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Ru G, Liu X, Ge Y, Wang L, Jiang L, Pielak G, Liu M, Li C. Trimethylamine N-oxide (TMAO) doubly locks the hydrophobic core and surfaces of protein against desiccation stress. Protein Sci 2024; 33:e5107. [PMID: 38989549 PMCID: PMC11237552 DOI: 10.1002/pro.5107] [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: 04/03/2024] [Revised: 06/14/2024] [Accepted: 06/23/2024] [Indexed: 07/12/2024]
Abstract
Interactions between proteins and osmolytes are ubiquitous within cells, assisting in response to environmental stresses. However, our understanding of protein-osmolyte interactions underlying desiccation tolerance is limited. Here, we employ solid-state NMR (ssNMR) to derive information about protein conformation and site-specific interactions between the model protein, SH3, and the osmolyte trimethylamine N-oxide (TMAO). The data show that SH3-TMAO interactions maintain key structured regions during desiccation and facilitate reversion to the protein's native state once desiccation stress is even slightly relieved. We identify 10 types of residues at 28 sites involved in the SH3-TMAO interactions. These sites comprise hydrophobic, positively charged, and aromatic amino acids located in SH3's hydrophobic core and surface clusters. TMAO locks both the hydrophobic core and surface clusters through its zwitterionic and trimethyl ends. This double locking is responsible for desiccation tolerance and differs from ideas based on exclusion, vitrification, and water replacement. ssNMR is a powerful tool for deepening our understanding of extremely weak protein-osmolyte interactions and providing insight into the evolutionary mechanism of environmental tolerance.
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Affiliation(s)
- Geying Ru
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Xiaoli Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Yuwei Ge
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Liying Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Ling Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Gary Pielak
- Department of Chemistry, Department of Biochemistry & Biophysics, Lineberger Cancer Center, Integrative Program for Biological and Genome Sciences of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
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2
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Kumar S, Stover L, Wang L, Bahramimoghaddam H, Zhou M, Russell DH, Laganowsky A. Native mass spectrometry of membrane protein-lipid interactions in different detergent environments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601044. [PMID: 38979331 PMCID: PMC11230385 DOI: 10.1101/2024.06.27.601044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Native mass spectrometry (MS) is revealing the role of specific lipids in modulating membrane protein structure and function. Membrane proteins solubilized in detergents are often introduced into the mass spectrometer; however, commonly used detergents for structural studies, such as dodecylmaltoside, tend to generate highly charged ions, leading to protein unfolding, thereby diminishing their utility for characterizing protein-lipid interactions. Thus, there is a critical need to develop approaches to investigate protein-lipid interactions in different detergents. Here, we demonstrate how charge-reducing molecules, such as spermine and trimethylamine-N-oxide, enable characterization of lipid binding to the bacterial water channel (AqpZ) and ammonia channel (AmtB) in complex with regulatory protein GlnK in different detergent environments. We find protein-lipid interactions are not only protein-dependent but can also be influenced by the detergent and type of charge-reducing molecule. AqpZ-lipid interactions are enhanced in LDAO (n-dodecyl-N,N-dimethylamine-N-oxide), whereas the interaction of AmtB-GlnK with lipids is comparable among different detergents. A fluorescent lipid binding assay also shows detergent dependence for AqpZ-lipid interactions, consistent with results from native MS. Taken together, native MS will play a pivotal role in establishing optimal experimental parameters that will be invaluable for various applications, such as drug discovery, as well as biochemical and structural investigations.
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Affiliation(s)
- Smriti Kumar
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lauren Stover
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lie Wang
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
| | | | - Ming Zhou
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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3
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Ng YK, Konermann L. Mechanism of Protein Aggregation Inhibition by Arginine: Blockage of Anionic Side Chains Favors Unproductive Encounter Complexes. J Am Chem Soc 2024; 146:8394-8406. [PMID: 38477601 DOI: 10.1021/jacs.3c14180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Aggregation refers to the assembly of proteins into nonphysiological higher order structures. While amyloid has been studied extensively, much less is known about amorphous aggregation, a process that interferes with protein expression and storage. Free arginine (Arg+) is a widely used aggregation inhibitor, but its mechanism remains elusive. Focusing on myoglobin (Mb), we recently applied atomistic molecular dynamics (MD) simulations for gaining detailed insights into amorphous aggregation (Ng J. Phys. Chem. B 2021, 125, 13099). Building on that approach, the current work for the first time demonstrates that MD simulations can directly elucidate aggregation inhibition mechanisms. Comparative simulations with and without Arg+ reproduced the experimental finding that Arg+ significantly decreased the Mb aggregation propensity. Our data reveal that, without Arg+, protein-protein encounter complexes readily form salt bridges and hydrophobic contacts, culminating in firmly linked dimeric aggregation nuclei. Arg+ promotes the dissociation of encounter complexes. These "unproductive" encounter complexes are favored because Arg+ binding to D- and E- lowers the tendency of these anionic residues to form interprotein salt bridges. Side chain blockage is mediated largely by the guanidinium group of Arg+, which binds carboxylates through H-bond-reinforced ionic contacts. Our MD data revealed Arg+ self-association into a dynamic quasi-infinite network, but we found no evidence that this self-association is important for protein aggregation inhibition. Instead, aggregation inhibition by Arg+ is similar to that mediated by free guanidinium ions. The computational strategy used here should be suitable for the rational design of aggregation inhibitors with enhanced potency.
