Аннотация
Липид–белковые взаимодействия играют центральную роль в поддержании структурного и функционального баланса биологических мембран, влияя на широкий спектр клеточных процессов. Однако данные взаимодействия становятся патологическими при нейродегенеративных заболеваниях, таких как болезни Альцгеймера, Паркинсона и Хантингтона. При этих нарушениях неправильное сворачивание и агрегация таких белков, как бета-амилоид (Aβ), альфа-синуклеин (α-syn) и мутантный хантингтин (mHtt), разрушают липидный бислой, повреждая целостность мембраны, ее текучесть и передачу сигналов. В этом обзоре мы исследуем решающую роль липид–белковых взаимодействий при нейродегенеративных заболеваниях, подчеркивая, что неправильное сворачивание белков приводит к образованию токсичных агрегатов, которые встраиваются в мембраны, вызывая нейротоксические явления. Передовые спектроскопические методы сыграли важную роль в изучении этих молекулярных взаимодействий. Световые методы, включая Фёрстеровский перенос энергии (FRET), круговой дихроизм (CD) и рамановскую спектроскопию, позволяют в режиме реального времени получить представление об агрегации белков и динамике липидных мембран. Методы, основанные на нейтронах, такие как нейтронная рефлектометрия и малоугловое рассеяние нейтронов (SANS), дополняют и обогащают анализ липид-белковых взаимодействий, особенно в контексте нейродегенеративной агрегации.
Кроме того, в обзоре подчеркивается важность липидных микродоменов, в частности богатых холестерином липидных рафтов, которые способствуют агрегации белков, влияющих на прогрессирование заболевания. Также обсуждаются терапевтические стратегии в отношении липид–белковых взаимодействий с акцентом на то, как спектроскопические исследования способствуют разработке лекарств, стабилизирующих целостность мембран или предотвращающих токсическую агрегацию. Наконец, интеграция спектроскопии с вычислительными моделями, такими как молекулярная динамика (MD), представляется как многообещающий подход для выявления особенностей сложной динамики липид–белковых взаимодействий, обеспечивая более полную картину механизмов развития заболевания.
Поддерживающие организации
Библиографические ссылки
[2] V. Corradi, B. I. Sejdiu, H. Mesa-Galloso, H. Abdizadeh, S. Yu. Noskov, S. J. Marrink,D. P. Tieleman, Emerging diversity in lipid–protein interactions, Chemical Reviews 119 (2019)5775–5848. https://doi.org/10.1021/acs.chemrev.8b00451.
[3] A. G. Lee, Lipid–protein interactions in biological membranes: A structural perspective,Biochimica et Biophysica Acta — Biomembranes 1612 (2003). https://doi.org/10.1016/S0005-2736(03)00056-7.
[4] M. F. Brown, Soft matter in lipid–protein interactions, Annual Review of Biophysics 46 (2017).https://doi.org/10.1146/annurev-biophys-070816-033843.
[5] W. Dowhan, M. Bogdanov, Lipid–protein interactions as determinants of membraneprotein structure and function, Biochemical Society Transactions, 39 (3) (2011).https://doi.org/10.1042/ BST0390767.
[6] K. Corin, J. U. Bowie, How bilayer properties influence membrane protein folding, Protein Science29 (12) (2020). https://doi.org/10.1002/pro.3973.
[7] I. Levental, E. Lyman, Author Correction: Regulation of membrane protein structure andfunction by their lipid nano-environment, Nature Reviews Molecular Cell Biology (2022).10.1038/s41580-022-00524-4, Nature Reviews Molecular Cell Biology 24 (2023). https://doi.org/10.1038/s41580-022-00560-0.
[8] K. Suga, D. Matsui, N. Watanabe, Y. Okamoto, H. Umakoshi, Insight into the exoso-mal membrane: From viewpoints of membrane fluidity and polarity, Langmuir 37 (2021).https://doi.org/10.1021/acs.langmuir.1c00687.
[9] K. A. Wilson, H. I. MacDermott-Opeskin, E. Riley, Y. Lin, M. L. O’Mara, Understanding thelink between lipid diversity and the biophysical properties of the Neuronal plasma membrane,Biochemistry 59 (2020). https://doi.org/10.1021/acs.biochem.0c00524.
[10] F. Collin, O. Cerlati, F. Couderc, B. Lonetti, J. D. Marty, A. F. Mingotaud, Multidisciplinaryanalysis of protein–lipid interactions and implications in neurodegenerative disorders, TrAC —Trends in Analytical Chemistry 132 (2020). https://doi.org/10.1016/j.trac.2020.116059.
[11] J. Peruzzi, J. Steinkuehler, T. Vu, P. Lu, D. Baker, N. Kamat, Organizing cell-free expressedmembrane proteins in synthetic membranes using lipid–protein interactions, Biophysical Journal121 (2022). https://doi.org/10.1016/j.bpj.2021.11.1194.
[12] R. Budvytyte, G. Valincius, The interactions of amyloidβaggregates with phospholipid mem-branes and the implications for neurodegeneration, Biochemical Society Transactions 51 (2023).https://doi.org/10.1042/BST20220434.
[13] M. Andreasen, N. Lorenzen, D. Otzen, Interactions between misfolded protein oligomers andmembranes: A central topic in neurodegenerative diseases?, Biochimica et Biophysica Acta —Biomembranes 1848 (2015). https://doi.org/10.1016/j.bbamem.2015.01.018.
[14] J. Gandhi, A.C. Antonelli, A. Afridi, S. Vatsia, G. Joshi, V. Romanov, I. V. J. Murray,S. A. Khan, Protein misfolding and aggregation in neurodegenerative diseases: A review of patho-geneses, novel detection strategies, and potential therapeutics, Reviews in the Neurosciences 30(2019). https://doi.org/10.1515/revneuro-2016-0035.
[15] C. Soto, S. Pritzkow, Protein misfolding, aggregation, and conformational strains in neurode-generative diseases, Nature Neuroscience 21 (2018). https://doi.org/10.1038/s41593-018-0235-9.
[16] V. V. Dyakin, T. M. Wisniewski, A. Lajtha, Chiral interface of amyloid beta (Aβ: Relevanceto protein aging, aggregation and neurodegeneration, Symmetry 12 (2020). https://doi.org/10.3390/SYM12040585.
