1
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Lin CP, Li H, Brogan DJ, Wang T, Akbari OS, Komives EA. CRISPR-RNA binding drives structural ordering that primes Cas7-11 for target cleavage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.01.606276. [PMID: 39211128 PMCID: PMC11360901 DOI: 10.1101/2024.08.01.606276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Type III-E CRISPR-Cas effectors, of which Cas7-11 is the first, are single proteins that cleave target RNAs without nonspecific collateral cleavage, opening new possibilities for RNA editing. Biochemical experiments combined with amide hydrogen-deuterium exchange (HDX-MS) experiments provide a first glimpse of the conformational dynamics of apo Cas7-11. HDX-MS revealed the backbone comprised of the four Cas7 zinc-binding RRM folds are well-folded but insertion sequences are highly dynamic and fold upon binding crRNA. The crRNA causes folding of disordered catalytic loops and β-hairpins, stronger interactions at domain-domain interfaces, and folding of the Cas7.1 processing site. Target RNA binding causes only minor ordering around the catalytic loops of Cas7.2 and Cas7.3. We show that Cas7-11 cannot fully process the CRISPR array and that binding of partially processed crRNA induces multiple states in Cas7-11 and reduces target RNA cleavage. The insertion domain shows the most ordering upon binding of mature crRNA. Finally, we show a crRNA-induced conformational change in one of the TPR-CHAT binding sites providing an explanation for why crRNA binding facilitates TPR-CHAT binding. The results provide the first glimpse of the apo state of Cas7-11 and reveal how its structure and function are regulated by crRNA binding.
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2
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Wagner WJ, Gross ML. Using mass spectrometry-based methods to understand amyloid formation and inhibition of alpha-synuclein and amyloid beta. MASS SPECTROMETRY REVIEWS 2024; 43:782-825. [PMID: 36224716 PMCID: PMC10090239 DOI: 10.1002/mas.21814] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Amyloid fibrils, insoluble β-sheets structures that arise from protein misfolding, are associated with several neurodegenerative disorders. Many small molecules have been investigated to prevent amyloid fibrils from forming; however, there are currently no therapeutics to combat these diseases. Mass spectrometry (MS) is proving to be effective for studying the high order structure (HOS) of aggregating proteins and for determining structural changes accompanying protein-inhibitor interactions. When combined with native MS (nMS), gas-phase ion mobility, protein footprinting, and chemical cross-linking, MS can afford regional and sometimes amino acid spatial resolution of the aggregating protein. The spatial resolution is greater than typical low-resolution spectroscopic, calorimetric, and the traditional ThT fluorescence methods used in amyloid research today. High-resolution approaches can struggle when investigating protein aggregation, as the proteins exist as complex oligomeric mixtures of many sizes and several conformations or polymorphs. Thus, MS is positioned to complement both high- and low-resolution approaches to studying amyloid fibril formation and protein-inhibitor interactions. This review covers basics in MS paired with ion mobility, continuous hydrogen-deuterium exchange (continuous HDX), pulsed hydrogen-deuterium exchange (pulsed HDX), fast photochemical oxidation of proteins (FPOP) and other irreversible labeling methods, and chemical cross-linking. We then review the applications of these approaches to studying amyloid-prone proteins with a focus on amyloid beta and alpha-synuclein. Another focus is the determination of protein-inhibitor interactions. The expectation is that MS will bring new insights to amyloid formation and thereby play an important role to prevent their formation.
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Affiliation(s)
- Wesley J Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
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3
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Torres-Paris C, Song HJ, Engelberger F, Ramírez-Sarmiento CA, Komives EA. The Light Chain Allosterically Enhances the Protease Activity of Murine Urokinase-Type Plasminogen Activator. Biochemistry 2024; 63:1434-1444. [PMID: 38780522 PMCID: PMC11154964 DOI: 10.1021/acs.biochem.4c00071] [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] [Received: 02/06/2024] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
The active form of the murine urokinase-type plasminogen activator (muPA) is formed by a 27-residue disordered light chain connecting the amino-terminal fragment (ATF) with the serine protease domain. The two chains are tethered by a disulfide bond between C1CT in the disordered light chain and C122CT in the protease domain. Previous work showed that the presence of the disordered light chain affected the inhibition of the protease domain by antibodies. Here we show that the disordered light chain induced a 3.7-fold increase in kcat of the protease domain of muPA. In addition, hydrogen-deuterium exchange mass spectrometry (HDX-MS) and accelerated molecular dynamics (AMD) were performed to identify the interactions between the disordered light chain and the protease domain. HDX-MS revealed that the light chain is contacting the 110s, the turn between the β10- and β11-strand, and the β7-strand. A reduction in deuterium uptake was also observed in the activation loop, the 140s loop and the 220s loop, which forms the S1-specificty pocket where the substrate binds. These loops are further away from where the light chain seems to be interacting with the protease domain. Our results suggest that the light chain most likely increases the activity of muPA by allosterically favoring conformations in which the specificity pocket is formed. We propose a model by which the allostery would be transmitted through the β-strands of the β-barrels to the loops on the other side of the protease domain.
