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Mamatkulov K, Zavatski S, Arynbek Y, Esawii HA, Burko A, Bandarenka H, Arzumanyan G. Conformational analysis of lipid membrane mimetics modified with A β42 peptide by Raman spectroscopy and computer simulations. J Biomol Struct Dyn 2024:1-14. [PMID: 38520152 DOI: 10.1080/07391102.2024.2330706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/08/2024] [Indexed: 03/25/2024]
Abstract
Peptide-lipid interactions play an important role in maintaining the integrity and function of the cell membrane. Even slight changes in these interactions can induce the development of various diseases. Specifically, peptide misfolding and aggregation in the membrane is considered to be one of the triggers of Alzheimer's disease (AD), however its exact mechanism is still unclear. To this end, an increase of amyloid-beta (Aβ) peptide concentration in the human brain is widely accepted to gradually produce cytotoxic Aβ aggregates (plaques). These plaques initiate a sequence of pathogenic events ending up in observable symptoms of dementia. Understanding the mechanism of the Aβ interaction with cells is crucial for early detection and prevention of Alzheimer's disease. Hence, in this work, a comprehensive Raman analysis of the Aβ42 conformational dynamics in water and in liposomes and lipodiscs that mimic the membrane system is presented. The obtained results show that the secondary structure of Aβ42 in liposomes is dominated by the α-helix conformation, which remains stable over time. However, it comes as a surprise to reveal that the lipodisc environment induces the transformation of the Aβ42 secondary structure to a β-turn/random coil. Our Raman spectroscopy findings are supported with molecular dynamics (MD) and density functional theory (DFT) simulations, showing their good agreement.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kahramon Mamatkulov
- Laboratory of Neutron Physics, Sector of Raman Spectroscopy, Joint Institute for Nuclear Research, Dubna, Russia
| | - Siarhei Zavatski
- Applied Plasmonics Laboratory, Belarusian State University of Informatics and Radioelectronics, Minsk, Belarus
| | - Yersultan Arynbek
- Laboratory of Neutron Physics, Sector of Raman Spectroscopy, Joint Institute for Nuclear Research, Dubna, Russia
- Faculty of Physics and Technology, al-Farabi, Kazakh National University, Almaty, Kazakhstan
| | - Heba A Esawii
- Laboratory of Neutron Physics, Sector of Raman Spectroscopy, Joint Institute for Nuclear Research, Dubna, Russia
- Biophysics Department, Faculty of Science, Cairo University, Egypt
| | - Aliaksandr Burko
- Applied Plasmonics Laboratory, Belarusian State University of Informatics and Radioelectronics, Minsk, Belarus
| | - Hanna Bandarenka
- Applied Plasmonics Laboratory, Belarusian State University of Informatics and Radioelectronics, Minsk, Belarus
| | - Grigory Arzumanyan
- Laboratory of Neutron Physics, Sector of Raman Spectroscopy, Joint Institute for Nuclear Research, Dubna, Russia
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Yamamoto S, Kimura F. Probing the solvation of the α-helix with extended amide III bands in Raman optical activity. Phys Chem Chem Phys 2022; 24:3191-3199. [PMID: 35043805 DOI: 10.1039/d1cp04480j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Experimental and theoretical Raman optical activity (ROA) study of α-helical peptides and proteins has suggested that the relative intensity of two extended amide III ROA bands at ∼1340 cm-1 (I band) and ∼1300 cm-1 (II band) can be used to monitor the permittivity of the surrounding medium of the α-helix. So far, the ROA intensity ratio, II/III, has been interpreted from two different viewpoints. The first one is in terms of a direct effect of permittivity around the α-helix. The second one is based on a structural equilibrium of two types of α-helical structures, "hydrated" and "unhydrated" ones. In the present study, temperature- and solvent-dependences of II/III are measured for highly-α-helical peptides and compared to the theoretical spectra while varying the permittivity or the type of α-helical structure. A fragment method with partial optimization in the normal modes is adopted in density functional theory calculations. The main features of the experimental spectra and a trend of the observed II/III are well reproduced by the simulations, which leads us to a conclusion that the II/III is dominantly governed by a direct influence of the permittivity of the environment and just accessorily by the equilibrium of the two types of α-helices. The simulations also opposed the conventional assignments of the I and II bands to "hydrated" and "unhydrated" α-helical structures, respectively. In the case of α-helical proteins, solvent exposure of the α-helix may be monitored by the ROA ratio.