[17] V. Ghiglieri, V. Calabrese, P. Calabresi, Alpha-synuclein: From early synaptic dysfunction toneurodegeneration, Frontiers in Neurology 9 (2018). https://doi.org/10.3389/fneur.2018.00295.
[18] G. Forloni, Alpha synuclein: Neurodegeneration and inflammation, International Journal ofMolecular Sciences 24 (2023). https://doi.org/10.3390/ijms24065914.
[19] B. Bernard, Huntington’s Disease, Humboldt-Universit ̈at zu Berlin, Mathematisch-Naturwissen-schaftliche Fakult ̈at, 2009. https://doi.org/https://doi.org/10.18452/15900.
[20] S. Boopathi, A. B. Poma, R. Gardu ̃no-Ju ́arez, An overview of several inhibitors for Alzheimer’sdisease: Characterization and failure, International Journal of Molecular Sciences 22 (2021).https://doi.org/10.3390/ijms221910798.
[21] Z. Niu, Z. Zhang, W. Zhao, J. Yang, Interactions between amyloidβpeptide and lipid mem-branes, Biochimica et Biophysica Acta — Biomembranes 1860 (2018). https://doi.org/10.1016/j.bbamem.2018.04.004.
[22] E. Popugaeva, E. Pchitskaya, I. Bezprozvanny, Dysregulation of intracellular calcium signalingin Alzheimer’s disease, Antioxidants and Redox Signaling 29 (2018). https://doi.org/10.1089/ars.2018.7506.
[23] I. N. Serratos, E. Hern ́andez-P ́erez, C. Campos, M. Aschner, A. Santamar ́ıa, An update onthe critical role ofα-synuclein in Parkinson’s disease and other synucleinopathies: From tissueto cellular and molecular levels, Molecular Neurobiology 59 (2022). https://doi.org/10.1007/s12035-021-02596-3.
[24] L. Liu, H. Tong, Y. Sun, X. Chen, T. Yang, G. Zhou, X. J. Li, S. Li, Huntingtin interactingproteins and pathological implications, International Journal of Molecular Sciences 24 (2023).https://doi.org/ 10.3390/ijms241713060.
[25] A. Shamim, T. Mahmood, F. Ahsan, A. Kumar, P. Bagga, Lipids: An insight into the neu-rodegenerative disorders, Clinical Nutrition Experimental 20 (2018). https://doi.org/10.1016/j.yclnex.2018.05.001.
[26] G. Xu, W. Li, H. Xie, J. Zhu, L. Song, J. Tang, Y. Miao, X. X. Han, In situ monitoring of mem-brane protein electron transfer via surface-enhanced resonance Raman spectroscopy, AnalyticalChemistry 96 (2024). https://doi.org/10.1021/acs.analchem.3c04700.
[27] A. Torreggiani, A. Tinti, Z. Jurasekova, M. Capdevila, M. Saracino, M. Di Foggia,Structural lesions of proteins connected to lipid membrane damages caused by radicalstress: Assessment by biomimetic systems and Raman spectroscopy, Biomolecules 9 (2019).https://doi.org/10.3390/biom9120794.
[28] V. Rondelli, S. Helmy, G. Passignani, P. Parisse, D. Di Silvestre, Integrated strategies fora holistic view of extracellular vesicles, ACS Omega 7 (2022). https://doi.org/10.1021/acso-mega.2c01003.
[29] A. Tukova, A. Rodger, Spectroscopy of model-membrane liposome–protein systems: Comple-mentarity of linear dichroism, circular dichroism, fluorescence and SERS, Emerging Topics inLife Sciences 5 (2021). https://doi.org/10.1042/ETLS20200354.
[30] D. Shrestha, A. Jenei, P. Nagy, G. Vereb, J. Sz ̈oll ̋osi, Understanding FRET as a researchtool for cellular studies, International Journal of Molecular Sciences 16 (2015). https://doi.org/10.3390/ijms16046718.
[31] A. J. P. Teunissen, C. P ́erez-Medina, A. Meijerink, W. J. M. Mulder, Investigating supramolec-ular systems using F ̈orster resonance energy transfer, Chemical Society Reviews 47 (2018).https://doi.org/10.1039/c8cs00278a. Annual Review of Physical Chemistry 70 (2019). https://doi.org/10.1146/annurev-physchem-042018-052527.
[32] V. Betaneli, J. M ̈ucksch, P. Schwille, Fluorescence correlation spectroscopy to examine protein–lipid interactions in membranes, in: Methods in Molecular Biology, 2019. https://doi.org/10.1007/978-1-4939-9512-7_18.[33] D. Sulzer, R. H. Edwards, The physiological role ofα-synuclein and its relationship to Parkinson’sdisease, Journal of Neurochemistry 150 (2019). https://doi.org/10.1111/jnc.14810.[34] S. A. Tatulian, FTIR analysis of proteins and protein–membrane interactions, in: Methods inMolecular Biology, 2019. https://doi.org/10.1007/978-1-4939-9512-7_13.[35] A. Ausili, M. S ́anchez, J. C. G ́omez-Fern ́andez, Attenuated total reflectance infrared spec-troscopy: A powerful method for the simultaneous study of structure and spatial orien-tation of lipids and membrane proteins, Biomedical Spectroscopy and Imaging 4 (2015).https://doi.org/10.3233/bsi-150104.
[36] M. G. Herrera, M. Giamp ́a, N. Tonali, V. I. Dodero, Multimodal methods to study proteinaggregation and fibrillation, in: Advances in Protein Molecular and Structural Biology Methods,2022. https://doi.org/10.1016/B978-0-323-90264-9.00006-4.
[37] Sidney Steven Dicke, Protein secondary structure identification in vitro and ex vivo using 2D IRspectroscopy: Kinetics and imaging, University of Wisconsin-Madison, 2023.
[38] D. Baghel, A. P. de Oliveira, S. Satyarthy, W. E. Chase, S. Banerjee, A. Ghosh, Structural charac-terization of amyloid aggregates with spatially resolved infrared spectroscopy, 2024, pp. 113–150.https://doi.org/10.1016/bs.mie.2024.02.013.
[39] D. J. Laird, M. M. Mulvihill, J. A. Whiles Lillig, Membrane-induced peptide structural changesmonitored by infrared and circular dichroism spectroscopy, Biophysical Chemistry 145 (2009).https://doi.org/10.1016/j.bpc.2009.09.002.
