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Löwe M, Kalacheva M, Boersma AJ, Kedrov A. The more the merrier: effects of macromolecular crowding on the structure and dynamics of biological membranes. FEBS J 2020; 287:5039-5067. [DOI: 10.1111/febs.15429] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Maryna Löwe
- Synthetic Membrane Systems Institute of Biochemistry Heinrich Heine University Düsseldorf Germany
| | | | | | - Alexej Kedrov
- Synthetic Membrane Systems Institute of Biochemistry Heinrich Heine University Düsseldorf Germany
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McClintic WT, Taylor GJ, Simpson ML, Collier CP. Macromolecular Crowding Affects Voltage-Dependent Alamethicin Pore Formation in Lipid Bilayer Membranes. J Phys Chem B 2020; 124:5095-5102. [DOI: 10.1021/acs.jpcb.0c01650] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- William T. McClintic
- The Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Graham J. Taylor
- The Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Michael L. Simpson
- The Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Nanophase Material Science, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - C. Patrick Collier
- The Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Nanophase Material Science, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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Shahid S, Hassan MI, Islam A, Ahmad F. Size-dependent studies of macromolecular crowding on the thermodynamic stability, structure and functional activity of proteins: in vitro and in silico approaches. Biochim Biophys Acta Gen Subj 2017; 1861:178-197. [DOI: 10.1016/j.bbagen.2016.11.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 11/27/2022]
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Danoff EJ, Fleming KG. Novel Kinetic Intermediates Populated along the Folding Pathway of the Transmembrane β-Barrel OmpA. Biochemistry 2016; 56:47-60. [PMID: 28001375 DOI: 10.1021/acs.biochem.6b00809] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We examined the folding of the β-barrel membrane protein OmpA from Escherichia coli. Although previous studies identified several intermediate states followed by a concerted translocation mechanism across the bilayer, some aspects of the pathway were still unclear, including the extent of secondary structure formation in the intermediate states and how the mechanism gave rise to multiple exponential phases in the folding kinetics. We addressed these questions by investigating the folding kinetics of the OmpA transmembrane β-barrel domain over a range of bilayer thicknesses, allowing us to observe different regions of the folding pathway. The fastest folding into the thinnest bilayers provided information about the later stages of the process, and the slowest folding into thicker bilayers revealed early kinetic steps. Folding was monitored using sodium dodecyl sulfate-polyacrylamide gel electrophoresis and circular dichroism spectroscopy, which provide complementary information about tertiary and secondary structure formation. We globally fit the folding data to kinetic schemes and found that the same core pathway was followed under all lipid conditions. We propose a multistep folding mechanism for OmpA that includes unstructured surface-adsorbed states converting through a partially inserted state with substantial β-sheet structure to the final natively inserted barrel. Kinetic models show that all steps of the main folding pathway are accelerated by membrane defects that occur as a result of thinning the bilayer or incubation of lipids at the phase transition temperature. In addition to suppressing off-pathway states, β-barrel assembly machinery-catalyzed folding in vivo could accelerate any or all of these main folding steps to ensure efficient outer membrane protein biogenesis in vivo.
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Affiliation(s)
- Emily J Danoff
- T. C. Jenkins Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Karen G Fleming
- T. C. Jenkins Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
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De Geyter J, Tsirigotaki A, Orfanoudaki G, Zorzini V, Economou A, Karamanou S. Protein folding in the cell envelope of Escherichia coli. Nat Microbiol 2016; 1:16107. [PMID: 27573113 DOI: 10.1038/nmicrobiol.2016.107] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/02/2016] [Indexed: 11/09/2022]
Abstract
While the entire proteome is synthesized on cytoplasmic ribosomes, almost half associates with, localizes in or crosses the bacterial cell envelope. In Escherichia coli a variety of mechanisms are important for taking these polypeptides into or across the plasma membrane, maintaining them in soluble form, trafficking them to their correct cell envelope locations and then folding them into the right structures. The fidelity of these processes must be maintained under various environmental conditions including during stress; if this fails, proteases are called in to degrade mislocalized or aggregated proteins. Various soluble, diffusible chaperones (acting as holdases, foldases or pilotins) and folding catalysts are also utilized to restore proteostasis. These responses can be general, dealing with multiple polypeptides, with functional overlaps and operating within redundant networks. Other chaperones are specialized factors, dealing only with a few exported proteins. Several complex machineries have evolved to deal with binding to, integration in and crossing of the outer membrane. This complex protein network is responsible for fundamental cellular processes such as cell wall biogenesis; cell division; the export, uptake and degradation of molecules; and resistance against exogenous toxic factors. The underlying processes, contributing to our fundamental understanding of proteostasis, are a treasure trove for the development of novel antibiotics, biopharmaceuticals and vaccines.
