail S. Pine nuts (
Pinus pinea
L.) as a potential novel plant‐based source of functional protein isolates: optimization of alkali extraction conditions, evaluation of functional properties and biochemical characterization. J FOOD PROCESS PRES 2022. [DOI: 10.1111/jfpp.16471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Nourelimane Benzitoune
- Laboratoire de Gestion et Valorisation des Ressources Naturelles et Assurance Qualité (LGVRNAQ) Faculté des Sciences de la Nature et de la Vie et des Sciences de la Terre Université de Bouira 10000 Bouira Algérie
- Département des Sciences Biologiques Faculté des Sciences de la Nature et de la Vie et des Sciences de la Terre Université de Bouira 10000 Bouira Algérie
| | - Nabil kadri
- Département des Sciences Biologiques Faculté des Sciences de la Nature et de la Vie et des Sciences de la Terre Université de Bouira 10000 Bouira Algérie
- Laboratoire de Biochimie Biophysique, Biomathématiques et Scientométrie (L3BS), Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000 Bejaia Algérie
| | - Meriem Adouane
- Laboratoire de Gestion et Valorisation des Ressources Naturelles et Assurance Qualité (LGVRNAQ) Faculté des Sciences de la Nature et de la Vie et des Sciences de la Terre Université de Bouira 10000 Bouira Algérie
- Département des Sciences Biologiques Faculté des Sciences de la Nature et de la Vie et des Sciences de la Terre Université de Bouira 10000 Bouira Algérie
| | - Farida Berkani
- Laboratoire de Gestion et Valorisation des Ressources Naturelles et Assurance Qualité (LGVRNAQ) Faculté des Sciences de la Nature et de la Vie et des Sciences de la Terre Université de Bouira 10000 Bouira Algérie
- Département des Sciences Biologiques Faculté des Sciences de la Nature et de la Vie et des Sciences de la Terre Université de Bouira 10000 Bouira Algérie
| | - Amina Abbou
- Laboratoire de Gestion et Valorisation des Ressources Naturelles et Assurance Qualité (LGVRNAQ) Faculté des Sciences de la Nature et de la Vie et des Sciences de la Terre Université de Bouira 10000 Bouira Algérie
- Département des Sciences Biologiques Faculté des Sciences de la Nature et de la Vie et des Sciences de la Terre Université de Bouira 10000 Bouira Algérie
| | - Farid Dahmoune
- Département des Sciences Biologiques Faculté des Sciences de la Nature et de la Vie et des Sciences de la Terre Université de Bouira 10000 Bouira Algérie
- Laboratoire de Biochimie Biophysique, Biomathématiques et Scientométrie (L3BS), Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000 Bejaia Algérie
| | - Hocine Remini
- Département des Sciences Biologiques Faculté des Sciences de la Nature et de la Vie et des Sciences de la Terre Université de Bouira 10000 Bouira Algérie
- Laboratoire de Biochimie Biophysique, Biomathématiques et Scientométrie (L3BS), Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000 Bejaia Algérie
| | - Souhila Bensmail
- Département des Sciences Biologiques Faculté des Sciences de la Nature et de la Vie et des Sciences de la Terre Université de Bouira 10000 Bouira Algérie
- Laboratoire de Recherche en Technologie Alimentaire (LRTA) Faculté des Sciences de l'Ingénieur Université de M'hamed Bougara 35000 Boumerdès Algérie
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26
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Tandon A, Subramani VK, Kim KK, Park SH. Interaction of Prion Peptides with DNA Structures. ACS OMEGA 2022; 7:176-186. [PMID: 35036689 PMCID: PMC8756453 DOI: 10.1021/acsomega.1c04328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/09/2021] [Indexed: 06/14/2023]
Abstract
Prion protein aggregation is known to be modulated by macromolecules including nucleic acids. To clarify the role of nucleic acids in PrP pathology, we investigated the interaction between nucleic acids and the prion peptide (PrP)-a synthetic prion protein model peptide resembling a portion of the human prion protein in structure and function spanning amino acid residues 106-126. We used synthetic DNA lattices and natural DNA duplexes extracted from salmon (sDNA) bound with PrP and studied their interaction using distinct physical measurements. The formation of DNA lattices with PrP was visualized by atomic force microscopy (AFM) to investigate the influence of the PrP. PrP inhibited the growth of the double-crossover (DX) lattices significantly compared to the control peptide (CoP). We also conducted optical measurements such as ultraviolet-visible (UV-Vis), circular dichroism (CD), and Fourier transform infrared (FTIR) spectroscopies to validate the interaction between PrP and DNA immediately (D0) and after a 30-day incubation (D30) period. UV-Vis spectra showed variation in the absorbance intensities, specific for the binding of CoP and PrP to DNA. The CD analysis revealed the presence of various secondary structures, such as α-helices and β-sheets, in PrP- and PrP-bound sDNA complexes. The PrP-sDNA interaction was confirmed using FTIR by the change and shift of the absorption peak intensity and the alteration of PrP secondary structures in the presence of DNA. The cytotoxic effects of the PrP-bound sDNA complexes were assessed by a cytotoxicity assay in human neuroblastoma cells in culture. It confirmed that PrP with sDNA was less cytotoxic than CoP. This study provides new applications for DNA molecules by investigating their effect in complex with aggregated proteins. Our study unequivocally showed the beneficial effect of the interaction between DNA and the pathological prion protein. It therefore provides valuable information to exploit this effect in the development of potential therapeutics. Moreover, our work might serve as a basis for further studies investigating the role of DNA interactions with other amyloidogenic proteins.