[40] M. Bucciantini, S. Rigacci, M. Stefani, Amyloid aggregation: Role of biological mem-branes and the aggregate-membrane system, Journal of Physical Chemistry Letters 5 (2014).https://doi.org/10.1021/jz4024354.
[41] M. F. Pignataro, M. G. Herrera, V. I. Dodero, Evaluation of peptide/protein self-assembly andaggregation by spectroscopic methods, Molecules 25 (2020). https://doi.org/10.3390/molecu-les25204854
[42] H. Li, F. Rahimi, S. Sinha, P. Maiti, G. Bitan, K. Murakami, Amyloids and protein aggregation-analytical methods, in: Encyclopedia of Analytical Chemistry, 2009. https://doi.org/10.1002/9780470027318.a9038.
[43] L. A. Clifton, C. Neylon, J. H. Lakey, Examining protein–lipid complexes using neutron scatter-ing, Methods in Molecular Biology 974 (2013). https://doi.org/10.1007/978-1-62703-275-9_7.
[44] R. Ashkar, H. Z. Bilheux, H. Bordallo, R. Briber, D. J. E. Callaway, et. al, Neutron scatteringin the biological sciences: Progress and prospects, Acta Crystallographica Section D: StructuralBiology 74 (2018). https://doi.org/10.1107/S2059798318017503.
[45] M. Sunder, N. Acharya, S. Nayak, N. Mazumder, Optical spectroscopy and microscopy techniquesfor assessment of neurological diseases, Applied Spectroscopy Reviews 56 (2021). https://doi.org/10.1080/05704928.2020.1851237.[46] F. Scollo, C. La Rosa, Amyloidogenic intrinsically disordered proteins: New insights into theirself-assembly and their interaction with membranes, Life 10 (2020). https://doi.org/10.3390/life10080144.
[47] L. A. Clifton, S. C. L. Hall, N. Mahmoudi, T. J. Knowles, F. Heinrich, J. H. Lakey, Structuralinvestigations of protein–lipid complexes using neutron scattering, in: Methods in MolecularBiology, 2019. https://doi.org/10.1007/978-1-4939-9512-7_11.
[48] S. Biswas, V. B. Gavra, A. K. Das, U. Tripathy, Biophotonics in disease diagnosis and therapy, in:Biomedical Engineering and Its Applications in Healthcare, 2019. https://doi.org/10.1007/978-981-13-3705-5_3.[49] J. D. Morris, C. K. Payne, Microscopy and cell biology: New methods and new questions, Annual Review of Physical Chemistry 70 (2019). https://doi.org/10.1146/annurev-physchem-042018-052527.
[50] H. Lotfipour, H. Sobhani, M. Khodabandeh, Quantum diagnosis of cancer with heralded singlephotons, Laser Physics Letters 19 (2022). https://doi.org/10.1088/1612-202X/ac8bd4.
[51] S. Pallen, Y. Shetty, S. Das, J. M. Vaz, N. Mazumder, Advances in nonlinear optical microscopytechniques for in vivo and in vitro neuroimaging, Biophysical Reviews 13 (2021). https://doi.org/10.1007/s12551-021-00832-7.
[52] R. Liu, S. Xia, H. Li, Native top-down mass spectrometry for higher-order structural charac-terization of proteins and complexes, Mass Spectrometry Reviews 42 (2023). https://doi.org/10.1002/mas.21793.
[53] A. V. Vlasov, N. L. Maliar, S. V. Bazhenov, E. I. Nikelshparg, N. A. Brazhe, A. D. Vlasova,S. D. Osipov, V. V. Sudarev, Y. L. Ryzhykau, A. O. Bogorodskiy, E. V. Zinovev, A. V. Rogachev,I. V. Manukhov, V. I. Borshchevskiy, A. I. Kuklin, J. Pokorn ́y, O. Sosnovtseva, G. V. Maksimov,V. I. Gordeliy, Raman scattering: From structural biology to medical applications, Crystals 10(2020). https://doi.org/10.3390/cryst10010038.
[54] G. Dorrington, N. P. Chmel, S. R. Norton, A. M. Wemyss, K. Lloyd, D. P. Amarasinghe,A. Rodger, Light scattering corrections to linear dichroism spectroscopy for liposomes in shearflow using calcein fluorescence and modified Rayleigh–Gans–Debye–Mie scattering, BiophysicalReviews 10 (2018). https://doi.org/10.1007/s12551-018-0458-8.
[55] R. A. Karaballi, Spectroscopic investigation of the interaction between biomimetic membranesand protein, Saint Mary’s University, Halifax, Nova Scotia, 2015.
[56] E. Smith, G. Dent, Modern Raman spectroscopy: A practical approach, Wiley, 2019.https://doi.org/ 10.1002/0470011831.
[57] A. C. S. Talari, Z. Movasaghi, S. Rehman, I. U. Rehman, Raman spectroscopy of biological tis-sues, Applied Spectroscopy Reviews 50 (2015). https://doi.org/10.1080/05704928.2014.923902.
[58] G. M. Arzumanyan, N. V. Doroshkevich, K. Z. Mamatkulov, S. N. Shashkov, E. V. Zinovev,A. V. Vlasov, E. S. Round, V. I. Gordeliy, Highly sensitive coherent anti-Stokes Raman scat-tering imaging of protein crystals, Journal of the American Chemical Society 138 (2016).https://doi.org/10.1021/jacs.6b04464.
[59] S. Zavatski, N. Khinevich, K. Girel, S. Redko, N. Kovalchuk, I. Komissarov, V. Lukashevich,I. Semak, K. Mamatkulov, M. Vorobyeva, G. Arzumanyan, H. Bandarenka, Surface enhancedRaman spectroscopy of lactoferrin adsorbed on silvered porous silicon covered with graphene,Biosensors 9 (2019). https://doi.org/10.3390/bios9010034.
[60] L. M. Miller, Infrared spectroscopy and imaging for understanding neurodegenerative protein-misfolding diseases, in: Vibrational Spectroscopy in Protein Research: From Purified Proteinsto Aggregates and Assemblies, 2020. https://doi.org/10.1016/B978-0-12-818610-7.00005-0.