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Affiliation(s)
- Constanza Torres-Paris
- Department
of Chemistry and Biochemistry, Mail Code 0309, University of California San Diego, 9325 S Scholars Dr, La Jolla, California 92161, United States
| | - Harriet J. Song
- Department
of Chemistry and Biochemistry, Mail Code 0309, University of California San Diego, 9325 S Scholars Dr, La Jolla, California 92161, United States
| | - Felipe Engelberger
- Institute
for Biological and Medical Engineering, Schools of Engineering, Medicine
and Biological Sciences, Pontificia Universidad
Católica de Chile, Santiago 7820436, Chile
- ANID
- Millennium Science Initiative Program - Millennium Institute for
Integrative Biology (iBio), Santiago 8331150, Chile
| | - César A. Ramírez-Sarmiento
- Institute
for Biological and Medical Engineering, Schools of Engineering, Medicine
and Biological Sciences, Pontificia Universidad
Católica de Chile, Santiago 7820436, Chile
- ANID
- Millennium Science Initiative Program - Millennium Institute for
Integrative Biology (iBio), Santiago 8331150, Chile
| | - Elizabeth A. Komives
- Department
of Chemistry and Biochemistry, Mail Code 0309, University of California San Diego, 9325 S Scholars Dr, La Jolla, California 92161, United States
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4
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Ham D, Ahn D, Chung C, Chung KY. Isolation and conformational analysis of the Gα α-helical domain. Biochem Biophys Res Commun 2023; 685:149153. [PMID: 37913692 DOI: 10.1016/j.bbrc.2023.149153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/03/2023]
Abstract
Heterotrimeric G proteins (G proteins), composed of Gα, Gβ, and Gγ subunits, are the major downstream signaling molecules of the G protein-coupled receptors. Upon activation, Gα undergoes conformational changes both in the Ras-like domain (RD) and the α-helical domain (AHD), leading to the dissociation of Gα from Gβγ and subsequent regulation of downstream effector proteins. Gα RD mediate the most of classical functions of Gα. However, the role of Gα AHD is relatively not well elucidated despite its much higher sequence differences between Gα subtypes than those between Gα RD. Here, we isolated AHD from Gαs, Gαi1, and Gαq to provide tools for examining Gα AHD. We investigated the conformational dynamics of the isolated Gα AHD compared to those of the GDP-bound Gα. The results showed higher local conformational dynamics of Gα AHD not only at the domain interfaces but also in regions further away from the domain interfaces. This finding is consistent with the conformation of Gα AHD in the receptor-bound nucleotide-free state. Therefore, the isolated Gα AHD could provide a platform for studying the functions of Gα AHD, such as identification of the Gα AHD-binding proteins.
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Affiliation(s)
- Donghee Ham
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Donghoon Ahn
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Chiwoon Chung
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea.
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5
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Hatvany JB, Gallagher ES. Hydrogen/deuterium exchange for the analysis of carbohydrates. Carbohydr Res 2023; 530:108859. [PMID: 37290371 DOI: 10.1016/j.carres.2023.108859] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 06/10/2023]
Abstract
Carbohydrates and glycans are integral to many biological processes, including cell-cell recognition and energy storage. However, carbohydrates are often difficult to analyze due to the high degree of isomerism present. One method being developed to distinguish these isomeric species is hydrogen/deuterium exchange-mass spectrometry (HDX-MS). In HDX-MS, carbohydrates are exposed to a deuterated reagent and the functional groups with labile hydrogen atoms, including hydroxyls and amides, exchange with the 1 amu heavier isotope, deuterium. These labels can then be detected by MS, which monitors the mass increase with the addition of D-labels. The observed rate of exchange is dependent on the exchanging functional group, the accessibility of the exchanging functional group, and the presence of hydrogen bonds. Herein, we discuss how HDX has been applied in the solution-phase, gas-phase, and during MS ionization to label carbohydrates and glycans. Additionally, we compare differences in the conformations that are labeled, the labeling timeframes, and applications of each of these methods. Finally, we comment on future opportunities for development and use of HDX-MS to analyze glycans and glycoconjugates.
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Affiliation(s)
- Jacob B Hatvany
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX, 76798, USA
| | - Elyssia S Gallagher
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX, 76798, USA.
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6
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Structural and Functional Implication of Natural Variants of Gαs. Int J Mol Sci 2023; 24:ijms24044064. [PMID: 36835474 PMCID: PMC9959179 DOI: 10.3390/ijms24044064] [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: 01/16/2023] [Revised: 02/09/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Heterotrimeric guanine nucleotide-binding proteins (G proteins) are among the most important cellular signaling components, especially G protein-coupled receptors (GPCRs). G proteins comprise three subunits, Gα, Gβ, and Gγ. Gα is the key subunit, and its structural state regulates the active status of G proteins. Interaction of guanosine diphosphate (GDP) or guanosine triphosphate (GTP) with Gα switches G protein into basal or active states, respectively. Genetic alteration in Gα could be responsible for the development of various diseases due to its critical role in cell signaling. Specifically, loss-of-function mutations of Gαs are associated with parathyroid hormone-resistant syndrome such as inactivating parathyroid hormone/parathyroid hormone-related peptide (PTH/PTHrP) signaling disorders (iPPSDs), whereas gain-of-function mutations of Gαs are associated with McCune-Albright syndrome and tumor development. In the present study, we analyzed the structural and functional implications of natural variants of the Gαs subtype observed in iPPSDs. Although a few tested natural variants did not alter the structure and function of Gαs, others induced drastic conformational changes in Gαs, resulting in improper folding and aggregation of the proteins. Other natural variants induced only mild conformational changes but altered the GDP/GTP exchange kinetics. Therefore, the results shed light on the relationship between natural variants of Gα and iPPSDs.
