1
|
Li Y, Li W, Zheng Y, Wang T, Pu R, Zhang Z. Desalting strategies for native mass spectrometry. Talanta 2024; 281:126824. [PMID: 39250868 DOI: 10.1016/j.talanta.2024.126824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 09/02/2024] [Accepted: 09/05/2024] [Indexed: 09/11/2024]
Abstract
In native mass spectrometry (MS) salts are indispensable for preserving the native structures of biomolecules, but detrimental to mass sensitivity, resolution, and accuracy. Such a conflict makes desalting in native MS more challenging, distinctive, and sample-dependent than in peptide-centric MS. This review first briefly introduces the charged residue mechanism whereby native-like gaseous protein ions are released from electrospray droplets, revealing a higher degree of salt adduction than denatured proteins. Subsequently, this review summarizes and explores the existing strategies, underlying mechanisms and future perspectives of desalting in native MS. These strategies mainly focus on buffer exchange into volatile salts (offline and online approaches), addition of solution additives (e.g., anion, supercharging reagent, solution phase chelator and amino acid), use of submicron electrospray emitters (down to 60 nm), and other potential approaches (e.g., induced and electrophoretic nanoelectrospray ionization). The strategies of online buffer exchange and using nanoscale electrospray emitters are highlighted. This review would not only be a valuable addition to the field of sample preparation in MS, but would also serve as a beginner's guide to desalting in native MS.
Collapse
Affiliation(s)
- Yun Li
- School of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an, 710065, China
| | - Weijie Li
- School of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an, 710065, China
| | - Yajun Zheng
- School of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an, 710065, China.
| | - Tong Wang
- School of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an, 710065, China
| | - Ruijin Pu
- School of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an, 710065, China
| | - Zhiping Zhang
- School of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an, 710065, China.
| |
Collapse
|
2
|
Zhang T, Lyu J, Yang B, Yun SD, Scott E, Zhao M, Laganowsky A. Native mass spectrometry and structural studies reveal modulation of MsbA-nucleotide interactions by lipids. Nat Commun 2024; 15:5946. [PMID: 39009687 PMCID: PMC11251056 DOI: 10.1038/s41467-024-50350-9] [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: 09/08/2023] [Accepted: 07/07/2024] [Indexed: 07/17/2024] Open
Abstract
The ATP-binding cassette (ABC) transporter, MsbA, plays a pivotal role in lipopolysaccharide (LPS) biogenesis by facilitating the transport of the LPS precursor lipooligosaccharide (LOS) from the cytoplasmic to the periplasmic leaflet of the inner membrane. Despite multiple studies shedding light on MsbA, the role of lipids in modulating MsbA-nucleotide interactions remains poorly understood. Here we use native mass spectrometry (MS) to investigate and resolve nucleotide and lipid binding to MsbA, demonstrating that the transporter has a higher affinity for adenosine 5'-diphosphate (ADP). Moreover, native MS shows the LPS-precursor 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)2-lipid A (KDL) can tune the selectivity of MsbA for adenosine 5'-triphosphate (ATP) over ADP. Guided by these studies, four open, inward-facing structures of MsbA are determined that vary in their openness. We also report a 2.7 Å-resolution structure of MsbA in an open, outward-facing conformation that is not only bound to KDL at the exterior site, but with the nucleotide binding domains (NBDs) adopting a distinct nucleotide-free structure. The results obtained from this study offer valuable insight and snapshots of MsbA during the transport cycle.
Collapse
Affiliation(s)
- Tianqi Zhang
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Bowei Yang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Sangho D Yun
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Elena Scott
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Minglei Zhao
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, USA.
| |
Collapse
|
3
|
Seewald M, Nielinger L, Alker K, Behnke JS, Wycisk V, Urner LH. Detergent Chemistry Modulates the Transgression of Planetary Boundaries including Antimicrobial Resistance and Drug Discovery. Angew Chem Int Ed Engl 2024; 63:e202403833. [PMID: 38619211 DOI: 10.1002/anie.202403833] [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: 02/23/2024] [Revised: 03/13/2024] [Accepted: 03/13/2024] [Indexed: 04/16/2024]
Abstract
Detergent chemistry enables applications in the world today while harming safe operating spaces that humanity needs for survival. Aim of this review is to support a holistic thought process in the design of detergent chemistry. We harness the planetary boundary concept as a framework for literature survey to identify progresses and knowledge gaps in context with detergent chemistry and five planetary boundaries that are currently transgressed, i.e., climate, freshwater, land system, novel entities, biosphere integrity. Our survey unveils the status of three critical challenges to be addressed in the years to come, including (i) the implementation of a holistically, climate-friendly detergent industry; (ii) the alignment of materialistic and social aspects in creating technical solutions by means of sustainable chemistry; (iii) the development of detergents that serve the purpose of applications but do not harm the biosphere in their role as novel entities. Specifically, medically relevant case reports revealed that even the most sophisticated detergent design cannot sufficiently accelerate drug discovery to outperform the antibiotic resistance development that detergents simultaneously promote as novel entities. Safe operating spaces that humanity needs for its survival may be secured by directing future efforts beyond sustainable chemistry, resource efficiency, and net zero emission targets.
Collapse
Affiliation(s)
- Marc Seewald
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
| | - Lena Nielinger
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
| | - Katharina Alker
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
| | - Jan-Simon Behnke
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
| | - Virginia Wycisk
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
| | - Leonhard H Urner
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
| |
Collapse
|
4
|
Wu D, Yan R, Song S, Swansiger AK, Li Y, Prell JS, Zhou Q, Robinson CV. The complete assembly of human LAT1-4F2hc complex provides insights into its regulation, function and localisation. Nat Commun 2024; 15:3711. [PMID: 38697966 PMCID: PMC11065870 DOI: 10.1038/s41467-024-47948-4] [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: 09/05/2023] [Accepted: 04/17/2024] [Indexed: 05/05/2024] Open
Abstract
The LAT1-4F2hc complex (SLC7A5-SLC3A2) facilitates uptake of essential amino acids, hormones and drugs. Its dysfunction is associated with many cancers and immune/neurological disorders. Here, we apply native mass spectrometry (MS)-based approaches to provide evidence of super-dimer formation (LAT1-4F2hc)2. When combined with lipidomics, and site-directed mutagenesis, we discover four endogenous phosphatidylethanolamine (PE) molecules at the interface and C-terminus of both LAT1 subunits. We find that interfacial PE binding is regulated by 4F2hc-R183 and is critical for regulation of palmitoylation on neighbouring LAT1-C187. Combining native MS with mass photometry (MP), we reveal that super-dimerization is sensitive to pH, and modulated by complex N-glycans on the 4F2hc subunit. We further validate the dynamic assemblies of LAT1-4F2hc on plasma membrane and in the lysosome. Together our results link PTM and lipid binding with regulation and localisation of the LAT1-4F2hc super-dimer.