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Affiliation(s)
- Yuen Ki Ng
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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4
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Emergence of mass spectrometry detergents for membrane proteomics. Anal Bioanal Chem 2023:10.1007/s00216-023-04584-z. [PMID: 36808272 PMCID: PMC10328889 DOI: 10.1007/s00216-023-04584-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 02/21/2023]
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.
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5
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Kumar S, Zhu Y, Stover L, Laganowsky A. Step toward Probing the Nonannular Belt of Membrane Proteins. Anal Chem 2022; 94:13906-13912. [PMID: 36170465 DOI: 10.1021/acs.analchem.2c02811] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Integral membrane proteins are embedded in the biological membrane, where they carry out numerous biological processes. Although lipids present in the membrane are crucial for membrane protein function, it remains difficult to characterize many lipid binding events to membrane proteins, such as those that form the annular belt. Here, we use native mass spectrometry along with the charge-reducing properties of trimethylamine N-oxide (TMAO) to characterize a large number of lipid binding events to the bacterial ammonia channel (AmtB). In the absence of TMAO, significant peak overlap between neighboring charge states is observed, resulting in erroneous abundances for different molecular species. With the addition of TMAO, the weighted average charge state (Zavg) was decreased. In addition, the increased spacing between nearby charge states enabled a higher number of lipid binding species to be observed while minimizing mass spectral peak overlap. These conditions helped us to determine the equilibrium binding constants (Kd) for up to 16 lipid binding events. The binding constants for the first few lipid binding events display the highest affinity, whereas the binding constants for higher lipid binding events converge to a similar value. These findings suggest a transition from nonannular to annular lipid binding to AmtB.
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Affiliation(s)
- Smriti Kumar
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yun Zhu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lauren Stover
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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6
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Serebryany E, Chowdhury S, Woods CN, Thorn DC, Watson NE, McClelland AA, Klevit RE, Shakhnovich EI. A native chemical chaperone in the human eye lens. eLife 2022; 11:76923. [PMID: 35723573 PMCID: PMC9246369 DOI: 10.7554/elife.76923] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/13/2022] [Indexed: 12/02/2022] Open
Abstract
Cataract is one of the most prevalent protein aggregation disorders and still the most common cause of vision loss worldwide. The metabolically quiescent core region of the human lens lacks cellular or protein turnover; it has therefore evolved remarkable mechanisms to resist light-scattering protein aggregation for a lifetime. We now report that one such mechanism involves an unusually abundant lens metabolite, myo-inositol, suppressing aggregation of lens crystallins. We quantified aggregation suppression using our previously well-characterized in vitro aggregation assays of oxidation-mimicking human γD-crystallin variants and investigated myo-inositol’s molecular mechanism of action using solution NMR, negative-stain TEM, differential scanning fluorometry, thermal scanning Raman spectroscopy, turbidimetry in redox buffers, and free thiol quantitation. Unlike many known chemical chaperones, myo-inositol’s primary target was not the native, unfolded, or final aggregated states of the protein; rather, we propose that it was the rate-limiting bimolecular step on the aggregation pathway. Given recent metabolomic evidence that it is severely depleted in human cataractous lenses compared to age-matched controls, we suggest that maintaining or restoring healthy levels of myo-inositol in the lens may be a simple, safe, and globally accessible strategy to prevent or delay lens opacification due to age-onset cataract.