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Affiliation(s)
- Anshula Tandon
- Department
of Physics, Sungkyunkwan University, Suwon 16419, Korea
- Sungkyunkwan
Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Vinod Kumar Subramani
- Department
of Precision Medicine, School of Medicine, Sungkyunkwan University, Suwon 16419, Korea
| | - Kyeong Kyu Kim
- Sungkyunkwan
Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
- Department
of Precision Medicine, School of Medicine, Sungkyunkwan University, Suwon 16419, Korea
| | - Sung Ha Park
- Department
of Physics, Sungkyunkwan University, Suwon 16419, Korea
- Sungkyunkwan
Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
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27
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Raussens V, Waeytens J. Characterization of Bacterial Amyloids by Nano-infrared Spectroscopy. Methods Mol Biol 2022; 2538:117-129. [PMID: 35951297 DOI: 10.1007/978-1-0716-2529-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Atomic force microscopy has been used for decades to study the topography of proteins during aggregation but with a lack of information on the secondary structure. On the contrary, infrared spectroscopy was able to study structural changes during the aggregation, but this analysis is complicated due to the presence of different species in mixtures and the poor spatial (~μm) resolution of the FTIR microscopy. Recently, Professor Alexandre Dazzi combined those techniques in the so-called AFM-IR. This method allows acquiring IR spectra at the nanometric scale and becomes a new standard method for the characterization of amyloid fibrils and, more generally, for the aggregation of proteins.
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Affiliation(s)
- Vincent Raussens
- Structure et Fonction des Membranes Biologiques, Université libre de Bruxelles, Bruxelles, Belgium
| | - Jehan Waeytens
- Structure et Fonction des Membranes Biologiques, Université libre de Bruxelles, Bruxelles, Belgium.
- Institut de Chimie Physique, CNRS UMR8000, Université Paris-Sud, Université Paris-Saclay, Orsay, France.
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28
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Ami D, Natalello A. Characterization of the Conformational Properties of Soluble and Insoluble Proteins by Fourier Transform Infrared Spectroscopy. Methods Mol Biol 2022; 2406:439-454. [PMID: 35089573 DOI: 10.1007/978-1-0716-1859-2_26] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The FTIR (micro-)spectroscopy method applied to the study of the structural properties of different soluble and insoluble proteins will be illustrated. In particular, we will discuss the procedure to analyze proteins in form of hydrated films and in solution by means of attenuated total reflection (ATR) measurements. Moreover, we will describe the procedure to characterize bacterial inclusion bodies (IBs) and amyloid deposits within human tissues by means of FTIR microspectroscopy.
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Affiliation(s)
- Diletta Ami
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.
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29
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Siri M, Herrera M, Moyano AJ, Celej MS. Influence of the macromolecular crowder alginate in the fibrillar organization of the functional amyloid FapC from Pseudomonas aeruginosa. Arch Biochem Biophys 2021; 713:109062. [PMID: 34688606 DOI: 10.1016/j.abb.2021.109062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 10/03/2021] [Accepted: 10/15/2021] [Indexed: 11/28/2022]
Abstract
Bacterial biofilms are an alternative lifestyle in which communities of bacteria are embedded in an extracellular matrix manly composed by polysaccharides, nucleic acids and proteins, being the hallmark of bacterial survival in a variety of ecological niches. Amyloid fibrils are one of the proteinaceous components of such extracellular crowded environments. FapC is the main component of the functional amyloid recently discovered in Pseudomonas species, including the opportunistic pathogen P. aeruginosa, which is a major cause of nosocomial infections and contamination of medical devices. Considering that several functional roles have been attributed to this bacterial amyloid, FapC emerged as a novel target to control Pseudomonas biofilm formation and to design new treatments against chronic infections. In this study, we used complementary biophysical techniques to evaluate conformational signatures of FapC amyloids formed in the presence of alginate, the major exopolysaccharide associated with the mucoid phenotype of P. aeruginosa strains isolated from cystic fibrosis patients. We found that the this naturally occurring macromolecular crowder leads to morphological similar yet polymorphic FapC fibrils, highlighting the importance of considering the complexity of the extracellular matrix in order to improve our understanding of microbial functional amyloids.
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Affiliation(s)
- Macarena Siri
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Melisa Herrera
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Alejandro J Moyano
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - M Soledad Celej
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina.
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30
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Katayama K, Suzuki K, Suno R, Kise R, Tsujimoto H, Iwata S, Inoue A, Kobayashi T, Kandori H. Vibrational spectroscopy analysis of ligand efficacy in human M 2 muscarinic acetylcholine receptor (M 2R). Commun Biol 2021; 4:1321. [PMID: 34815515 PMCID: PMC8635417 DOI: 10.1038/s42003-021-02836-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 11/01/2021] [Indexed: 12/30/2022] Open
Abstract
The intrinsic efficacy of ligand binding to G protein-coupled receptors (GPCRs) reflects the ability of the ligand to differentially activate its receptor to cause a physiological effect. Here we use attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy to examine the ligand-dependent conformational changes in the human M2 muscarinic acetylcholine receptor (M2R). We show that different ligands affect conformational alteration appearing at the C=O stretch of amide-I band in M2R. Notably, ATR-FTIR signals strongly correlated with G-protein activation levels in cells. Together, we propose that amide-I band serves as an infrared probe to distinguish the ligand efficacy in M2R and paves the path to rationally design ligands with varied efficacy towards the target GPCR.