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Affiliation(s)
- Shigeki Yamamoto
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka 560-0043, Japan.
| | - Fumiya Kimura
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka 560-0043, Japan.
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Gianolio E, Mohan R, Berkessel A. EnantiopureN-Benzyloxycarbonyl-β2-amino Acid Allyl Esters from Racemic β-Lactams by Dynamic Kinetic Resolution usingCandida antarcticaLipase B. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500820] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Yamamoto S, Bouř P. Detection of Molecular Chirality by Induced Resonance Raman Optical Activity in Europium Complexes. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204765] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Yamamoto S, Bouř P. Detection of Molecular Chirality by Induced Resonance Raman Optical Activity in Europium Complexes. Angew Chem Int Ed Engl 2012; 51:11058-61. [DOI: 10.1002/anie.201204765] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Indexed: 11/07/2022]
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Conformational analyses of peptides and proteins by vibrational Raman optical activity. Anal Bioanal Chem 2012; 403:2203-12. [DOI: 10.1007/s00216-012-5891-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 02/09/2012] [Accepted: 02/20/2012] [Indexed: 10/28/2022]
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Merten C, Barron LD, Hecht L, Johannessen C. Determination of the Helical Screw Sense and Side-Group Chirality of a Synthetic Chiral Polymer from Raman Optical Activity. Angew Chem Int Ed Engl 2011; 50:9973-6. [DOI: 10.1002/anie.201104345] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Indexed: 11/11/2022]
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Johannessen C, Hecht L, Merten C. Comparative Study of Measured and Computed Raman Optical Activity of a Chiral Transition Metal Complex. Chemphyschem 2011; 12:1419-21. [DOI: 10.1002/cphc.201100128] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Indexed: 11/09/2022]
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Berkessel A, Jurkiewicz I, Mohan R. Enzymatic Dynamic Kinetic Resolution of Oxazinones: A New Approach to Enantiopure β2-Amino Acids. ChemCatChem 2011. [DOI: 10.1002/cctc.201000343] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Luber S, Reiher M. Prediction of Raman Optical Activity Spectra of Chiral 3-Acetylcamphorato-Cobalt Complexes. Chemphyschem 2010; 11:1876-87. [DOI: 10.1002/cphc.201000121] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Luber S, Neugebauer J, Reiher M. Enhancement and de-enhancement effects in vibrational resonance Raman optical activity. J Chem Phys 2010; 132:044113. [DOI: 10.1063/1.3300069] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Jacob C, Luber S, Reiher M. Understanding the Signatures of Secondary-Structure Elements in Proteins with Raman Optical Activity Spectroscopy. Chemistry 2009; 15:13491-508. [DOI: 10.1002/chem.200901840] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Ebert MO, Gardiner J, Ballet S, Abell A, Seebach D. Synthesis and High-Resolution NMR Structure of a β3-Octapeptide with and without a Tether Introduced by Olefin Metathesis. Helv Chim Acta 2009. [DOI: 10.1002/hlca.200900311] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Luber S, Reiher M. Intensity-Carrying Modes in Raman and Raman Optical Activity Spectroscopy. Chemphyschem 2009; 10:2049-57. [DOI: 10.1002/cphc.200900255] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Liégeois V. A Vibrational Raman Optical Activity Study of 1,1′-Binaphthyl Derivatives. Chemphyschem 2009; 10:2017-25. [DOI: 10.1002/cphc.200900115] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Guthmuller J, Cecchet F, Lis D, Caudano Y, Mani AA, Thiry PA, Peremans A, Champagne B. Theoretical Simulation of Vibrational Sum-Frequency Generation Spectra from Density Functional Theory: Application top-Nitrothiophenol and 2,4-Dinitroaniline. Chemphyschem 2009; 10:2132-42. [DOI: 10.1002/cphc.200900184] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Luber S, Reiher M. Calculated Raman Optical Activity Spectra of 1,6-Anhydro-β-d-glucopyranose. J Phys Chem A 2009; 113:8268-77. [DOI: 10.1021/jp902828r] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sandra Luber
- Laboratorium für Physikalische Chemie, ETH Zürich, Wolfgang − Pauli-Str. 10, CH-8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie, ETH Zürich, Wolfgang − Pauli-Str. 10, CH-8093 Zürich, Switzerland
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Jacob CR, Luber S, Reiher M. Calculated Raman Optical Activity Signatures of Tryptophan Side Chains. Chemphyschem 2008; 9:2177-80. [DOI: 10.1002/cphc.200800448] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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