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For: Paiz EA, Allen JH, Correia JJ, Fitzkee NC, Hough LE, Whitten ST. Beta turn propensity and a model polymer scaling exponent identify intrinsically disordered phase-separating proteins. J Biol Chem 2021;297:101343. [PMID: 34710373 PMCID: PMC8592878 DOI: 10.1016/j.jbc.2021.101343] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 12/14/2022]  Open
Number Cited by Other Article(s)
1
Feng M, Liu L, Xian ZN, Wei X, Li K, Yan W, Lu Q, Shi Y, He G. PSTP: accurate residue-level phase separation prediction using protein conformational and language model embeddings. Brief Bioinform 2025;26:bbaf171. [PMID: 40315433 PMCID: PMC12047702 DOI: 10.1093/bib/bbaf171] [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: 01/18/2025] [Revised: 03/07/2025] [Accepted: 03/19/2025] [Indexed: 05/04/2025]  Open
2
Saar D, Lennartsson CLE, Weidner P, Burgermeister E, Kragelund BB. The Myotubularin Related Proteins and the Untapped Interaction Potential of Their Disordered C-Terminal Regions. Proteins 2025;93:831-854. [PMID: 39614773 PMCID: PMC11878207 DOI: 10.1002/prot.26774] [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: 09/23/2024] [Revised: 11/11/2024] [Accepted: 11/13/2024] [Indexed: 03/05/2025]
3
Newell NE. ExploreTurns: A web tool for the exploration, analysis, and classification of beta turns and structured loops in proteins; application to beta-bulge and Schellman loops, Asx helix caps, beta hairpins, and other hydrogen-bonded motifs. Protein Sci 2025;34:e70046. [PMID: 39968865 PMCID: PMC11836897 DOI: 10.1002/pro.70046] [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: 05/08/2024] [Revised: 12/14/2024] [Accepted: 01/14/2025] [Indexed: 02/20/2025]
4
Chatterjee H, Sengupta N. Molecular crowding and amyloidogenic self-assembly: Emergent perspectives from modern computations. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2025;211:209-247. [PMID: 39947750 DOI: 10.1016/bs.pmbts.2024.10.001] [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: 05/09/2025]
5
Morey‐Yagi SR, Hashida Y, Okamoto M, Odahara M, Suzuki T, Thagun C, Foong CP, Numata K. Expression of spider silk protein in tobacco improves drought tolerance with minimal effects on its mechanotype. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2025;121:e17213. [PMID: 39866095 PMCID: PMC11771620 DOI: 10.1111/tpj.17213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/05/2024] [Accepted: 11/29/2024] [Indexed: 01/28/2025]
6
Motorin NA, Makarov GI, Rekstina VV, Evtushenko EG, Sabirzyanov FA, Ziganshin RH, Shaytan AK, Kalebina TS. Yeast Glucan Remodeling Protein Bgl2p: Amyloid Properties and the Mode of Attachment in Cell Wall. Int J Mol Sci 2024;25:13703. [PMID: 39769468 PMCID: PMC11677059 DOI: 10.3390/ijms252413703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2024] [Revised: 12/15/2024] [Accepted: 12/19/2024] [Indexed: 01/11/2025]  Open
7
Kaundal S, Anish R, Ayyar BV, Shanker S, Kaur G, Crawford SE, Pollet J, Stossi F, Estes MK, Prasad BVV. RNA-dependent RNA polymerase of predominant human norovirus forms liquid-liquid phase condensates as viral replication factories. SCIENCE ADVANCES 2024;10:eadp9333. [PMID: 39705355 DOI: 10.1126/sciadv.adp9333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 11/14/2024] [Indexed: 12/22/2024]
8
Kaundal S, Anish R, Ayyar BV, Shanker S, Kaur G, Crawford SE, Pollet J, Stossi F, Estes MK, Prasad BV. RNA-dependent RNA polymerase of predominant human norovirus forms liquid-liquid phase condensates as viral replication factories. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.24.554692. [PMID: 39345611 PMCID: PMC11429606 DOI: 10.1101/2023.08.24.554692] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
9
Whited AM, Jungreis I, Allen J, Cleveland CL, Mudge JM, Kellis M, Rinn JL, Hough LE. Biophysical characterization of high-confidence, small human proteins. BIOPHYSICAL REPORTS 2024;4:100167. [PMID: 38909903 PMCID: PMC11305224 DOI: 10.1016/j.bpr.2024.100167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/09/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024]
10