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Affiliation(s)
- Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan.
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan.
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
| | - Kohei Suzuki
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
| | - Ryoji Suno
- Department of Medical Chemistry, Kansai Medical University, Hirakata, 573-1010, Japan
| | - Ryoji Kise
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, 980-8578, Japan
| | - Hirokazu Tsujimoto
- Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - So Iwata
- Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, 980-8578, Japan
| | - Takuya Kobayashi
- Department of Medical Chemistry, Kansai Medical University, Hirakata, 573-1010, Japan
- Japan Agency for Medical Research and Development, Core Research for Evolutional Science and Technology (AMED-CREST), Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan.
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan.
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31
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Fischer P, Mukherjee S, Schiewer E, Broser M, Bartl F, Hegemann P. The inner mechanics of rhodopsin guanylyl cyclase during cGMP-formation revealed by real-time FTIR spectroscopy. eLife 2021; 10:e71384. [PMID: 34665128 PMCID: PMC8575461 DOI: 10.7554/elife.71384] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/18/2021] [Indexed: 01/01/2023] Open
Abstract
Enzymerhodopsins represent a recently discovered class of rhodopsins which includes histidine kinase rhodopsin, rhodopsin phosphodiesterases, and rhodopsin guanylyl cyclases (RGCs). The regulatory influence of the rhodopsin domain on the enzyme activity is only partially understood and holds the key for a deeper understanding of intra-molecular signaling pathways. Here, we present a UV-Vis and FTIR study about the light-induced dynamics of a RGC from the fungus Catenaria anguillulae, which provides insights into the catalytic process. After the spectroscopic characterization of the late rhodopsin photoproducts, we analyzed truncated variants and revealed the involvement of the cytosolic N-terminus in the structural rearrangements upon photo-activation of the protein. We tracked the catalytic reaction of RGC and the free GC domain independently by UV-light induced release of GTP from the photolabile NPE-GTP substrate. Our results show substrate binding to the dark-adapted RGC and GC alike and reveal differences between the constructs attributable to the regulatory influence of the rhodopsin on the conformation of the binding pocket. By monitoring the phosphate rearrangement during cGMP and pyrophosphate formation in light-activated RGC, we were able to confirm the M state as the active state of the protein. The described setup and experimental design enable real-time monitoring of substrate turnover in light-activated enzymes on a molecular scale, thus opening the pathway to a deeper understanding of enzyme activity and protein-protein interactions.
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Affiliation(s)
- Paul Fischer
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu BerlinBerlinGermany
| | - Shatanik Mukherjee
- Institute of Biology, Biophysical Chemistry, Humboldt University of BerlinBerlinGermany
| | - Enrico Schiewer
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu BerlinBerlinGermany
| | - Matthias Broser
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu BerlinBerlinGermany
| | - Franz Bartl
- Institute of Biology, Biophysical Chemistry, Humboldt University of BerlinBerlinGermany
| | - Peter Hegemann
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu BerlinBerlinGermany
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32
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De Meutter J, Goormaghtigh E. Protein Structural Denaturation Evaluated by MCR-ALS of Protein Microarray FTIR Spectra. Anal Chem 2021; 93:13441-13449. [PMID: 34592098 DOI: 10.1021/acs.analchem.1c01416] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The loss of native structure is common in proteins. Among others, aggregation is one structural modification of particular importance as it is a major concern for the efficiency and safety of biotherapeutic proteins. Yet, recognizing the structural features associated with intermolecular bridging in a high-throughput manner remains a challenge. We combined here the use of protein microarrays spotted at a density of ca 2500 samples per cm2 and Fourier transform infrared (FTIR) imaging to analyze structural modifications in a set of 85 proteins characterized by widely different secondary structure contents, submitted or not to mild denaturing conditions. Multivariate curve resolution alternating least squares (MCR-ALS) was used to model a new spectral component appearing in the protein set subject to denaturing conditions. In the native protein set, 6 components were found to be sufficient to obtain good modeling of the spectra. Furthermore, their shape allowed them to be assigned to α-helix, β-sheet, and other structures. Their content in each protein was correlated with the known secondary structure, confirming these assignments. In the denatured proteins, a new component was necessary and modeled by MCR-ALS. This new component could be assigned to the intermolecular β-sheet, bridging protein molecules. MCR-ALS, therefore, unveiled a potential spectroscopic marker of protein aggregation and allowed a semiquantitative evaluation of its content. Insight into other structural rearrangements was also obtained.
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Affiliation(s)
- Joëlle De Meutter
- Center for Structural Biology and Bioinformatics, Laboratory for the Structure and Function of Biological Membranes, Campus Plaine, Université Libre de Bruxelles CP206/2, B1050 Brussels, Belgium
| | - Erik Goormaghtigh
- Center for Structural Biology and Bioinformatics, Laboratory for the Structure and Function of Biological Membranes, Campus Plaine, Université Libre de Bruxelles CP206/2, B1050 Brussels, Belgium
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El Khoury Y, Schirer A, Patte-Mensah C, Klein C, Meyer L, Rataj-Baniowska M, Bernad S, Moss D, Lecomte S, Mensah-Nyagan AG, Hellwig P. Raman Imaging Reveals Accumulation of Hemoproteins in Plaques from Alzheimer's Diseased Tissues. ACS Chem Neurosci 2021; 12:2940-2945. [PMID: 34292705 DOI: 10.1021/acschemneuro.1c00289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Hemes have been suggested to play a central role in Alzheimer's disease since they show high peroxidase reactivity when bound to amyloid β peptides, leading to the production of reactive oxygen species. Here we used Fourier transform infrared and Raman imaging on Alzheimer's diseased mice and human brain tissue. Our finding suggests the accumulation of hemes in the senile plaques of both murine and human samples. We compared the Raman signature of the plaques to the ones of various hemeoproteins and to the hemin-Aβ-42 complex. The detected Raman signature of the plaques does not allow identifying the type of heme accumulating in the plaques.
