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Abstract
To exchange and communicate with their surroundings, bacteria have evolved multiple active and passive mechanisms for trans-envelope transport. Among the pore-forming complexes found in the outer membrane of Gram-negative bacteria, secretins are distinctive homo-oligomeric channels dedicated to the active translocation of voluminous structures such as folded proteins, assembled fibers, virus particles or DNA. Members of the bacterial secretin family share a common cylinder-shaped structure with a gated pore-forming part inserted in the outer membrane, and a periplasmic channel connected to the inner membrane components of the corresponding nanomachine. In this mini-review, we will present what recently determined 3D structures have told us about the mechanisms of translocation through secretins of large substrates to the bacterial surface or in the extracellular milieu.
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Affiliation(s)
- Brice Barbat
- LCB-UMR7283, CNRS, Aix Marseille Université, IMM, 13009, Marseille, France
| | | | - Romé Voulhoux
- LCB-UMR7283, CNRS, Aix Marseille Université, IMM, 13009, Marseille, France.
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2
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Achatz S, Jarasch A, Skerra A. Structural plasticity in the loop region of engineered lipocalins with novel ligand specificities, so-called Anticalins. J Struct Biol X 2022; 6:100054. [PMID: 34988429 PMCID: PMC8693463 DOI: 10.1016/j.yjsbx.2021.100054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 12/30/2022] Open
Abstract
The lipocalins exhibit four structurally variable loops at one end of a β-barrel. Binding sites for diverse ligands occur in the natural lipocalin family members. Loop reshaping via combinatorial protein design leads to novel ligand specificities. Many crystal structures of Anticalins derived from the Lcn2 scaffold are available. Graphical analysis reveals high structural plasticity of the lipocalin loop region.
Anticalins are generated via combinatorial protein design on the basis of the lipocalin protein scaffold and constitute a novel class of small and robust engineered binding proteins that offer prospects for applications in medical therapy as well as in vivo diagnostics as an alternative to antibodies. The lipocalins are natural binding proteins with diverse ligand specificities which share a simple architecture with a central eight-stranded antiparallel β-barrel and an α-helix attached to its side. At the open end of the β-barrel, four structurally variable loops connect the β-strands in a pair-wise manner and, together, shape the ligand pocket. Using targeted random mutagenesis in combination with molecular selection techniques, this loop region can be reshaped to generate pockets for the tight binding of various ligands ranging from small molecules over peptides to proteins. While such Anticalin proteins can be derived from different natural lipocalins, the human lipocalin 2 (Lcn2) scaffold proved particularly successful for the design of binding proteins with novel specificities and, over the years, more than 20 crystal structures of Lcn2-based Anticalins have been elucidated. In this graphical structural biology review we illustrate the conformational variability that emerged in the loop region of these functionally diverse artificial binding proteins in comparison with the natural scaffold. Our present analysis provides picturesque evidence of the high structural plasticity around the binding site of the lipocalins which explains the proven tolerance toward excessive mutagenesis, thus demonstrating remarkable resemblance to the complementarity-determining region of antibodies (immunoglobulins).
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Affiliation(s)
- S Achatz
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - A Jarasch
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - A Skerra
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
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3
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Abstract
Pore-forming proteins (PFPs) of the diverse life forms have emerged as the potent cell-killing entities owing to their specialized membrane-damaging properties. PFPs have the unique ability to perforate the plasma membranes of their target cells, and they exert this functionality by creating oligomeric pores in the membrane lipid bilayer. Pathogenic bacteria employ PFPs as toxins to execute their virulence mechanisms, whereas in the higher vertebrates PFPs are deployed as the part of the immune system and to generate inflammatory responses. PFPs are the unique dimorphic proteins that are generally synthesized as water-soluble molecules, and transform into membrane-inserted oligomeric pore assemblies upon interacting with the target membranes. In spite of sharing very little sequence similarity, PFPs from diverse organisms display incredible structural similarity. Yet, at the same time, structure-function mechanisms of the PFPs document remarkable versatility. Such notions establish PFPs as the fascinating model system to explore variety of unsolved issues pertaining to the structure-function paradigm of the proteins that interact and act in the membrane environment. In this article, we discuss our current understanding regarding the structural basis of the pore-forming functions of the diverse class of PFPs. We attempt to highlight the similarities and differences in their structures, membrane pore-formation mechanisms, and their implications for the various biological processes, ranging from the bacterial virulence mechanisms to the inflammatory immune response generation in the higher animals.
