TY - JOUR AU - Kardos, József AU - Nyiri, Márton Péter AU - Moussong, Éva AU - Wien, Frank AU - Molnár, Tamás AU - Murvai, Nikoletta AU - Tóth, Vilmos AU - Vadászi, Henrietta AU - Kun, Judit AU - Jamme, Frederic AU - Micsonai, András TI - Guide to the structural characterization of protein aggregates and amyloid fibrils by CD spectroscopy JF - PROTEIN SCIENCE J2 - PROTEIN SCI VL - 34 PY - 2025 IS - 3 PG - 16 SN - 0961-8368 DO - 10.1002/pro.70066 UR - https://m2.mtmt.hu/api/publication/35835997 ID - 35835997 N1 - Funding Agency and Grant Number: Richter Gedeon Talentum Alapitvany; Magyar Tudomanyos Akademia; Eotvos Lorand Tudomanyegyetem; Nemzeti Kutatasi Fejlesztesi es Innovacios Hivatal; National Research, Development, and Innovation Fund; Hungarian Academy of Sciences; Eotvos Lorand University Excellence Fund Funding text: Richter Gedeon Talentum Alapitvany; Magyar Tudomanyos Akademia; Eotvos Lorand Tudomanyegyetem; Nemzeti Kutatasi Fejlesztesi es Innovacios Hivatal; National Research, Development, and Innovation Fund; Hungarian Academy of Sciences; Eotvos Lorand University Excellence Fund LA - English DB - MTMT ER - TY - JOUR AU - Micsonai, András AU - Wien, Frank AU - Murvai, Nikoletta AU - Nyiri, Márton Péter AU - Balatoni, Bori AU - Lee, Young-Ho AU - Molnár, Tamás AU - Goto, Yuji AU - Jamme, Frédéric AU - Kardos, József TI - BeStSel: analysis site for protein CD spectra—2025 update JF - NUCLEIC ACIDS RESEARCH J2 - NUCLEIC ACIDS RES VL - 53 PY - 2025 IS - W1 SP - W73 EP - W83 SN - 0305-1048 DO - 10.1093/nar/gkaf378 UR - https://m2.mtmt.hu/api/publication/36141720 ID - 36141720 N1 - Funding Agency and Grant Number: National Research, Development and Innovation Fund of Hungary [K138937]; Hungarian Academy of Sciences [NAP3.0 Program] [NAP2022-I-3/2022]; Eotvos Lorand University Excellence Fund [EKA 2022/045-P278-1]; DKOEP-23 Doctoral Excellence Program of the Ministry for Culture and Innovation from NRDI Fund; SOLEIL Synchrotron, France [20230777, 20231948, 20240797, 20241998]; National Research Foundation of Korea grant - Korean government [RS-2022-NR069719, RS-2021-NR057690]; KBSI fund [A412580, A423310, A439200, C512120, C523200, C539200]; National Research, Development and Innovation Fund of Hungary [K138937] Funding text: This work was supported by the National Research, Development and Innovation Fund of Hungary [grant #K138937], by the Hungarian Academy of Sciences [NAP3.0 Program NAP2022-I-3/2022] and by the Eotvos Lorand University Excellence Fund [EKA 2022/045-P278-1]. M.P.N. was supported by the DKOEP-23 Doctoral Excellence Program of the Ministry for Culture and Innovation from the source of the NRDI Fund. SRCD measurements were supported by SOLEIL Synchrotron, France (proposals 20230777, 20231948, 20240797, and 20241998). Y.-H.L. was supported by the National Research Foundation of Korea grant funded by the Korean government [RS-2022-NR069719, RS-2021-NR057690] and the KBSI fund [A412580, A423310, A439200, C512120, C523200, and C539200]. Funding to pay the Open Access publication charges for this article was provided by the National Research, Development and Innovation Fund of Hungary [grant # K138937]. AB - Circular dichroism (CD) spectroscopy is a widely used technique to characterize the secondary structure composition of proteins. We have developed the Beta Structure Selection (BeStSel) method (PNAS, 112, E3095), which solves the main problem of protein CD spectroscopy—namely, the spectral variability of β-structures. The BeStSel web server utilizes this method to provide tools to the community for CD spectrum analysis. BeStSel uniquely provides information on eight secondary structure components, including parallel β-structure and antiparallel β-sheets with three different twist groups. It outperforms all available methods in accuracy and information content, and is also able to predict protein folds down to the topology/homology level of the CATH classification. The algorithm has been further developed, and the accuracy of the estimation of the secondary structure elements is improved by 0.7% as an average on the reference dataset. A new module of the web server calculates protein stability from the thermal denaturation profile followed by CD. Secondary structure calculations of uploaded PDB and mmcif files support the experimental verification of MD simulations and AlphaFold models by CD spectroscopy. Well-proven modules for disorder–order classification and extinction