1
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Lutomski CA, El‐Baba TJ, Hinkle JD, Liko I, Bennett JL, Kalmankar NV, Dolan A, Kirschbaum C, Greis K, Urner LH, Kapoor P, Yen H, Pagel K, Mullen C, Syka JEP, Robinson CV. Infrared Multiphoton Dissociation Enables Top-Down Characterization of Membrane Protein Complexes and G Protein-Coupled Receptors. Angew Chem Int Ed Engl 2023; 62:e202305694. [PMID: 37329506 PMCID: PMC7615181 DOI: 10.1002/anie.202305694] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/20/2023] [Accepted: 06/15/2023] [Indexed: 06/19/2023]
Abstract
Membrane proteins are challenging to analyze by native mass spectrometry (MS) as their hydrophobic nature typically requires stabilization in detergent micelles that are removed prior to analysis via collisional activation. There is however a practical limit to the amount of energy which can be applied, which often precludes subsequent characterization by top-down MS. To overcome this barrier, we have applied a modified Orbitrap Eclipse Tribrid mass spectrometer coupled to an infrared laser within a high-pressure linear ion trap. We show how tuning the intensity and time of incident photons enables liberation of membrane proteins from detergent micelles. Specifically, we relate the ease of micelle removal to the infrared absorption of detergents in both condensed and gas phases. Top-down MS via infrared multiphoton dissociation (IRMPD), results in good sequence coverage enabling unambiguous identification of membrane proteins and their complexes. By contrasting and comparing the fragmentation patterns of the ammonia channel with two class A GPCRs, we identify successive cleavage of adjacent amino acids within transmembrane domains. Using gas-phase molecular dynamics simulations, we show that areas prone to fragmentation maintain aspects of protein structure at increasing temperatures. Altogether, we propose a rationale to explain why and where in the protein fragment ions are generated.
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Affiliation(s)
- Corinne A. Lutomski
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Tarick J. El‐Baba
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | | | | | - Jack L. Bennett
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Neha V. Kalmankar
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Andrew Dolan
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Carla Kirschbaum
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | - Kim Greis
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | - Leonhard H. Urner
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
- Department of Chemistry and Chemical BiologyTU Dortmund UniversityDortmund44227Germany
| | | | - Hsin‐Yung Yen
- OMass TherapeuticsOxfordOX4 2GXUK
- Institute of Biological ChemistryAcademia SinicaTaipei115Taiwan
| | - Kevin Pagel
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | | | | | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
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2
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Lutomski CA, El‐Baba TJ, Hinkle JD, Liko I, Bennett JL, Kalmankar NV, Dolan A, Kirschbaum C, Greis K, Urner LH, Kapoor P, Yen H, Pagel K, Mullen C, Syka JEP, Robinson CV. Infrared Multiphoton Dissociation Enables Top-Down Characterization of Membrane Protein Complexes and G Protein-Coupled Receptors. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202305694. [PMID: 38516403 PMCID: PMC10953453 DOI: 10.1002/ange.202305694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Indexed: 03/23/2024]
Abstract
Membrane proteins are challenging to analyze by native mass spectrometry (MS) as their hydrophobic nature typically requires stabilization in detergent micelles that are removed prior to analysis via collisional activation. There is however a practical limit to the amount of energy which can be applied, which often precludes subsequent characterization by top-down MS. To overcome this barrier, we have applied a modified Orbitrap Eclipse Tribrid mass spectrometer coupled to an infrared laser within a high-pressure linear ion trap. We show how tuning the intensity and time of incident photons enables liberation of membrane proteins from detergent micelles. Specifically, we relate the ease of micelle removal to the infrared absorption of detergents in both condensed and gas phases. Top-down MS via infrared multiphoton dissociation (IRMPD), results in good sequence coverage enabling unambiguous identification of membrane proteins and their complexes. By contrasting and comparing the fragmentation patterns of the ammonia channel with two class A GPCRs, we identify successive cleavage of adjacent amino acids within transmembrane domains. Using gas-phase molecular dynamics simulations, we show that areas prone to fragmentation maintain aspects of protein structure at increasing temperatures. Altogether, we propose a rationale to explain why and where in the protein fragment ions are generated.
