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For: Loos MS, Ramakrishnan R, Vranken W, Tsirigotaki A, Tsare EP, Zorzini V, Geyter JD, Yuan B, Tsamardinos I, Klappa M, Schymkowitz J, Rousseau F, Karamanou S, Economou A. Structural Basis of the Subcellular Topology Landscape of Escherichia coli. Front Microbiol 2019;10:1670. [PMID: 31404336 PMCID: PMC6677119 DOI: 10.3389/fmicb.2019.01670] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/08/2019] [Indexed: 11/21/2022]  Open
Number Cited by Other Article(s)
1
Moon J, Hu G, Hayashi T. Application of Machine Learning in the Quantitative Analysis of the Surface Characteristics of Highly Abundant Cytoplasmic Proteins: Toward AI-Based Biomimetics. Biomimetics (Basel) 2024;9:162. [PMID: 38534847 DOI: 10.3390/biomimetics9030162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/12/2024] [Accepted: 02/29/2024] [Indexed: 03/28/2024]  Open
2
Sanaboyana VR, Elcock AH. Improving Signal and Transit Peptide Predictions Using AlphaFold2-predicted Protein Structures. J Mol Biol 2024;436:168393. [PMID: 38065275 PMCID: PMC10843742 DOI: 10.1016/j.jmb.2023.168393] [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: 09/12/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023]
3
Kunze M, Alder NN, Hwang I, Roussel G, Karamyshev AL. Editorial: Targeting signals in protein trafficking and transport. Front Physiol 2023;14:1338852. [PMID: 38143916 PMCID: PMC10748493 DOI: 10.3389/fphys.2023.1338852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023]  Open
4
Heithoff DM, Mahan SP, Barnes V L, Leyn SA, George CX, Zlamal JE, Limwongyut J, Bazan GC, Fried JC, Fitzgibbons LN, House JK, Samuel CE, Osterman AL, Low DA, Mahan MJ. A broad-spectrum synthetic antibiotic that does not evoke bacterial resistance. EBioMedicine 2023;89:104461. [PMID: 36801104 PMCID: PMC10025758 DOI: 10.1016/j.ebiom.2023.104461] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 02/17/2023]  Open
5
Rettenbacher LA, von der Haar T. A quantitative interpretation of oxidative protein folding activity in Escherichia coli. Microb Cell Fact 2022;21:268. [PMID: 36550495 PMCID: PMC9773447 DOI: 10.1186/s12934-022-01982-3] [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: 10/24/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022]  Open
6
McCaul N, Braakman I. Hold the fold: how delayed folding aids protein secretion. EMBO J 2022;41:e112787. [PMID: 36314692 PMCID: PMC9713708 DOI: 10.15252/embj.2022112787] [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: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022]  Open
7
Smets D, Tsirigotaki A, Smit JH, Krishnamurthy S, Portaliou AG, Vorobieva A, Vranken W, Karamanou S, Economou A. Evolutionary adaptation of the protein folding pathway for secretability. EMBO J 2022;41:e111344. [PMID: 36031863 PMCID: PMC9713715 DOI: 10.15252/embj.2022111344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 07/14/2022] [Accepted: 08/02/2022] [Indexed: 01/15/2023]  Open
8
Cylke KC, Si F, Banerjee S. Effects of antibiotics on bacterial cell morphology and their physiological origins. Biochem Soc Trans 2022;50:1269-1279. [PMID: 36093840 PMCID: PMC10152891 DOI: 10.1042/bst20210894] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 08/05/2022] [Accepted: 08/17/2022] [Indexed: 11/17/2022]
9
Smets D, Smit J, Xu Y, Karamanou S, Economou A. Signal Peptide-rheostat Dynamics Delay Secretory Preprotein Folding. J Mol Biol 2022;434:167790. [PMID: 35970402 DOI: 10.1016/j.jmb.2022.167790] [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: 06/27/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 10/15/2022]
10
Just Add Data: automated predictive modeling for knowledge discovery and feature selection. NPJ Precis Oncol 2022;6:38. [PMID: 35710826 PMCID: PMC9203777 DOI: 10.1038/s41698-022-00274-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 04/13/2022] [Indexed: 01/20/2023]  Open
11
Mandela E, Stubenrauch CJ, Ryoo D, Hwang H, Cohen EJ, Torres VVL, Deo P, Webb CT, Huang C, Schittenhelm RB, Beeby M, Gumbart JC, Lithgow T, Hay ID. Adaptation of the periplasm to maintain spatial constraints essential for cell envelope processes and cell viability. eLife 2022;11:73516. [PMID: 35084330 PMCID: PMC8824477 DOI: 10.7554/elife.73516] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/21/2022] [Indexed: 11/17/2022]  Open
12
Parisi G, Palopoli N, Tosatto SC, Fornasari MS, Tompa P. "Protein" no longer means what it used to. Curr Res Struct Biol 2021;3:146-152. [PMID: 34308370 PMCID: PMC8283027 DOI: 10.1016/j.crstbi.2021.06.002] [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: 04/12/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 01/02/2023]  Open
13
Dautin N. Folding Control in the Path of Type 5 Secretion. Toxins (Basel) 2021;13:341. [PMID: 34064645 PMCID: PMC8151025 DOI: 10.3390/toxins13050341] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 12/17/2022]  Open
14
Oswald J, Njenga R, Natriashvili A, Sarmah P, Koch HG. The Dynamic SecYEG Translocon. Front Mol Biosci 2021;8:664241. [PMID: 33937339 PMCID: PMC8082313 DOI: 10.3389/fmolb.2021.664241] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022]  Open
15
Effective Small Molecule Antibacterials from a Novel Anti-Protein Secretion Screen. Microorganisms 2021;9:microorganisms9030592. [PMID: 33805695 PMCID: PMC8000395 DOI: 10.3390/microorganisms9030592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/03/2022]  Open
16
Signal Recognition Particle Suppressor Screening Reveals the Regulation of Membrane Protein Targeting by the Translation Rate. mBio 2021;12:mBio.02373-20. [PMID: 33436432 PMCID: PMC7844537 DOI: 10.1128/mbio.02373-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
17
Elfageih R, Karyolaimos A, Kemp G, de Gier J, von Heijne G, Kudva R. Cotranslational folding of alkaline phosphatase in the periplasm of Escherichia coli. Protein Sci 2020;29:2028-2037. [PMID: 32790204 PMCID: PMC7513700 DOI: 10.1002/pro.3927] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/08/2020] [Accepted: 08/11/2020] [Indexed: 01/10/2023]
18
Horne JE, Brockwell DJ, Radford SE. Role of the lipid bilayer in outer membrane protein folding in Gram-negative bacteria. J Biol Chem 2020;295:10340-10367. [PMID: 32499369 PMCID: PMC7383365 DOI: 10.1074/jbc.rev120.011473] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/03/2020] [Indexed: 01/09/2023]  Open
19
De Geyter J, Portaliou AG, Srinivasu B, Krishnamurthy S, Economou A, Karamanou S. Trigger factor is a bona fide secretory pathway chaperone that interacts with SecB and the translocase. EMBO Rep 2020;21:e49054. [PMID: 32307852 DOI: 10.15252/embr.201949054] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 03/09/2020] [Accepted: 03/19/2020] [Indexed: 11/09/2022]  Open
20
Sueki A, Stein F, Savitski MM, Selkrig J, Typas A. Systematic Localization of Escherichia coli Membrane Proteins. mSystems 2020;5:e00808-19. [PMID: 32127419 PMCID: PMC7055658 DOI: 10.1128/msystems.00808-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/14/2020] [Indexed: 11/20/2022]  Open
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