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Article ; Online: LipidII: Just Another Brick in the Wall?

Scheffers, Dirk-Jan / Tol, Menno B

2015 Volume 11, Issue 12, Page(s) e1005213

Abstract: Nearly all bacteria contain a peptidoglycan cell wall. The peptidoglycan precursor molecule is LipidII, containing the basic peptidoglycan building block attached to a lipid. Although the suitability of LipidII as an antibacterial target has long been ... ...

Abstract	Nearly all bacteria contain a peptidoglycan cell wall. The peptidoglycan precursor molecule is LipidII, containing the basic peptidoglycan building block attached to a lipid. Although the suitability of LipidII as an antibacterial target has long been recognized, progress on elucidating the role(s) of LipidII in bacterial cell biology has been slow. The focus of this review is on exciting new developments, both with respect to antibacterials targeting LipidII as well as the emerging role of LipidII in organizing the membrane and cell wall synthesis. It appears that on both sides of the membrane, LipidII plays crucial roles in organizing cytoskeletal proteins and peptidoglycan synthesis machineries. Finally, the recent discovery of no less than three different categories of LipidII flippases will be discussed.
MeSH term(s)	Bacterial Proteins/metabolism ; Cell Wall/metabolism ; Peptidoglycan/metabolism
Chemical Substances	Bacterial Proteins ; Peptidoglycan
Language	English
Publishing date	2015-12-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7366
ISSN (online)	1553-7374
ISSN	1553-7366
DOI	10.1371/journal.ppat.1005213
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Article ; Online: In vivo cluster formation of nisin and lipid II is correlated with membrane depolarization.

Tol, Menno B / Morales Angeles, Danae / Scheffers, Dirk-Jan

Antimicrobial agents and chemotherapy

2015 Volume 59, Issue 6, Page(s) 3683–3686

Abstract: Nisin and related lantibiotics kill bacteria by pore formation or by sequestering lipid II. Some lantibiotics sequester lipid II into clusters, which were suggested to kill cells through delocalized peptidoglycan synthesis. Here, we show that cluster ... ...

Abstract	Nisin and related lantibiotics kill bacteria by pore formation or by sequestering lipid II. Some lantibiotics sequester lipid II into clusters, which were suggested to kill cells through delocalized peptidoglycan synthesis. Here, we show that cluster formation is always concomitant with (i) membrane pore formation and (ii) membrane depolarization. Nisin variants that cluster lipid II kill L-form bacteria with similar efficiency, suggesting that delocalization of peptidoglycan synthesis is not the primary killing mechanism of these lantibiotics.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Bacteriocins/pharmacology ; Cell Membrane/drug effects ; Nisin/pharmacology ; Peptidoglycan/metabolism ; Uridine Diphosphate N-Acetylmuramic Acid/analogs & derivatives ; Uridine Diphosphate N-Acetylmuramic Acid/metabolism
Chemical Substances	Anti-Bacterial Agents ; Bacteriocins ; Peptidoglycan ; Uridine Diphosphate N-Acetylmuramic Acid ; muramyl-NAc-(pentapeptide)pyrophosphoryl-undecaprenol ; Nisin (1414-45-5)
Language	English
Publishing date	2015
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	217602-6
ISSN	1098-6596 ; 0066-4804
ISSN (online)	1098-6596
ISSN	0066-4804
DOI	10.1128/AAC.04781-14
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Article ; Online: Thermal unfolding of a mammalian pentameric ligand-gated ion channel proceeds at consecutive, distinct steps.

Tol, Menno B / Deluz, Cédric / Hassaine, Gherici / Graff, Alexandra / Stahlberg, Henning / Vogel, Horst

The Journal of biological chemistry

2012 Volume 288, Issue 8, Page(s) 5756–5769

Abstract: Pentameric ligand-gated ion channels (LGICs) play an important role in fast synaptic signal transduction. Binding of agonists to the β-sheet-structured extracellular domain opens an ion channel in the transmembrane α-helical region of the LGIC. How the ... ...