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Affiliation(s)
- Youssef El Khoury
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie De La Matière Complexe, Université de Strasbourg-CNRS, 4 Rue Blaise Pascal, 67081 Strasbourg, France
| | - Alicia Schirer
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie De La Matière Complexe, Université de Strasbourg-CNRS, 4 Rue Blaise Pascal, 67081 Strasbourg, France
| | - Christine Patte-Mensah
- Biopathologie de la Myéline, Neuroprotection et Stratégies Thérapeutiques, INSERM U1119, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, 1 Rue Eugène Boeckel, 67000 Strasbourg, France
| | - Christian Klein
- Biopathologie de la Myéline, Neuroprotection et Stratégies Thérapeutiques, INSERM U1119, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, 1 Rue Eugène Boeckel, 67000 Strasbourg, France
| | - Laurence Meyer
- Biopathologie de la Myéline, Neuroprotection et Stratégies Thérapeutiques, INSERM U1119, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, 1 Rue Eugène Boeckel, 67000 Strasbourg, France
| | - Monika Rataj-Baniowska
- Biopathologie de la Myéline, Neuroprotection et Stratégies Thérapeutiques, INSERM U1119, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, 1 Rue Eugène Boeckel, 67000 Strasbourg, France
| | - Sophie Bernad
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
| | - David Moss
- Synchrotron Light Source ANKA, Karlsruhe Research Center, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Sophie Lecomte
- Chimie Biologie des Membranes et Nanoobjets, UMR 5248, Université de Bordeaux-CNRS, 14 Allée Geoffroy St. Hilaire, 33600 Pessac, France
| | - Ayikoe-Guy Mensah-Nyagan
- Biopathologie de la Myéline, Neuroprotection et Stratégies Thérapeutiques, INSERM U1119, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, 1 Rue Eugène Boeckel, 67000 Strasbourg, France
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie De La Matière Complexe, Université de Strasbourg-CNRS, 4 Rue Blaise Pascal, 67081 Strasbourg, France
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A photoswitchable helical peptide with light-controllable interface/transmembrane topology in lipidic membranes. iScience 2021; 24:102771. [PMID: 34286233 PMCID: PMC8273423 DOI: 10.1016/j.isci.2021.102771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/02/2021] [Accepted: 06/19/2021] [Indexed: 11/21/2022] Open
Abstract
The spontaneous insertion of helical transmembrane (TM) polypeptides into lipid bilayers is driven by three sequential equilibria: solution-to-membrane interface (MI) partition, unstructured-to-helical folding, and MI-to-TM helix insertion. A bottleneck for understanding these three steps is the lack of experimental approaches to perturb membrane-bound hydrophobic polypeptides out of equilibrium rapidly and reversibly. Here, we report on a 24-residues-long hydrophobic α-helical polypeptide, covalently coupled to an azobenzene photoswitch (KCALP-azo), which displays a light-controllable TM/MI equilibrium in hydrated lipid bilayers. FTIR spectroscopy reveals that trans KCALP-azo folds as a TM α-helix (TM topology). After trans-to-cis photoisomerization of the azobenzene moiety with UV light (reversed with blue light), the helical structure of KCALP-azo is maintained, but its helix tilt increased from 32 ± 5° to 79 ± 8°, indication of a reversible TM-to-MI transition. Further analysis indicates that this transition is incomplete, with cis KCALP-azo existing in a ∼90% TM and ∼10% MI mixture. We present an α-helical transmembrane peptide modified with a molecular photoswitch The peptide exhibits reversible photocontrol of its membrane topology A fraction moves to the membrane interface with UV and inserts back with blue light This system will be useful to address the molecular mechanism for membrane insertion
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Waeytens J, Mathurin J, Deniset-Besseau A, Arluison V, Bousset L, Rezaei H, Raussens V, Dazzi A. Probing amyloid fibril secondary structures by infrared nanospectroscopy: experimental and theoretical considerations. Analyst 2021; 146:132-145. [PMID: 33107501 DOI: 10.1039/d0an01545h] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Amyloid fibrils are composed of aggregated peptides or proteins in a fibrillary structure with a higher β-sheet content than their native structure. Attenuated total reflection Fourier transform infrared spectroscopy only provides bulk analysis of a sample therefore it is impossible to discriminate between different aggregated structures. To overcome this limitation, near-field techniques like AFM-IR have emerged in the last twenty years to allow infrared nanospectroscopy. This technique obtains IR spectra with a spatial resolution of ten nanometres, the size of isolated fibrils. Here, we present essential practical considerations to avoid misinterpretations and artefacts during these analyses. Effects of polarization of the incident IR laser, illumination configuration and coating of the AFM probes are discussed, including the advantages and drawbacks of their use. This approach will improve interpretation of AFM-IR spectra especially for the determination of secondary structures of species not accessible using classical ATR-FTIR.
