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For: Ahmed AB, Znassi N, Château MT, Kajava AV. A structure-based approach to predict predisposition to amyloidosis. Alzheimers Dement 2014;11:681-90. [PMID: 25150734 DOI: 10.1016/j.jalz.2014.06.007] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 04/22/2014] [Accepted: 06/06/2014] [Indexed: 10/24/2022]
Number Cited by Other Article(s)
1
Basha S, Mukunda DC, Pai AR, Mahato KK. Assessing amyloid fibrils and amorphous aggregates: A review. Int J Biol Macromol 2025;311:143725. [PMID: 40324497 DOI: 10.1016/j.ijbiomac.2025.143725] [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: 01/23/2025] [Revised: 04/23/2025] [Accepted: 04/29/2025] [Indexed: 05/07/2025]
2
Polańska O, Szulc N, Dyrka W, Wojciechowska AW, Kotulska M, Żak AM, Gąsior-Głogowska ME, Szefczyk M. Environmental sensitivity of amyloidogenic motifs in fungal NOD-like receptor-mediated immunity: Molecular and structural insights into amyloid assembly. Int J Biol Macromol 2025;304:140773. [PMID: 39924043 DOI: 10.1016/j.ijbiomac.2025.140773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 01/13/2025] [Accepted: 02/05/2025] [Indexed: 02/11/2025]
3
Pyankov IA, Gonay V, Stepanov YA, Shestun P, Kostareva AA, Uspenskaya MV, Petukhov MG, Kajava AV. A computational approach to predict the effects of missense mutations on protein amyloidogenicity: A case study in hereditary transthyretin cardiomyopathy. J Struct Biol 2025;217:108176. [PMID: 39933599 DOI: 10.1016/j.jsb.2025.108176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Revised: 02/06/2025] [Accepted: 02/07/2025] [Indexed: 02/13/2025]
4
Kachkin D, Zelinsky AA, Romanova NV, Kulichikhin KY, Zykin PA, Khorolskaya JI, Deckner ZJ, Kajava AV, Rubel AA, Chernoff YO. Prion-like Properties of Short Isoforms of Human Chromatin Modifier PHC3. Int J Mol Sci 2025;26:1512. [PMID: 40003978 PMCID: PMC11855497 DOI: 10.3390/ijms26041512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2024] [Revised: 02/06/2025] [Accepted: 02/07/2025] [Indexed: 02/27/2025]  Open
5
Gonay V, Dunne MP, Caceres‐Delpiano J, Kajava AV. Developing machine-learning-based amyloidogenicity predictors with Cross-Beta DB. Alzheimers Dement 2025;21:e14510. [PMID: 39776173 PMCID: PMC11848165 DOI: 10.1002/alz.14510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2024] [Accepted: 12/06/2024] [Indexed: 01/11/2025]
6
Hassan M, Shahzadi S, Li MS, Kloczkowski A. Prediction and Evaluation of Protein Aggregation with Computational Methods. Methods Mol Biol 2025;2867:299-314. [PMID: 39576588 DOI: 10.1007/978-1-0716-4196-5_17] [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: 11/24/2024]
7
Zhou Y, Liu W, Luo C, Huang Z, Samarappuli Mudiyanselage Savini G, Zhao L, Wang R, Huang J. Ab-Amy 2.0: Predicting light chain amyloidogenic risk of therapeutic antibodies based on antibody language model. Methods 2025;233:11-18. [PMID: 39550021 DOI: 10.1016/j.ymeth.2024.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 10/28/2024] [Accepted: 11/06/2024] [Indexed: 11/18/2024]  Open
8
Iglesias V, Chilimoniuk J, Pintado-Grima C, Bárcenas O, Ventura S, Burdukiewicz M. Aggregating amyloid resources: A comprehensive review of databases on amyloid-like aggregation. Comput Struct Biotechnol J 2024;23:4011-4018. [PMID: 39582896 PMCID: PMC11585477 DOI: 10.1016/j.csbj.2024.10.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 10/24/2024] [Accepted: 10/27/2024] [Indexed: 11/26/2024]  Open
9
Sulyok-Eiler M, Harmat V, Perczel A. Unravelling the Complexity of Amyloid Peptide Core Interfaces. J Chem Inf Model 2024;64:8628-8640. [PMID: 39473194 PMCID: PMC11600497 DOI: 10.1021/acs.jcim.4c01479] [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: 08/16/2024] [Revised: 10/07/2024] [Accepted: 10/14/2024] [Indexed: 11/26/2024]
