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Article ; Online: Tailoring Purification and Analysis of Membrane Proteins with Modular Detergents.

Urner, Leonhard H

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2507, Page(s) 359–374

Abstract: Detergents are crucially needed for the purification of drug targets: membrane proteins. Here, a method is described that combines tunable detergent technology and established laboratory techniques to tailor the affinity purification and structural ... ...

Abstract	Detergents are crucially needed for the purification of drug targets: membrane proteins. Here, a method is described that combines tunable detergent technology and established laboratory techniques to tailor the affinity purification and structural analysis of membrane proteins.
MeSH term(s)	Detergents/chemistry ; Membrane Proteins/metabolism ; Micelles
Chemical Substances	Detergents ; Membrane Proteins ; Micelles
Language	English
Publishing date	2022-06-30
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2368-8_19
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Article ; Online: Advances in membrane mimetics and mass spectrometry for understanding membrane structure and function.

Urner, Leonhard H

Current opinion in chemical biology

2022 Volume 69, Page(s) 102157

Abstract: Membrane proteins and lipids play roles in regulating biological functions of cells. However, the analysis of interactions between membrane proteins and lipids in biological membranes remains challenging. Native membranes typically contain heterogenous ... ...

Abstract	Membrane proteins and lipids play roles in regulating biological functions of cells. However, the analysis of interactions between membrane proteins and lipids in biological membranes remains challenging. Native membranes typically contain heterogenous lipid mixtures and low amounts of membrane proteins. This review presents recent developments in membrane mimetics and complementary mass spectrometry approaches for the investigation of membrane protein-lipid interactions after protein expression and purification. Furthermore, it is exemplified how delipidation knowledge on membrane mimetics can be used to gain insights into the role of lipids for protein structure and function. Because every technology has its strengths and weaknesses, it becomes apparent that integrated research approaches will facilitate the investigation of complex membrane environments in the future.
MeSH term(s)	Biomimetics ; Cell Membrane/metabolism ; Mass Spectrometry/methods ; Membrane Lipids/chemistry ; Membrane Lipids/metabolism ; Membrane Proteins/metabolism
Chemical Substances	Membrane Lipids ; Membrane Proteins
Language	English
Publishing date	2022-05-14
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	1439176-4
ISSN	1879-0402 ; 1367-5931
ISSN (online)	1879-0402
ISSN	1367-5931
DOI	10.1016/j.cbpa.2022.102157
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Article ; Online: Protocol to test the utility of detergents for E. coli membrane protein extraction and delipidation.

Wycisk, Virginia / Urner, Leonhard H

STAR protocols

2023 Volume 4, Issue 2, Page(s) 102146

Abstract: We present a protocol to evaluate the utility of detergents for purification and delipidation of E. coli membrane proteins. We determine the critical aggregation concentration of detergents. Furthermore, we compare the ability of detergents to extract ... ...

Abstract	We present a protocol to evaluate the utility of detergents for purification and delipidation of E. coli membrane proteins. We determine the critical aggregation concentration of detergents. Furthermore, we compare the ability of detergents to extract membrane proteins and to maintain protein-lipid interactions during purification. The protocol describes steps for isolating and delipidating membrane proteins from E. coli membranes by extraction and affinity purification using detergents. The protocol does not enable an absolute quantification of purification outcomes. For complete details on the use and execution of this protocol, please refer to Urner et al.
Language	English
Publishing date	2023-03-17
Publishing country	United States
Document type	Journal Article
ISSN	2666-1667
ISSN (online)	2666-1667
DOI	10.1016/j.xpro.2023.102146
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Article ; Online: Emergence of mass spectrometry detergents for membrane proteomics.

Behnke, Jan-Simon / Urner, Leonhard H

Analytical and bioanalytical chemistry

2023 Volume 415, Issue 18, Page(s) 3897–3909

Abstract: Detergents enable the investigation of membrane proteins by mass spectrometry. Detergent designers aim to improve underlying methodologies and are confronted with the challenge to design detergents with optimal solution and gas-phase properties. Herein, ... ...