Collapse
Affiliation(s)
- Di Wu
- Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU, UK.
| | - Renhong Yan
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong Province, China
| | - Siyuan Song
- Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU, UK
| | - Andrew K Swansiger
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, Oregon, 97403-1253, USA
| | - Yaning Li
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - James S Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, Oregon, 97403-1253, USA
| | - Qiang Zhou
- Research Center for Industries of the Future, Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang Province, China
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU, UK.
| |
Collapse
|
5
|
Pirona L, Ballabio F, Alfonso-Prieto M, Capelli R. Calcium-Driven In Silico Inactivation of a Human Olfactory Receptor. J Chem Inf Model 2024; 64:2971-2978. [PMID: 38523266 DOI: 10.1021/acs.jcim.4c00249] [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: 03/26/2024]
Abstract
Conformational changes as well as molecular determinants related to the activation and inactivation of olfactory receptors are still poorly understood due to the intrinsic difficulties in the structural determination of this GPCR family. Here, we perform, for the first time, the in silico inactivation of human olfactory receptor OR51E2, highlighting the possible role of calcium in this receptor state transition. Using molecular dynamics simulations, we show that a divalent ion in the ion binding site, coordinated by two acidic residues at positions 2.50 and 3.39 conserved across most ORs, stabilizes the receptor in its inactive state. In contrast, protonation of the same two acidic residues is not sufficient to drive inactivation within the microsecond timescale of our simulations. Our findings suggest a novel molecular mechanism for OR inactivation, potentially guiding experimental validation and offering insights into the possible broader role of divalent ions in GPCR signaling.
Collapse
Affiliation(s)
- Lorenza Pirona
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, I-20133 Milano, Italy
| | - Federico Ballabio
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, I-20133 Milano, Italy
| | - Mercedes Alfonso-Prieto
- Computational Biomedicine, Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, D-54248 Jülich, Germany
| | - Riccardo Capelli
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, I-20133 Milano, Italy
| |
Collapse
|
6
|
Wycisk V, Wagner MC, Urner LH. Trends in the Diversification of the Detergentome. Chempluschem 2024; 89:e202300386. [PMID: 37668309 DOI: 10.1002/cplu.202300386] [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: 07/24/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/06/2023]
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.
Collapse
Affiliation(s)
- Virginia Wycisk
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
| | - Marc-Christian Wagner
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
| | - Leonhard H Urner
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
| |
Collapse
|
7
|
Brown KA, Morris R, Eckhardt SJ, Ge Y, Gellman SH. Phosphorylation Sites of the Gastric Inhibitory Polypeptide Receptor (GIPR) Revealed by Trapped-Ion-Mobility Spectrometry Coupled to Time-of-Flight Mass Spectrometry (TIMS-TOF MS). J Am Chem Soc 2023; 145:28030-28037. [PMID: 38091482 PMCID: PMC10842860 DOI: 10.1021/jacs.3c09078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The gastric inhibitory polypeptide receptor (GIPR), a G protein-coupled receptor (GPCR) that regulates glucose metabolism and insulin secretion, is a target for the development of therapeutic agents to address type 2 diabetes and obesity. Signal transduction processes mediated by GPCR activation typically result in receptor phosphorylation, but very little is known about GIPR phosphorylation. Mass spectrometry (MS) is a powerful tool for detecting phosphorylation and other post-translational modifications of proteins and for identifying modification sites. However, applying MS methods to GPCRs is challenging because the native expression levels are low and the hydrophobicity of these proteins complicates isolation and enrichment. Here we use a widely available technique, trapped-ion-mobility spectrometry coupled to time-of-flight mass spectrometry (TIMS-TOF MS), to characterize the phosphorylation status of the GIPR. We identified eight serine residues that are phosphorylated, one in an intracellular loop and the remainder in the C-terminal domain. Stimulation with the native agonist GIP enhanced phosphorylation at four of these sites. For comparison, we evaluated tirzepatide (TZP), a dual agonist of the glucagon-like peptide-1 (GLP-1) receptor and the GIPR that has recently been approved for the treatment of type 2 diabetes. Stimulation with TZP enhanced phosphorylation at the same four sites that were enhanced with GIP; however, TZP also enhanced phosphorylation at a fifth site that is unique to this synthetic agonist. This work establishes an important and accessible tool for the characterization of signal transduction via the GIPR and reveals an unanticipated functional difference between GIP and TZP.