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Affiliation(s)
- Corinne A. Lutomski
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Tarick J. El‐Baba
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | | | | | - Jack L. Bennett
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Neha V. Kalmankar
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Andrew Dolan
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Carla Kirschbaum
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | - Kim Greis
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | - Leonhard H. Urner
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
- Department of Chemistry and Chemical BiologyTU Dortmund UniversityDortmund44227Germany
| | | | - Hsin‐Yung Yen
- OMass TherapeuticsOxfordOX4 2GXUK
- Institute of Biological ChemistryAcademia SinicaTaipei115Taiwan
| | - Kevin Pagel
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | | | | | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
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3
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Wu R, Benzenberg LR, Svingou D, Zenobi R. The Structure of Cyclic Neuropeptide Somatostatin and Octapeptide Octreotide in the Presence of Copper Ions: Insights from Transition Metal Ion FRET and Native Ion Mobility-Mass Spectrometry. J Am Chem Soc 2023; 145:10542-10547. [PMID: 37146120 DOI: 10.1021/jacs.2c13613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The conformation and function of somatostatin (SST), a cyclic neuropeptide, was recently found to be altered in the presence of Cu(II) ions, which leads to self-aggregation and loss of biological function as a neurotransmitter. However, the impact of Cu(II) ions on the structure and function of SST is not fully understood. In this work, transition metal ion Förster resonance energy transfer (tmFRET) and native ion mobility-mass spectrometry (IM-MS) were utilized to study the structures of well-defined gas-phase ions of SST and of a smaller analogue, octreotide (OCT). The tmFRET results suggest two binding sites of Cu(II) ions in both native-like SST and OCT ions, either in close proximity to the disulfide bond or complexed by two aromatic residues, consistent with results obtained from collision-induced dissociation (CID). The former binding site was reported to initiate aggregation of SST, while the latter binding site could directly affect the essential motif for receptor binding and therefore impair the biological function of SST and OCT when bound to SST receptors. Our results demonstrate that tmFRET is capable of locating transition metal ion binding sites in neuropeptides. Furthermore, multiple distance constraints (tmFRET) and global shape (IM-MS) provide additional structural insights of SST and OCT ions upon metal binding, which is related to the self-aggregation mechanisms and overall biological functions.
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Affiliation(s)
- Ri Wu
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Lukas R Benzenberg
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Despoina Svingou
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Renato Zenobi
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
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4
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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.
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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
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5
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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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6
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Zhou L, Liu Z, Guo Y, Liu S, Zhao H, Zhao S, Xiao C, Feng S, Yang X, Wang F. Ultraviolet Photodissociation Reveals the Molecular Mechanism of Crown Ether Microsolvation Effect on the Gas-Phase Native-like Protein Structure. J Am Chem Soc 2023; 145:1285-1291. [PMID: 36584399 DOI: 10.1021/jacs.2c11210] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Maintaining the protein high-order structures and interactions during the transition from aqueous solution to gas phase is essential to the structural analysis of native mass spectrometry (nMS). Herein, we systematically interrogate the effects of charge state and crown ether (CE) complexation on the gas-phase native-like protein structure by integrating nMS with 193 nm ultraviolet photodissociation (UVPD). The alterations of photofragmentation yields of protein residues and the charge site distribution of fragment ions reveal the specific sites and sequence regions where charge and CE take effect. Our results exhibit the CE complexation on protonated residues can largely alleviate the structure disruption induced by the intramolecular solvation of charged side chains. The influences of CE complexation and positive charge on gas-phase protein structure exhibit generally opposite trends because the CE microsolvation avoids the hydrogen-bonding formation between the charged side chains with backbone carbonyls. Thus, CE complexation leads to a more stable and native-like protein structure in the gas phase.
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Affiliation(s)
- Lingqiang Zhou
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China.,CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongjie Guo
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Shiwen Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Heng Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Shan Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chunlei Xiao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Shun Feng
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Xueming Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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7
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Pérez-Robles R, Salmerón-García A, Clemente-Bautista S, Jiménez-Lozano I, Cabañas-Poy MJ, Cabeza J, Navas N. Method for identification and quantification of intact teduglutide peptide using (RP)UHPLC-UV-(HESI/ORBITRAP)MS. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:4359-4369. [PMID: 36263764 DOI: 10.1039/d2ay01254e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Teduglutide (Revestive®, 10 mg mL-1) is a recombinant human glucagon-like peptide 2 analogue, used in the treatment of short bowel syndrome, a serious and highly disabling condition which results from either too small a length of intestine or loss of critical intestinal function. The determination of therapeutic compounds of protein-nature is always challenging due to their complex structure. In this work, we present a fast, straightforward reversed phase (RP)UHPLC-UV-(HESI/ORBITRAP)MS method for the identification and quantification of the intact teduglutide peptide. The method has been developed and validated in accordance with the International Council for Harmonization of Technical Requirements for Pharmaceuticals for Human Use (ICH) guidelines; therefore, linearity, limits of detection and quantification, accuracy (precision and trueness), robustness, system suitability and specificity using the signal from the UV and MS, have been evaluated. The validation performance parameters obtained from the UV and MS signals were compared throughout the work, to select the most suitable. To study the specificity of the method and the impact of medicine mishandling under hospital conditions, force degradation studies were performed, i.e. thermal (40 °C and 60 °C), shaking (mechanical) and light (accelerated exposition) effects. Identification by the exact mass of teduglutide was achieved and it was confirmed that the peptide does not undergo any post-translational modifications (PTMs). To the best of our knowledge, the present work reports the first method developed for the simultaneous identification, structural characterization, and quantification of the therapeutic teduglutide peptide. Finally, the proposed method is able to indicate stability when quantifying the intact teduglutide since detects and characterises the exact mass of the degradation/modification products.