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Affiliation(s)
- Eugene Serebryany
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Sourav Chowdhury
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Christopher N Woods
- Department of Biochemistry, University of Washington, Seattle, United States
| | - David C Thorn
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Nicki E Watson
- Center for Nanoscale Systems, Harvard University, Cambridge, United States
| | | | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
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7
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Yen HY, Abramsson ML, Agasid MT, Lama D, Gault J, Liko I, Kaldmäe M, Saluri M, Qureshi AA, Suades A, Drew D, Degiacomi MT, Marklund EG, Allison TM, Robinson CV, Landreh M. Electrospray ionization of native membrane proteins proceeds via a charge equilibration step. RSC Adv 2022; 12:9671-9680. [PMID: 35424940 PMCID: PMC8972943 DOI: 10.1039/d2ra01282k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/21/2022] [Indexed: 11/21/2022] Open
Abstract
Electrospray ionization mass spectrometry is increasingly applied to study the structures and interactions of membrane protein complexes. However, the charging mechanism is complicated by the presence of detergent micelles during ionization. Here, we show that the final charge of membrane proteins can be predicted by their molecular weight when released from the non-charge reducing saccharide detergents. Our data indicate that PEG detergents lower the charge depending on the number of detergent molecules in the surrounding micelle, whereas fos-choline detergents may additionally participate in ion–ion reactions after desolvation. The supercharging reagent sulfolane, on the other hand, has no discernible effect on the charge of detergent-free membrane proteins. Taking our observations into the context of protein-detergent interactions in the gas phase, we propose a charge equilibration model for the generation of native-like membrane protein ions. During ionization of the protein-detergent complex, the ESI charges are distributed between detergent and protein according to proton affinity of the detergent, number of detergent molecules, and surface area of the protein. Charge equilibration influenced by detergents determines the final charge state of membrane proteins. This process likely contributes to maintaining a native-like fold after detergent release and can be harnessed to stabilize particularly labile membrane protein complexes in the gas phase. The electrospray ionization mechanism contributes to preserving the structures and interactions of membrane protein complexes in native mass spectrometry.![]()
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Affiliation(s)
- Hsin-Yung Yen
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK .,Institute of Biological Chemistry, Academia Sinica 128, Academia Road Sec. 2, Nankang Taipei 115 Taiwan
| | - Mia L Abramsson
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Tomtebodavägen 23A 17165 Stockholm Sweden
| | - Mark T Agasid
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Dilraj Lama
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Tomtebodavägen 23A 17165 Stockholm Sweden
| | - Joseph Gault
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Idlir Liko
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Margit Kaldmäe
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Tomtebodavägen 23A 17165 Stockholm Sweden
| | - Mihkel Saluri
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Tomtebodavägen 23A 17165 Stockholm Sweden
| | - Abdul Aziz Qureshi
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK .,Department of Biochemistry and Biophysics, Stockholm University 10691 Stockholm Sweden
| | - Albert Suades
- Department of Biochemistry and Biophysics, Stockholm University 10691 Stockholm Sweden
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm University 10691 Stockholm Sweden
| | | | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University Box 576 75123 Uppsala Sweden
| | - Timothy M Allison
- Biomolecular Interaction Centre, School of Physical and Chemical Sciences, University of Canterbury Christchurch 8140 New Zealand
| | - Carol V Robinson
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Tomtebodavägen 23A 17165 Stockholm Sweden
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8
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Abramsson ML, Sahin C, Hopper JTS, Branca RMM, Danielsson J, Xu M, Chandler SA, Österlund N, Ilag LL, Leppert A, Costeira-Paulo J, Lang L, Teilum K, Laganowsky A, Benesch JLP, Oliveberg M, Robinson CV, Marklund EG, Allison TM, Winther JR, Landreh M. Charge Engineering Reveals the Roles of Ionizable Side Chains in Electrospray Ionization Mass Spectrometry. JACS AU 2021; 1:2385-2393. [PMID: 34977906 PMCID: PMC8717373 DOI: 10.1021/jacsau.1c00458] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Indexed: 05/03/2023]
Abstract
In solution, the charge of a protein is intricately linked to its stability, but electrospray ionization distorts this connection, potentially limiting the ability of native mass spectrometry to inform about protein structure and dynamics. How the behavior of intact proteins in the gas phase depends on the presence and distribution of ionizable surface residues has been difficult to answer because multiple chargeable sites are present in virtually all proteins. Turning to protein engineering, we show that ionizable side chains are completely dispensable for charging under native conditions, but if present, they are preferential protonation sites. The absence of ionizable side chains results in identical charge state distributions under native-like and denaturing conditions, while coexisting conformers can be distinguished using ion mobility separation. An excess of ionizable side chains, on the other hand, effectively modulates protein ion stability. In fact, moving a single ionizable group can dramatically alter the gas-phase conformation of a protein ion. We conclude that although the sum of the charges is governed solely by Coulombic terms, their locations affect the stability of the protein in the gas phase.