Heredia-Torrejón M, Montañez R, González-Meneses A, Carcavilla A, Medina MA, Lechuga-Sancho AM. VUS next in rare diseases? Deciphering genetic determinants of biomolecular condensation. Orphanet J Rare Dis 2024;19:327. [PMID: 39243101 PMCID: PMC11380411 DOI: 10.1186/s13023-024-03307-6] [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: 08/21/2023] [Accepted: 08/06/2024] [Indexed: 09/09/2024]  Open
11
Zaman S, Lengerer B, Van Lindt J, Saenen I, Russo G, Bossaer L, Carpentier S, Tompa P, Flammang P, Roelants K. Recurrent evolution of adhesive defence systems in amphibians by parallel shifts in gene expression. Nat Commun 2024;15:5612. [PMID: 38987280 PMCID: PMC11237159 DOI: 10.1038/s41467-024-49917-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 06/17/2024] [Indexed: 07/12/2024]  Open
12
Whited AM, Jungreis I, Allen J, Cleveland CL, Mudge JM, Kellis M, Rinn JL, Hough LE. Biophysical characterization of high-confidence, small human proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589296. [PMID: 38659920 PMCID: PMC11042228 DOI: 10.1101/2024.04.12.589296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
13
Amarasekara DL, Kariyawasam CS, Hejny MA, Torgall VB, Werfel TA, Fitzkee NC. Protein-Functionalized Gold Nanospheres with Tunable Photothermal Efficiency for the Near-Infrared Photothermal Ablation of Biofilms. ACS APPLIED MATERIALS & INTERFACES 2024;16:4321-4332. [PMID: 38236953 PMCID: PMC10843580 DOI: 10.1021/acsami.3c13288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
14
Wang J, Ma X, Hu Y, Feng G, Guo C, Zhang X, Ma H. Regulation of micro- and small-exon retention and other splicing processes by GRP20 for flower development. NATURE PLANTS 2024;10:66-85. [PMID: 38195906 PMCID: PMC10808074 DOI: 10.1038/s41477-023-01605-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/29/2023] [Indexed: 01/11/2024]
15
do Amaral MJ, Mohapatra S, Passos AR, Lopes da Silva TS, Carvalho RS, da Silva Almeida M, Pinheiro AS, Wegmann S, Cordeiro Y. Copper drives prion protein phase separation and modulates aggregation. SCIENCE ADVANCES 2023;9:eadi7347. [PMID: 37922348 PMCID: PMC10624353 DOI: 10.1126/sciadv.adi7347] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/03/2023] [Indexed: 11/05/2023]
16
Wilson C, Lewis KA, Fitzkee NC, Hough LE, Whitten ST. ParSe 2.0: A web tool to identify drivers of protein phase separation at the proteome level. Protein Sci 2023;32:e4756. [PMID: 37574757 PMCID: PMC10464302 DOI: 10.1002/pro.4756] [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: 06/23/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
17
Amarasekara DL, Kariyawasam CS, Hejny MA, Torgall VB, Werfel TA, Fitzkee NC. Near-Infrared Photothermal Ablation of Biofilms using ProteinFunctionalized Gold Nanospheres with a Tunable Temperature Response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.12.553096. [PMID: 37645901 PMCID: PMC10462018 DOI: 10.1101/2023.08.12.553096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
18
López-Palacios TP, Andersen JL. Kinase regulation by liquid-liquid phase separation. Trends Cell Biol 2023;33:649-666. [PMID: 36528418 PMCID: PMC10267292 DOI: 10.1016/j.tcb.2022.11.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022]
19
Pavlova I, Iudin M, Surdina A, Severov V, Varizhuk A. G-Quadruplexes in Nuclear Biomolecular Condensates. Genes (Basel) 2023;14:genes14051076. [PMID: 37239436 DOI: 10.3390/genes14051076] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023]  Open
20
Ibrahim AY, Khaodeuanepheng NP, Amarasekara DL, Correia JJ, Lewis KA, Fitzkee NC, Hough LE, Whitten ST. Intrinsically disordered regions that drive phase separation form a robustly distinct protein class. J Biol Chem 2022;299:102801. [PMID: 36528065 PMCID: PMC9860499 DOI: 10.1016/j.jbc.2022.102801] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/29/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]  Open
21
Cai H, Vernon RM, Forman-Kay JD. An Interpretable Machine-Learning Algorithm to Predict Disordered Protein Phase Separation Based on Biophysical Interactions. Biomolecules 2022;12:biom12081131. [PMID: 36009025 PMCID: PMC9405563 DOI: 10.3390/biom12081131] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/21/2022]  Open
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