[61] K. Mamatkulov, S. Zavatski, Y. Arynbek, H. A. Esawii, A. Burko, H. Bandarenka, G. Arzu-manyan, Conformational analysis of lipid membrane mimetics modified with Aβ42 peptide byRaman spectroscopy and computer simulations, Journal of Biomolecular Structure and Dynamics1–14 (2024). https://doi.org/10.1080/07391102.2024.2330706.
[62] J. Wu, C. Cao, R. A. Loch, A. Tiiman, J. Luo, Single-molecule studies of amyloid proteins: Frombiophysical properties to diagnostic perspectives, Quarterly Reviews of Biophysics 53 (2020) e12.https://doi.org/DOI: 10.1017/S0033583520000086.
[63] P. Madhu, D. Das, S. Mukhopadhyay, Conformation-specific perturbation of membrane dynamicsby structurally distinct oligomers of Alzheimer’s amyloid-βpeptide, Physical Chemistry Chem-ical Physics 23 (2021). https://doi.org/10.1039/d0cp06456d.
[64] A. K. Ganapati, Biophysical exploration of membrane–protein interactions in Alzheimer’s disease,University of California, 2023.
[65] Q. Chen, Y. Xie, J. Xi, Y. Guo, H. Qian, Y. Cheng, Y. Chen, W. Yao, Characterization of lipid oxidation process of beef during repeated freeze-thaw by electron spin resonance technology and Ra-man spectroscopy, Food Chemistry 243 (2018). https://doi.org/10.1016/j.foodchem.2017.09.115.
[66] T. Vo-Dinh, F. Yan, M. B. Wabuyele, Surface-enhanced Raman scattering for medical di-agnostics and biological imaging, Journal of Raman Spectroscopy 36 (2005). https://doi.org/10.1002/jrs.1348.
[67] Z. Q. Tian, B. Ren, D. Y. Wu, Surface-enhanced Raman scattering: From noble to transitionmetals and from rough surfaces to ordered nanostructures, Journal of Physical Chemistry B 106(2002). https://doi.org/10.1021/jp0257449.
[68] Y. Zhou, J. Liu, T. Zheng, Y. Tian, Label-free SERS strategy for in situ monitoring and real-timeimaging of Aβaggregation process in live neurons and brain tissues, Analytical Chemistry 92(2020). https://doi.org/10.1021/acs.analchem.9b05837.
[69] V. Voiciuk, G. Valincius, R. Budvytyte, A. Matijoˇska, I. Matulaitiene, G. Niaura, Surface-enhanced Raman spectroscopy for detection of toxic amyloidβoligomers adsorbed on self-assembled monolayers, Spectrochimica Acta — Part A: Molecular and Biomolecular Spectroscopy95 (2012). https://doi.org/10.1016/j.saa.2012.04.043.
[70] Y. Zheng, L. Zhang, J. Zhao, L. Li, M. Wang, P. Gao, Q. Wang, X. Zhang, W. Wang, Advancesin aptamers against Aβand applications in Aβdetection and regulation for Alzheimer’s disease,Theranostics 12 (2022). https://doi.org/10.7150/thno.69465.
[71] L. A. Munishkina, A. L. Fink, Fluorescence as a method to reveal structures and membrane-interactions of amyloidogenic proteins, Biochimica et Biophysica Acta — Biomembranes 1768(2007). https://doi.org/10.1016/j.bbamem.2007.03.015.
[72] Z. Yang, H. Xu, J. Wang, W. Chen, M. Zhao, Single-molecule fluorescence techniques formembrane protein dynamics analysis, Applied Spectroscopy 75 (2021). https://doi.org/10.1177/00037028211009973.
[73] S. Sarabipour, N. Del Piccolo, K. Hristova, Characterization of membrane protein interactions inplasma membrane derived vesicles with quantitative imaging F ̈urster resonance energy transfer,Accounts of Chemical Research 48 (2015). https://doi.org/10.1021/acs.accounts.5b00238.
[74] S. Zadran, S. Standley, K. Wong, E. Otiniano, A. Amighi, M. Baudry, Fluorescence resonanceenergy transfer (FRET)–based biosensors: Visualizing cellular dynamics and bioenergetics, Ap-plied Microbiology and Biotechnology 96 (2012). https://doi.org/10.1007/s00253-012-4449-6.
[75] G. Krainer, S. Keller, M. Schlierf, Structural dynamics of membrane–protein folding from single-molecule FRET, Current Opinion in Structural Biology 58 (2019). https://doi.org/10.1016/j.sbi.2019.05.025.
[76] J. W. Taraska, M. C. Puljung, N. B. Olivier, G. E. Flynn, W. N. Zagotta, Mapping the structureand conformational movements of proteins with transition metal ion FRET, Nature Methods 6(2009). https://doi.org/10.1038/nmeth.1341.
[77] J. H. Ha, S. N. Loh, Protein conformational switches: From nature to design, Chemistry —A European Journal 18 (2012). https://doi.org/10.1002/chem.201200348.
[78] J. W. Taraska, Mapping membrane protein structure with fluorescence, Current Opinion inStructural Biology 22 (2012). https://doi.org/10.1016/j.sbi.2012.02.004.
[79] A. S. Khadria, A. Senes, Review fluorophores, environments, and quantification techniquesin the analysis of transmembrane helix interaction using FRET, Biopolymers 104 (2015).https://doi.org/10.1002/BIP.22667.
[80] S. J. Leblanc, P. Kulkarni, K. R. Weninger, Single molecule FRET: A powerful tool to studyintrinsically disordered proteins, Biomolecules 8 (2018). https://doi.org/10.3390/biom8040140.
[81] D. Maurel, L. Comps-Agrar, C. Brock, M. L. Rives, E. Bourrier, M. A. Ayoub, H. Bazin, N. Tinel,T. Durroux, L. Pr ́ezeau, E. Trinquet, J. P. Pin, Cell-surface protein–protein interaction analysiswith time-resolved FRET and snap-tag technologies: Application to GPCR oligomerization,Nature Methods 5 (2008). https://doi.org/10.1038/nmeth.1213.
[82] E. K. L. Yeow, A. H. A. Clayton, Enumeration of oligomerization states of membrane proteins inliving cells by homo-FRET spectroscopy and microscopy: Theory and application, BiophysicalJournal 92 (2007). https://doi.org/10.1529/biophysj.106.099424.