Collapse
Affiliation(s)
- Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Rylie Morris
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Samantha J. Eckhardt
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| |
Collapse
|
8
|
Scott-Dennis M, Rafani FA, Yi Y, Perera T, Harwood CR, Guba W, Rufer AC, Grether U, Veprintsev DB, Sykes DA. Development of a membrane-based Gi-CASE biosensor assay for profiling compounds at cannabinoid receptors. Front Pharmacol 2023; 14:1158091. [PMID: 37637423 PMCID: PMC10450933 DOI: 10.3389/fphar.2023.1158091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/05/2023] [Indexed: 08/29/2023] Open
Abstract
Introduction: The cannabinoid receptor (CBR) subtypes 1 (CB1R) and 2 (CB2R) are key components of the endocannabinoid system (ECS), playing a central role in the control of peripheral pain, inflammation and the immune response, with further roles in the endocrine regulation of food intake and energy balance. So far, few medicines targeting these receptors have reached the clinic, suggesting that a better understanding of the receptor signalling properties of existing tool compounds and clinical candidates may open the door to the development of more effective and safer treatments. Both CB1R and CB2R are Gαi protein-coupled receptors but detecting Gαi protein signalling activity reliably and reproducibly is challenging. This is due to the inherent variability in live cell-based assays and restrictions around the use of radioactive [35S]-GTPγS, a favoured technology for developing higher-throughput membrane-based Gαi protein activity assays. Methods: Here, we describe the development of a membrane-based Gαi signalling system, produced from membrane preparations of HEK293TR cells, stably overexpressing CB1R or CB2R, and components of the Gαi-CASE biosensor. This BRET-based system allows direct detection of Gαi signalling in both cells and membranes by monitoring bioluminescence resonance energy transfer (BRET) between the α and the βγ subunits. Cells and membranes were subject to increasing concentrations of reference cannabinoid compounds, with 10 μM furimazine added to generate RET signals, which were detected on a PHERAstar FSX plate reader, then processed using MARS software and analysed in GraphPad PRISM 9.2. Results: In membranes expressing the Gi-CASE biosensor, the cannabinoid ligands profiled were found to show agonist and inverse agonist activity. Agonist activity elicited a decrease in the BRET signal, indicative of receptor activation and G protein dissociation. Inverse agonist activity caused an increase in BRET signal, indicative of receptor inactivation, and the accumulation of inactive G protein. Our membrane-based Gi-CASE NanoBRET system successfully characterised the potency (pEC50) and efficacy (Emax) of CBR agonists and inverse agonists in a 384-well screening format. Values obtained were in-line with whole-cell Gi-CASE assays and consistent with literature values obtained in the GTPγS screening format. Discussion: This novel, membrane-based Gαi protein activation assay is applicable to other Gαi-coupled GPCRs, including orphan receptors, allowing real-time higher-throughput measurements of receptor activation.
Collapse
Affiliation(s)
- Morgan Scott-Dennis
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Midlands, United Kingdom
| | - Fikri A. Rafani
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Midlands, United Kingdom
| | - Yicheng Yi
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Midlands, United Kingdom
| | - Themiya Perera
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Midlands, United Kingdom
| | - Clare R. Harwood
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Midlands, United Kingdom
| | - Wolfgang Guba
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Arne C. Rufer
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Uwe Grether
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Dmitry B. Veprintsev
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Midlands, United Kingdom
- Z7 Biotech Limited, London, United Kingdom
| | - David A. Sykes
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Midlands, United Kingdom
- Z7 Biotech Limited, London, United Kingdom
| |
Collapse
|
9
|
Tajiri M, Imai S, Konuma T, Shimamoto K, Shimada I, Akashi S. Evaluation of Drug Responses to Human β 2AR Using Native Mass Spectrometry. ACS OMEGA 2023; 8:24544-24551. [PMID: 37457453 PMCID: PMC10339329 DOI: 10.1021/acsomega.3c02737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023]
Abstract
We aimed to develop a platform to rapidly investigate the responses of agonists and antagonists to G-protein-coupled receptors (GPCRs) using native mass spectrometry (MS). We successfully observed the ligand-bound human β2 adrenergic receptor (hβ2AR); however, it was challenging to quantitatively discuss drug efficacy from MS data alone. Since ligand-bound GPCRs are stabilized by the Gα subunit of G proteins on the membrane, mini-Gs and nanobody80 (Nb80) that can mimic the Gα interface of the GPCR were utilized. Ternary complexes of hβ2AR, ligand, and mini-Gs or Nb80 were prepared and subjected to native MS. We found a strong correlation between the hβ2AR-mini-Gs or -Nb80 complex ratio observed in the mass spectra and agonist/antagonist efficacy obtained using a cell-based assay. This method does not require radioisotope labeling and would be applicable to the analysis of other GPCRs, facilitating the characterization of candidate compounds as GPCR agonists and antagonists.
Collapse
Affiliation(s)
- Michiko Tajiri
- Graduate
School of Medical Life Science, Yokohama
City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shunsuke Imai
- Biosystems
Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tsuyoshi Konuma
- Graduate
School of Medical Life Science, Yokohama
City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Keiko Shimamoto
- Suntory
Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Ichio Shimada
- Biosystems
Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Graduate
School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi, Hiroshima City, Hiroshima 739-8528, Japan
| | - Satoko Akashi
- Graduate
School of Medical Life Science, Yokohama
City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| |
Collapse
|
10
|
James AD, Unthank KP, Jones I, Sajjaboontawee N, Sizer RE, Chawla S, Evans GJO, Brackenbury WJ. Sodium regulates PLC and IP 3 R-mediated calcium signaling in invasive breast cancer cells. Physiol Rep 2023; 11:e15663. [PMID: 37017052 PMCID: PMC10074044 DOI: 10.14814/phy2.15663] [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: 08/10/2022] [Revised: 03/03/2023] [Accepted: 03/21/2023] [Indexed: 04/06/2023] Open
Abstract
Intracellular Ca2+ signaling and Na+ homeostasis are inextricably linked via ion channels and co-transporters, with alterations in the concentration of one ion having profound effects on the other. Evidence indicates that intracellular Na+ concentration ([Na+ ]i ) is elevated in breast tumors, and that aberrant Ca2+ signaling regulates numerous key cancer hallmark processes. The present study therefore aimed to determine the effects of Na+ depletion on intracellular Ca2+ handling in metastatic breast cancer cell lines. The relationship between Na+ and Ca2+ was probed using fura-2 and SBFI fluorescence imaging and replacement of extracellular Na+ with equimolar N-methyl-D-glucamine (0Na+ /NMDG) or choline chloride (0Na+ /ChoCl). In triple-negative MDA-MB-231 and MDA-MB-468 cells and Her2+ SKBR3 cells, but not ER+ MCF-7 cells, 0Na+ /NMDG and 0Na+ /ChoCl resulted in a slow, sustained depletion in [Na+ ]i that was accompanied by a rapid and sustained increase in intracellular Ca2+ concentration ([Ca2+ ]i ). Application of La3+ in nominal Ca2+ -free conditions had no effect on this response, ruling out reverse-mode NCX activity and Ca2+ entry channels. Moreover, the Na+ -linked [Ca2+ ]i increase was independent of membrane potential hyperpolarization (NS-1619), but was inhibited by pharmacological blockade of IP3 receptors (2-APB), phospholipase C (PLC, U73122) or following depletion of endoplasmic reticulum Ca2+ stores (cyclopiazonic acid). Thus, Na+ is linked to PLC/IP3 -mediated activation of endoplasmic reticulum Ca2+ release in metastatic breast cancer cells and this may have an important role in breast tumors where [Na+ ]i is perturbed.