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Affiliation(s)
- Mia L. Abramsson
- Department
of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 171 65 Stockholm, Sweden
| | - Cagla Sahin
- Department
of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 171 65 Stockholm, Sweden
- Linderstrøm-Lang
Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen, Denmark
| | - Jonathan T. S. Hopper
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Rui M. M. Branca
- Department
of Oncology-Pathology, Science for Life
Laboratory and Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Jens Danielsson
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Mingming Xu
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Shane A. Chandler
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Nicklas Österlund
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Leopold L. Ilag
- Department
of Material and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
| | - Axel Leppert
- Department
of Biosciences and Nutrition, Karolinska
Institutet, Neo, 141 83 Huddinge, Sweden
| | - Joana Costeira-Paulo
- Department
of Chemistry−BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Lisa Lang
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Kaare Teilum
- Linderstrøm-Lang
Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen, Denmark
| | - Arthur Laganowsky
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Justin L. P. Benesch
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Mikael Oliveberg
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Carol V. Robinson
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Erik G. Marklund
- Department
of Chemistry−BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Timothy M. Allison
- Biomolecular
Interaction Centre, School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Jakob R. Winther
- Linderstrøm-Lang
Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen, Denmark
| | - Michael Landreh
- Department
of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 171 65 Stockholm, Sweden
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9
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Pharmacological targeting of endoplasmic reticulum stress in disease. Nat Rev Drug Discov 2021; 21:115-140. [PMID: 34702991 DOI: 10.1038/s41573-021-00320-3] [Citation(s) in RCA: 181] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2021] [Indexed: 02/08/2023]
Abstract
The accumulation of misfolded proteins in the endoplasmic reticulum (ER) leads to ER stress, resulting in activation of the unfolded protein response (UPR) that aims to restore protein homeostasis. However, the UPR also plays an important pathological role in many diseases, including metabolic disorders, cancer and neurological disorders. Over the last decade, significant effort has been invested in targeting signalling proteins involved in the UPR and an array of drug-like molecules is now available. However, these molecules have limitations, the understanding of which is crucial for their development into therapies. Here, we critically review the existing ER stress and UPR-directed drug-like molecules, highlighting both their value and their limitations.
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10
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McCabe JW, Hebert MJ, Shirzadeh M, Mallis CS, Denton JK, Walker TE, Russell DH. THE IMS PARADOX: A PERSPECTIVE ON STRUCTURAL ION MOBILITY-MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:280-305. [PMID: 32608033 PMCID: PMC7989064 DOI: 10.1002/mas.21642] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/03/2020] [Indexed: 05/06/2023]
Abstract
Studies of large proteins, protein complexes, and membrane protein complexes pose new challenges, most notably the need for increased ion mobility (IM) and mass spectrometry (MS) resolution. This review covers evolutionary developments in IM-MS in the authors' and key collaborators' laboratories with specific focus on developments that enhance the utility of IM-MS for structural analysis. IM-MS measurements are performed on gas phase ions, thus "structural IM-MS" appears paradoxical-do gas phase ions retain their solution phase structure? There is growing evidence to support the notion that solution phase structure(s) can be retained by the gas phase ions. It should not go unnoticed that we use "structures" in this statement because an important feature of IM-MS is the ability to deal with conformationally heterogeneous systems, thus providing a direct measure of conformational entropy. The extension of this work to large proteins and protein complexes has motivated our development of Fourier-transform IM-MS instruments, a strategy first described by Hill and coworkers in 1985 (Anal Chem, 1985, 57, pp. 402-406) that has proved to be a game-changer in our quest to merge drift tube (DT) and ion mobility and the high mass resolution orbitrap MS instruments. DT-IMS is the only method that allows first-principles determinations of rotationally averaged collision cross sections (CSS), which is essential for studies of biomolecules where the conformational diversities of the molecule precludes the use of CCS calibration approaches. The Fourier transform-IM-orbitrap instrument described here also incorporates the full suite of native MS/IM-MS capabilities that are currently employed in the most advanced native MS/IM-MS instruments. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - Michael J Hebert
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | | | - Joanna K Denton
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - Thomas E Walker
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
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11
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Affiliation(s)
- James E. Keener
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Guozhi Zhang
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Michael T. Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
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12
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Barth M, Schmidt C. Native mass spectrometry-A valuable tool in structural biology. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4578. [PMID: 32662584 DOI: 10.1002/jms.4578] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 05/16/2023]
Abstract
Proteins and the complexes they form with their ligands are the players of cellular action. Their function is directly linked with their structure making the structural analysis of protein-ligand complexes essential. Classical techniques of structural biology include X-ray crystallography, nuclear magnetic resonance spectroscopy and recently distinguished cryo-electron microscopy. However, protein-ligand complexes are often dynamic and heterogeneous and consequently challenging for these techniques. Alternative approaches are therefore needed and gained importance during the last decades. One alternative is native mass spectrometry, which is the analysis of intact protein complexes in the gas phase. To achieve this, sample preparation and instrument conditions have to be optimised. Native mass spectrometry then reveals stoichiometry, protein interactions and topology of protein assemblies. Advanced techniques such as ion mobility and high-resolution mass spectrometry further add to the range of applications and deliver information on shape and microheterogeneity of the complexes. In this tutorial, we explain the basics of native mass spectrometry including sample requirements, instrument modifications and interpretation of native mass spectra. We further discuss the developments of native mass spectrometry and provide example spectra and applications.