[83] S. Christie, X. Shi, A.W. Smith, Resolving membrane protein–protein interactions in live cellswith pulsed interleaved excitation fluorescence cross-correlation spectroscopy, Accounts of Chem-ical Research 53 (2020). https://doi.org/10.1021/acs.accounts.9b00625.
[84] K. Hemmen, S. Choudhury, M. Friedrich, J. Balkenhol, F. Knote, M. J. Lohse, K. G. Heinze,Dual-color fluorescence cross-correlation spectroscopy to study protein–protein interactionand protein dynamics in live cells, Journal of Visualized Experiments 2021 (2021).https://doi.org/10.3791/62954.
[85] Z. Saedi, M. Nikkhah, A FRET-based aptasensor for the detection ofα-synuclein oligomersas biomarkers of Parkinson’s disease, Analytical Methods 14 (2022). https://doi.org/10.1039/d2ay00611a.
[86] A. Svanbergsson, F. Ek, I. Martinsson, J. Rodo, D. Liu, E. Brandi, C. Haikal, L. Torres-Garcia,W. Li, G. Gouras, R. Olsson, T. Bj ̈orklund, J. Y. Li, FRET-based screening identifies p38 MAPKand PKC inhibition as targets for prevention of seededα-synuclein aggregation, Neurotherapeu-tics 18 (2021). https://doi.org/10.1007/s13311-021-01070-1.
[87] N. P. Reynolds, A. Soragni, M. Rabe, D. Verdes, E. Liverani, S. Handschin, R. Riek, S. Seeger,Mechanism of membrane interaction and disruption byα-synuclein, Journal of the AmericanChemical Society 133 (2011). https://doi.org/10.1021/ja2029848.
[88] C. M. Pfefferkorn, Z. Jiang, J. C. Lee, Biophysics ofα-synuclein membrane interactions, Bio-chimica et Biophysica Acta — Biomembranes 1818 (2012). https://doi.org/10.1016/j.bbamem.2011.07.032.
[89] A. R. Braun, Understanding the membrane biophysics of alpha-synuclein and its role in mem-brane curvature induction and structural remodeling, University of Minnesota, 2014.
[90] C. Sanluca, P. Spagnolo, R. Mancinelli, M. I. De Bartolo, M. Fava, M. Maccarrone, S. Carotti,E. Gaudio, A. Leuti, G. Vivacqua, Interaction betweenα-synuclein and bioactive lipids:Neurodegeneration, disease biomarkers and emerging therapies, Metabolites 14 (2024) 352.https://doi.org/ 10.3390/metabo14070352.
[91] J. Wu, Amyloid oligomer formation and interferences, Faculty of Science, Structural Biology &Biophysics, Nano-diffraction of Biological Specimen, 2024.
[92] R. Hu, J. Diao, J. Li, Z. Tang, X. Li, J. Leitz, J. Long, J. Liu, D. Yu, Q. Zhao, Intrinsicand membrane-facilitatedα-synuclein oligomerization revealed by label-free detection throughsolid-state nanopores, Scientific Reports 6 (2016). https://doi.org/10.1038/srep20776.
[93] S. Ray, N. Singh, K. Patel, G. Krishnamoorthy, S. K. Maji, FRAP and FRET investigation ofα-synuclein fibrillization via liquid–liquid phase separation in vitro and in heLa cells, in: Methodsin Molecular Biology, 2023. https://doi.org/10.1007/978-1-0716-2597-2_26.[94] R. W. Woody, Circular dichroism, Methods in Enzymology 246 (1995) 34–71. https://doi.org/10.1016/0076-6879(95)46006-3.
[95] B. A. Wallace, The role of circular dichroism spectroscopy in the era of integrative structural biol-ogy, Current Opinion in Structural Biology 58 (2019). https://doi.org/10.1016/j.sbi.2019.04.001.
[96] D. M. Rogers, S. B. Jasim, N. T. Dyer, F. Auvray, M. R ́efr ́egiers, J. D. Hirst, Electroniccircular dichroism spectroscopy of proteins, Chem 5 (2019). https://doi.org/10.1016/j.chempr.2019.07.008.
[97] L. A. Linhares, C. H. I. Ramos, Unlocking insights into folding, structure, and function ofproteins through circular dichroism spectroscopy — A short review, Applied Biosciences 2 (2023).https://doi.org/10.3390/applbiosci2040040.
[98] S. Kelly, N. Price, The use of circular dichroism in the investigation of protein structure and func-tion, Current Protein & Peptide Science 1 (2005). https://doi.org/10.2174/1389203003381315.
[99] R. A. Copeland, Spectroscopic probes of protein structure, in: Methods for Protein Analysis,1994. https://doi.org/10.1007/978-1-4757-1505-7_9.
[100] O. C. Mancini, A multi-disciplinary study of the early stages of beta amyloid aggregation, Uni-versity of Strathclyde, 2017. https://doi.org/10.48730/950a-6q28.
[101] M. A. Haque, P. Kaur, A. Islam, M. I. Hassan, Application of circular dichroism spectroscopyin studying protein folding, stability, and interaction, in: Advances in Protein Molecular andStructural Biology Methods, 2022. https://doi.org/10.1016/B978-0-323-90264-9.00014-3.
[102] G. Siligardi, R. Hussain, S. G. Patching, M. K. Phillips-Jones, Ligand- and drug-binding studiesof membrane proteins revealed through circular dichroism spectroscopy, Biochimica et BiophysicaActa — Biomembranes 1838 (2014). https://doi.org/10.1016/j.bbamem.2013.06.019.
[103] W. Rog ́o ̇z, A. Owczarzy, K. Kulig, M. Macia ̨ ̇zek-Jurczyk, Ligand-human serum albumin anal-ysis: The near-UV CD and UV-Vis spectroscopic studies, Naunyn-Schmiedeberg’s Archives ofPharmacology (2024). https://doi.org/10.1007/s00210-024-03471-3.
[104] C. S. Braun, L. A. Kueltzo, C. R. Middaugh, Ultraviolet absorption and circular dichroismspectroscopy of nonviral gene delivery complexes, in: Nonviral Vectors for Gene Therapy, 2003.https://doi.org/10.1385/1-59259-139-6:253.