Abstract	Detergents enable the investigation of membrane proteins by mass spectrometry. Detergent designers aim to improve underlying methodologies and are confronted with the challenge to design detergents with optimal solution and gas-phase properties. Herein, we review literature related to the optimization of detergent chemistry and handling and identify an emerging research direction: the optimization of mass spectrometry detergents for individual applications in mass spectrometry-based membrane proteomics. We provide an overview about qualitative design aspects including their relevance for the optimization of detergents in bottom-up proteomics, top-down proteomics, native mass spectrometry, and Nativeomics. In addition to established design aspects, such as charge, concentration, degradability, detergent removal, and detergent exchange, it becomes apparent that detergent heterogeneity is a promising key driver for innovation. We anticipate that rationalizing the role of detergent structures in membrane proteomics will serve as an enabling step for the analysis of challenging biological systems.
MeSH term(s)	Detergents/chemistry ; Proteomics/methods ; Mass Spectrometry/methods ; Membrane Proteins/analysis
Chemical Substances	Detergents ; Membrane Proteins
Language	English
Publishing date	2023-02-18
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	201093-8
ISSN	1618-2650 ; 0016-1152 ; 0372-7920
ISSN (online)	1618-2650
ISSN	0016-1152 ; 0372-7920
DOI	10.1007/s00216-023-04584-z
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Article ; Online: Trends in the Diversification of the Detergentome.

Wycisk, Virginia / Wagner, Marc-Christian / Urner, Leonhard H

ChemPlusChem

2023 Volume 89, Issue 1, Page(s) e202300386

Abstract: Detergents are amphiphilic molecules that serve as enabling steps for today's world applications. The increasing diversity of the detergentome is key to applications enabled by detergent science. Regardless of the application, the optimal design of ... ...

Abstract	Detergents are amphiphilic molecules that serve as enabling steps for today's world applications. The increasing diversity of the detergentome is key to applications enabled by detergent science. Regardless of the application, the optimal design of detergents is determined empirically, which leads to failed preparations, and raising costs. To facilitate project planning, here we review synthesis strategies that drive the diversification of the detergentome. Synthesis strategies relevant for industrial and academic applications include linear, modular, combinatorial, bio-based, and metric-assisted detergent synthesis. Scopes and limitations of individual synthesis strategies in context with industrial product development and academic research are discussed. Furthermore, when designing detergents, the selection of molecular building blocks, i. e., head, linker, tail, is as important as the employed synthesis strategy. To facilitate the design of safe-to-use and tailor-made detergents, we provide an overview of established head, linker, and tail groups and highlight selected scopes and limitations for applications. It becomes apparent that most recent contributions to the increasing chemical diversity of detergent building blocks originate from the development of detergents for membrane protein studies. The overview of synthesis strategies and molecular blocks will bring us closer to the ability to predictably design and synthesize optimal detergents for challenging future applications.
MeSH term(s)	Detergents/chemistry ; Membrane Proteins/chemistry
Chemical Substances	Detergents ; Membrane Proteins
Language	English
Publishing date	2023-09-28
Publishing country	Germany
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ISSN	2192-6506
ISSN (online)	2192-6506
DOI	10.1002/cplu.202300386
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Article: Combinatorial synthesis enables scalable designer detergents for membrane protein studies.

Urner, Leonhard H / Ariamajd, Armin / Weikum, Alex

Chemical science

2022 Volume 13, Issue 35, Page(s) 10299–10307

Abstract: Non-ionic detergents with tailor-made properties are indispensable tools for today's world applications, such as cleaning, disinfection, and drug discovery. To facilitate their challenging production, herein we introduce a new detergent class, namely ... ...