coefficient calculation continue to work. The BeStSel server is freely accessible at https://bestsel.elte.hu. LA - English DB - MTMT ER - TY - JOUR AU - Kalydi, Eszter AU - Murvai, Nikoletta AU - Saridakis, Emmanuel AU - Mavridis, Irene M. AU - Malanga, Milo AU - Kardos, József AU - Yannakopoulou, Konstantina AU - Béni, Szabolcs TI - Molecular encapsulation of the aminosteroid phytotoxins solanidine and α-solanine by sugammadex: new insights into atomic-level interactions JF - CARBOHYDRATE POLYMERS J2 - CARBOHYD POLYM VL - 366 PY - 2025 PG - 12 SN - 0144-8617 DO - 10.1016/j.carbpol.2025.123824 UR - https://m2.mtmt.hu/api/publication/36172461 ID - 36172461 N1 - Department of Pharmacognosy, Faculty of Pharmacy, Semmelweis University, Üllői út. 26, Budapest, 1085, Hungary ELTE-Functional Nucleic Acid Motifs Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary Institute of Nanoscience and Nanotechnology, National Center for Scientific Research “Demokritos”, Patr. Grigoriou & 27 Neapoleos Str., Aghia Paraskevi Attikis, 15341, Greece CarboHyde Zrt., Berlini u. 47-49, Budapest, 1045, Hungary ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/c, Budapest, 1117, Hungary Integrative Health and Environmental Analysis Research Laboratory, Department of Analytical Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/a, Budapest, 1117, Hungary Export Date: 18 July 2025; Cited By: 0; Correspondence Address: S. Béni; Department of Pharmacognosy, Faculty of Pharmacy, Semmelweis University, Budapest, Üllői út. 26, 1085, Hungary; email: szabolcs.beni@ttk.elte.hu; CODEN: CAPOD LA - English DB - MTMT ER - TY - JOUR AU - Kardos, József AU - Wien, Frank AU - Moussong, Éva AU - Murvai, Nikoletta AU - Nyiri, Márton Péter AU - Molnár, Tamás AU - Jamme, Frederic AU - Micsonai, András TI - BPS2025 - From prediction to proof: High-throughput validation of AlphaFold-generated structures by circular dichroism spectroscopy JF - BIOPHYSICAL JOURNAL J2 - BIOPHYS J VL - 124 PY - 2025 IS - 3 SP - 214a SN - 0006-3495 DO - 10.1016/j.bpj.2024.11.1184 UR - https://m2.mtmt.hu/api/publication/36335112 ID - 36335112 LA - English DB - MTMT ER - TY - JOUR AU - Moussong, Éva AU - Nyiri, Márton Péter AU - Murvai, Nikoletta AU - Kun, Judit AU - Kovács, Attila AU - Molnár, Tamás AU - Micsonai, András AU - Kardos, József TI - Effect of nanoparticles on the aggregation and amyloid formation of amyloid-beta peptide JF - BIOPHYSICAL JOURNAL J2 - BIOPHYS J VL - 122 PY - 2023 IS - 3 SP - 332a SN - 0006-3495 DO - 10.1016/j.bpj.2022.11.1854 UR - https://m2.mtmt.hu/api/publication/33641256 ID - 33641256 LA - English DB - MTMT ER - TY - JOUR AU - Micsonai, András AU - Moussong, Éva AU - Wien, Frank AU - Boros, Eszter AU - Vadászi, Henrietta AU - Murvai, Nikoletta AU - Lee, Young-Ho AU - Molnár, Tamás AU - Réfrégiers, Matthieu AU - Goto, Yuji AU - Tantos, Ágnes AU - Kardos, József TI - Bestsel: Updated webserver for secondary structure and fold prediction for protein CD spectroscopy JF - BIOPHYSICAL JOURNAL J2 - BIOPHYS J VL - 122 PY - 2023 IS - 3 SP - 179a SN - 0006-3495 DO - 10.1016/j.bpj.2022.11.1110 UR - https://m2.mtmt.hu/api/publication/33641398 ID - 33641398 LA - English DB - MTMT ER - TY - JOUR AU - Murvai, Nikoletta AU - Lin, Yuxi AU - Molnár, Tamás AU - Kovács, Attila AU - Micsonai, András AU - Kyu Bang, Jeong AU - Lee, Young-Ho AU - Kardos, József TI - Inhibition studies on aggregation and cytotoxicity of Alzheimer's amyloid-β peptide JF - BIOPHYSICAL JOURNAL J2 - BIOPHYS J VL - 122 PY - 2023 IS - 3S1 SP - 350a EP - 351a SN - 0006-3495 DO - 10.1016/j.bpj.2022.11.1945 UR - https://m2.mtmt.hu/api/publication/33641452 ID - 33641452 LA - English DB - MTMT ER - TY - JOUR AU - Micsonai, András AU - Moussong, Éva AU - Murvai, Nikoletta AU - Tantos, Ágnes AU - Tőke, Orsolya AU - Réfrégiers, Matthieu AU - Wien, Frank AU - Kardos, József TI - Disordered-ordered protein binary classification by circular dichroism spectroscopy JF - BIOPHYSICAL JOURNAL J2 - BIOPHYS J VL - 122 PY - 2023 IS - 3 SP - 344a SN - 0006-3495 DO - 10.1016/j.bpj.2022.11.1915 UR - https://m2.mtmt.hu/api/publication/33660819 ID - 33660819 LA - English DB - MTMT ER - TY - JOUR AU - Murvai, Nikoletta AU - Gellén, Gabriella AU - Micsonai, András AU - Schlosser, Gitta AU - Kardos, József TI - Cross-Linked α-Synuclein as Inhibitor of Amyloid Formation JF - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES J2 - INT J MOL SCI VL - 24 PY - 2023 IS - 17 SN - 1661-6596 DO - 10.3390/ijms241713403 