Collapse
Affiliation(s)
- Andrew D. James
- Department of BiologyUniversity of YorkYorkUK
- York Biomedical Research InstituteUniversity of YorkYorkUK
| | | | | | - Nattanan Sajjaboontawee
- Department of BiologyUniversity of YorkYorkUK
- York Biomedical Research InstituteUniversity of YorkYorkUK
| | | | - Sangeeta Chawla
- Department of BiologyUniversity of YorkYorkUK
- York Biomedical Research InstituteUniversity of YorkYorkUK
| | - Gareth J. O. Evans
- Department of BiologyUniversity of YorkYorkUK
- York Biomedical Research InstituteUniversity of YorkYorkUK
| | - William J. Brackenbury
- Department of BiologyUniversity of YorkYorkUK
- York Biomedical Research InstituteUniversity of YorkYorkUK
| |
Collapse
|
11
|
Fiorentino F, Rotili D, Mai A. Native mass spectrometry-directed drug discovery: Recent advances in investigating protein function and modulation. Drug Discov Today 2023; 28:103548. [PMID: 36871843 DOI: 10.1016/j.drudis.2023.103548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/15/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
Native mass spectrometry (nMS) is a biophysical method for studying protein complexes and can provide insights into subunit stoichiometry and composition, protein-ligand, and protein-protein interactions (PPIs). These analyses are made possible by preserving non-covalent interactions in the gas phase, thereby allowing the analysis of proteins in their native state. Consequently, nMS has been increasingly applied in early drug discovery campaigns for the characterization of protein-drug interactions and the evaluation of PPI modulators. Here, we discuss recent developments in nMS-directed drug discovery and provide a timely perspective on the possible applications of this technology in drug discovery.
Collapse
Affiliation(s)
- Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| |
Collapse
|
12
|
Mass spectrometry of intact membrane proteins: shifting towards a more native-like context. Essays Biochem 2023; 67:201-213. [PMID: 36807530 PMCID: PMC10070488 DOI: 10.1042/ebc20220169] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 02/23/2023]
Abstract
Integral membrane proteins are involved in a plethora of biological processes including cellular signalling, molecular transport, and catalysis. Many of these functions are mediated by non-covalent interactions with other proteins, substrates, metabolites, and surrounding lipids. Uncovering such interactions and deciphering their effect on protein activity is essential for understanding the regulatory mechanisms underlying integral membrane protein function. However, the detection of such dynamic complexes has proven to be challenging using traditional approaches in structural biology. Native mass spectrometry has emerged as a powerful technique for the structural characterisation of membrane proteins and their complexes, enabling the detection and identification of protein-binding partners. In this review, we discuss recent native mass spectrometry-based studies that have characterised non-covalent interactions of membrane proteins in the presence of detergents or membrane mimetics. We additionally highlight recent progress towards the study of membrane proteins within native membranes and provide our perspective on how these could be combined with recent developments in instrumentation to investigate increasingly complex biomolecular systems.
Collapse
|
13
|
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.
Collapse
|
14
|
Davies A, Tomas A. Appreciating the potential for GPCR crosstalk with ion channels. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 195:101-120. [PMID: 36707150 DOI: 10.1016/bs.pmbts.2022.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
G protein-coupled receptors (GPCRs) are expressed by most tissues in the body and are exploited pharmacologically in a variety of pathological conditions including diabetes, cardiovascular disease, neurological diseases, and cancers. Numerous cell signaling pathways can be regulated by GPCR activation, depending on the specific GPCR, ligand and cell type. Ion channels are among the many effector proteins downstream of these signaling pathways. Saliently, ion channels are also recognized as druggable targets, and there is evidence that their activity may regulate GPCR function via membrane potential and cytoplasmic ion concentration. Overall, there appears to be a large potential for crosstalk between ion channels and GPCRs. This might have implications not only for targeting GPCRs for drug development, but also opens the possibility of co-targeting them with ion channels to achieve improved therapeutic outcomes. In this review, we highlight the large variety of possible GPCR-ion channel crosstalk modes.
Collapse
Affiliation(s)
- Amy Davies
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Alejandra Tomas
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom.
| |
Collapse
|
15
|
Lei W, Hu J, Chen HY, Xu JJ. Nanopore Liberates G-Quadruplexes from Biochemical Buffers for Accurate Mass Spectrometric Examination. Anal Chem 2022; 94:17972-17979. [PMID: 36515943 DOI: 10.1021/acs.analchem.2c04099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Achieving accurate measurements of G-quadruplexes (G4s), especially the characterization of their complicated non-covalent interactions with various components (such as metal ions and ligands) under physiological conditions, is of fundamental significance in unveiling their biological roles and developing antitumor drugs. By employing a nanopore ion emitter (∼30 nm), we demonstrated for the first time that G4 ions, which are free of non-specific adduction and meanwhile maintaining their pre-existing specific bindings with metal ions or ligands, can be directly liberated from common biochemical buffers (consisting of concentrated non-volatile salts of >150 mM) for mass spectrometric examination. Notably, the intermediate complexes of G4s with mixed di-cation coordination formed during the Na+/K+ exchange were successfully observed by mass spectrometry, whose structures were also revealed by the reconstructed circular dichroism spectra. We believe the nanopore-based ion emitters have built a solid bridge between native G4s in aqueous buffers and their accurate stoichiometries obtained by mass spectrometric examination.