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Affiliation(s)
- Jehan Waeytens
- Structure et Fonction des Membranes Biologiques, Université libre de Bruxelles, Bruxelles, Belgique.
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Claro B, Goormaghtigh E, Bastos M. Attenuated total reflection-Fourier transform infrared spectroscopy: a tool to characterize antimicrobial cyclic peptide-membrane interactions. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:629-639. [PMID: 33743025 DOI: 10.1007/s00249-020-01495-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/16/2020] [Accepted: 12/31/2020] [Indexed: 11/24/2022]
Abstract
Attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) has been used for the structural characterization of peptides and their interactions with membranes. Antimicrobial peptides (AMPs) are part of our immune system and widely studied in recent years. Many linear AMPs have been studied, but their cyclization was shown to enhance the peptide's activity. We have used cyclic peptides (CPs) of an even number of alternating D- and L-α-amino acids, an emerging class of potential AMPs. These CPs can adopt a flat-ring shape that can stack into an antiparallel structure, forming intermolecular hydrogen bonds between different units, creating a tubular β-sheet structure - self-assembled cyclic peptide nanotubes (SCPNs). To get the structural information on peptides in solution and/or in contact with membranes, Amide I and II absorptions are used as they can adopt frequency and shape band characteristics that are influenced by the strength of existing hydrogen bonds between the amide CO and NH involved in secondary structures such as helix, β-sheet or aperiodic structures. The combination of polarized lens with ATR-FTIR provides an important tool to study the orientation of peptides when interacting with lipid membranes as the information can be derived on the position relative to the membrane normal. This work shows how ATR-FTIR used together with polarized light was successfully used to characterize structurally two CPs (RSKSWPgKQ and RSKSWXC10KQ) in solution and upon interaction with negatively charged membranes of DMPG, assessing the formation and orientation of tubular structures (SCPNs) that were shown to be enhanced by the presence of the lipid membrane.
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Affiliation(s)
- Bárbara Claro
- Departamento de Química e Bioquímica, Centro de Investigação em Química, Faculdade de Ciências, CIQUP, Universidade do Porto, Porto, Portugal
| | - Erik Goormaghtigh
- Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, ULB, Brussels, Belgium
| | - Margarida Bastos
- Departamento de Química e Bioquímica, Centro de Investigação em Química, Faculdade de Ciências, CIQUP, Universidade do Porto, Porto, Portugal.
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37
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Kwak TJ, Jung H, Allen BD, Demirel MC, Chang WJ. Dielectrophoretic separation of randomly shaped protein particles. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2020.118280] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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38
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Banerjee S. Long-term incubation of myoglobin with glyoxal induces amyloid like aggregation of the heme protein: Implications of advanced glycation end products in protein conformational disorders. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.115256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abedin F, Tatulian SA. Mutual structural effects of unmodified and pyroglutamylated amyloid β peptides during aggregation. J Pept Sci 2021; 27:e3312. [PMID: 33631839 DOI: 10.1002/psc.3312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 02/05/2021] [Accepted: 02/16/2021] [Indexed: 11/09/2022]
Abstract
Amyloid β (Aβ) peptide aggregates are linked to Alzheimer's disease (AD). Posttranslationally pyroglutamylated Aβ (pEAβ) occurs in AD brains in significant quantities and is hypertoxic, but the underlying structural and aggregation properties remain poorly understood. Here, the structure and aggregation of Aβ1-40 and pEAβ3-40 are analyzed separately and in equimolar combination. Circular dichroism data show that Aβ1-40 , pEAβ3-40 , and their combination assume α-helical structure in dry state and transition to unordered structure in aqueous buffer. Aβ1-40 and the 1:1 combination gradually acquire β-sheet structure while pEAβ3-40 adopts an α-helix/β-sheet conformation. Thioflavin-T fluorescence studies suggest that the two peptides mutually inhibit fibrillogenesis. Fourier transform infrared (FTIR) spectroscopy identifies the presence of β-turn and α-helical structures in addition to β-sheet structure in peptides in aqueous buffer. The kinetics of transitions from the initial α-helical structure to β-sheet structure were resolved by slow hydration of dry peptides by D2 O vapor, coupled with isotope-edited FTIR. These data confirmed the mutual suppression of β-sheet formation by the two peptides. Remarkably, pEAβ3-40 maintained a significant fraction of α-helical structure in the combined sample, implying a reduced β-sheet propensity of pEAβ3-40 . Altogether, the data imply that the combination of unmodified and pyroglutamylated Aβ peptides resists fibrillogenesis and favors the prefibrillar state, which may underlie hypertoxicity of pEAβ.