[105] J. Kypr, I. Kejnovsk ́a, D. Renˇciuk, M. Vorl ́ıˇckov ́a, Circular dichroism and conformational poly-morphism of DNA, Nucleic Acids Research 37 (2009). https://doi.org/10.1093/nar/gkp026.
[106] P. Changenet, F. Hache, Recent advances in the development of ultrafast electronic circulardichroism for probing the conformational dynamics of biomolecules in solution, European Phys-ical Journal: Special Topics 232 (2023). https://doi.org/10.1140/epjs/s11734-022-00679-3.
[107] S. J. Opella, Structure determination of membrane proteins by nuclear magnetic resonance spec-troscopy, Annual Review of Analytical Chemistry 6 (2013). https://doi.org/10.1146/annurev-anchem-062012-092631.
[108] D. Marion, An introduction to biological NMR spectroscopy, Molecular and Cellular Proteomics12 (2013). https://doi.org/10.1074/mcp.O113.030239.
[109] J. T. Pelton, L. R. McLean, Spectroscopic methods for analysis of protein secondary structure,Analytical Biochemistry 277 (2000). https://doi.org/10.1006/abio.1999.4320.
[110] A. J. Miles, R. W. Janes, B. A. Wallace, Tools and methods for circular dichroism spectroscopyof proteins: A tutorial review, Chemical Society Reviews 50 (2021). https://doi.org/10.1039/d0cs00558d.
[111] A. J. Miles, B. A. Wallace, Circular dichroism spectroscopy of membrane proteins, ChemicalSociety Reviews 45 (2016) 4859–4872. https://doi.org/10.1039/C5CS00084J.
[112] A. J. Miles, B. A. Wallace, Circular dichroism spectroscopy for protein characterization: Bio-pharmaceutical applications, in: Biophysical Characterization of Proteins in Developing Bio-pharmaceuticals, 2015. https://doi.org/10.1016/B978-0-444-59573-7.00006-3.
[113] M. Naldi, S. Giannoni, E. Betti, S. Ferroni, C. Valle, S. Giusto, M. Galvani, Amyloidβ-peptide25–35 self-assembly and its inhibition: A model undecapeptide system to gain atomistic andsecondary structure details of the Alzheimer’s disease process and treatment, ACS ChemicalNeuroscience 3 (11) (2012) 952–962. https://doi.org/10.1021/cn3000982.
[114] M. S. H. Mubin, A Structural study of liposome formation (thesis), La Trobe University, 2012.https://doi.org/10.26181/21850818.v1
[115] S. Kurakin, D. Badreeva, E. Dushanov, A. Shutikov, S. Efimov, A. Timerova, T. Mukhamet-zyanov, T. Murugova, O. Ivankov, K. Mamatkulov, G. Arzumanyan, V. Klochkov, N. Kuˇcerka,Arrangement of lipid vesicles and bicelle-like structures formed in the presence of Aβ(25–35)peptide, Biochimica et Biophysica Acta — Biomembranes 1866 (2024). https://doi.org/10.1016/j.bbamem.2023.184237.
[116] M. A. Mohamed, J. Jaafar, A. F. Ismail, M. H. D. Othman, M. A. Rahman, Fourier transforminfrared (FTIR) spectroscopy, in: Membrane Characterization, 2017. https://doi.org/10.1016/
B978-0-444-63776-5.00001-2.
[117] M. P. Brown, C. Royer, Fluorescence spectroscopy as a tool to investigate protein interactions,Current Opinion in Biotechnology 8 (1997). https://doi.org/10.1016/S0958-1669(97)80156-5.
[118] A. A. Ismail, F. R. van de Voort, J. Sedman, Chapter 4 Fourier transform infrared spectroscopy:Principles and applications, Techniques and Instrumentation in Analytical Chemistry 18 (1997).https://doi.org/10.1016/S0167-9244(97)80013-3.
[119] S. A. Tatulian, Structural characterization of membrane proteins and peptides by FTIR andATR-FTIR spectroscopy, Methods in Molecular Biology 974 (2013). https://doi.org/10.1007/978-1-62703-275-9_9.
[120] J. A. Hering, P. I. Haris, FTIR spectroscopy for analysis of protein secondary structure, Advancesin Biomedical Spectroscopy 2 (2009). https://doi.org/10.3233/978-1-60750-045-2-129.
[121] M. Carbonaro, A. Nucara, Secondary structure of food proteins by Fourier transform spec-troscopy in the mid-infrared region, Amino Acids 38 (2010). https://doi.org/10.1007/s00726-009-0274-3.
[122] J. L. R. Arrondo, F. M. Go ̃ni, Infrared spectroscopic studies of lipid–protein interactions inmembranes, New Comprehensive Biochemistry 25 (1993). https://doi.org/10.1016/S0167-7306(08)60242-2.
[123] S. P. O. Danielsen, H. K. Beech, S. Wang, B. M. El-Zaatari, X. Wang, L. Sapir, T. Ouchi,Z. Wang, P. N. Johnson, Y. Hu, D. J. Lundberg, G. Stoychev, S. L. Craig, J. A. Johnson,J. A. Kalow, B. D. Olsen, M. Rubinstein, Molecular characterization of polymer networks, Chem-ical Reviews 121 (2021). https://doi.org/10.1021/acs.chemrev.0c01304.
[124] S. Sangamnerkar, Application of ATR-FTIR spectroscopy for the direct detection of stimulantsin biofluids, University of Strathclyde, 2024.
[125] H. Tiernan, B. Byrne, S. G. Kazarian, ATR-FTIR spectroscopy and spectroscopic imaging forthe analysis of biopharmaceuticals, Spectrochimica Acta — Part A: Molecular and BiomolecularSpectroscopy 241 (2020). https://doi.org/10.1016/j.saa.2020.118636.
[126] J. S. Randhawa, Advanced analytical techniques for microplastics in the environment: A review,Bulletin of the National Research Centre 47 (2023). https://doi.org/10.1186/s42269-023-01148-0.
[127] C. Lamberti, A. Zecchina, E. Groppo, S. Bordiga, Probing the surfaces of heterogeneouscatalysts by in situ IR spectroscopy, Chemical Society Reviews 39 (2010). https://doi.org/10.1039/c0cs00117a.