Collapse
Affiliation(s)
- Wen Lei
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Jun Hu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| |
Collapse
|
16
|
Yen HY, Liko I, Song W, Kapoor P, Almeida F, Toporowska J, Gherbi K, Hopper JTS, Charlton SJ, Politis A, Sansom MSP, Jazayeri A, Robinson CV. Mass spectrometry captures biased signalling and allosteric modulation of a G-protein-coupled receptor. Nat Chem 2022; 14:1375-1382. [PMID: 36357787 PMCID: PMC9758051 DOI: 10.1038/s41557-022-01041-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 08/09/2022] [Indexed: 11/12/2022]
Abstract
G-protein-coupled receptors signal through cognate G proteins. Despite the widespread importance of these receptors, their regulatory mechanisms for G-protein selectivity are not fully understood. Here we present a native mass spectrometry-based approach to interrogate both biased signalling and allosteric modulation of the β1-adrenergic receptor in response to various ligands. By simultaneously capturing the effects of ligand binding and receptor coupling to different G proteins, we probed the relative importance of specific interactions with the receptor through systematic changes in 14 ligands, including isoprenaline derivatives, full and partial agonists, and antagonists. We observed enhanced dynamics of the intracellular loop 3 in the presence of isoprenaline, which is capable of acting as a biased agonist. We also show here that endogenous zinc ions augment the binding in receptor-Gs complexes and propose a zinc ion-binding hotspot at the TM5/TM6 intracellular interface of the receptor-Gs complex. Further interrogation led us to propose a mechanism in which zinc ions facilitate a structural transition of the intermediate complex towards the stable state.
Collapse
Affiliation(s)
- Hsin-Yung Yen
- Chemical Research Laboratory, University of Oxford, Oxford, UK.
- OMass Therapeutics, Oxford, UK.
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
| | - Idlir Liko
- Chemical Research Laboratory, University of Oxford, Oxford, UK
- OMass Therapeutics, Oxford, UK
| | - Wanling Song
- Department of Biochemistry, University of Oxford, Oxford, UK
- Rahko, London, UK
| | | | | | | | | | | | - Steven J Charlton
- OMass Therapeutics, Oxford, UK
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Argyris Politis
- Department of Chemistry, King's College London, London, UK
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Carol V Robinson
- Chemical Research Laboratory, University of Oxford, Oxford, UK.
- Kavli Institute for Nanoscience Discovery, Oxford, UK.
| |
Collapse
|
17
|
Advances in membrane mimetics and mass spectrometry for understanding membrane structure and function. Curr Opin Chem Biol 2022; 69:102157. [DOI: 10.1016/j.cbpa.2022.102157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/01/2022] [Accepted: 04/12/2022] [Indexed: 12/19/2022]
|
18
|
Dafun AS, Marcoux J. Structural mass spectrometry of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140813. [PMID: 35750312 DOI: 10.1016/j.bbapap.2022.140813] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/10/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
The analysis of proteins and protein complexes by mass spectrometry (MS) has come a long way since the invention of electrospray ionization (ESI) in the mid 80s. Originally used to characterize small soluble polypeptide chains, MS has progressively evolved over the past 3 decades towards the analysis of samples of ever increasing heterogeneity and complexity, while the instruments have become more and more sensitive and resolutive. The proofs of concepts and first examples of most structural MS methods appeared in the early 90s. However, their application to membrane proteins, key targets in the biopharma industry, is more recent. Nowadays, a wealth of information can be gathered from such MS-based methods, on all aspects of membrane protein structure: sequencing (and more precisely proteoform characterization), but also stoichiometry, non-covalent ligand binding (metals, drug, lipids, carbohydrates), conformations, dynamics and distance restraints for modelling. In this review, we present the concept and some historical and more recent applications on membrane proteins, for the major structural MS methods.
Collapse
Affiliation(s)
- Angelique Sanchez Dafun
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France.
| |
Collapse
|
19
|
Liu R, Xia S, Li H. Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes. MASS SPECTROMETRY REVIEWS 2022:e21793. [PMID: 35757976 DOI: 10.1002/mas.21793] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Progress in structural biology research has led to a high demand for powerful and yet complementary analytical tools for structural characterization of proteins and protein complexes. This demand has significantly increased interest in native mass spectrometry (nMS), particularly native top-down mass spectrometry (nTDMS) in the past decade. This review highlights recent advances in nTDMS for structural research of biological assemblies, with a particular focus on the extra multi-layers of information enabled by TDMS. We include a short introduction of sample preparation and ionization to nMS, tandem fragmentation techniques as well as mass analyzers and software/analysis pipelines used for nTDMS. We highlight unique structural information offered by nTDMS and examples of its broad range of applications in proteins, protein-ligand interactions (metal, cofactor/drug, DNA/RNA, and protein), therapeutic antibodies and antigen-antibody complexes, membrane proteins, macromolecular machineries (ribosome, nucleosome, proteosome, and viruses), to endogenous protein complexes. The challenges, potential, along with perspectives of nTDMS methods for the analysis of proteins and protein assemblies in recombinant and biological samples are discussed.
Collapse
Affiliation(s)
- Ruijie Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shujun Xia
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
20
|
Abstract
Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.
Collapse
Affiliation(s)
- Amber D. Rolland
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA 97403-1253
| | - James S. Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA 97403-1253
- Materials Science Institute, 1252 University of Oregon, Eugene, OR, USA 97403-1252
| |
Collapse
|
21
|
Gavriilidou AFM, Sokratous K, Yen HY, De Colibus L. High-Throughput Native Mass Spectrometry Screening in Drug Discovery. Front Mol Biosci 2022; 9:837901. [PMID: 35495635 PMCID: PMC9047894 DOI: 10.3389/fmolb.2022.837901] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/15/2022] [Indexed: 12/15/2022] Open
Abstract
The design of new therapeutic molecules can be significantly informed by studying protein-ligand interactions using biophysical approaches directly after purification of the protein-ligand complex. Well-established techniques utilized in drug discovery include isothermal titration calorimetry, surface plasmon resonance, nuclear magnetic resonance spectroscopy, and structure-based drug discovery which mainly rely on protein crystallography and, more recently, cryo-electron microscopy. Protein-ligand complexes are dynamic, heterogeneous, and challenging systems that are best studied with several complementary techniques. Native mass spectrometry (MS) is a versatile method used to study proteins and their non-covalently driven assemblies in a native-like folded state, providing information on binding thermodynamics and stoichiometry as well as insights on ternary and quaternary protein structure. Here, we discuss the basic principles of native mass spectrometry, the field's recent progress, how native MS is integrated into a drug discovery pipeline, and its future developments in drug discovery.