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7
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Hammerschmid D, Calvaresi V, Bailey C, Russell Lewis B, Politis A, Morris M, Denbigh L, Anderson M, Reading E. Chromatographic Phospholipid Trapping for Automated H/D Exchange Mass Spectrometry of Membrane Protein-Lipid Assemblies. Anal Chem 2023; 95:3002-3011. [PMID: 36706021 PMCID: PMC9909672 DOI: 10.1021/acs.analchem.2c04876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Lipid interactions modulate the function, folding, structure, and organization of membrane proteins. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) has emerged as a useful tool to understand the structural dynamics of these proteins within lipid environments. Lipids, however, have proven problematic for HDX-MS analysis of membrane-embedded proteins due to their presence of impairing proteolytic digestion, causing liquid chromatography column fouling, ion suppression, and/or mass spectral overlap. Herein, we describe the integration of a chromatographic phospholipid trap column into the HDX-MS apparatus to enable online sample delipidation prior to protease digestion of deuterium-labeled protein-lipid assemblies. We demonstrate the utility of this method on membrane scaffold protein-lipid nanodisc─both empty and loaded with the ∼115 kDa transmembrane protein AcrB─proving efficient and automated phospholipid capture with minimal D-to-H back-exchange, peptide carry-over, and protein loss. Our results provide insights into the efficiency of phospholipid capture by ZrO2-coated and TiO2 beads and describe how solution conditions can be optimized to maximize not only the performance of our online but also the existing offline, delipidation workflows for HDX-MS. We envision that this HDX-MS method will significantly ease membrane protein analysis, allowing to better interrogate their dynamics in artificial lipid bilayers or even native cell membranes.
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Affiliation(s)
- Dietmar Hammerschmid
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB London, U.K.
| | - Valeria Calvaresi
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB London, U.K.
| | - Chloe Bailey
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB London, U.K.
| | | | - Argyris Politis
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB London, U.K.
| | - Michael Morris
- Waters
Corporation, Stamford Avenue, Altrincham Road, SK9
4AX Wilmslow, U.K.
| | - Laetitia Denbigh
- Waters
Corporation, Stamford Avenue, Altrincham Road, SK9
4AX Wilmslow, U.K.
| | - Malcolm Anderson
- Waters
Corporation, Stamford Avenue, Altrincham Road, SK9
4AX Wilmslow, U.K.
| | - Eamonn Reading
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB London, U.K.
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8
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Solomon TL, Delaglio F, Giddens JP, Marino JP, Yu YB, Taraban MB, Brinson RG. Correlated analytical and functional evaluation of higher order structure perturbations from oxidation of NISTmAb. MAbs 2023; 15:2160227. [PMID: 36683157 PMCID: PMC9872951 DOI: 10.1080/19420862.2022.2160227] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The clinical efficacy and safety of protein-based drugs such as monoclonal antibodies (mAbs) rely on the integrity of the protein higher order structure (HOS) during product development, manufacturing, storage, and patient administration. As mAb-based drugs are becoming more prevalent in the treatment of many illnesses, the need to establish metrics for quality attributes of mAb therapeutics through high-resolution techniques is also becoming evident. To this end, here we used a forced degradation method, time-dependent oxidation by hydrogen peroxide, on the model biotherapeutic NISTmAb and evaluated the effects on HOS with orthogonal analytical methods and a functional assay. To monitor the oxidation process, the experimental workflow involved incubation of NISTmAb with hydrogen peroxide in a benchtop nuclear magnetic resonance spectrometer (NMR) that followed the reaction kinetics, in real-time through the water proton transverse relaxation rate R2(1H2O). Aliquots taken at defined time points were further analyzed by high-field 2D 1H-13C methyl correlation fingerprint spectra in parallel with other analytical techniques, including thermal unfolding, size-exclusion chromatography, and surface plasmon resonance, to assess changes in stability, heterogeneity, and binding affinities. The complementary measurement outputs from the different techniques demonstrate the utility of combining NMR with other analytical tools to monitor oxidation kinetics and extract the resulting structural changes in mAbs that are functionally relevant, allowing rigorous assessment of HOS attributes relevant to the efficacy and safety of mAb-based drug products.
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Affiliation(s)
- Tsega L. Solomon
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland, United States
| | - Frank Delaglio
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland, United States
| | - John P. Giddens
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland, United States
| | - John P. Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland, United States
| | - Yihua Bruce Yu
- Bio- and Nano-Technology Center, University of Maryland School of Pharmacy, and Institute for Bioscience and Biotechnology Research, Rockville, Maryland, United States
| | - Marc B. Taraban
- Bio- and Nano-Technology Center, University of Maryland School of Pharmacy, and Institute for Bioscience and Biotechnology Research, Rockville, Maryland, United States
| | - Robert G. Brinson
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland, United States,CONTACT Robert G. Brinson Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, 9600 Gudelsky Drive Rockville, Rockville, Maryland20850, United States
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9
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Effect of α-helical domain of Gi/o α subunit on GDP/GTP turnover. Biochem J 2022; 479:1843-1855. [PMID: 36000572 DOI: 10.1042/bcj20220163] [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: 04/04/2022] [Revised: 08/11/2022] [Accepted: 08/24/2022] [Indexed: 11/17/2022]
Abstract
Heterotrimeric guanine nucleotide-binding proteins (G proteins) are composed of α, β, and γ subunits, and Gα has a GDP/GTP-binding pocket. When a guanine nucleotide exchange factor (GEF) interacts with Gα, GDP is released, and GTP interacts to Gα. The GTP-bound activated Gα dissociates from GEF and Gβγ, mediating the induction of various intracellular signaling pathways. Depending on the sequence similarity and cellular function, Gα subunits are subcategorized into four subfamilies: Gαi/o, Gαs, Gαq/11, and Gα12/13. Although the Gαi/o subtype family proteins, Gαi3 and GαoA, share similar sequences and functions, they differ in their GDP/GTP turnover profiles, with GαoA possessing faster rates than Gαi3. The structural factors responsible for these differences remain unknown. In this study, we employed hydrogen/deuterium exchange mass spectrometry and mutational studies to investigate the factors responsible for these functional differences. The Gα subunit consists of a Ras-like domain (RD) and an α-helical domain (AHD). The RD has GTPase activity and receptor-binding and effector-binding regions; however, the function of the AHD has not yet been extensively studied. In this study, the chimeric construct containing the RD of Gαi3 and the AHD of GαoA showed a GDP/GTP turnover profile similar to that of GαoA, suggesting that the AHD is the major regulator of the GDP/GTP turnover profile. Additionally, site-directed mutagenesis revealed the importance of the N-terminal part of αA and αA/αB loops in the AHD for the GDP/GTP exchange. These results suggest that the AHD regulates the nucleotide exchange rate within the Gα subfamily.