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Affiliation(s)
- Faisal Abedin
- Physics Graduate Program, University of Central Florida, Orlando, Florida, USA
| | - Suren A Tatulian
- Department of Physics, University of Central Florida, Orlando, Florida, USA
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40
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Zheng RH, Wei WM, Liu YY. Theoretical study on spectral differences of polypeptides constituted by L- and D-amino acids. Mol Phys 2021. [DOI: 10.1080/00268976.2020.1812747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Ren-Hui Zheng
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Wen-Mei Wei
- School of Basic Medical Science, Anhui Medical University, Hefei, People’s Republic of China
| | - Yan-Ying Liu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, People’s Republic of China
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41
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Amino acid side chain contribution to protein FTIR spectra: impact on secondary structure evaluation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:641-651. [PMID: 33558954 PMCID: PMC8189991 DOI: 10.1007/s00249-021-01507-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 01/13/2021] [Accepted: 01/25/2021] [Indexed: 01/25/2023]
Abstract
Prediction of protein secondary structure from FTIR spectra usually relies on the absorbance in the amide I–amide II region of the spectrum. It assumes that the absorbance in this spectral region, i.e., roughly 1700–1500 cm−1 is solely arising from amide contributions. Yet, it is accepted that, on the average, about 20% of the absorbance is due to amino acid side chains. The present paper evaluates the contribution of amino acid side chains in this spectral region and the potential to improve secondary structure prediction after correcting for their contribution. We show that the β-sheet content prediction is improved upon subtraction of amino acid side chain contributions in the amide I–amide II spectral range. Improvement is relatively important, for instance, the error of prediction of β-sheet content decreases from 5.42 to 4.97% when evaluated by ascending stepwise regression. Other methods tested such as partial least square regression and support vector machine have also improved accuracy for β-sheet content evaluation. The other structures such as α-helix do not significantly benefit from side chain contribution subtraction, in some cases prediction is even degraded. We show that co-linearity between secondary structure content and amino acid composition is not a main limitation for improving secondary structure prediction. We also show that, even though based on different criteria, secondary structures defined by DSSP and XTLSSTR both arrive at the same conclusion: only the β-sheet structure clearly benefits from side chain subtraction. It must be concluded that side chain contribution subtraction benefit for the evaluation of other secondary structure contents is limited by the very rough description of side chain absorbance which does not take into account the variations related to their environment. The study was performed on a large protein set. To deal with the large number of proteins present, we worked on protein microarrays deposited on BaF2 slides and FTIR spectra were acquired with an imaging system.
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42
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Evaluation of protein secondary structure from FTIR spectra improved after partial deuteration. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:613-628. [PMID: 33534058 PMCID: PMC8189984 DOI: 10.1007/s00249-021-01502-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/08/2021] [Accepted: 01/13/2021] [Indexed: 11/11/2022]
Abstract
FTIR spectroscopy has become a major tool to determine protein secondary structure. One of the identified obstacle for reaching better predictions is the strong overlap of bands assigned to different secondary structures. Yet, while for instance disordered structures and α-helical structures absorb almost at the same wavenumber, the absorbance bands are differentially shifted upon deuteration, in part because exchange is much faster for disordered structures. We recorded the FTIR spectra of 85 proteins at different stages of hydrogen/deuterium exchange process using protein microarrays and infrared imaging for high throughput measurements. Several methods were used to relate spectral shape to secondary structure content. While in absolute terms, β-sheet is always better predicted than α-helix content, results consistently indicate an improvement of secondary structure predictions essentially for the α-helix and the category called “Others” (grouping random, turns, bends, etc.) after 15 min of exchange. On the contrary, the β-sheet fraction is better predicted in non-deuterated conditions. Using partial least square regression, the error of prediction for the α-helix content is reduced after 15-min deuteration. Further deuteration degrades the prediction. Error on the prediction for the “Others” structures also decreases after 15-min deuteration. Cross-validation or a single 25-protein test set result in the same overall conclusions.
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43
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Bernier SC, Millette MA, Roy S, Cantin L, Coutinho A, Salesse C. Structural information and membrane binding of truncated RGS9-1 Anchor Protein and its C-terminal hydrophobic segment. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183566. [PMID: 33453187 DOI: 10.1016/j.bbamem.2021.183566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/22/2020] [Accepted: 01/10/2021] [Indexed: 01/19/2023]
Abstract
Visual phototransduction takes place in photoreceptor cells. Light absorption by rhodopsin leads to the activation of transducin as a result of the exchange of its GDP for GTP. The GTP-bound ⍺-subunit of transducin then activates phosphodiesterase (PDE), which in turn hydrolyzes cGMP leading to photoreceptor hyperpolarization. Photoreceptors return to the dark state upon inactivation of these proteins. In particular, PDE is inactivated by the protein complex R9AP/RGS9-1/Gβ5. R9AP (RGS9-1 anchor protein) is responsible for the membrane anchoring of this protein complex to photoreceptor outer segment disk membranes most likely by the combined involvement of its C-terminal hydrophobic domain as well as other types of interactions. This study thus aimed to gather information on the structure and membrane binding of the C-terminal hydrophobic segment of R9AP as well as of truncated R9AP (without its C-terminal domain, R9AP∆TM). Circular dichroism and infrared spectroscopic measurements revealed that the secondary structure of R9AP∆TM mainly includes ⍺-helical structural elements. Moreover, intrinsic fluorescence measurements of native R9AP∆TM and individual mutants lacking one tryptophan demonstrated that W79 is more buried than W173 but that they are both located in a hydrophobic environment. This method also revealed that membrane binding of R9AP∆TM does not involve regions near its tryptophan residues, while infrared spectroscopy validated its binding to lipid vesicles. Additional fluorescence measurements showed that the C-terminal segment of R9AP is membrane embedded. Maximum insertion pressure and synergy data using Langmuir monolayers suggest that interactions with specific phospholipids could be involved in the membrane binding of R9AP∆TM.