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Affiliation(s)
- Marie Barth
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
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13
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Lyu J, Liu Y, McCabe JW, Schrecke S, Fang L, Russell DH, Laganowsky A. Discovery of Potent Charge-Reducing Molecules for Native Ion Mobility Mass Spectrometry Studies. Anal Chem 2020; 92:11242-11249. [PMID: 32672445 DOI: 10.1021/acs.analchem.0c01826] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
There is growing interest in the characterization of protein complexes and their interactions with ligands using native ion mobility mass spectrometry. A particular challenge, especially for membrane proteins, is preserving noncovalent interactions and maintaining native-like structures. Different approaches have been developed to minimize activation of protein complexes by manipulating charge on protein complexes in solution and the gas-phase. Here, we report the utility of polyamines that have exceptionally high charge-reducing potencies with some molecules requiring 5-fold less than trimethylamine oxide to elicit the same effect. The charge-reducing molecules do not adduct to membrane protein complexes and are also compatible with ion-mobility mass spectrometry, paving the way for improved methods of charge reduction.
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Affiliation(s)
- Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yang Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Samantha Schrecke
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lei Fang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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14
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Ganguly P, Polák J, van der Vegt NFA, Heyda J, Shea JE. Protein Stability in TMAO and Mixed Urea–TMAO Solutions. J Phys Chem B 2020; 124:6181-6197. [DOI: 10.1021/acs.jpcb.0c04357] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Pritam Ganguly
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California 93106, United States
| | - Jakub Polák
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, Darmstadt 64287, Germany
| | - Jan Heyda
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California 93106, United States
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, United States
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15
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Urner LH, Schulze M, Maier YB, Hoffmann W, Warnke S, Liko I, Folmert K, Manz C, Robinson CV, Haag R, Pagel K. A new azobenzene-based design strategy for detergents in membrane protein research. Chem Sci 2020; 11:3538-3546. [PMID: 34109026 PMCID: PMC8152689 DOI: 10.1039/d0sc01022g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 03/09/2020] [Indexed: 12/02/2022] Open
Abstract
Mass spectrometry enables the in-depth structural elucidation of membrane protein complexes, which is of great interest in structural biology and drug discovery. Recent breakthroughs in this field revealed the need for design rules that allow fine-tuning the properties of detergents in solution and gas phase. Desirable features include protein charge reduction, because it helps to preserve native features of protein complexes during transfer from solution into the vacuum of a mass spectrometer. Addressing this challenge, we here present the first systematic gas-phase study of azobenzene detergents. The utility of gas-phase techniques for monitoring light-driven changes of isomer ratios and molecular properties are investigated in detail. This leads to the first azobenzene detergent that enables the native mass spectrometry analysis of membrane proteins and whose charge-reducing properties can be tuned by irradiation with light. More broadly, the presented work outlines new avenues for the high-throughput characterization of supramolecular systems and opens a new design strategy for detergents in membrane protein research.
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Affiliation(s)
- Leonhard H Urner
- Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society Faradayweg 4-6 14195 Berlin Germany
- Physical and Theoretical Chemistry Laboratory, University of Oxford South Parks Road OX13QZ Oxford UK
| | - Maiko Schulze
- Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Yasmine B Maier
- Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Waldemar Hoffmann
- Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society Faradayweg 4-6 14195 Berlin Germany
| | - Stephan Warnke
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society Faradayweg 4-6 14195 Berlin Germany
| | - Idlir Liko
- Physical and Theoretical Chemistry Laboratory, University of Oxford South Parks Road OX13QZ Oxford UK
| | - Kristin Folmert
- Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Christian Manz
- Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford South Parks Road OX13QZ Oxford UK
| | - Rainer Haag
- Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society Faradayweg 4-6 14195 Berlin Germany
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16
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Bolla JR, Corey RA, Sahin C, Gault J, Hummer A, Hopper JTS, Lane DP, Drew D, Allison TM, Stansfeld PJ, Robinson CV, Landreh M. A Mass‐Spectrometry‐Based Approach to Distinguish Annular and Specific Lipid Binding to Membrane Proteins. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jani Reddy Bolla
- Department of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Robin A. Corey
- Department of BiochemistryUniversity of Oxford South Parks Road Oxford OX1 3QU UK
| | - Cagla Sahin
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet 17165 Solna Sweden
- Department of BiologyUniversity of Copenhagen Copenhagen N 2200 Denmark