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10
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Hydrogen‑deuterium exchange mass spectrometry to study interactions and conformational changes of proteins in paints. Biophys Chem 2022; 289:106861. [DOI: 10.1016/j.bpc.2022.106861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/07/2022] [Accepted: 07/24/2022] [Indexed: 11/18/2022]
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11
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Advances in Mass Spectrometry-based Epitope Mapping of Protein Therapeutics. J Pharm Biomed Anal 2022; 215:114754. [DOI: 10.1016/j.jpba.2022.114754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/16/2022] [Accepted: 04/03/2022] [Indexed: 11/21/2022]
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12
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Protein folding stabilities are a major determinant of oxidation rates for buried methionine residues. J Biol Chem 2022; 298:101872. [PMID: 35346688 PMCID: PMC9062257 DOI: 10.1016/j.jbc.2022.101872] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 12/20/2022] Open
Abstract
The oxidation of protein-bound methionines to form methionine sulfoxides has a broad range of biological ramifications, making it important to delineate factors that influence methionine oxidation rates within a given protein. This is especially important for biopharmaceuticals, where oxidation can lead to deactivation and degradation. Previously, neighboring residue effects and solvent accessibility have been shown to impact the susceptibility of methionine residues to oxidation. In this study, we provide proteome-wide evidence that oxidation rates of buried methionine residues are also strongly influenced by the thermodynamic folding stability of proteins. We surveyed the Escherichia coli proteome using several proteomic methodologies and globally measured oxidation rates of methionine residues in the presence and absence of tertiary structure, as well as the folding stabilities of methionine-containing domains. These data indicated that buried methionines have a wide range of protection factors against oxidation that correlate strongly with folding stabilities. Consistent with this, we show that in comparison to E. coli, the proteome of the thermophile Thermus thermophilus is significantly more stable and thus more resistant to methionine oxidation. To demonstrate the utility of this correlation, we used native methionine oxidation rates to survey the folding stabilities of E. coli and T. thermophilus proteomes at various temperatures and propose a model that relates the temperature dependence of the folding stabilities of these two species to their optimal growth temperatures. Overall, these results indicate that oxidation rates of buried methionines from the native state of proteins can be used as a metric of folding stability.
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13
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Keramisanou D, Vasantha Kumar M, Boose N, Abzalimov RR, Gelis I. Assembly mechanism of early Hsp90-Cdc37-kinase complexes. SCIENCE ADVANCES 2022; 8:eabm9294. [PMID: 35294247 PMCID: PMC8926337 DOI: 10.1126/sciadv.abm9294] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/25/2022] [Indexed: 05/27/2023]
Abstract
Molecular chaperones have an essential role for the maintenance of a balanced protein homeostasis. Here, we investigate how protein kinases are recruited and loaded to the Hsp90-Cdc37 complex, the first step during Hsp90-mediated chaperoning that leads to enhanced client kinase stability and activation. We show that conformational dynamics of all partners is a critical feature of the underlying loading mechanism. The kinome co-chaperone Cdc37 exists primarily in a dynamic extended conformation but samples a low-populated, well-defined compact structure. Exchange between these two states is maintained in an assembled Hsp90-Cdc37 complex and is necessary for substrate loading. Breathing motions at the N-lobe of a free kinase domain partially expose the kinase segment trapped in the Hsp90 dimer downstream in the cycle. Thus, client dynamics poise for chaperone dependence. Hsp90 is not directly involved during loading, and Cdc37 is assigned the task of sensing clients by stabilizing the preexisting partially unfolded client state.
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Affiliation(s)
| | | | - Nicole Boose
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA
| | - Rinat R. Abzalimov
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
| | - Ioannis Gelis
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA
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14
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Devaurs D, Antunes DA, Borysik AJ. Computational Modeling of Molecular Structures Guided by Hydrogen-Exchange Data. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:215-237. [PMID: 35077179 DOI: 10.1021/jasms.1c00328] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Data produced by hydrogen-exchange monitoring experiments have been used in structural studies of molecules for several decades. Despite uncertainties about the structural determinants of hydrogen exchange itself, such data have successfully helped guide the structural modeling of challenging molecular systems, such as membrane proteins or large macromolecular complexes. As hydrogen-exchange monitoring provides information on the dynamics of molecules in solution, it can complement other experimental techniques in so-called integrative modeling approaches. However, hydrogen-exchange data have often only been used to qualitatively assess molecular structures produced by computational modeling tools. In this paper, we look beyond qualitative approaches and survey the various paradigms under which hydrogen-exchange data have been used to quantitatively guide the computational modeling of molecular structures. Although numerous prediction models have been proposed to link molecular structure and hydrogen exchange, none of them has been widely accepted by the structural biology community. Here, we present as many hydrogen-exchange prediction models as we could find in the literature, with the aim of providing the first exhaustive list of its kind. From purely structure-based models to so-called fractional-population models or knowledge-based models, the field is quite vast. We aspire for this paper to become a resource for practitioners to gain a broader perspective on the field and guide research toward the definition of better prediction models. This will eventually improve synergies between hydrogen-exchange monitoring and molecular modeling.