10
Valina AA, Siniukova VA, Belashova TA, Kanapin AA, Samsonova AA, Masharsky AE, Lykholay AN, Galkina SA, Zadorsky SP, Galkin AP. Amyloid Fibrils of the s36 Protein Modulate the Morphogenesis of Drosophila melanogaster Eggshell. Int J Mol Sci 2024;25:12499. [PMID: 39684212 DOI: 10.3390/ijms252312499] [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: 10/03/2024] [Revised: 11/14/2024] [Accepted: 11/17/2024] [Indexed: 12/18/2024]  Open
11
Kell DB, Pretorius E. Proteomic Evidence for Amyloidogenic Cross-Seeding in Fibrinaloid Microclots. Int J Mol Sci 2024;25:10809. [PMID: 39409138 PMCID: PMC11476703 DOI: 10.3390/ijms251910809] [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: 09/17/2024] [Revised: 10/01/2024] [Accepted: 10/03/2024] [Indexed: 10/20/2024]  Open
12
Bondarev SA, Uspenskaya MV, Leclercq J, Falgarone T, Zhouravleva GA, Kajava AV. AmyloComp: A Bioinformatic Tool for Prediction of Amyloid Co-aggregation. J Mol Biol 2024;436:168437. [PMID: 38185324 DOI: 10.1016/j.jmb.2024.168437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/13/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
13
Bárcenas O, Kuriata A, Zalewski M, Iglesias V, Pintado-Grima C, Firlik G, Burdukiewicz M, Kmiecik S, Ventura S. Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation. Nucleic Acids Res 2024;52:W170-W175. [PMID: 38738618 PMCID: PMC11223845 DOI: 10.1093/nar/gkae382] [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: 03/11/2024] [Revised: 04/11/2024] [Accepted: 04/29/2024] [Indexed: 05/14/2024]  Open
14
Ghosh D, Biswas A, Radhakrishna M. Advanced computational approaches to understand protein aggregation. BIOPHYSICS REVIEWS 2024;5:021302. [PMID: 38681860 PMCID: PMC11045254 DOI: 10.1063/5.0180691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/18/2024] [Indexed: 05/01/2024]
15
Szulc N, Gąsior-Głogowska M, Żyłka P, Szefczyk M, Wojciechowski JW, Żak AM, Dyrka W, Kaczorowska A, Burdukiewicz M, Tarek M, Kotulska M. Structural effects of charge destabilization and amino acid substitutions in amyloid fragments of CsgA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024;313:124094. [PMID: 38503257 DOI: 10.1016/j.saa.2024.124094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/21/2024]
16
Khalili K, Farzam F, Dabirmanesh B, Khajeh K. Prediction of protein aggregation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024;206:229-263. [PMID: 38811082 DOI: 10.1016/bs.pmbts.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
17
Liao S, Zhang Y, Han X, Wang T, Wang X, Yan Q, Li Q, Qi Y, Zhang Z. A sequence-based model for identifying proteins undergoing liquid-liquid phase separation/forming fibril aggregates via machine learning. Protein Sci 2024;33:e4927. [PMID: 38380794 PMCID: PMC10880426 DOI: 10.1002/pro.4927] [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: 08/15/2023] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/22/2024]
18
Wojciechowski JW, Szczurek W, Szulc N, Szefczyk M, Kotulska M. PACT - Prediction of amyloid cross-interaction by threading. Sci Rep 2023;13:22268. [PMID: 38097650 PMCID: PMC10721876 DOI: 10.1038/s41598-023-48886-9] [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: 02/13/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023]  Open
19
Galkin AP, Sysoev EI, Valina AA. Amyloids and prions in the light of evolution. Curr Genet 2023;69:189-202. [PMID: 37165144 DOI: 10.1007/s00294-023-01270-6] [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: 04/14/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/12/2023]
20