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Affiliation(s)
- Sarah C Bernier
- CUO-Recherche, Centre de recherche du CHU de Québec and Département d'ophtalmologie, Faculté de Médecine, and Regroupement Stratégique PROTEO, Université Laval, Québec, Québec, Canada
| | - Marc-Antoine Millette
- CUO-Recherche, Centre de recherche du CHU de Québec and Département d'ophtalmologie, Faculté de Médecine, and Regroupement Stratégique PROTEO, Université Laval, Québec, Québec, Canada
| | - Sarah Roy
- CUO-Recherche, Centre de recherche du CHU de Québec and Département d'ophtalmologie, Faculté de Médecine, and Regroupement Stratégique PROTEO, Université Laval, Québec, Québec, Canada
| | - Line Cantin
- CUO-Recherche, Centre de recherche du CHU de Québec and Département d'ophtalmologie, Faculté de Médecine, and Regroupement Stratégique PROTEO, Université Laval, Québec, Québec, Canada
| | - Ana Coutinho
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; Department of Chemistry and Biochemistry, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Christian Salesse
- CUO-Recherche, Centre de recherche du CHU de Québec and Département d'ophtalmologie, Faculté de Médecine, and Regroupement Stratégique PROTEO, Université Laval, Québec, Québec, Canada.
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Aisenbrey C, Rifi O, Bechinger B. Structure, membrane topology and influence of cholesterol of the membrane proximal region: transmembrane helical anchor sequence of gp41 from HIV. Sci Rep 2020; 10:22278. [PMID: 33335248 PMCID: PMC7746737 DOI: 10.1038/s41598-020-79327-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
During the first steps of HIV infection the Env subunit gp41 is thought to establish contact between the membranes and to be the main driver of fusion. Here we investigated in liquid crystalline membranes the structure and cholesterol recognition of constructs made of a gp41 external region carrying a cholesterol recognition amino acid consensus (CRAC) motif and a hydrophobic membrane anchoring sequence. CD- und ATR-FTIR spectroscopies indicate that the constructs adopt a high degree of helical secondary structure in membrane environments. Furthermore, 15N and 2H solid-state NMR spectra of gp41 polypeptides reconstituted into uniaxially oriented bilayers agree with the CRAC domain being an extension of the transmembrane helix. Upon addition of cholesterol the CRAC NMR spectra remain largely unaffected when being associated with the native gp41 transmembrane sequence but its topology changes when anchored in the membrane by a hydrophobic model sequence. The 2H solid-state NMR spectra of deuterated cholesterol are indicative of a stronger influence of the model sequence on this lipid when compared to the native gp41 sequence. These observations are suggestive of a strong coupling between the transmembrane and the membrane proximal region of gp41 possibly enforced by oligomerization of the transmembrane helical region.
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Affiliation(s)
- Christopher Aisenbrey
- Institut de chimie de Strasbourg, UMR7177, University of Strasbourg/CNRS, 4, Rue Blaise Pascal, 67070, Strasbourg, France
| | - Omar Rifi
- Institut de chimie de Strasbourg, UMR7177, University of Strasbourg/CNRS, 4, Rue Blaise Pascal, 67070, Strasbourg, France
| | - Burkhard Bechinger
- Institut de chimie de Strasbourg, UMR7177, University of Strasbourg/CNRS, 4, Rue Blaise Pascal, 67070, Strasbourg, France.
- Institut Universitaire de France, Paris, France.
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45
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Contribution of Secondary Structure Changes to the Surface Activity of Proteins. J Biotechnol 2020; 323:208-220. [DOI: 10.1016/j.jbiotec.2020.07.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/13/2020] [Accepted: 07/20/2020] [Indexed: 11/22/2022]
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46
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Telnaya EA, Plotnikova LV, Garifullin AD, Kuvshinov AY, Voloshin SV, Polyanichko AM. Infrared Spectroscopy of Blood Serum from Patients with Oncohematological Diseases. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s0006350920060214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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47
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Blond P, Bevernaegie R, Troian-Gautier L, Lagrost C, Hubert J, Reniers F, Raussens V, Jabin I. Ready-to-Use Germanium Surfaces for the Development of FTIR-Based Biosensors for Proteins. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:12068-12076. [PMID: 33007158 DOI: 10.1021/acs.langmuir.0c02681] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Germanium is particularly suitable for the design of FTIR-based biosensors for proteins. The grafting of stable and thin organic layers on germanium surfaces remains, however, challenging. To tackle this problem, we developed a calix[4]arene-tetradiazonium salt decorated with four oligo(ethylene glycol) chains and a terminal reactive carboxyl group. This versatile molecular platform was covalently grafted on germanium surfaces to yield robust ready-to-use surfaces for biosensing applications. The grafted calixarene monolayer prevents nonspecific adsorption of proteins while allowing bioconjugation with biomolecules such as bovine serum albumin (BSA) or biotin. It is shown that the native form of the investigated proteins was maintained upon immobilization. As a proof of concept, the resulting calix[4]arene-based germanium biosensors were used through a combination of ATR-FTIR spectroscopy and fluorescence microscopy for the selective detection of streptavidin from a complex medium. This study opens real possibilities for the development of sensitive and selective FTIR-based biosensors devoted to the detection of proteins.