| | - Joseph Gault
- Department of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Alissa Hummer
- Department of BiochemistryUniversity of Oxford South Parks Road Oxford OX1 3QU UK
| | - Jonathan T. S. Hopper
- OMass Therapeutics The Oxford Science Park, The Schrödinger Building Kidlington OX4 4GE UK
| | - David P. Lane
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet 17165 Solna Sweden
| | - David Drew
- Department of Biochemistry and BiophysicsStockholm University 10691 Stockholm Sweden
| | - Timothy M. Allison
- Biomolecular Interaction Centre and School of Physical and Chemical SciencesUniversity of Canterbury Christchurch 8140 New Zealand
| | - Phillip J. Stansfeld
- Department of BiochemistryUniversity of Oxford South Parks Road Oxford OX1 3QU UK
- School of Life Sciences & Department of ChemistryUniversity of Warwick Coventry CV4 7AL UK
| | - Carol V. Robinson
- Department of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet 17165 Solna Sweden
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17
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Bolla JR, Corey RA, Sahin C, Gault J, Hummer A, Hopper JTS, Lane DP, Drew D, Allison TM, Stansfeld PJ, Robinson CV, Landreh M. A Mass-Spectrometry-Based Approach to Distinguish Annular and Specific Lipid Binding to Membrane Proteins. Angew Chem Int Ed Engl 2020; 59:3523-3528. [PMID: 31886601 PMCID: PMC7065234 DOI: 10.1002/anie.201914411] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/29/2019] [Indexed: 01/21/2023]
Abstract
Membrane proteins engage in a variety of contacts with their surrounding lipids, but distinguishing between specifically bound lipids, and non-specific, annular interactions is a challenging problem. Applying native mass spectrometry to three membrane protein complexes with different lipid-binding properties, we explore the ability of detergents to compete with lipids bound in different environments. We show that lipids in annular positions on the presenilin homologue protease are subject to constant exchange with detergent. By contrast, detergent-resistant lipids bound at the dimer interface in the leucine transporter show decreased koff rates in molecular dynamics simulations. Turning to the lipid flippase MurJ, we find that addition of the natural substrate lipid-II results in the formation of a 1:1 protein-lipid complex, where the lipid cannot be displaced by detergent from the highly protected active site. In summary, we distinguish annular from non-annular lipids based on their exchange rates in solution.
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Affiliation(s)
- Jani Reddy Bolla
- Department of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QZUK
| | - Robin A. Corey
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
| | - Cagla Sahin
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet17165SolnaSweden
- Department of BiologyUniversity of CopenhagenCopenhagen N2200Denmark
| | - Joseph Gault
- Department of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QZUK
| | - Alissa Hummer
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
| | - Jonathan T. S. Hopper
- OMass TherapeuticsThe Oxford Science Park, The Schrödinger BuildingKidlingtonOX4 4GEUK
| | - David P. Lane
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet17165SolnaSweden
| | - David Drew
- Department of Biochemistry and BiophysicsStockholm University10691StockholmSweden
| | - Timothy M. Allison
- Biomolecular Interaction Centre and School of Physical and Chemical SciencesUniversity of CanterburyChristchurch8140New Zealand
| | - Phillip J. Stansfeld
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
- School of Life Sciences & Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
| | - Carol V. Robinson
- Department of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QZUK
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet17165SolnaSweden
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18
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Urner LH, Liko I, Yen HY, Hoi KK, Bolla JR, Gault J, Almeida FG, Schweder MP, Shutin D, Ehrmann S, Haag R, Robinson CV, Pagel K. Modular detergents tailor the purification and structural analysis of membrane proteins including G-protein coupled receptors. Nat Commun 2020; 11:564. [PMID: 31992701 PMCID: PMC6987200 DOI: 10.1038/s41467-020-14424-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/19/2019] [Indexed: 01/29/2023] Open
Abstract
Detergents enable the purification of membrane proteins and are indispensable reagents in structural biology. Even though a large variety of detergents have been developed in the last century, the challenge remains to identify guidelines that allow fine-tuning of detergents for individual applications in membrane protein research. Addressing this challenge, here we introduce the family of oligoglycerol detergents (OGDs). Native mass spectrometry (MS) reveals that the modular OGD architecture offers the ability to control protein purification and to preserve interactions with native membrane lipids during purification. In addition to a broad range of bacterial membrane proteins, OGDs also enable the purification and analysis of a functional G-protein coupled receptor (GPCR). Moreover, given the modular design of these detergents, we anticipate fine-tuning of their properties for specific applications in structural biology. Seen from a broader perspective, this represents a significant advance for the investigation of membrane proteins and their interactions with lipids. Detergents are indispensable reagents in membrane protein structural biology. Here, L. H. Urner and co-workers introduce oligoglycerol detergents (OGDs) and use native mass spectrometry to show how interactions of membrane proteins with native membrane lipids can be preserved during purification.