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Affiliation(s)
- Didier Devaurs
- MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, U.K
| | - Dinler A Antunes
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77005, United States
| | - Antoni J Borysik
- Department of Chemistry, King's College London, London SE1 1DB, U.K
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15
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James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
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Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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16
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Chiu D, Pan L, Fay L, Eakin C, Valliere-Douglass J. Structural characterization of a monomethylauristatin-E based ADC that contains 8 drugs conjugated at interchain cysteine residues. J Pharm Biomed Anal 2021; 205:114309. [PMID: 34403866 DOI: 10.1016/j.jpba.2021.114309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/31/2021] [Accepted: 08/04/2021] [Indexed: 10/20/2022]
Abstract
Antibody-drug conjugates (ADCs) with a drug-to-antibody ratio (DAR) of 8 are attractive as therapeutic anti-cancer agents due to the higher levels of cytotoxic payload delivered to tumors. Biophysical characterization of a DAR 8 ADC fully conjugated at all interchain cysteine residues was carried out to determine if IgG1 interchain disulfide reduction and conjugation led to structural perturbations that impacted product stability. Comparisons between the DAR 8 ADC and the unconjugated parent antibody identified minor tertiary and quaternary structural changes localized to the CL, CH1, and CH2 domains and CH2-CH3 domain interface. Stability studies of the DAR 8 ADC indicated that the structural changes had minimal impacts to product stability as demonstrated by low levels of fragmentation and aggregation under nominal storage and temperature stress stability conditions. Additionally, no detectable higher order structural changes were observed by CD or DSC in the DAR 8 ADC after 3 months at (25 °C) stability conditions. The structural and stability results support the developability of DAR 8 ADCs fully conjugated to interchain cysteines residues with an optimized and clinically relevant second generation monomethylauristatin-E (MMAE) drug-linker.
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Affiliation(s)
- David Chiu
- Quality Control, Seagen Inc., 21823 30th Drive Southeast, Bothell, WA, 98021, United States.
| | - Lucy Pan
- Quality Control, Seagen Inc., 21823 30th Drive Southeast, Bothell, WA, 98021, United States.
| | - Lindsay Fay
- Pharmaceutical Sciences, Seagen Inc., 21823 30th Drive Southeast, Bothell, WA, 98021, United States.
| | - Catherine Eakin
- Analytical Sciences, Seagen Inc., 21823 30th Drive Southeast, Bothell, WA, 98021, United States.
| | - John Valliere-Douglass
- Analytical Sciences, Seagen Inc., 21823 30th Drive Southeast, Bothell, WA, 98021, United States.
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17
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Merkle PS, Trabjerg E, Hongjian S, Ferber M, Cuendet MA, Jørgensen TJD, Luescher I, Irving M, Zoete V, Michielin O, Rand KD. Probing the Conformational Dynamics of Affinity-Enhanced T Cell Receptor Variants upon Binding the Peptide-Bound Major Histocompatibility Complex by Hydrogen/Deuterium Exchange Mass Spectrometry. Biochemistry 2021; 60:859-872. [PMID: 33689297 DOI: 10.1021/acs.biochem.1c00035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Binding of the T cell receptor (TCR) to its cognate, peptide antigen-loaded major histocompatibility complex (pMHC) is a key interaction for triggering T cell activation and ultimately elimination of the target cell. Despite the importance of this interaction for cellular immunity, a comprehensive molecular understanding of TCR specificity and affinity is lacking. We conducted hydrogen/deuterium exchange mass spectrometry (HDX-MS) analyses of individual affinity-enhanced TCR variants and clinically relevant pMHC class I molecules (HLA-A*0201/NY-ESO-1157-165) to investigate the causality between increased binding affinity and conformational dynamics in TCR-pMHC complexes. Differential HDX-MS analyses of TCR variants revealed that mutations for affinity enhancement in TCR CDRs altered the conformational response of TCR to pMHC ligation. Improved pMHC binding affinity was in general observed to correlate with greater differences in HDX upon pMHC binding in modified TCR CDR loops, thereby providing new insights into the TCR-pMHC interaction. Furthermore, a specific point mutation in the β-CDR3 loop of the NY-ESO-1 TCR associated with a substantial increase in binding affinity resulted in a substantial change in pMHC binding kinetics (i.e., very slow kon, revealed by the detection of EX1 HDX kinetics), thus providing experimental evidence for a slow induced-fit binding mode. We also examined the conformational impact of pMHC binding on an unrelated TRAV12-2 gene-encoded TCR directed against the immunodominant MART-126-35 cancer antigen restricted by HLA-A*0201. Our findings provide a molecular basis for the observed TRAV12-2 gene bias in natural CD8+ T cell-based immune responses against the MART-1 antigen, with potential implications for general ligand discrimination and TCR cross-reactivity processes.