Abstract	Non-ionic detergents with tailor-made properties are indispensable tools for today's world applications, such as cleaning, disinfection, and drug discovery. To facilitate their challenging production, herein we introduce a new detergent class, namely scalable hybrid detergents. We report a combinatorial synthesis strategy that allows us to fuse head groups of different detergents into hybrid detergents with unbeatable ease. Importantly, combinatorial synthesis also enables the choice between (i) high-throughput preparation of detergents for small scale applications and (ii) large scale preparation of individual detergents. This combinatorial synthesis strategy enables an unprecedented fine tuning of detergent properties, such as overall polarity and shape, which are determining factors in applications, such as membrane protein research. Our data show that membrane protein purification parameters, such as protein yields and activity, can be linked to overall polarity and shape. Conveniently, both parameters can be theoretically described by means of the hydrophilic-lipophilic balance (HLB) and packing parameter concepts. Both concepts are principally applicable to all non-ionic detergent classes, which facilitates the identification of widely applicable design guidelines for the predictable optimization of non-ionic detergents. Our findings permit access to a yet unexplored chemical space of the detergentome, therefore creating new possibilities for structure-property relationship studies. Seen from a broader perspective, combinatorial synthesis will facilitate the preparation of designer detergents with tailor-made properties for future applications in today's world.
Language	English
Publishing date	2022-08-30
Publishing country	England
Document type	Journal Article
ZDB-ID	2559110-1
ISSN	2041-6539 ; 2041-6520
ISSN (online)	2041-6539
ISSN	2041-6520
DOI	10.1039/d2sc03130b
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Article ; Online: Non-ionic hybrid detergents for protein delipidation.

Urner, Leonhard H / Liko, Idlir / Pagel, Kevin / Haag, Rainer / Robinson, Carol V

Biochimica et biophysica acta. Biomembranes

2022 Volume 1864, Issue 9, Page(s) 183958

Abstract: Non-ionic detergents are important tools for the investigation of interactions between membrane proteins and lipid membranes. Recent studies led to the question as to whether the ability to capture protein-lipid interactions depends on the properties of ... ...

Abstract	Non-ionic detergents are important tools for the investigation of interactions between membrane proteins and lipid membranes. Recent studies led to the question as to whether the ability to capture protein-lipid interactions depends on the properties of detergents or their concentration in purification buffers. To address this question, we present the synthesis of an asymmetric, hybrid detergent that combines the head groups of detergents with opposing delipidating properties. We discuss detergent properties and protein purification outcomes to reveal whether the properties of detergent micelles or the detergent concentration in purification buffers drive membrane protein delipidation. We anticipate that our findings will enable the development of rationally design detergents for future applications in membrane protein research.
MeSH term(s)	Detergents/metabolism ; Lipids ; Membrane Proteins/metabolism ; Micelles
Chemical Substances	Detergents ; Lipids ; Membrane Proteins ; Micelles
Language	English
Publishing date	2022-05-10
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	60-7
ISSN	1879-2642 ; 1879-2596 ; 1879-260X ; 1872-8006 ; 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)	1879-2642 ; 1879-2596 ; 1879-260X ; 1872-8006 ; 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.2022.183958
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Article ; Online: Rationalizing the Optimization of Detergents for Membrane Protein Purification.

Urner, Leonhard H / Junge, Florian / Fiorentino, Francesco / El-Baba, Tarick J / Shutin, Denis / Nölte, Gideon / Haag, Rainer / Robinson, Carol V

Chemistry (Weinheim an der Bergstrasse, Germany)

2023 Volume 29, Issue 30, Page(s) e202300159

Abstract: Membrane protein purification by means of detergents is key to isolating membrane-bound therapeutic targets. The role of the detergent structure in this process, however, is not well understood. Detergents are optimized empirically, leading to failed ... ...

Abstract	Membrane protein purification by means of detergents is key to isolating membrane-bound therapeutic targets. The role of the detergent structure in this process, however, is not well understood. Detergents are optimized empirically, leading to failed preparations, and thereby raising costs. Here we evaluate the utility of the hydrophilic-lipophilic balance (HLB) concept, which was introduced by Griffin in 1949, for guiding the optimization of the hydrophobic tail in first-generation, dendritic oligoglycerol detergents ([G1] OGDs). Our findings deliver qualitative HLB guidelines for rationalizing the optimization of detergents. Moreover, [G1] OGDs exhibit strongly delipidating properties, regardless of the structure of the hydrophobic tail, which delivers a methodological enabling step for investigating binding strengths of endogenous lipids and their role for membrane protein oligomerization. Our findings will facilitate the analysis of challenging drug targets in the future.
MeSH term(s)	Detergents/chemistry ; Hydrophobic and Hydrophilic Interactions ; Membrane Proteins/chemistry ; alpha-Synuclein
Chemical Substances	Detergents ; FUS protein, human ; Membrane Proteins ; alpha-Synuclein
Language	English
Publishing date	2023-04-19
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1478547-X
ISSN	1521-3765 ; 0947-6539
ISSN (online)	1521-3765
ISSN	0947-6539
DOI	10.1002/chem.202300159
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Article ; Online: Detergents with Scalable Properties Identify Noncanonical Lipopolysaccharide Binding to Bacterial Inner Membrane Proteins.