Qi X, Wang Y, Yu H, Liu R, Leppert A, Zheng Z, Zhong X, Jin Z, Wang H, Li X, Wang X, Landreh M, A Morozova-Roche L, Johansson J, Xiong S, Iashchishyn I, Chen G. Spider Silk Protein Forms Amyloid-Like Nanofibrils through a Non-Nucleation-Dependent Polymerization Mechanism. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023;19:e2304031. [PMID: 37455347 DOI: 10.1002/smll.202304031] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/29/2023] [Indexed: 07/18/2023]
21
Falgarone T, Villain E, Richard F, Osmanli Z, Kajava AV. Census of exposed aggregation-prone regions in proteomes. Brief Bioinform 2023;24:bbad183. [PMID: 37200152 DOI: 10.1093/bib/bbad183] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/30/2023] [Accepted: 04/21/2023] [Indexed: 05/20/2023]  Open
22
Danilov LG, Sukhanova XV, Rogoza TM, Antonova EY, Trubitsina NP, Zhouravleva GA, Bondarev SA. Identification of New FG-Repeat Nucleoporins with Amyloid Properties. Int J Mol Sci 2023;24:ijms24108571. [PMID: 37239918 DOI: 10.3390/ijms24108571] [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: 03/31/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023]  Open
23
Frenkel A, Zecharia E, Gómez-Pérez D, Sendersky E, Yegorov Y, Jacob A, Benichou JIC, Stierhof YD, Parnasa R, Golden SS, Kemen E, Schwarz R. Cell specialization in cyanobacterial biofilm development revealed by expression of a cell-surface and extracellular matrix protein. NPJ Biofilms Microbiomes 2023;9:10. [PMID: 36864092 PMCID: PMC9981879 DOI: 10.1038/s41522-023-00376-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 02/06/2023] [Indexed: 03/04/2023]  Open
24
Beckwith SL, Nomberg EJ, Newman AC, Taylor JV, Guerrero RC, Garfinkel DJ. An interchangeable prion-like domain is required for Ty1 retrotransposition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530227. [PMID: 36909481 PMCID: PMC10002725 DOI: 10.1101/2023.02.27.530227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
25
Molecular Determinants of Fibrillation in a Viral Amyloidogenic Domain from Combined Biochemical and Biophysical Studies. Int J Mol Sci 2022;24:ijms24010399. [PMID: 36613842 PMCID: PMC9820236 DOI: 10.3390/ijms24010399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022]  Open
26
Wojciechowski JW, Tekoglu E, Gąsior-Głogowska M, Coustou V, Szulc N, Szefczyk M, Kopaczyńska M, Saupe SJ, Dyrka W. Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins. PLoS Comput Biol 2022;18:e1010787. [PMID: 36542665 PMCID: PMC9815663 DOI: 10.1371/journal.pcbi.1010787] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 01/05/2023] [Accepted: 12/02/2022] [Indexed: 12/24/2022]  Open
27
Osmanli Z, Falgarone T, Samadova T, Aldrian G, Leclercq J, Shahmuradov I, Kajava AV. The Difference in Structural States between Canonical Proteins and Their Isoforms Established by Proteome-Wide Bioinformatics Analysis. Biomolecules 2022;12:1610. [PMID: 36358962 PMCID: PMC9687161 DOI: 10.3390/biom12111610] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/14/2022] [Accepted: 10/27/2022] [Indexed: 09/02/2023]  Open
28
Kachkin DV, Volkov KV, Sopova JV, Bobylev AG, Fedotov SA, Inge-Vechtomov SG, Galzitskaya OV, Chernoff YO, Rubel AA, Aksenova AY. Human RAD51 Protein Forms Amyloid-like Aggregates In Vitro. Int J Mol Sci 2022;23:ijms231911657. [PMID: 36232958 PMCID: PMC9570251 DOI: 10.3390/ijms231911657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 12/30/2022]  Open
29
Liu Y, Yeung WSB, Chiu PCN, Cao D. Computational approaches for predicting variant impact: An overview from resources, principles to applications. Front Genet 2022;13:981005. [PMID: 36246661 PMCID: PMC9559863 DOI: 10.3389/fgene.2022.981005] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022]  Open
30