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MESH Headings
- Humans
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/immunology
- HLA-A2 Antigen/chemistry
- HLA-A2 Antigen/immunology
- HLA-A2 Antigen/metabolism
- HLA-A2 Antigen/genetics
- Protein Conformation
- Hydrogen Deuterium Exchange-Mass Spectrometry
- Protein Binding
- Peptides/chemistry
- Peptides/metabolism
- Peptides/immunology
- Major Histocompatibility Complex
- Antigens, Neoplasm/chemistry
- Antigens, Neoplasm/metabolism
- Antigens, Neoplasm/immunology
- Antigens, Neoplasm/genetics
- Peptide Fragments/chemistry
- Peptide Fragments/metabolism
- Peptide Fragments/genetics
- Peptide Fragments/immunology
- Deuterium Exchange Measurement
- Mutation
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Affiliation(s)
- Patrick S Merkle
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Esben Trabjerg
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Song Hongjian
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Mathias Ferber
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Michel A Cuendet
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
- Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, United States
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Immanuel Luescher
- Ludwig Branch for Cancer Research of the University of Lausanne, 8001 Zurich, Switzerland
| | - Melita Irving
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
- Ludwig Branch for Cancer Research of the University of Lausanne, 8001 Zurich, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Olivier Michielin
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
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18
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Stocks BB, Bird GH, Walensky LD, Melanson JE. Characterizing Native and Hydrocarbon-Stapled Enfuvirtide Conformations with Ion Mobility Mass Spectrometry and Hydrogen-Deuterium Exchange. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:753-761. [PMID: 33534566 DOI: 10.1021/jasms.0c00453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The number of approved peptide therapeutics, as well as those in development, has been increasing in recent years. Frequently, the biological activity of such peptides is elicited through the adoption of secondary structural elements upon interaction with their cellular target. However, many therapeutic peptides are unstructured in solution and accordingly exhibit a poor bioavailability due to rapid proteolysis in vivo. To combat this degradation, numerous naturally occurring peptides with therapeutic properties contain stabilizing features, such as N-to-C cyclization or disulfide bonds. Recently, hydrocarbon stapling via non-native amino acid substitution followed by ring-closing metathesis has been shown to induce a dramatic stabilization of α-helical peptides. Identifying the ideal staple location along the peptide backbone is a critical developmental step, and methods to streamline this optimization are needed. Mass spectrometry-based methods such as ion mobility (IM) and hydrogen-deuterium exchange (HDX) can detect multiple discrete peptide conformations, a significant advantage over bulk spectroscopic techniques. In this study we use IM-MS and HDX-MS to demonstrate that the native 36-residue enfuvirtide peptide is highly dynamic in solution and the conformational ensemble populated by stabilized constructs depends heavily on the staple location. Further, our measurements yielded results that correlate well with the average α-helical content measured by circular dichroism. The MS-based approaches described herein represent sensitive and potentially high-throughput methods for characterizing and identifying optimally stapled peptides.
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Affiliation(s)
- Bradley B Stocks
- Metrology, National Research Council Canada, 1200 Montreal Road, Ottawa, Ontario K1A 0R6, Canada
| | - Gregory H Bird
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Loren D Walensky
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Jeremy E Melanson
- Metrology, National Research Council Canada, 1200 Montreal Road, Ottawa, Ontario K1A 0R6, Canada
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19
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Ozohanics O, Ambrus A. Hydrogen-Deuterium Exchange Mass Spectrometry: A Novel Structural Biology Approach to Structure, Dynamics and Interactions of Proteins and Their Complexes. Life (Basel) 2020; 10:E286. [PMID: 33203161 PMCID: PMC7696067 DOI: 10.3390/life10110286] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/12/2020] [Accepted: 11/12/2020] [Indexed: 11/16/2022] Open
Abstract
Hydrogen/Deuterium eXchange Mass Spectrometry (HDX-MS) is a rapidly evolving technique for analyzing structural features and dynamic properties of proteins. It may stand alone or serve as a complementary method to cryo-electron-microscopy (EM) or other structural biology approaches. HDX-MS is capable of providing information on individual proteins as well as large protein complexes. Owing to recent methodological advancements and improving availability of instrumentation, HDX-MS is becoming a routine technique for some applications. When dealing with samples of low to medium complexity and sizes of less than 150 kDa, conformation and ligand interaction analyses by HDX-MS are already almost routine applications. This is also well supported by the rapid evolution of the computational (software) background that facilitates the analysis of the obtained experimental data. HDX-MS can cope at times with analytes that are difficult to tackle by any other approach. Large complexes like viral capsids as well as disordered proteins can also be analyzed by this method. HDX-MS has recently become an established tool in the drug discovery process and biopharmaceutical development, as it is now also capable of dissecting post-translational modifications and membrane proteins. This mini review provides the reader with an introduction to the technique and a brief overview of the most common applications. Furthermore, the most challenging likely applications, the analyses of glycosylated and membrane proteins, are also highlighted.
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Affiliation(s)
- Oliver Ozohanics
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, 37–47 Tuzolto Street, 1094 Budapest, Hungary
| | - Attila Ambrus
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, 37–47 Tuzolto Street, 1094 Budapest, Hungary
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20
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Ziemianowicz DS, Sarpe V, Crowder D, Pells TJ, Raval S, Hepburn M, Rafiei A, Schriemer DC. Harmonizing structural mass spectrometry analyses in the mass spec studio. J Proteomics 2020; 225:103844. [DOI: 10.1016/j.jprot.2020.103844] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/23/2020] [Accepted: 05/24/2020] [Indexed: 01/06/2023]
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21
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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22
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Zhang Z. Complete Extraction of Protein Dynamics Information in Hydrogen/Deuterium Exchange Mass Spectrometry Data. Anal Chem 2020; 92:6486-6494. [DOI: 10.1021/acs.analchem.9b05724] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Zhongqi Zhang
- Process Development, Amgen Incorporated, One Amgen Center Drive, Thousand Oaks, California 91320, United States
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23
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Hong J, Wu H, Zhang R, He M, Xu W. The Coupling of Taylor Dispersion Analysis and Mass Spectrometry to Differentiate Protein Conformations. Anal Chem 2020; 92:5200-5206. [DOI: 10.1021/acs.analchem.9b05745] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jie Hong
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Haimei Wu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Rongkai Zhang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Muyi He
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
- Institute of Food Safety, Chinese Academy of Inspection & Quarantine, Beijing 100176, China
| | - Wei Xu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
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24
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Conformational Dynamics and Functional Implications of Phosphorylated β-Arrestins. Structure 2020; 28:314-323.e3. [DOI: 10.1016/j.str.2019.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 11/25/2019] [Accepted: 12/21/2019] [Indexed: 12/18/2022]
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25
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The Impact of Immunoglobulin G1 Fc Sialylation on Backbone Amide H/D Exchange. Antibodies (Basel) 2019; 8:antib8040049. [PMID: 31581521 PMCID: PMC6963987 DOI: 10.3390/antib8040049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/24/2019] [Accepted: 09/26/2019] [Indexed: 12/17/2022] Open
Abstract
The usefulness of higher-order structural information provided by hydrogen/deuterium exchange-mass spectrometry (H/DX-MS) for the structural impact analyses of chemical and post-translational antibody modifications has been demonstrated in various studies. However, the structure-function assessment for protein drugs in biopharmaceutical research and development is often impeded by the relatively low-abundance (below 5%) of critical quality attributes or by overlapping effects of modifications, such as glycosylation, with chemical amino acid modifications; e.g., oxidation or deamidation. We present results demonstrating the applicability of the H/DX-MS technique to monitor conformational changes of specific Fc glycosylation variants produced by in vitro glyco-engineering technology. A trend towards less H/DX in Fc Cγ2 domain segments correlating with larger glycan structures could be confirmed. Furthermore, significant deuterium uptake differences and corresponding binding properties to Fc receptors (as monitored by SPR) between α-2,3- and α-2,6-sialylated Fc glycosylation variants were verified at sensitive levels.