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Affiliation(s)
- Raquel Pérez-Robles
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Department of Analytical Chemistry, Science Faculty, University of Granada, Granada, Spain
- Fundación para la Investigación Biosanitaria de Andalucía Oriental-Alejandro Otero, Granada, Spain
| | - Antonio Salmerón-García
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Department of Clinical Pharmacy, San Cecilio University Hospital, Granada, Spain
| | | | - Inés Jiménez-Lozano
- Maternal and Child Pharmacy Service, Vall d'Hebron Hospital, Pharmacy, Barcelona, Spain
| | | | - Jose Cabeza
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Department of Clinical Pharmacy, San Cecilio University Hospital, Granada, Spain
| | - Natalia Navas
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Department of Analytical Chemistry, Science Faculty, University of Granada, Granada, Spain
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8
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Wu R, Metternich JB, Tiwari P, Benzenberg LR, Harrison JA, Liu Q, Zenobi R. Structural Studies of a Stapled Peptide with Native Ion Mobility-Mass Spectrometry and Transition Metal Ion Förster Resonance Energy Transfer in the Gas Phase. J Am Chem Soc 2022; 144:14441-14445. [PMID: 35943275 DOI: 10.1021/jacs.2c02776] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Native mass spectrometry has emerged as an important tool for gas-phase structural biology. However, the conformations that a biomolecular ion adopts in the gas phase can differ from those found in solution. Herein, we report a synergistic, native ion mobility-mass spectrometry (IM-MS) and transition metal ion Förster resonance energy transfer (tmFRET)-based approach to probe the gas-phase ion structures of a nonstapled peptide (nsp; Ac-CAARAAHAAAHARARA-NH2) and a stapled peptide (sp; Ac-CXARAXHAAAHARARA-NH2). The stapled peptide contains a single hydrocarbon chain connecting the peptide backbone in the i and i + 4 positions via a Grubbs ring-closure metathesis. Fluorescence lifetime measurements indicated that the Cu-bound complexes of carboxyrhodamine 6g (crh6g)-labeled stapled peptide (sp-crh6g) had a shorter donor-acceptor distance (rDA) than the labeled nonstapled peptide (nsp-crh6g). Experimental collision cross-section (CCS) values were then determined by native IM-MS, which could separate the conformations of Cu-bound complexes of nsp-crh6g and sp-crh6g. Finally, the experimental CCS (i.e., shape) and rDA (i.e., distance) values were used as constraints for computational studies, which unambiguously revealed how a staple reduces the elongation of the peptide ions in the gas phase. This study demonstrates the superiority of combining native IM-MS, tmFRET, and computational studies to investigate the structure of biomolecular ions.
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Affiliation(s)
- Ri Wu
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Jonas B Metternich
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Prince Tiwari
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Lukas R Benzenberg
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Julian A Harrison
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Qinlei Liu
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Renato Zenobi
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
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9
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Dragan P, Atzei A, Sanmukh SG, Latek D. Computational and experimental approaches to probe GPCR activation and signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 193:1-36. [PMID: 36357073 DOI: 10.1016/bs.pmbts.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
G protein-coupled receptors (GPCRs) regulate different physiological functions, e.g., sensation, growth, digestion, reproductivity, nervous and immune systems response, and many others. In eukaryotes, they are also responsible for intercellular communication in response to pathogens. The major primary messengers binding to these cell-surface receptors constitute small-molecule or peptide hormones and neurotransmitters, nucleotides, lipids as well as small proteins. The simplicity of the way how GPCR signaling can be regulated by their endogenous agonists prompted the usage of GPCRs as major drug targets in modern pharmacology. Drugs targeting GPCRs inhibit pathological processes at the very beginning. This enables to significantly reduce the occurrence of morphological changes caused by diseases. Until recently, X-ray crystallography was the method of the first choice to obtain high-resolution structural information about GPCRs. Following X-ray crystallography, cryo-EM gained attention in GPCR studies as a quick and low-cost alternative. FRET microscopy is also widely used for GPCRs in the analysis of protein-protein interactions (PPIs) in intact cells as well as for screening purposes. Regarding computational methods, molecular dynamics (MD) for many years has proven its usefulness in studying the GPCR activation. MODELLER and Rosetta were widely used to generate preliminary homology models of GPCRs for MD simulation systems. Apart from the conventional all-atom approach with explicitly defined solvent, also other techniques have been applied to GPCRs, e.g., MARTINI or hybrid methods involving the coarse-grained representation, less demanding regarding computational resources, and thus offering much larger simulation timescales.