Abstract	Pentameric ligand-gated ion channels (LGICs) play an important role in fast synaptic signal transduction. Binding of agonists to the β-sheet-structured extracellular domain opens an ion channel in the transmembrane α-helical region of the LGIC. How the structurally distinct and distant domains are functionally coupled for such central transmembrane signaling processes remains an open question. To obtain detailed information about the stability of and the coupling between these different functional domains, we analyzed the thermal unfolding of a homopentameric LGIC, the 5-hydroxytryptamine receptor (ligand binding, secondary structure, accessibility of Trp and Cys residues, and aggregation), in plasma membranes as well as during detergent extraction, purification, and reconstitution into artificial lipid bilayers. We found a large loss in thermostability correlating with the loss of the lipid bilayer during membrane solubilization and purification. Thermal unfolding of the 5-hydroxytryptamine receptor occurred in consecutive steps at distinct protein locations. A loss of ligand binding was detected first, followed by formation of different transient low oligomeric states of receptor pentamers, followed by partial unfolding of helical parts of the protein, which finally lead to the formation receptor aggregates. Structural destabilization of the receptor in detergents could be partially reversed by reconstituting the receptor into lipid bilayers. Our results are important because they quantify the stability of LGICs during detergent extraction and purification and can be used to create stabilized receptor proteins for structural and functional studies.
MeSH term(s)	Animals ; CHO Cells ; Cell Membrane/metabolism ; Cricetinae ; DNA, Complementary/metabolism ; Detergents/chemistry ; Detergents/pharmacology ; Hot Temperature ; Ligand-Gated Ion Channels/metabolism ; Ligands ; Lipid Bilayers/chemistry ; Mice ; Microscopy, Electron, Transmission/methods ; Microscopy, Fluorescence/methods ; Models, Biological ; Protein Denaturation ; Protein Structure, Tertiary ; Receptors, Serotonin, 5-HT2/metabolism ; Spectrometry, Fluorescence/methods ; Temperature
Chemical Substances	DNA, Complementary ; Detergents ; Ligand-Gated Ion Channels ; Ligands ; Lipid Bilayers ; Receptors, Serotonin, 5-HT2
Language	English
Publishing date	2012-12-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M112.422287
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Article ; Online: Bicyclic enol cyclocarbamates inhibit penicillin-binding proteins.

Dockerty, Paul / Edens, Jerre G / Tol, Menno B / Morales Angeles, Danae / Domenech, Arnau / Liu, Yun / Hirsch, Anna K H / Veening, Jan-Willem / Scheffers, Dirk-Jan / Witte, Martin D

Organic & biomolecular chemistry

2017 Volume 15, Issue 4, Page(s) 894–910

Abstract: Natural products form attractive leads for the development of chemical probes and drugs. The antibacterial lipopeptide Brabantamide A contains an unusual enol cyclocarbamate and we used this scaffold as inspiration for the synthesis of a panel of enol ... ...

Abstract	Natural products form attractive leads for the development of chemical probes and drugs. The antibacterial lipopeptide Brabantamide A contains an unusual enol cyclocarbamate and we used this scaffold as inspiration for the synthesis of a panel of enol cyclocarbamate containing compounds. By equipping the scaffold with different groups, we identified structural features that are essential for antibacterial activity. Some of the derivatives block incorporation of hydroxycoumarin carboxylic acid-amino d-alanine into the newly synthesized peptidoglycan. Activity-based protein-profiling experiments revealed that the enol carbamates inhibit a specific subset of penicillin-binding proteins in B. subtilis and S. pneumoniae.
Language	English
Publishing date	2017-01-25
Publishing country	England
Document type	Journal Article
ZDB-ID	2097583-1
ISSN	1477-0539 ; 1477-0520
ISSN (online)	1477-0539
ISSN	1477-0520
DOI	10.1039/c6ob01664b
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Article: Large scale expression and purification of the mouse 5-HT3 receptor.

Hassaine, Ghérici / Deluz, Cédric / Tol, Menno B / Li, Xiao-Dan / Graff, Alexandra / Vogel, Horst / Nury, Hugues

Biochimica et biophysica acta

2013 Volume 1828, Issue 11, Page(s) 2544–2552

Abstract: Receptors of the Cys-loop family are central to neurotransmission and primary therapeutic targets. In order to decipher their gating and modulation mechanisms, structural data is essential. However, structural studies require large amounts of pure, ... ...