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26
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Du Y, Duc NM, Rasmussen SGF, Hilger D, Kubiak X, Wang L, Bohon J, Kim HR, Wegrecki M, Asuru A, Jeong KM, Lee J, Chance MR, Lodowski DT, Kobilka BK, Chung KY. Assembly of a GPCR-G Protein Complex. Cell 2019; 177:1232-1242.e11. [PMID: 31080064 DOI: 10.1016/j.cell.2019.04.022] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 02/25/2019] [Accepted: 04/09/2019] [Indexed: 12/30/2022]
Abstract
The activation of G proteins by G protein-coupled receptors (GPCRs) underlies the majority of transmembrane signaling by hormones and neurotransmitters. Recent structures of GPCR-G protein complexes obtained by crystallography and cryoelectron microscopy (cryo-EM) reveal similar interactions between GPCRs and the alpha subunit of different G protein isoforms. While some G protein subtype-specific differences are observed, there is no clear structural explanation for G protein subtype-selectivity. All of these complexes are stabilized in the nucleotide-free state, a condition that does not exist in living cells. In an effort to better understand the structural basis of coupling specificity, we used time-resolved structural mass spectrometry techniques to investigate GPCR-G protein complex formation and G-protein activation. Our results suggest that coupling specificity is determined by one or more transient intermediate states that serve as selectivity filters and precede the formation of the stable nucleotide-free GPCR-G protein complexes observed in crystal and cryo-EM structures.
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Affiliation(s)
- Yang Du
- Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Nguyen Minh Duc
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Søren G F Rasmussen
- Department of Neuroscience, University of Copenhagen, Copenhagen 2200, Denmark
| | - Daniel Hilger
- Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Xavier Kubiak
- Department of Neuroscience, University of Copenhagen, Copenhagen 2200, Denmark
| | - Liwen Wang
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jennifer Bohon
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; Case Center for Synchrotron Biosciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Hee Ryung Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Marcin Wegrecki
- Department of Neuroscience, University of Copenhagen, Copenhagen 2200, Denmark
| | - Awuri Asuru
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Kyung Min Jeong
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jeongmi Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Mark R Chance
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; Case Center for Synchrotron Biosciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - David T Lodowski
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Brian K Kobilka
- Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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27
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Maleknia SD, Downard KM. Protein Footprinting with Radical Probe Mass Spectrometry- Two Decades of Achievement. Protein Pept Lett 2019; 26:4-15. [PMID: 30484400 DOI: 10.2174/0929866526666181128124241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/31/2018] [Accepted: 09/11/2018] [Indexed: 01/19/2023]
Abstract
BACKGROUND Radical Probe Mass Spectrometry (RP-MS) describes a pioneering methodology in structural biology that enables the study of protein structures, their interactions, and dynamics on fast timescales (down to sub-milliseconds). Hydroxyl radicals (•OH) generated directly from water within aqueous solutions induce the oxidation of reactive, solvent accessible amino acid side chains that are then analyzed by mass spectrometry. Introduced in 1998 at the American Society for Mass Spectrometry annual conference, RP-MS was first published on in 1999. OBJECTIVE This review article describes developments and applications of the RP-MS methodology over the past two decades. METHODS The RP-MS method has been variously referred to as synchrotron X-ray radiolysis footprinting, Hydroxyl Radical Protein Footprinting (HRPF), X-ray Footprinting with Mass Spectrometry (XF-MS), Fast Photochemical Oxidation of Proteins (FPOP), oxidative labelling, covalent oxidative labelling, and even the Stability of Proteins from Rates of Oxidation (SPROX). RESULTS The article describes the utility of hydroxyl radicals as a protein structural probe, the advantages of RP-MS in comparison to other MS-based approaches, its proof of concept using ion mobility mass spectrometry, its application to protein structure, folding, complex and aggregation studies, its extension to study the onset of protein damage, its implementation using a high throughput sample loading approach, and the development of protein docking algorithms to aid with data analysis and visualization. CONCLUSION RP-MS represents a powerful new structural approach that can aid in our understanding of the structure and functions of proteins, and the impact of sustained oxidation on proteins in disease pathogenesis.