[128] A. Muga, H. H. Mantsch, W. K. Surewicz, Membrane binding induces destabilization of cy-tochrome c structure, Biochemistry 30 (1991). https://doi.org/10.1021/bi00243a025.
[129] R. Kranz, R. Lill, B. Goldman, G. Bonnard, S. Merchant, Molecular mechanisms of cytochrome cbiogenesis: Three distinct systems, Molecular Microbiology 29 (1998). https://doi.org/10.1046/j.1365-2958.1998.00869.x.
[130] M. Ott, B. Zhivotovsky, S. Orrenius, Role of cardiolipin in cytochrome c release from mitochon-dria, Cell Death and Differentiation 14 (2007). https://doi.org/10.1038/sj.cdd.4402135.
[131] K. El Kirat, S. Morandat, Cytochrome c interaction with neutral lipid membranes: Influenceof lipid packing and protein charges, Chemistry and Physics of Lipids 162 (1) (2009) 17–24.https://doi.org/10.1016/j.chemphyslip.2009.08.002.
[132] T. Heimburg, D. Marsh, Investigation of secondary and tertiary structural changes of cytochromec in complexes with anionic lipids using amide hydrogen exchange measurements: An FTIR study,Biophysical Journal 65 (1993). https://doi.org/10.1016/S0006-3495(93)81299-2.
[133] S. Halder, S. Kumari, S. Kumar, V. K. Aswal, S. K. Saha, Fluorescence resonance energy transfer,small-angle neutron scattering, and dynamic light scattering study on interactions of geminisurfactants having different spacer groups with protein at various regions of binding isotherms,ACS Omega 3 (2018). https://doi.org/10.1021/acsomega.8b01471.
[134] T. A. Harroun, N. Kuˇcerka, M. P. Nieh, J. Katsaras, Neutron and X-ray scattering for biophysics and biotechnology: Examples of self-assembled lipid systems, Soft Matter 5 (2009).https://doi.org/10.1039/b819799g.
[135] D. K. Rai, V. K. Sharma, D. Anunciado, H. O’Neill, E. Mamontov, V. Urban, W. T. Heller,S. Qian, Neutron scattering studies of the interplay of amyloidβpeptide (1–40) and an anioniclipid 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol, Scientific Reports 6 (2016). https://doi.org/10.1038/srep30983.
[136] F. A. Heberle, D. A. A. Myles, J. Katsaras, Biomembranes research using thermal and coldneutrons, Chemistry and Physics of Lipids 192 (2015). https://doi.org/10.1016/j.chemphyslip.2015.07.020.
[137] M. Haertlein, M. Moulin, J. M. Devos, V. Laux, O. Dunne, V. T. Forsyth, Biomoleculardeuteration for neutron structural biology and dynamics, in: Methods in Enzymology, 2016.https://doi.org/10.1016/bs.mie.2015.11.001.
[138] X. Hu, M. Liao, K. Ding, J. Wang, H. Xu, K. Tao, F. Zhou, J. R. Lu, Neutron reflection andscattering in characterising peptide assemblies, Advances in Colloid and Interface Science 322(2023). https://doi.org/10.1016/j.cis.2023.103033.
[139] O. Ivankov, T. Kondela, E. B. Dushanov, E. V. Ermakova, T. N. Murugova, D. Soloviov,A. I. Kuklin, N. Kuˇcerka, Cholesterol and melatonin regulated membrane fluidity does not affectthe membrane breakage triggered by amyloid-beta peptide, Biophysical Chemistry 298 (2023).https://doi.org/10.1016/j.bpc.2023.107023.
[140] T. Kondela, E. Dushanov, M. Vorobyeva, K. Mamatkulov, E. Drolle, D. Soloviov, P. Hrubovˇc ́ak,K. Kholmurodov, G. Arzumanyan, Z. Leonenko, N. Kuˇcerka, Investigating the competitive ef-fects of cholesterol and melatonin in model lipid membranes, Biochimica et Biophysica Acta —Biomembranes 1863 (2021). https://doi.org/10.1016/j.bbamem.2021.183651.
[141] J. Birch, H. Cheruvara, N. Gamage, P. J. Harrison, R. Lithgo, A. Quigley, Changes in membraneprotein structural biology, Biology 9 (2020). https://doi.org/10.3390/biology9110401.
[142] T. O. C. Kwan, D. Axford, I. Moraes, Membrane protein crystallography in the era of mod-ern structural biology, Biochemical Society Transactions 48 (2020) 2505–2524. https://doi.org/10.1042/BST20200066.
[143] J. Zha, D. Li, Lipid cubic phase for membrane protein X-ray crystallography, in: MembraneBiophysics: New Insights and Methods, 2017. https://doi.org/10.1007/978-981-10-6823-2_7.
[144] J. M. Sanderson, Resolving the kinetics of lipid, protein and peptide diffusion in membranes,Molecular Membrane Biology 29 (2012). https://doi.org/10.3109/09687688.2012.678018.
[145] E. Mahieu, F. Gabel, Biological small-angle neutron scattering: Recent results and develop-ment, Acta Crystallographica Section D: Structural Biology 74 (2018). https://doi.org/10.1107/S2059798318005016.
[146] E. Sezgin, P. Schwille, Fluorescence techniques to study lipid dynamics, Cold Spring HarborPerspectives in Biology 3 (2011). https://doi.org/10.1101/cshperspect.a009803.
[147] J. E. Nielsen, V. A. Bjørnestad, R. Lund, Resolving the structural interactions between an-timicrobial peptides and lipid membranes using small-angle scattering methods: The case ofindolicidin, Soft Matter 14 (2018). https://doi.org/10.1039/c8sm01888j.
[148] J. E. Nielsen, S. F. Pr ́evost, H. Jenssen, R. Lund, Impact of antimicrobial peptides on E. coli-mimicking lipid model membranes: Correlating structural and dynamic effects using scatteringmethods, Faraday Discussions 232 (2021). https://doi.org/10.1039/d0fd00046a.
[149] J. E. Nielsen, V. A. Bjørnestad, V. Pipich, H. Jenssen, R. Lund, Beyond structural models forthe mode of action: How natural antimicrobial peptides affect lipid transport, Journal of Colloidand Interface Science 582 (2021). https://doi.org/10.1016/j.jcis.2020.08.094.