Collapse
|
22
|
Bueschbell B, Manga P, Schiedel AC. The Many Faces of G Protein-Coupled Receptor 143, an Atypical Intracellular Receptor. Front Mol Biosci 2022; 9:873777. [PMID: 35495622 PMCID: PMC9039016 DOI: 10.3389/fmolb.2022.873777] [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: 02/11/2022] [Accepted: 03/10/2022] [Indexed: 12/24/2022] Open
Abstract
GPCRs transform extracellular stimuli into a physiological response by activating an intracellular signaling cascade initiated via binding to G proteins. Orphan G protein-coupled receptors (GPCRs) hold the potential to pave the way for development of new, innovative therapeutic strategies. In this review we will introduce G protein-coupled receptor 143 (GPR143), an enigmatic receptor in terms of classification within the GPCR superfamily and localization. GPR143 has not been assigned to any of the GPCR families due to the lack of common structural motifs. Hence we will describe the most important motifs of classes A and B and compare them to the protein sequence of GPR143. While a precise function for the receptor has yet to be determined, the protein is expressed abundantly in pigment producing cells. Many GPR143 mutations cause X-linked Ocular Albinism Type 1 (OA1, Nettleship-Falls OA), which results in hypopigmentation of the eyes and loss of visual acuity due to disrupted visual system development and function. In pigment cells of the skin, loss of functional GPR143 results in abnormally large melanosomes (organelles in which pigment is produced). Studies have shown that the receptor is localized internally, including at the melanosomal membrane, where it may function to regulate melanosome size and/or facilitate protein trafficking to the melanosome through the endolysosomal system. Numerous additional roles have been proposed for GPR143 in determining cancer predisposition, regulation of blood pressure, development of macular degeneration and signaling in the brain, which we will briefly describe as well as potential ligands that have been identified. Furthermore, GPR143 is a promiscuous receptor that has been shown to interact with multiple other melanosomal proteins and GPCRs, which strongly suggests that this orphan receptor is likely involved in many different physiological actions.
Collapse
Affiliation(s)
- Beatriz Bueschbell
- Department of Pharmaceutical and Medicinal Chemistry, Pharmaceutical Institute, University of Bonn, Bonn, Germany
| | - Prashiela Manga
- Ronald O. Perelman Department of Dermatology, Grossman School of Medicine, New York University, New York City, NY, United States
| | - Anke C. Schiedel
- Department of Pharmaceutical and Medicinal Chemistry, Pharmaceutical Institute, University of Bonn, Bonn, Germany
- *Correspondence: Anke C. Schiedel,
| |
Collapse
|
23
|
Jordan JS, Xia Z, Williams ER. Tips on Making Tiny Tips: Secrets to Submicron Nanoelectrospray Emitters. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:607-611. [PMID: 35157433 DOI: 10.1021/jasms.1c00372] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nanoelectrospray ionization emitters with submicron tip diameters have significant advantages for use in native mass spectrometry, including the ability to produce resolved charge-state distributions for proteins and macromolecular complexes from standard biochemical buffers that contain high concentrations of nonvolatile salts and to prevent nonspecific aggregation that can occur during droplet evaporation. We report on various factors affecting the tip morphology and provide suggestions for producing and using emitters with submicron tips. Effects of pulling parameters for a Sutter Instrument P-87 tip puller on the resulting tip diameter and morphology are shown. The "Pull" parameter has the largest effect on tip diameter, followed by "Velocity", "Pressure", and "Heat", whereas the "Time" parameter has minimal effect beyond a lower threshold. High "Pull" values generate emitters with multiple tapers, whereas high "Velocity" values generate a tip with only a single tapered region. A protocol for producing reproducible emitters in the submicron size range, as well as guidelines and tips for using these emitters with standard biochemical buffers that contain high concentrations of nonvolatile salts, is presented with the aim of expanding their use within the native mass spectrometry community.
Collapse
Affiliation(s)
- Jacob S Jordan
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Zijie Xia
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Evan R Williams
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| |
Collapse
|
24
|
Swansiger AK, Marty MT, Prell JS. Fourier-Transform Approach for Reconstructing Macromolecular Mass Defect Profiles. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:172-180. [PMID: 34913687 DOI: 10.1021/jasms.1c00317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
State-of-the-art native mass spectrometry (MS) methods have been developed for analysis of highly heterogeneous intact complexes and have provided much insight into the structure and properties of noncovalent assemblies that can be difficult to study using denatured proteins. These native MS methods can often be used to study even highly polydisperse membrane proteins embedded in detergent micelles, nanodiscs, and other membrane mimics. However, characterizing highly polydisperse native complexes which are also heterogeneous presents additional challenges for native MS. Macromolecular mass defect (MMD) analysis aims to characterize heterogeneous ion populations obfuscated by adduct polydispersity and reveal the distribution of "base" masses, and was recently implemented in the Bayesian analysis software UniDec. Here, we illustrate an alternative, orthogonal MMD analysis method implemented in the deconvolution program iFAMS, which takes advantage of Fourier transform (FT) to deconvolve low-resolution data with few user-input parameters and which can provide high quality results even for mass spectra with a signal-to-noise ratio of ∼5:1. Agreement between this method, which is based on frequency-domain data, and the mass-domain algorithm of UniDec provides strong evidence that both methods can accurately characterize highly polydisperse and heterogeneous ion populations. The FT algorithm is expected to be very useful in characterizing many types of analytes ranging from membrane proteins to polymer-conjugated proteins, branched polymers, and other large analytes, as well as for reconstructing isotope profiles for highly complex but still isotope-resolved mass spectra.