Abstract	Receptors of the Cys-loop family are central to neurotransmission and primary therapeutic targets. In order to decipher their gating and modulation mechanisms, structural data is essential. However, structural studies require large amounts of pure, functional receptors. Here, we present the expression and purification of the mouse serotonin 5-HT3 receptor to high purity and homogeneity levels. Inducible expression in human embryonic kidney 293 cells in suspension cultures with orbital shaking resulted in yields of 6-8mg receptor per liter of culture. Affinity purification using a strep tag provided pure protein in active form. Further deglycosylation and removal of the purification tag led to a pentameric receptor after size-exclusion chromatography, at the milligram scale. This material is suitable for crystallography, as demonstrated by X-ray diffraction of receptor crystals at low resolution.
MeSH term(s)	Animals ; Chromatography, Affinity ; Chromatography, Gel ; Crystallization ; Electrophoresis, Polyacrylamide Gel ; Glycosylation ; Mice ; Receptors, Serotonin, 5-HT3/isolation & purification ; Receptors, Serotonin, 5-HT3/metabolism ; Recombinant Proteins/isolation & purification ; Recombinant Proteins/metabolism
Chemical Substances	Receptors, Serotonin, 5-HT3 ; Recombinant Proteins
Language	English
Publishing date	2013-11
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	60-7
ISSN	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbamem.2013.05.028
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Article: Flavin binding to the high affinity riboflavin transporter RibU.

Duurkens, Ria H / Tol, Menno B / Geertsma, Eric R / Permentier, Hjalmar P / Slotboom, Dirk Jan

The Journal of biological chemistry

2007 Volume 282, Issue 14, Page(s) 10380–10386

Abstract: The first biochemical and spectroscopic characterization of a purified membrane transporter for riboflavin (vitamin B(2)) is presented. The riboflavin transporter RibU from the bacterium Lactococcus lactis was overexpressed, solubilized, and purified. ... ...

Abstract	The first biochemical and spectroscopic characterization of a purified membrane transporter for riboflavin (vitamin B(2)) is presented. The riboflavin transporter RibU from the bacterium Lactococcus lactis was overexpressed, solubilized, and purified. The purified transporter was bright yellow when the cells had been cultured in rich medium. We used a detergent-compatible matrix-assisted laser desorption ionization time-of-flight mass spectrometry method (Cadene, M., and Chait, B. T. (2000) Anal. Chem. 72, 5655-5658) to show that the source of the yellow color was riboflavin that had been co-purified with the transporter. The method appears generally applicable for substrate identification of purified membrane proteins. Substrate-free RibU was produced by expressing the protein in cells cultured in chemically defined medium. Riboflavin, FMN, and roseoflavin bound to RibU with high affinity and 1:1 stoichiometry (K(d) for riboflavin is 0.6 nM), but FAD did not bind to the transporter. The absorption spectrum of riboflavin changed dramatically when the substrate bound to RibU. Well resolved bands appeared at 441, 464, and 486 nm, indicating a hydrophobic binding pocket. The fluorescence of riboflavin was almost completely quenched upon binding to RibU, and also the tryptophan fluorescence of the transporter was quenched when flavins bound. The results indicate that riboflavin is stacked with one or more tryptophan residues in the binding pocket of RibU. Mutagenesis experiments showed that Trp-68 was involved directly in the riboflavin binding. The structural properties of the binding site and mechanistic consequences of the exceptionally high affinity of RibU for its substrate are discussed in relation to soluble riboflavin-binding proteins of known structure.
MeSH term(s)	Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Binding Sites/physiology ; Flavin Mononucleotide/chemistry ; Flavin Mononucleotide/metabolism ; Lactococcus lactis/chemistry ; Lactococcus lactis/genetics ; Lactococcus lactis/metabolism ; Membrane Transport Proteins/chemistry ; Membrane Transport Proteins/genetics ; Membrane Transport Proteins/metabolism ; Protein Binding/physiology ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Riboflavin/chemistry ; Riboflavin/metabolism ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Tryptophan/chemistry ; Tryptophan/metabolism
Chemical Substances	Bacterial Proteins ; Membrane Transport Proteins ; Recombinant Proteins ; Flavin Mononucleotide (7N464URE7E) ; Tryptophan (8DUH1N11BX) ; Riboflavin (TLM2976OFR)
Language	English
Publishing date	2007-02-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M608583200
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Article ; Online: X-ray structure of the mouse serotonin 5-HT3 receptor.