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Affiliation(s)
- Anish Kumar Mondal
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India
| | - Kausik Chattopadhyay
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India.
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Schubeis T, Schwarzer TS, Le Marchand T, Stanek J, Movellan KT, Castiglione K, Pintacuda G, Andreas LB. Resonance assignment of the outer membrane protein AlkL in lipid bilayers by proton-detected solid-state NMR. Biomol NMR Assign 2020; 14:295-300. [PMID: 32607893 DOI: 10.1007/s12104-020-09964-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
Most commonly small outer membrane proteins, possessing between 8 and 12 β-strands, are not involved in transport but fulfill diverse functions such as cell adhesion or binding of ligands. An intriguing exception are the 8-stranded β-barrel proteins of the OmpW family, which are implicated in the transport of small molecules. A representative example is AlkL from Pseudomonas putida GPoI, which functions as a passive importer of hydrophobic molecules. This role is of high interest with respect to both fundamental biological understanding and industrial applications in biocatalysis, since this protein is frequently utilized in biotransformation of alkanes. While the transport function of AlkL is generally accepted, a controversy in the transport mechanism still exists. In order to address this, we are pursuing a structural study of recombinantly produced AlkL reconstituted in lipid bilayers using solid-state NMR spectroscopy. In this manuscript we present 1H, 13C and 15N chemical shift assignments obtained via a suite of 3D experiments employing high magnetic fields (1 GHz and 800 MHz) and the latest magic-angle spinning (MAS) approaches at fast (60-111) kHz rates. We additionally analyze the secondary structure prediction in comparison with those of published structures of homologous proteins.
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Affiliation(s)
- Tobias Schubeis
- Centre de RMN à Très Hauts Champs de Lyon (FRE 2034 - CNRS, UCB Lyon 1, ENS Lyon), Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Tom S Schwarzer
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstraße 15, 85748, Garching, Germany
| | - Tanguy Le Marchand
- Centre de RMN à Très Hauts Champs de Lyon (FRE 2034 - CNRS, UCB Lyon 1, ENS Lyon), Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Jan Stanek
- Centre de RMN à Très Hauts Champs de Lyon (FRE 2034 - CNRS, UCB Lyon 1, ENS Lyon), Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Kumar Tekwani Movellan
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Kathrin Castiglione
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstraße 15, 85748, Garching, Germany
- Institute of Bioprocess Engineering, FAU Erlangen-Nürnberg, Paul-Gordan Str. 3, 91052, Erlangen, Germany
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs de Lyon (FRE 2034 - CNRS, UCB Lyon 1, ENS Lyon), Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France.
| | - Loren B Andreas
- Centre de RMN à Très Hauts Champs de Lyon (FRE 2034 - CNRS, UCB Lyon 1, ENS Lyon), Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France.
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany.
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Roche DB, Viet PD, Bakulina A, Hirsh L, Tosatto SCE, Kajava AV. Classification of β-hairpin repeat proteins. J Struct Biol 2017; 201:130-138. [PMID: 29017817 DOI: 10.1016/j.jsb.2017.10.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/02/2017] [Accepted: 10/04/2017] [Indexed: 12/11/2022]
Abstract
In recent years, a number of new protein structures that possess tandem repeats have emerged. Many of these proteins are comprised of tandem arrays of β-hairpins. Today, the amount and variety of the data on these β-hairpin repeat (BHR) structures have reached a level that requires detailed analysis and further classification. In this paper, we classified the BHR proteins, compared structures, sequences of repeat motifs, functions and distribution across the major taxonomic kingdoms of life and within organisms. As a result, we identified six different BHR folds in tandem repeat proteins of Class III (elongated structures) and one BHR fold (up-and-down β-barrel) in Class IV ("closed" structures). Our survey reveals the high incidence of the BHR proteins among bacteria and viruses and their possible relationship to the structures of amyloid fibrils. It indicates that BHR folds will be an attractive target for future structural studies, especially in the context of age-related amyloidosis and emerging infectious diseases. This work allowed us to update the RepeatsDB database, which contains annotated tandem repeat protein structures and to construct sequence profiles based on BHR structural alignments.