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Affiliation(s)
- Pascale Blond
- Laboratoire de Chimie Organique, Université libre de Bruxelles (ULB), Avenue F. D. Roosevelt 50, CP160/06, B-1050 Brussels, Belgium
- Laboratory for the Structure and Function of Biological Membranes, Centre for Structural Biology and Bioinformatics, Université libre de Bruxelles (ULB), Boulevard du Triomphe, CP206/02, B-1050 Brussels, Belgium
| | - Robin Bevernaegie
- Laboratoire de Chimie Organique, Université libre de Bruxelles (ULB), Avenue F. D. Roosevelt 50, CP160/06, B-1050 Brussels, Belgium
| | - Ludovic Troian-Gautier
- Laboratoire de Chimie Organique, Université libre de Bruxelles (ULB), Avenue F. D. Roosevelt 50, CP160/06, B-1050 Brussels, Belgium
| | | | - Julie Hubert
- Chemistry of Surfaces, Interfaces and Nanomaterials, Université libre de Bruxelles (ULB), Boulevard du Triomphe, CP 255, B-1050 Brussels, Belgium
| | - François Reniers
- Chemistry of Surfaces, Interfaces and Nanomaterials, Université libre de Bruxelles (ULB), Boulevard du Triomphe, CP 255, B-1050 Brussels, Belgium
| | - Vincent Raussens
- Laboratory for the Structure and Function of Biological Membranes, Centre for Structural Biology and Bioinformatics, Université libre de Bruxelles (ULB), Boulevard du Triomphe, CP206/02, B-1050 Brussels, Belgium
| | - Ivan Jabin
- Laboratoire de Chimie Organique, Université libre de Bruxelles (ULB), Avenue F. D. Roosevelt 50, CP160/06, B-1050 Brussels, Belgium
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48
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Kvick M, Tasiopoulos CP, Barth A, Söderberg LD, Lundell F, Hedhammar M. Cyclic Expansion/Compression of the Air-Liquid Interface as a Simple Method to Produce Silk Fibers. Macromol Biosci 2020; 21:e2000227. [PMID: 33016002 DOI: 10.1002/mabi.202000227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/01/2020] [Indexed: 01/23/2023]
Abstract
Self-assembly of recombinant spider silk protein at air-liquid interfaces is used as a starting point to produce homogeneous fiber bundles. The film that is formed on a silk protein solution in a vertically placed syringe is subjected to repeated controlled extension and compression by an oscillating vertical motion. Thereby, a precise breakup of the film can be achieved, followed by transport and roll-up against the syringe wall prior to extraction. Advantages of the method are that it 1) is simple to use; 2) requires a small volume of protein solution (1 mL) at relatively low concentration (1 mg mL-1 ); 3) can be performed under sterile conditions; 4) does not require any use of coagulants; and 5) is compatible with the addition of viable cells during the process, which thereby are integrated uniformly throughout the fiber.
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Affiliation(s)
| | - Christos P Tasiopoulos
- Institute of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, School of Biotechnology, Stockholm, SE-100 44, Sweden
| | - Andreas Barth
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, 106 91, Sweden
| | - Lars Daniel Söderberg
- Linné FLOW Centre, KTH Mechanics, KTH Royal Institute of Technology, Stockholm, SE-100 44, Sweden.,Wallenberg Wood Science Center, KTH Royal Institute of Technology, Stockholm, SE-100 44, Sweden
| | - Fredrik Lundell
- Linné FLOW Centre, KTH Mechanics, KTH Royal Institute of Technology, Stockholm, SE-100 44, Sweden.,Wallenberg Wood Science Center, KTH Royal Institute of Technology, Stockholm, SE-100 44, Sweden
| | - My Hedhammar
- Institute of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, School of Biotechnology, Stockholm, SE-100 44, Sweden
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49
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Melin F, Hellwig P. Redox Properties of the Membrane Proteins from the Respiratory Chain. Chem Rev 2020; 120:10244-10297. [DOI: 10.1021/acs.chemrev.0c00249] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Frederic Melin
- Chimie de la Matière Complexe UMR 7140, Laboratoire de Bioelectrochimie et Spectroscopie, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
| | - Petra Hellwig
- Chimie de la Matière Complexe UMR 7140, Laboratoire de Bioelectrochimie et Spectroscopie, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
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50
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On the Secondary Structure of Silk Fibroin Nanoparticles Obtained Using Ionic Liquids: An Infrared Spectroscopy Study. Polymers (Basel) 2020; 12:polym12061294. [PMID: 32516911 PMCID: PMC7361871 DOI: 10.3390/polym12061294] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/27/2020] [Accepted: 06/02/2020] [Indexed: 12/30/2022] Open
Abstract
Silk fibroin from Bombyx mori caterpillar is an outstanding biocompatible polymer for the production of biomaterials. Its impressive combination of strength, flexibility, and degradability are related to the protein’s secondary structure, which may be altered during the manufacture of the biomaterial. The present study looks at the silk fibroin secondary structure during nanoparticle production using ionic liquids and high-power ultrasound using novel infrared spectroscopic approaches. The infrared spectrum of silk fibroin fibers shows that they are composed of 58% β-sheet, 9% turns, and 33% irregular and/or turn-like structures. When fibroin was dissolved in ionic liquids, its amide I band resembled that of soluble silk and no β-sheet absorption was detected. Silk fibroin nanoparticles regenerated from the ionic liquid solution exhibited an amide I band that resembled that of the silk fibers but had a reduced β-sheet content and a corresponding higher content of turns, suggesting an incomplete turn-to-sheet transition during the regeneration process. Both the analysis of the experimental infrared spectrum and spectrum calculations suggest a particular type of β-sheet structure that was involved in this deficiency, whereas the two other types of β-sheet structure found in silk fibroin fibers were readily formed.
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