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Affiliation(s)
- Paulina Dragan
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | | | | | - Dorota Latek
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland.
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10
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LILBID-MS: using lasers to shed light on biomolecular architectures. Biochem Soc Trans 2022; 50:1057-1067. [PMID: 35695670 PMCID: PMC9317959 DOI: 10.1042/bst20190881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/15/2022] [Accepted: 05/20/2022] [Indexed: 11/17/2022]
Abstract
Structural Biology has moved beyond the aim of simply identifying the components of a cellular subsystem towards analysing the dynamics and interactions of multiple players within a cell. This focal shift comes with additional requirements for the analytical tools used to investigate these systems of increased size and complexity, such as Native Mass Spectrometry, which has always been an important tool for structural biology. Scientific advance and recent developments, such as new ways to mimic a cell membrane for a membrane protein, have caused established methods to struggle to keep up with the increased demands. In this review, we summarize the possibilities, which Laser Induced Liquid Bead Ion Desorption (LILBID) mass spectrometry offers with regard to the challenges of modern structural biology, like increasingly complex sample composition, novel membrane mimics and advanced structural analysis, including next neighbor relations and the dynamics of complex formation.
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11
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Fiorentino F, Bolla JR. Mass Spectrometry Analysis of Dynamics and Interactions of the LPS Translocon LptDE. Methods Mol Biol 2022; 2548:109-128. [PMID: 36151495 DOI: 10.1007/978-1-0716-2581-1_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The presence of lipopolysaccharide (LPS) in the outer leaflet of the outer membrane (OM) is essential for Gram-negative bacteria OM barrier function and for maintaining its cell integrity. As such, comprehensive information about its biosynthesis and translocation represents a successful strategy for the development of antibacterial drugs. LPS is a complex glycolipid, and probing its interactions with LPS transport (Lpt) proteins has been extremely challenging. However, mass spectrometry (MS) techniques have recently catalyzed tremendous advancements in the characterization of LPS transport (Lpt) proteins and probed associated conformational dynamics upon substrate binding. Here, we describe the application of MS methods to study the dynamics of LPS translocon LptDE in the presence of natural substrates and inhibitors.
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Affiliation(s)
- Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Jani R Bolla
- The Kavli Institute for Nanoscience Discovery, Oxford, UK.
- Department of Plant Sciences, University of Oxford, Oxford, UK.
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12
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Hauser AS, Kooistra AJ, Munk C, Heydenreich FM, Veprintsev DB, Bouvier M, Babu MM, Gloriam DE. GPCR activation mechanisms across classes and macro/microscales. Nat Struct Mol Biol 2021; 28:879-888. [PMID: 34759375 PMCID: PMC8580822 DOI: 10.1038/s41594-021-00674-7] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 09/22/2021] [Indexed: 12/27/2022]
Abstract
Two-thirds of human hormones and one-third of clinical drugs activate ~350 G-protein-coupled receptors (GPCR) belonging to four classes: A, B1, C and F. Whereas a model of activation has been described for class A, very little is known about the activation of the other classes, which differ by being activated by endogenous ligands bound mainly or entirely extracellularly. Here we show that, although they use the same structural scaffold and share several 'helix macroswitches', the GPCR classes differ in their 'residue microswitch' positions and contacts. We present molecular mechanistic maps of activation for each GPCR class and methods for contact analysis applicable for any functional determinants. This provides a superfamily residue-level rationale for conformational selection and allosteric communication by ligands and G proteins, laying the foundation for receptor-function studies and drugs with the desired modality.
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Affiliation(s)
- Alexander S Hauser
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Albert J Kooistra
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Christian Munk
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- Data Tools Department, Novozymes A/S, Copenhagen, Denmark
| | - Franziska M Heydenreich
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biochemistry and Molecular Medicine, Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
- Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Dmitry B Veprintsev
- Centre of Membrane Proteins and Receptors (COMPARE), University of Nottingham, Nottingham, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Michel Bouvier
- Department of Biochemistry and Molecular Medicine, Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - M Madan Babu
- Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David E Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
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