Collapse
Affiliation(s)
- Andrew K Swansiger
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
- Materials Science Institute, University of Oregon, Eugene, Oregon 97403-1252, United States
| |
Collapse
|
25
|
Webb IK. Recent technological developments for native mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140732. [PMID: 34653668 DOI: 10.1016/j.bbapap.2021.140732] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 11/16/2022]
Abstract
Native mass spectrometry (MS), the analysis of proteins and protein complexes from solutions that stabilize native solution structures, is a rapidly expanding area. There is strong evidence supporting the retention of proteins' native folds in the absence of solvent under the experimental timescales of MS experiments. Therefore, instrumentation has been developed to use gas-phase native-like protein ions to exploit the speed, sensitivity, and selectivity of mass spectrometry approaches to solve emerging problems in structural biology. This article reviews some of the recent advances and applications in gas-phase instrumentation for structural proteomics.
Collapse
Affiliation(s)
- Ian K Webb
- Department of Chemistry and Chemical Biology, Purdue School of Science, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, United States of America; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, United States of America.
| |
Collapse
|
26
|
Nguyen GTH, Bennett JL, Liu S, Hancock SE, Winter DL, Glover DJ, Donald WA. Multiplexed Screening of Thousands of Natural Products for Protein-Ligand Binding in Native Mass Spectrometry. J Am Chem Soc 2021; 143:21379-21387. [PMID: 34886668 DOI: 10.1021/jacs.1c10408] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The structural diversity of natural products offers unique opportunities for drug discovery, but challenges associated with their isolation and screening can hinder the identification of drug-like molecules from complex natural product extracts. Here we introduce a mass spectrometry-based approach that integrates untargeted metabolomics with multistage, high-resolution native mass spectrometry to rapidly identify natural products that bind to therapeutically relevant protein targets. By directly screening crude natural product extracts containing thousands of drug-like small molecules using a single, rapid measurement, we could identify novel natural product ligands of human drug targets without fractionation. This method should significantly increase the efficiency of target-based natural product drug discovery workflows.
Collapse
Affiliation(s)
- Giang T H Nguyen
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Jack L Bennett
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Sherrie Liu
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Sarah E Hancock
- School of Medical Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Daniel L Winter
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Dominic J Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| |
Collapse
|
27
|
Peris-Díaz M, Guran R, Domene C, de los Rios V, Zitka O, Adam V, Krężel A. An Integrated Mass Spectrometry and Molecular Dynamics Simulations Approach Reveals the Spatial Organization Impact of Metal-Binding Sites on the Stability of Metal-Depleted Metallothionein-2 Species. J Am Chem Soc 2021; 143:16486-16501. [PMID: 34477370 PMCID: PMC8517974 DOI: 10.1021/jacs.1c05495] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Indexed: 12/16/2022]
Abstract
Mammalian metallothioneins (MTs) are a group of cysteine-rich proteins that bind metal ions in two α- and β-domains and represent a major cellular Zn(II)/Cu(I) buffering system in the cell. At cellular free Zn(II) concentrations (10-11-10-9 M), MTs do not exist in fully loaded forms with seven Zn(II)-bound ions (Zn7MTs). Instead, MTs exist as partially metal-depleted species (Zn4-6MT) because their Zn(II) binding affinities are on the nano- to picomolar range comparable to the concentrations of cellular Zn(II). The mode of action of MTs remains poorly understood, and thus, the aim of this study is to characterize the mechanism of Zn(II) (un)binding to MTs, the thermodynamic properties of the Zn1-6MT2 species, and their mechanostability properties. To this end, native mass spectrometry (MS) and label-free quantitative bottom-up and top-down MS in combination with steered molecular dynamics simulations, well-tempered metadynamics (WT-MetaD), and parallel-bias WT-MetaD (amounting to 3.5 μs) were integrated to unravel the chemical coordination of Zn(II) in all Zn1-6MT2 species and to explain the differences in binding affinities of Zn(II) ions to MTs. Differences are found to be the result of the degree of water participation in MT (un)folding and the hyper-reactive character of Cys21 and Cys29 residues. The thermodynamics properties of Zn(II) (un)binding to MT2 are found to differ from those of Cd(II), justifying their distinctive roles. The potential of this integrated strategy in the investigation of numerous unexplored metalloproteins is attested by the results highlighted in the present study.
Collapse
Affiliation(s)
- Manuel
David Peris-Díaz
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Roman Guran
- Department
of Chemistry and Biochemistry, Mendel University
in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
- Central
European Institute of Technology, Brno University
of Technology, Purkynova
123, 612 00 Brno, Czech Republic
| | - Carmen Domene
- Department
of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Vivian de los Rios
- Functional
Proteomics, Department of Cellular and Molecular Medicine and Proteomic
Facility, Centro de Investigaciones Biológicas
(CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Ondrej Zitka
- Department
of Chemistry and Biochemistry, Mendel University
in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
- Central
European Institute of Technology, Brno University
of Technology, Purkynova
123, 612 00 Brno, Czech Republic
| | - Vojtech Adam
- Department
of Chemistry and Biochemistry, Mendel University
in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
- Central
European Institute of Technology, Brno University
of Technology, Purkynova
123, 612 00 Brno, Czech Republic
| | - Artur Krężel
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
| |
Collapse
|
28
|
Dong Y, Laaksonen A, Gao Q, Ji X. Molecular Mechanistic Insights into the Ionic-Strength-Controlled Interfacial Behavior of Proteins on a TiO 2 Surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11499-11507. [PMID: 34549968 DOI: 10.1021/acs.langmuir.1c01726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
By adjusting the ionic strengths through changing the concentration of the buffer ions, the molecular force and the interfacial behavior of cytochrome c (Cyt c) and TiO2 are systematically studied. The molecular forces determined by combining the adhesion force and adsorption capacity are found to first increase and then decrease with the increasing ionic strength, with a peak obtained at an ionic strength between 0.8 and 1.0 M. The mechanism is explained based on the dissociation and hydration of ions at the interfaces, where the buffer ions could be completely dissociated at ionic strengths of <0.8 M but were partially associated when the ionic strength increased to a high value (>1.2 M), and the strongest hydration was observed around 1.0 M. The hydrodynamic size and the zeta potential value representing the effective contact area and protein stability of the Cyt c molecule, respectively, are also affected by the hydration and are proportional to the molecular forces. The interfacial behavior of Cyt c molecules on the TiO2 surface, determined through surface-enhanced Raman scattering (SERS), is extremely affected by the ionic strength of the solution as the ion dissociation and hydration also increase the electron transfer ability, where the best SERS enhancement is observed at the ionic strength of around 1.0 M, corresponding to the largest molecular force. Our results provide a detailed understanding at the nanoscale on controlling the protein interfacial behavior with solid surfaces, adjusted by the buffer ions.