NOS1AP Interacts with α-Synuclein and Aggregates in Yeast and Mammalian Cells. Int J Mol Sci 2022;23:ijms23169102. [PMID: 36012368 PMCID: PMC9409085 DOI: 10.3390/ijms23169102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/11/2022] [Accepted: 08/11/2022] [Indexed: 11/24/2022]  Open
31
Amyloid Properties of the FXR1 Protein Are Conserved in Evolution of Vertebrates. Int J Mol Sci 2022;23:ijms23147997. [PMID: 35887344 PMCID: PMC9319111 DOI: 10.3390/ijms23147997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/16/2022] [Accepted: 07/18/2022] [Indexed: 12/10/2022]  Open
32
Computational methods to predict protein aggregation. Curr Opin Struct Biol 2022;73:102343. [PMID: 35240456 DOI: 10.1016/j.sbi.2022.102343] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/20/2021] [Accepted: 01/17/2022] [Indexed: 01/13/2023]
33
Bioinformatics Methods in Predicting Amyloid Propensity of Peptides and Proteins. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022;2340:1-15. [PMID: 35167067 DOI: 10.1007/978-1-0716-1546-1_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
34
Falgarone T, Villain É, Guettaf A, Leclercq J, Kajava AV. TAPASS: Tool for Annotation of Protein Amyloidogenicity in the context of other Structural States. J Struct Biol 2022;214:107840. [PMID: 35149212 DOI: 10.1016/j.jsb.2022.107840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/03/2022] [Accepted: 02/04/2022] [Indexed: 12/28/2022]
35
Danilov LG, Moskalenko SE, Matveenko AG, Sukhanova XV, Belousov MV, Zhouravleva GA, Bondarev SA. The Human NUP58 Nucleoporin Can Form Amyloids In Vitro and In Vivo. Biomedicines 2021;9:biomedicines9101451. [PMID: 34680573 PMCID: PMC8533070 DOI: 10.3390/biomedicines9101451] [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: 09/01/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 12/20/2022]  Open
36
Δ133p53β isoform pro-invasive activity is regulated through an aggregation-dependent mechanism in cancer cells. Nat Commun 2021;12:5463. [PMID: 34526502 PMCID: PMC8443592 DOI: 10.1038/s41467-021-25550-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 08/04/2021] [Indexed: 11/09/2022]  Open
37
Salladini E, Gondelaud F, Nilsson JF, Pesce G, Bignon C, Murrali MG, Fabre R, Pierattelli R, Kajava AV, Horvat B, Gerlier D, Mathieu C, Longhi S. Identification of a Region in the Common Amino-terminal Domain of Hendra Virus P, V, and W Proteins Responsible for Phase Transition and Amyloid Formation. Biomolecules 2021;11:1324. [PMID: 34572537 PMCID: PMC8471210 DOI: 10.3390/biom11091324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 12/14/2022]  Open
38
Surin AK, Grishin SY, Galzitskaya OV. Determination of amyloid core regions of insulin analogues fibrils. Prion 2021;14:149-162. [PMID: 32543316 PMCID: PMC7518739 DOI: 10.1080/19336896.2020.1776062] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]  Open
39
Mier P, Paladin L, Tamana S, Petrosian S, Hajdu-Soltész B, Urbanek A, Gruca A, Plewczynski D, Grynberg M, Bernadó P, Gáspári Z, Ouzounis CA, Promponas VJ, Kajava AV, Hancock JM, Tosatto SCE, Dosztanyi Z, Andrade-Navarro MA. Disentangling the complexity of low complexity proteins. Brief Bioinform 2021;21:458-472. [PMID: 30698641 PMCID: PMC7299295 DOI: 10.1093/bib/bbz007] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/19/2018] [Accepted: 01/07/2019] [Indexed: 12/31/2022]  Open
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Szulc N, Gąsior-Głogowska M, Wojciechowski JW, Szefczyk M, Żak AM, Burdukiewicz M, Kotulska M. Variability of Amyloid Propensity in Imperfect Repeats of CsgA Protein of Salmonella enterica and Escherichia coli. Int J Mol Sci 2021;22:ijms22105127. [PMID: 34066237 PMCID: PMC8151669 DOI: 10.3390/ijms22105127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/22/2021] [Accepted: 05/07/2021] [Indexed: 11/18/2022]  Open