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Affiliation(s)
- Leonhard H Urner
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany.,Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ, UK
| | - Idlir Liko
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ, UK.,OMass Therapeutics, The Schrödinger Building, Heatley Road, The Oxford Science Park, Oxford, OX4 4GE, UK
| | - Hsin-Yung Yen
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ, UK.,OMass Therapeutics, The Schrödinger Building, Heatley Road, The Oxford Science Park, Oxford, OX4 4GE, UK
| | - Kin-Kuan Hoi
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ, UK
| | - Jani Reddy Bolla
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ, UK
| | - Joseph Gault
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ, UK
| | - Fernando Gonçalves Almeida
- OMass Therapeutics, The Schrödinger Building, Heatley Road, The Oxford Science Park, Oxford, OX4 4GE, UK
| | - Marc-Philip Schweder
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
| | - Denis Shutin
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ, UK
| | - Svenja Ehrmann
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
| | - Rainer Haag
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany.
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ, UK.
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany. .,Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, 14195, Berlin, Germany.
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19
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Azoulay‐Ginsburg S, Trobiani L, Setini A, Favaloro FL, Giorda E, Jacob A, Hauschner H, Levy L, Cestra G, De Jaco A, Gruzman A. A Lipophilic 4‐Phenylbutyric Acid Derivative That Prevents Aggregation and Retention of Misfolded Proteins. Chemistry 2020; 26:1834-1845. [DOI: 10.1002/chem.201904292] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/17/2019] [Indexed: 12/20/2022]
Affiliation(s)
| | - Laura Trobiani
- Department of Biology and Biotechnology “Charles Darwin”, andPasteur Institute—Cenci Bolognetti FoundationSapienza University of Rome Piazzale Aldo Moro 5 Rome 00185 Italy
| | - Andrea Setini
- Department of Biology and Biotechnology “Charles Darwin”, andPasteur Institute—Cenci Bolognetti FoundationSapienza University of Rome Piazzale Aldo Moro 5 Rome 00185 Italy
| | - Flores Lietta Favaloro
- Department of Biology and Biotechnology “Charles Darwin”, andPasteur Institute—Cenci Bolognetti FoundationSapienza University of Rome Piazzale Aldo Moro 5 Rome 00185 Italy
| | - Ezio Giorda
- Ospedale Pediatrico Bambin Gesù-Rome Piazza di Sant'Onofrio 4 Rome 00165 Italy
| | - Avi Jacob
- Faculty of Life SciencesBar-Ilan University Ramat-Gan 5290002 Israel
| | - Hagit Hauschner
- Faculty of Life SciencesBar-Ilan University Ramat-Gan 5290002 Israel
| | - Laura Levy
- Department of ChemistryBar-Ilan University Ramat-Gan 5290002 Israel
| | - Gianluca Cestra
- Department of Biology and Biotechnology “Charles Darwin”, andPasteur Institute—Cenci Bolognetti FoundationSapienza University of Rome Piazzale Aldo Moro 5 Rome 00185 Italy
- Institute of Molecular Biology and Pathology—National Research CouncilSapienza University of Rome Piazzale Aldo Moro 5 Rome 00185 Italy
| | - Antonella De Jaco
- Department of Biology and Biotechnology “Charles Darwin”, andPasteur Institute—Cenci Bolognetti FoundationSapienza University of Rome Piazzale Aldo Moro 5 Rome 00185 Italy
| | - Arie Gruzman
- Department of ChemistryBar-Ilan University Ramat-Gan 5290002 Israel
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20
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Townsend JA, Keener JE, Miller ZM, Prell JS, Marty MT. Imidazole Derivatives Improve Charge Reduction and Stabilization for Native Mass Spectrometry. Anal Chem 2019; 91:14765-14772. [PMID: 31638377 DOI: 10.1021/acs.analchem.9b04263] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Noncovalent interactions between biomolecules are critical to their activity. Native mass spectrometry (MS) has enabled characterization of these interactions by preserving noncovalent assemblies for mass analysis, including protein-ligand and protein-protein complexes for a wide range of soluble and membrane proteins. Recent advances in native MS of lipoprotein nanodiscs have also allowed characterization of antimicrobial peptides and membrane proteins embedded in intact lipid bilayers. However, conventional native electrospray ionization (ESI) can disrupt labile interactions. To stabilize macromolecular complexes for native MS, charge reducing reagents can be added to the solution prior to ESI, such as triethylamine, trimethylamine oxide, and imidazole. Lowering the charge acquired during ESI reduces Coulombic repulsion that leads to dissociation, and charge reduction reagents may also lower the internal energy of the ions through evaporative cooling. Here, we tested a range of imidazole derivatives to discover improved charge reducing reagents and to determine how their chemical properties influence charge reduction efficacy. We measured their effects on a soluble protein complex, a membrane protein complex in detergent, and lipoprotein nanodiscs with and without embedded peptides, and used computational chemistry to understand the observed charge-reduction behavior. Together, our data revealed that hydrophobic substituents at the 2 position on imidazole can significantly improve both charge reduction and gas-phase stability over existing reagents. These new imidazole derivatives will be immediately beneficial for a range of native MS applications and provide chemical principles to guide development of novel charge reducing reagents.