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Affiliation(s)
- Daniel B Roche
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, 1919 Route de Mende, Cedex 5, Montpellier 34293, France; Institut de Biologie Computationnelle, Montpellier, France
| | - Phuong Do Viet
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, 1919 Route de Mende, Cedex 5, Montpellier 34293, France; Institut de Biologie Computationnelle, Montpellier, France
| | - Anastasia Bakulina
- Novosibirsk State University, Pirogova str. 1, Novosibirsk 630090, Russia; State Research Center of Virology and Biotechnology VECTOR, Koltsovo, Russia
| | - Layla Hirsh
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy; Engineering Department, Pontifical Catholic University of Peru, Lima 32, Peru
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, 1919 Route de Mende, Cedex 5, Montpellier 34293, France; Institut de Biologie Computationnelle, Montpellier, France.
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Höhr AIC, Straub SP, Warscheid B, Becker T, Wiedemann N. Assembly of β-barrel proteins in the mitochondrial outer membrane. Biochim Biophys Acta 2014; 1853:74-88. [PMID: 25305573 DOI: 10.1016/j.bbamcr.2014.10.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 09/25/2014] [Accepted: 10/01/2014] [Indexed: 12/15/2022]
Abstract
Mitochondria evolved through endosymbiosis of a Gram-negative progenitor with a host cell to generate eukaryotes. Therefore, the outer membrane of mitochondria and Gram-negative bacteria contain pore proteins with β-barrel topology. After synthesis in the cytosol, β-barrel precursor proteins are first transported into the mitochondrial intermembrane space. Folding and membrane integration of β-barrel proteins depend on the mitochondrial sorting and assembly machinery (SAM) located in the outer membrane, which is related to the β-barrel assembly machinery (BAM) in bacteria. The SAM complex recognizes β-barrel proteins by a β-signal in the C-terminal β-strand that is required to initiate β-barrel protein insertion into the outer membrane. In addition, the SAM complex is crucial to form membrane contacts with the inner mitochondrial membrane by interacting with the mitochondrial contact site and cristae organizing system (MICOS) and shares a subunit with the endoplasmic reticulum-mitochondria encounter structure (ERMES) that links the outer mitochondrial membrane to the endoplasmic reticulum (ER).
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Affiliation(s)
- Alexandra I C Höhr
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; Fakultät für Biologie, Universität Freiburg, 79104 Freiburg, Germany
| | - Sebastian P Straub
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; Fakultät für Biologie, Universität Freiburg, 79104 Freiburg, Germany
| | - Bettina Warscheid
- BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany; Abteilung Biochemie und Funktionelle Proteomik, Institut für Biologie II, Fakultät für Biologie, Universität Freiburg, 79104 Freiburg, Germany
| | - Thomas Becker
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany
| | - Nils Wiedemann
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany.
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Krammer EM, Saidani H, Prévost M, Homblé F. Origin of ion selectivity in Phaseolus coccineus mitochondrial VDAC. Mitochondrion 2014; 19 Pt B:206-13. [PMID: 24742372 DOI: 10.1016/j.mito.2014.04.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 03/14/2014] [Accepted: 04/04/2014] [Indexed: 12/23/2022]
Abstract
The mitochondrial voltage-dependent a nion-selective channel (VDAC) is the major permeation pathway for small ions and metabolites. Although a wealth of electrophysiological data has been obtained on different VDAC species, the physical mechanisms of their ionic selectivity are still elusive. We addressed this issue using electrophysiological experiments performed on plant VDAC. A simple macroscopic electrodiffusion model accounting for ion diffusion and for an effective fixed charge of the channel describes well its selectivity. Brownian Dynamics simulations of ion permeation performed on plant and mammalian VDACs point to the role of specific charged residues located at about the middle of the pore.
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Affiliation(s)
- Eva-Maria Krammer
- Structure et Fonction des Membranes Biologiques, Centre de Biologie Structurale et de Bioinformatique, Université Libre de Bruxelles (ULB), Bld du Triomphe, 1050 Brussels, Belgium
| | - Hayet Saidani
- Structure et Fonction des Membranes Biologiques, Centre de Biologie Structurale et de Bioinformatique, Université Libre de Bruxelles (ULB), Bld du Triomphe, 1050 Brussels, Belgium
| | - Martine Prévost
- Structure et Fonction des Membranes Biologiques, Centre de Biologie Structurale et de Bioinformatique, Université Libre de Bruxelles (ULB), Bld du Triomphe, 1050 Brussels, Belgium
| | - Fabrice Homblé
- Structure et Fonction des Membranes Biologiques, Centre de Biologie Structurale et de Bioinformatique, Université Libre de Bruxelles (ULB), Bld du Triomphe, 1050 Brussels, Belgium.
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