UR - https://m2.mtmt.hu/api/publication/34141758 ID - 34141758 N1 - Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest, H-1117, Hungary ELTE—Functional Nucleic Acid Motifs Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest, H-1117, Hungary MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Department of Analytical Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, H-1117, Hungary Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Egyetem tér 1, Debrecen, H-4032, Hungary Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen, H-4032, Hungary ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest, H-1117, Hungary Export Date: 10 October 2023 Correspondence Address: Kardos, J.; Department of Biochemistry, Hungary; email: kardos@elte.hu AB - The aggregation and amyloid formation of α-synuclein is associated with Parkinson’s disease and other synucleinopathies. In its native, monomeric form α-synuclein is an intrinsically disordered protein represented by highly dynamic conformational ensembles. Inhibition of α-synuclein aggregation using small molecules, peptides, or proteins has been at the center of interest in recent years. Our aim was to explore the effects of cross-linking on the structure and aggregation/amyloid formation properties of α-synuclein. Comparative analysis of available high-resolution amyloid structures and representative structural models and MD trajectory of monomeric α-synuclein revealed that potential cross-links in the monomeric protein are mostly incompatible with the amyloid forms and thus might inhibit fibrillation. Monomeric α-synuclein has been intramolecularly chemically cross-linked under various conditions using different cross-linkers. We determined the location of cross-links and their frequency using mass spectrometry and found that most of them cannot be realized in the amyloid structures. The inhibitory potential of cross-linked proteins has been experimentally investigated using various methods, including thioflavin-T fluorescence and transmission electron microscopy. We found that conformational constraints applied by cross-linking fully blocked α-synuclein amyloid formation. Moreover, DTSSP-cross-linked molecules exhibited an inhibitory effect on the aggregation of unmodified α-synuclein as well. LA - English DB - MTMT ER - TY - JOUR AU - Micsonai, András AU - Moussong, Éva AU - Murvai, Nikoletta AU - Tantos, Ágnes AU - Tőke, Orsolya AU - Réfrégiers, Matthieu AU - Wien, Frank AU - Kardos, József TI - Disordered–Ordered Protein Binary Classification by Circular Dichroism Spectroscopy JF - FRONTIERS IN MOLECULAR BIOSCIENCES J2 - FRONT MOL BIOSCI VL - 9 PY - 2022 PG - 10 SN - 2296-889X DO - 10.3389/fmolb.2022.863141 UR - https://m2.mtmt.hu/api/publication/32819946 ID - 32819946 AB - Intrinsically disordered proteins lack a stable tertiary structure and form dynamic conformational ensembles due to their characteristic physicochemical properties and amino acid composition. They are abundant in nature and responsible for a large variety of cellular functions. While numerous bioinformatics tools have been developed for in silico disorder prediction in the last decades, there is a need for experimental methods to verify the disordered state. CD spectroscopy is widely used for protein secondary structure analysis. It is usable in a wide concentration range under various buffer conditions. Even without providing high-resolution information, it is especially useful when NMR, X-ray, or other techniques are problematic or one simply needs a fast technique to verify the structure of proteins. Here, we propose an automatized binary disorder–order classification method by analyzing far-UV CD spectroscopy data. The method needs CD data at only three wavelength points, making high-throughput data collection possible. The mathematical analysis applies the k-nearest neighbor algorithm with cosine distance function, which is independent of the spectral amplitude and thus free of concentration determination errors. Moreover, the method can be used even for strong absorbing samples, such as the case of crowded environmental conditions, if the spectrum can be recorded down to the wavelength of 212 nm. We believe the classification method will be useful in identifying disorder and will also facilitate the growth of experimental data in IDP databases. The method is implemented on a webserver and freely available for academic users. LA - English DB - MTMT ER -