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Affiliation(s)
- Jozefien De Geyter
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
| | - Alexandra Tsirigotaki
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
| | - Georgia Orfanoudaki
- Institute of Molecular Biology and Biotechnology, FORTH and Department of Biology, University of Crete, PO Box 1385, GR-711 10 Iraklio, Crete, Greece
| | - Valentina Zorzini
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
| | - Anastassios Economou
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium.,Institute of Molecular Biology and Biotechnology, FORTH and Department of Biology, University of Crete, PO Box 1385, GR-711 10 Iraklio, Crete, Greece
| | - Spyridoula Karamanou
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
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Bekal S, Vincent A, Lin A, Harel J, Côté JC, Tremblay C. A Fatal Case of Necrotizing Fasciitis Caused by a Highly Virulent Escherichia coli Strain. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2016; 2016:2796412. [PMID: 27366162 PMCID: PMC4906195 DOI: 10.1155/2016/2796412] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 05/12/2016] [Indexed: 12/17/2022]
Abstract
Necrotizing fasciitis is a serious disease characterized by the necrosis of the subcutaneous tissues and fascia. E. coli as the etiologic agent of necrotizing fasciitis is a rare occurrence. A 66-year-old woman underwent total abdominal hysterectomy with bilateral salpingo-oophorectomy. She rapidly developed necrotizing fasciitis which led to her death 68 hours following surgery. An E. coli strain was isolated from blood and fascia cultures. DNA microarray revealed the presence of 20 virulence genes.
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Affiliation(s)
- Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada H9X 3R5
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada H3T 1J4
| | - André Vincent
- Centre Hospitalier Affilié Universitaire, Hôtel-Dieu de Lévis, Lévis, QC, Canada G6V 3Z1
| | - Alex Lin
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada H9X 3R5
| | - Josée Harel
- Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada J2S 2M2
| | - Jean-Charles Côté
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada H9X 3R5
| | - Cécile Tremblay
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada H9X 3R5
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada H3T 1J4
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Yoshitake T, Toyooka T, Nakasone Y, Zikihara K, Tokutomi S, Terazima M. Macromolecular crowding effect for photoreactions of LOV2 domains of Arabidopsis thaliana phototropin 1. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2015.08.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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What macromolecular crowding can do to a protein. Int J Mol Sci 2014; 15:23090-140. [PMID: 25514413 PMCID: PMC4284756 DOI: 10.3390/ijms151223090] [Citation(s) in RCA: 355] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 01/17/2023] Open
Abstract
The intracellular environment represents an extremely crowded milieu, with a limited amount of free water and an almost complete lack of unoccupied space. Obviously, slightly salted aqueous solutions containing low concentrations of a biomolecule of interest are too simplistic to mimic the “real life” situation, where the biomolecule of interest scrambles and wades through the tightly packed crowd. In laboratory practice, such macromolecular crowding is typically mimicked by concentrated solutions of various polymers that serve as model “crowding agents”. Studies under these conditions revealed that macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, protein-protein interactions, protein-nucleic acid interactions, and pathological aggregation. The goal of this review is to systematically analyze currently available experimental data on the variety of effects of macromolecular crowding on a protein molecule. The review covers more than 320 papers and therefore represents one of the most comprehensive compendia of the current knowledge in this exciting area.
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