Urner, Leonhard H / Fiorentino, Francesco / Shutin, Denis / Sauer, Joshua B / Agasid, Mark T / El-Baba, Tarick J / Bolla, Jani R / Stansfeld, Phillip J / Robinson, Carol V

Journal of the American Chemical Society

2024

Abstract: Lipopolysaccharide (LPS) is vital for maintaining the outer membrane barrier in Gram-negative bacteria. LPS is also frequently obtained in complex with the inner membrane proteins after detergent purification. The question of whether or not LPS binding ... ...

Abstract	Lipopolysaccharide (LPS) is vital for maintaining the outer membrane barrier in Gram-negative bacteria. LPS is also frequently obtained in complex with the inner membrane proteins after detergent purification. The question of whether or not LPS binding to inner membrane proteins not involved in outer membrane biogenesis reflects native lipid environments remains unclear. Here, we leverage the control of the hydrophilic-lipophilic balance and packing parameter concepts to chemically tune detergents that can be used to qualitatively differentiate the degree to which proteins copurify with phospholipids (PLs) and/or LPS. Given the scalable properties of these detergents, we demonstrate a detergent fine-tuning that enables the facile investigation of intact proteins and their complexes with lipids by native mass spectrometry (nMS). We conclude that LPS, a lipid that is believed to be important for outer membranes, can also affect the activity of membrane proteins that are currently not assigned to be involved in outer membrane biogenesis. Our results deliver a scalable detergent chemistry for a streamlined biophysical characterization of protein-lipid interactions, provide a rationale for the high affinity of LPS-protein binding, and identify noncanonical associations between LPS and inner membrane proteins with relevance for membrane biology and antibiotic research.
Language	English
Publishing date	2024-04-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.3c14358
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Article: The Effects of Sodium Ions on Ligand Binding and Conformational States of G Protein-Coupled Receptors—Insights from Mass Spectrometry

Agasid, Mark T / Sørensen, Lars / Urner, Leonhard H / Yan, Jun / Robinson, Carol V

Journal of the American Chemical Society. 2021 Mar. 12, v. 143, no. 11

2021

Abstract: The use of mass spectrometry to investigate proteins is now well established and provides invaluable information for both soluble and membrane protein assemblies. Maintaining transient noncovalent interactions under physiological conditions, however, ... ...

Abstract	The use of mass spectrometry to investigate proteins is now well established and provides invaluable information for both soluble and membrane protein assemblies. Maintaining transient noncovalent interactions under physiological conditions, however, remains challenging. Here, using nanoscale electrospray ionization emitters, we establish conditions that enable mass spectrometry of two G protein-coupled receptors (GPCR) from buffers containing high concentrations of sodium ions. For the Class A GPCR, the adenosine 2A receptor, we observe ligand-induced changes to sodium binding of the receptor at the level of individual sodium ions. We find that antagonists promote sodium binding while agonists attenuate sodium binding. These findings are in line with high-resolution X-ray crystallography wherein only inactive conformations retain sodium ions in allosteric binding pockets. For the glucagon receptor (a Class B GPCR) we observed enhanced ligand binding in electrospray buffers containing high concentrations of sodium, as opposed to ammonium acetate buffers. A combination of native and -omics mass spectrometry revealed the presence of a lipophilic negative allosteric modulator. These experiments highlight the advantages of implementing native mass spectrometry, from electrospray buffers containing high concentrations of physiologically relevant salts, to inform on allosteric ions or ligands with the potential to define their roles on GPCR function.
Keywords	X-ray diffraction ; adenosine ; ammonium acetate ; electrospray ionization mass spectrometry ; glucagon receptors ; ligands ; lipophilicity ; sodium
Language	English
Dates of publication	2021-0312
Size	p. 4085-4089.
Publishing place	American Chemical Society
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.0c11837
Database	NAL-Catalogue (AGRICOLA)

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