[150] R. Guidelli, L. Becucci, Functional activity of peptide ion channels in tethered bilayer lipidmembranes: Review, Electrochemical Science Advances 2 (2022). https://doi.org/10.1002/elsa.202100180.
[151] M. Forstner, SAXS, SANS and X-ray crystallography as complementary methods in thestudy of biological form and function, Journal of Applied Crystallography 33 (2000) 519–523.https://doi.org/ 10.1107/S0021889899014363.
[152] S. Kurakin, O. Ivankov, E. Dushanov, T. Murugova, E. Ermakova, S. Efimov, T. Mukhamet-zyanov, S. Smerdova, V. Klochkov, A. Kuklin, N. Kuˇcerka, Calcium ions do not influencethe Aβ(25–35) triggered morphological changes of lipid membranes, Biophysical Chemistry 313(2024) 107292. https://doi.org/10.1016/j.bpc.2024.107292.
[153] M. Beliˇcka, Y. Gerelli, N. Kuˇcerka, G. Fragneto, The component group structure of DPPC bilay-ers obtained by specular neutron reflectometry, Soft Matter 11 (2015). https://doi.org/10.1039/c5sm00274e.
[154] L. Ebersberger, T. Schindler, S.A. Kirsch, K. Pluhackova, A. Schambony, T. Seydel, R.A. B ̈ock-mann, T. Unruh, Lipid dynamics in membranes slowed down by transmembrane proteins, Fron-tiers in Cell and Developmental Biology 8 (2020). https://doi.org/10.3389/fcell.2020.579388.
[155] T. Matsuo, A. De Francesco, J. Peters, Molecular dynamics of lysozyme amyloid polymorphsstudied by incoherent neutron scattering, Frontiers in Molecular Biosciences 8 (2022) 812096.https://doi.org/10.3389/fmolb.2021.812096
[156] L. Lautner, C. Harries, E. Boukari, C. Krywka, A. Hassan, H. Frielinghaus, T. Salditt, Dynamicprocesses in biological membrane mimics revealed by quasielastic neutron scattering, Chemistryand Physics of Lipids 206 (2017) 28–42. https://doi.org/10.1016/j.chemphyslip.2017.05.009
[157] E. Fagerberg, E. Takai, H. Martinez-Seara, R. Baron, Self-diffusive properties of the intrinsi-cally disordered protein histatin 5 and the impact of crowding thereon: A combined neutronspectroscopy and molecular dynamics simulation study, Journal of Physical Chemistry B 126 (4)(2022) 789–801. https://doi.org/10.1021/acs.jpcb.1c08976.
[158] D. Lingwood and K. Simons, Lipid rafts as a membrane-organizing principle, Science 327 (5961)(2010) 46–50. https://doi.org/10.1126/science.1174621
[159] G. van Meer, D. R. Voelker, G. W. Feigenson, Membrane lipids: Where they are and how theybehave, Nature Reviews Molecular Cell Biology 9 (2) (2008) 112–124. https://doi.org/10.1038/nrm2330.
[160] C. H. Camp, Jr., M. T. Cicerone, Chemically sensitive bioimaging with coherent Raman scat-tering, Nature Photonics 9 (5) (2015) 295–305. https://doi.org/10.1038/nphoton.2015.60.
[161] D. M. Owen, K. Gaus, Imaging lipid domains in cell membranes: The advent of super-resolutionfluorescence microscopy, Frontiers in Plant Science 4 (2013) 503. https://doi.org/10.3389/fpls.2013.00503.
[162] G. Di Paolo, T.-W. Kim, Linking lipids to Alzheimer’s disease: Cholesterol and beyond, NatureReviews Neuroscience 12 (5) (2011) 284–296. https://doi.org/10.1038/nrn3012.
[163] B. Harke, J. Keller et al., Resolution scaling in STED microscopy, Optics Express 16 (2008)4154–4162. https://doi.org/10.1364/OE.16.004154.
[164] G. H. Patterson, J. Lippincott-Schwartz, A photoactivatable GFP for selective photolabelingof proteins and cells, Science 297 (5588) (2002) 1873–1877. https://doi.org/10.1126/science.1074952.
[165] H. Cho, D. Lenevich, D. Holtzman et al., Latest developments in experimental and computa-tional approaches to characterize protein–lipid interactions, Proteomics 12 (22) (2012) 3273–3285.https://doi.org/10.1002/pmic.201200255
[166] T. Brueckel, German Neutron Scattering Conference. Programme and abstracts, July 1, 2012.https://www.osti.gov/etdeweb/biblio/22151533.
[167] F. Heinrich, J. L. M ̊ansson, J. Gustafsson et al., Information gain from isotopic contrast vari-ation in neutron reflectometry on protein–membrane complex structures, Journal of AppliedCrystallography 53 (Pt 3) (2020) 800–810. https://doi.org/10.1107/S1600576720005634.
[168] R. B. G. Ravelli, S. M. McSweeney, The “fingerprint” that X-rays can leave on structures, Structure 8 (3) (2000) 315–328. https://doi.org/10.1016/S0969-2126(00)00109-X.
[169] V. Corradi, B. I. Sejdiu et al., Emerging diversity in lipid–protein interactions, Chemical Reviews119 (9) (2019) 5775–5848. https://doi.org/10.1021/acs.chemrev.8b00451.
[170] J. G. Almeida, A.J. Preto et al., Membrane proteins structures: A review on computationalmodeling tools, ScienceDirect 1859 (10) (2024) 2021–2039. https://doi.org/10.1016/j.bbamem.2017.07.008.
[171] I. Kumari, S. Ghosh, B. Tiwari et al., Molecular dynamics simulations, challenges and opportu-nities: A biologist’s prospective, Current Protein and Peptide Science 18 (11) (2017) 1163–1179.https://doi.org/10.2174/1389203718666170622074741.
[172] H. Zhong, H. Liu, H. Liu, Molecular mechanism of tau misfolding and aggregation: Insightsfrom molecular dynamics simulation, Current Medicinal Chemistry 31 (20) (2024) 2855–2871.https://doi.org/10.2174/0929867330666230409145247.
[173] P. A. Barredo, M. P. Balanay, Recent advances in molecular dynamics simulations of tau fibrilsand oligomers, Membranes 13 (3) (2023) 277. https://www.mdpi.com/2077-0375/13/3/277