Collapse
Affiliation(s)
- Yihui Dong
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 210009, P. R. China
| | - Aatto Laaksonen
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 210009, P. R. China
- Energy Engineering, Division of Energy Science, Luleå University of Technology, 97187 Luleå, Sweden
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry Aleea Grigore Ghica-Voda, No. 41A, 700487 Iasi, Romania
| | - Qingwei Gao
- State Key Laboratory of Chemical Engineering and School of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xiaoyan Ji
- Energy Engineering, Division of Energy Science, Luleå University of Technology, 97187 Luleå, Sweden
| |
Collapse
|
29
|
Use of tandem affinity-buffer exchange chromatography online with native mass spectrometry for optimizing overexpression and purification of recombinant proteins. Methods Enzymol 2021; 659:37-70. [PMID: 34752295 DOI: 10.1016/bs.mie.2021.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Purification of recombinant proteins typically entails overexpression in heterologous systems and subsequent chromatography-based isolation. While denaturing sodium dodecyl sulfate-polyacrylamide gel electrophoresis is routinely used to screen a variety of overexpression conditions (e.g., host, medium, inducer concentration, post-induction temperature and/or incubation time) and to assess the purity of the final product, its limitations, including aberrant protein migration due to compositional eccentricities or incomplete denaturation, often preclude firm conclusions regarding the extent of overexpression and/or purification. Therefore, we recently reported an automated liquid chromatography-mass spectrometry-based strategy that couples immobilized metal affinity chromatography (IMAC) with size exclusion-based online buffer exchange (OBE) and native mass spectrometry (nMS) to directly analyze cell lysates for the presence of target proteins. IMAC-OBE-nMS can be used to assess whether target proteins (1) are overexpressed in soluble form, (2) bind and elute from an IMAC resin, (3) oligomerize, and (4) have the expected mass. Here, we use four poly-His-tagged proteins to demonstrate the potential of IMAC-OBE-nMS for expedient optimization of overexpression and purification conditions for recombinant protein production.
Collapse
|
30
|
Cruz SL, Carranza-Aguilar CJ, Pérez-García IP. Sodium chloride injection to treat opioid overdose; Does it work? A preclinical study. Neurotoxicology 2021; 87:24-29. [PMID: 34478770 DOI: 10.1016/j.neuro.2021.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/15/2021] [Accepted: 08/28/2021] [Indexed: 12/22/2022]
Abstract
Opioid overdoses (ODs) are increasing in Mexico's northern border. Because naloxone is usually not available, witnesses inject common salt (NaCl) into a vein of OD victims in an attempt to help them regain consciousness. Despite this widespread practice, no preclinical studies have addressed the efficacy of NaCl as an opioid antidote. Here we tested saline solutions at different concentrations. Because the highest (31.6 %) caused tail necrosis, we selected 17.7 % as a hypertonic saline solution (HSS) to determine if it could prevent the lethal effect of morphine (Mor), fentanyl (Fen), or Mor + Fen in adult Wistar male rats. We also evaluated if NaCl could modify the opioid antagonist effect of naloxone. Our results show that HSS: a) sensitizes animals to thermal but not mechanical stimuli; b) does not prevent mortality caused by high morphine or fentanyl doses; c) decreases the latency to recovery from the sedative effects caused by low doses of morphine or fentanyl; and d) increases naloxone's efficacy to prevent the lethality produced by Mor or Fen, but not by Mor + Fen. These results suggest that HSS is marginally effective in shortening the recovery time from nonfatal opioid ODs and increases naloxone's efficacy to counteract opioid-induced ODs.
Collapse
Affiliation(s)
- Silvia L Cruz
- Departamento de Farmacobiología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav, IPN), Calzada de los Tenorios No. 235, Mexico City, 14330, Mexico; Member of the Global Studies Seminar, Faculty of Medicine, National Autonomous University of Mexico, Mexico.
| | - César J Carranza-Aguilar
- Departamento de Farmacobiología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav, IPN), Calzada de los Tenorios No. 235, Mexico City, 14330, Mexico
| | - Iker P Pérez-García
- Departamento de Farmacobiología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav, IPN), Calzada de los Tenorios No. 235, Mexico City, 14330, Mexico
| |
Collapse
|
31
|
Bennett JL, Nguyen GTH, Donald WA. Protein-Small Molecule Interactions in Native Mass Spectrometry. Chem Rev 2021; 122:7327-7385. [PMID: 34449207 DOI: 10.1021/acs.chemrev.1c00293] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Small molecule drug discovery has been propelled by the continual development of novel scientific methodologies to occasion therapeutic advances. Although established biophysical methods can be used to obtain information regarding the molecular mechanisms underlying drug action, these approaches are often inefficient, low throughput, and ineffective in the analysis of heterogeneous systems including dynamic oligomeric assemblies and proteins that have undergone extensive post-translational modification. Native mass spectrometry can be used to probe protein-small molecule interactions with unprecedented speed and sensitivity, providing unique insights into polydisperse biomolecular systems that are commonly encountered during the drug discovery process. In this review, we describe potential and proven applications of native MS in the study of interactions between small, drug-like molecules and proteins, including large multiprotein complexes and membrane proteins. Approaches to quantify the thermodynamic and kinetic properties of ligand binding are discussed, alongside a summary of gas-phase ion activation techniques that have been used to interrogate the structure of protein-small molecule complexes. We additionally highlight some of the key areas in modern drug design for which native mass spectrometry has elicited significant advances. Future developments and applications of native mass spectrometry in drug discovery workflows are identified, including potential pathways toward studying protein-small molecule interactions on a whole-proteome scale.
Collapse
Affiliation(s)
- Jack L Bennett
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Giang T H Nguyen
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| |
Collapse
|