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Affiliation(s)
- Julia A Townsend
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - James E Keener
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Zachary M Miller
- Department of Chemistry and Biochemistry , University of Oregon , Eugene , Oregon 97403 , United States
| | - James S Prell
- Department of Chemistry and Biochemistry , University of Oregon , Eugene , Oregon 97403 , United States.,Materials Science Institute , University of Oregon , Eugene , Oregon 97403 , United States
| | - Michael T Marty
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
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21
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Kaldmäe M, Österlund N, Lianoudaki D, Sahin C, Bergman P, Nyman T, Kronqvist N, Ilag LL, Allison TM, Marklund EG, Landreh M. Gas-Phase Collisions with Trimethylamine-N-Oxide Enable Activation-Controlled Protein Ion Charge Reduction. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1385-1388. [PMID: 31286443 PMCID: PMC6669196 DOI: 10.1007/s13361-019-02177-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/20/2019] [Accepted: 03/01/2019] [Indexed: 05/19/2023]
Abstract
Modulating protein ion charge is a useful tool for the study of protein folding and interactions by electrospray ionization mass spectrometry. Here, we investigate activation-dependent charge reduction of protein ions with the chemical chaperone trimethylamine-N-oxide (TMAO). Based on experiments carried out on proteins ranging from 4.5 to 35 kDa, we find that when combined with collisional activation, TMAO removes approximately 60% of the charges acquired under native conditions. Ion mobility measurements furthermore show that TMAO-mediated charge reduction produces the same end charge state and arrival time distributions for native-like and denatured protein ions. Our results suggest that gas-phase collisions between the protein ions and TMAO result in proton transfer, in line with previous findings for dimethyl- and trimethylamine. By adjusting the energy of the collisions experienced by the ions, it is possible to control the degree of charge reduction, making TMAO a highly dynamic charge reducer that opens new avenues for manipulating protein charge states in ESI-MS and for investigating the relationship between protein charge and conformation. ᅟ.
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Affiliation(s)
- Margit Kaldmäe
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Nicklas Österlund
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden
- Department of Environmental Science and Analytical Chemistry, Stockholm University, 106 91, Stockholm, Sweden
| | - Danai Lianoudaki
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Cagla Sahin
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Peter Bergman
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, 141 86, Huddinge, Sweden
| | - Tomas Nyman
- Protein Science Facility, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Nina Kronqvist
- Division for Neurogeriatrics, Department of Neurobiology, Care Sciences and Society (NVS), Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Leopold L Ilag
- Department of Environmental Science and Analytical Chemistry, Stockholm University, 106 91, Stockholm, Sweden
| | - Timothy M Allison
- Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, Box 576, 751 23, Uppsala, Sweden
| | - Michael Landreh
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65, Stockholm, Sweden.
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22
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Patrick JW, Laganowsky A. Generation of Charge-Reduced Ions of Membrane Protein Complexes for Native Ion Mobility Mass Spectrometry Studies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:886-892. [PMID: 30887461 PMCID: PMC6504596 DOI: 10.1007/s13361-019-02187-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/27/2019] [Accepted: 03/05/2019] [Indexed: 05/15/2023]
Abstract
Recent advances in native mass spectrometry (MS) have enabled the elucidation of how small molecule binding to membrane proteins modulates their structure and function. The protein-stabilizing osmolyte, trimethylamine oxide (TMAO), exhibits attractive properties for native MS studies. Here, we report significant charge reduction, nearly threefold, for three membrane protein complexes in the presence of this osmolyte without compromising mass spectral resolution. TMAO improves the ability to resolve individual lipid-binding events to the ammonia channel (AmtB) by over 200% compared to typical native conditions. The generation of ions with compact structure and access to a larger number of lipid-binding events through the incorporation of TMAO increases the utility of IM-MS for structural biology studies. Graphical Abstract.
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Affiliation(s)
- John W Patrick
- Department of Chemistry, Texas A&M University, College Station, TX, 77842, USA
- Janssen Research & Development, 1400 Mckean Road, Spring House, PA, 19477, USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, 77842, USA.
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