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Dyrka W, Gąsior-Głogowska M, Szefczyk M, Szulc N. Searching for universal model of amyloid signaling motifs using probabilistic context-free grammars. BMC Bioinformatics 2021;22:222. [PMID: 33926372 PMCID: PMC8086366 DOI: 10.1186/s12859-021-04139-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 04/19/2021] [Indexed: 11/16/2022]  Open
42
Barbitoff YA, Matveenko AG, Matiiv AB, Maksiutenko EM, Moskalenko SE, Drozdova PB, Polev DE, Beliavskaia AY, Danilov LG, Predeus AV, Zhouravleva GA. Chromosome-level genome assembly and structural variant analysis of two laboratory yeast strains from the Peterhof Genetic Collection lineage. G3-GENES GENOMES GENETICS 2021;11:6129118. [PMID: 33677552 PMCID: PMC8759820 DOI: 10.1093/g3journal/jkab029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/22/2021] [Indexed: 01/23/2023]
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Prabakaran R, Rawat P, Thangakani AM, Kumar S, Gromiha MM. Protein aggregation: in silico algorithms and applications. Biophys Rev 2021;13:71-89. [PMID: 33747245 PMCID: PMC7930180 DOI: 10.1007/s12551-021-00778-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/01/2021] [Indexed: 01/08/2023]  Open
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Andreychuk YV, Zadorsky SP, Zhuk AS, Stepchenkova EI, Inge-Vechtomov SG. Relationship between Type I and Type II Template Processes: Amyloids and Genome Stability. Mol Biol 2020. [DOI: 10.1134/s0026893320050027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Charoenkwan P, Kanthawong S, Nantasenamat C, Hasan MM, Shoombuatong W. iAMY-SCM: Improved prediction and analysis of amyloid proteins using a scoring card method with propensity scores of dipeptides. Genomics 2020;113:689-698. [PMID: 33017626 DOI: 10.1016/j.ygeno.2020.09.065] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/21/2020] [Accepted: 09/30/2020] [Indexed: 01/09/2023]
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Saupe SJ. Amyloid Signaling in Filamentous Fungi and Bacteria. Annu Rev Microbiol 2020;74:673-691. [DOI: 10.1146/annurev-micro-011320-013555] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Rozniakowski K, Fraczyk A, Galecki K, Wietrzyk J, Filip-Psurska B, Fraczyk J, Kaminski ZJ, Kolesinska B. New Human Islet Amyloid Polypeptide Fragments Susceptible to Aggregation. Chem Biodivers 2020;17:e2000501. [PMID: 32876375 DOI: 10.1002/cbdv.202000501] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 07/28/2020] [Indexed: 12/21/2022]
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Sulatskaya AI, Bondarev SA, Sulatsky MI, Trubitsina NP, Belousov MV, Zhouravleva GA, Llanos MA, Kajava AV, Kuznetsova IM, Turoverov KK. Point mutations affecting yeast prion propagation change the structure of its amyloid fibrils. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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The hot sites of α-synuclein in amyloid fibril formation. Sci Rep 2020;10:12175. [PMID: 32699326 PMCID: PMC7376172 DOI: 10.1038/s41598-020-68887-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 07/01/2020] [Indexed: 01/06/2023]  Open
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Aggregation and Prion-Inducing Properties of the G-Protein Gamma Subunit Ste18 are Regulated by Membrane Association. Int J Mol Sci 2020;21:ijms21145038. [PMID: 32708832 PMCID: PMC7403958 DOI: 10.3390/ijms21145038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/03/2020] [Accepted: 07/09/2020] [Indexed: 12/17/2022]  Open
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