Hassaine, Ghérici / Deluz, Cédric / Grasso, Luigino / Wyss, Romain / Tol, Menno B / Hovius, Ruud / Graff, Alexandra / Stahlberg, Henning / Tomizaki, Takashi / Desmyter, Aline / Moreau, Christophe / Li, Xiao-Dan / Poitevin, Frédéric / Vogel, Horst / Nury, Hugues

Nature

2014 Volume 512, Issue 7514, Page(s) 276–281

Abstract: Neurotransmitter-gated ion channels of the Cys-loop receptor family mediate fast neurotransmission throughout the nervous system. The molecular processes of neurotransmitter binding, subsequent opening of the ion channel and ion permeation remain poorly ... ...

Abstract	Neurotransmitter-gated ion channels of the Cys-loop receptor family mediate fast neurotransmission throughout the nervous system. The molecular processes of neurotransmitter binding, subsequent opening of the ion channel and ion permeation remain poorly understood. Here we present the X-ray structure of a mammalian Cys-loop receptor, the mouse serotonin 5-HT3 receptor, at 3.5 Å resolution. The structure of the proteolysed receptor, made up of two fragments and comprising part of the intracellular domain, was determined in complex with stabilizing nanobodies. The extracellular domain reveals the detailed anatomy of the neurotransmitter binding site capped by a nanobody. The membrane domain delimits an aqueous pore with a 4.6 Å constriction. In the intracellular domain, a bundle of five intracellular helices creates a closed vestibule where lateral portals are obstructed by loops. This 5-HT3 receptor structure, revealing part of the intracellular domain, expands the structural basis for understanding the operating mechanism of mammalian Cys-loop receptors.
MeSH term(s)	Amino Acid Sequence ; Animals ; Binding Sites ; Crystallography, X-Ray ; Mice ; Models, Molecular ; Molecular Sequence Data ; Neurotransmitter Agents/metabolism ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Protein Subunits/metabolism ; Receptors, Serotonin, 5-HT3/chemistry ; Receptors, Serotonin, 5-HT3/metabolism
Chemical Substances	Neurotransmitter Agents ; Protein Subunits ; Receptors, Serotonin, 5-HT3
Language	English
Publishing date	2014-08-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/nature13552
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Article: Flavin Binding to the High Affinity Riboflavin Transporter RibU

Duurkens, Ria H / Tol, Menno B / Geertsma, Eric R / Permentier, Hjalmar P / Slotboom, Dirk Jan

Journal of biological chemistry. 2007 Apr. 6, v. 282, no. 14

2007

Abstract: The first biochemical and spectroscopic characterization of a purified membrane transporter for riboflavin (vitamin B₂) is presented. The riboflavin transporter RibU from the bacterium Lactococcus lactis was overexpressed, solubilized, and purified. The ... ...

Abstract	The first biochemical and spectroscopic characterization of a purified membrane transporter for riboflavin (vitamin B₂) is presented. The riboflavin transporter RibU from the bacterium Lactococcus lactis was overexpressed, solubilized, and purified. The purified transporter was bright yellow when the cells had been cultured in rich medium. We used a detergent-compatible matrix-assisted laser desorption ionization time-of-flight mass spectrometry method (Cadene, M., and Chait, B. T. (2000) ANAL: Chem. 72, 5655-5658) to show that the source of the yellow color was riboflavin that had been co-purified with the transporter. The method appears generally applicable for substrate identification of purified membrane proteins. Substrate-free RibU was produced by expressing the protein in cells cultured in chemically defined medium. Riboflavin, FMN, and roseoflavin bound to RibU with high affinity and 1:1 stoichiometry (Kd for riboflavin is 0.6 nM), but FAD did not bind to the transporter. The absorption spectrum of riboflavin changed dramatically when the substrate bound to RibU. Well resolved bands appeared at 441, 464, and 486 nm, indicating a hydrophobic binding pocket. The fluorescence of riboflavin was almost completely quenched upon binding to RibU, and also the tryptophan fluorescence of the transporter was quenched when flavins bound. The results indicate that riboflavin is stacked with one or more tryptophan residues in the binding pocket of RibU. Mutagenesis experiments showed that Trp-68 was involved directly in the riboflavin binding. The structural properties of the binding site and mechanistic consequences of the exceptionally high affinity of RibU for its substrate are discussed in relation to soluble riboflavin-binding proteins of known structure.
Language	English
Dates of publication	2007-0406
Size	p. 10380-10386.
Publishing place	American Society for Biochemistry and Molecular Biology
Document type	Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
Database	NAL-Catalogue (AGRICOLA)

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