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Affiliation(s)
- Simin D Maleknia
- School of Mathematical and Physical Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Kevin M Downard
- Infectious Disease Responses Laboratory, University of New South Wales-Medicine, Sydney, NSW, Australia
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28
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Downard KM, Maleknia SD. Mass spectrometry in structural proteomics: The case for radical probe protein footprinting. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.11.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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29
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Affiliation(s)
- Vlastimil Dorčák
- Department of Biophysical Chemistry and Molecular OncologyInstitute of Biophysics of the CAS, v.v.i. Kralovopolska 135 612 65 Brno
| | - Emil Paleček
- Department of Biophysical Chemistry and Molecular OncologyInstitute of Biophysics of the CAS, v.v.i. Kralovopolska 135 612 65 Brno
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30
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Murcia Rios A, Vahidi S, Dunn SD, Konermann L. Evidence for a Partially Stalled γ Rotor in F 1-ATPase from Hydrogen-Deuterium Exchange Experiments and Molecular Dynamics Simulations. J Am Chem Soc 2018; 140:14860-14869. [PMID: 30339028 DOI: 10.1021/jacs.8b08692] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
F1-ATPase uses ATP hydrolysis to drive rotation of the γ subunit. The γ C-terminal helix constitutes the rotor tip that is seated in an apical bearing formed by α3β3. It remains uncertain to what extent the γ conformation during rotation differs from that seen in rigid crystal structures. Existing models assume that the entire γ subunit participates in every rotation. Here we interrogated E. coli F1-ATPase by hydrogen-deuterium exchange (HDX) mass spectrometry. Rotation of γ caused greatly enhanced deuteration in the γ C-terminal helix. The HDX kinetics implied that most F1 complexes operate with an intact rotor at any given time, but that the rotor tip is prone to occasional unfolding. A molecular dynamics (MD) strategy was developed to model the off-axis forces acting on γ. MD runs showed stalling of the rotor tip and unfolding of the γ C-terminal helix. MD-predicted H-bond opening events coincided with experimental HDX patterns. Our data suggest that in vitro operation of F1-ATPase is associated with significant rotational resistance in the apical bearing. These conditions cause the γ C-terminal helix to get "stuck" (and unfold) sporadically while the remainder of γ continues to rotate. This scenario contrasts the traditional "greasy bearing" model that envisions smooth rotation of the γ C-terminal helix. The fragility of the apical rotor tip in F1-ATPase is attributed to the absence of a c10 ring that stabilizes the rotation axis in intact FoF1. Overall, the MD/HDX strategy introduced here appears well suited for interrogating the inner workings of molecular motors.
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Affiliation(s)
- Angela Murcia Rios
- Departments of Chemistry and Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada
| | - Siavash Vahidi
- Departments of Chemistry and Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada
| | - Stanley D Dunn
- Departments of Chemistry and Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada
| | - Lars Konermann
- Departments of Chemistry and Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada
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31
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Oganesyan I, Lento C, Wilson DJ. Contemporary hydrogen deuterium exchange mass spectrometry. Methods 2018; 144:27-42. [DOI: 10.1016/j.ymeth.2018.04.023] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/16/2018] [Accepted: 04/21/2018] [Indexed: 02/07/2023] Open
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32
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Kaltashov IA. Mass spectrometry-based methods to study macromolecular higher order structure and interactions. Methods 2018; 144:1-2. [DOI: 10.1016/j.ymeth.2018.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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33
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Liu H, Kim HR, Deepak RNVK, Wang L, Chung KY, Fan H, Wei Z, Zhang C. Orthosteric and allosteric action of the C5a receptor antagonists. Nat Struct Mol Biol 2018; 25:472-481. [PMID: 29867214 DOI: 10.1038/s41594-018-0067-z] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/16/2018] [Indexed: 01/09/2023]
Abstract
The C5a receptor (C5aR) is a G-protein-coupled receptor (GPCR) that can induce strong inflammatory response to the anaphylatoxin C5a. Targeting C5aR has emerged as a novel anti-inflammatory therapeutic method. However, developing potent C5aR antagonists as drugs has proven difficult. Here, we report two crystal structures of human C5aR in ternary complexes with the peptide antagonist PMX53 and a non-peptide antagonist, either avacopan or NDT9513727. The structures, together with other biophysical, computational docking and cell-based signaling data, reveal the orthosteric action of PMX53 and its effect of stabilizing the C5aR structure, as well as the allosteric action of chemically diverse non-peptide C5aR antagonists with different binding poses. Structural comparison analysis suggests the presence of similar allosteric sites in other GPCRs. We also discuss critical structural features of C5aR in activation, including a novel conformation of helix 8. On the basis of our results, we suggest novel strategies for developing C5aR-targeting drugs.
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Affiliation(s)
- Heng Liu
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hee Ryung Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - R N V Krishna Deepak
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Lei Wang
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Hao Fan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Zhiyi Wei
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Cheng Zhang
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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34
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Kiselar J, Chance MR. High-Resolution Hydroxyl Radical Protein Footprinting: Biophysics Tool for Drug Discovery. Annu Rev Biophys 2018. [DOI: 10.1146/annurev-biophys-070317-033123] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hydroxyl radical footprinting (HRF) of proteins with mass spectrometry (MS) is a widespread approach for assessing protein structure. Hydroxyl radicals react with a wide variety of protein side chains, and the ease with which radicals can be generated (by radiolysis or photolysis) has made the approach popular with many laboratories. As some side chains are less reactive and thus cannot be probed, additional specific and nonspecific labeling reagents have been introduced to extend the approach. At the same time, advances in liquid chromatography and MS approaches permit an examination of the labeling of individual residues, transforming the approach to high resolution. Lastly, advances in understanding of the chemistry of the approach have led to the determination of absolute protein topologies from HRF data. Overall, the technology can provide precise and accurate measures of side-chain solvent accessibility in a wide range of interesting and useful contexts for the study of protein structure and dynamics in both academia and industry.
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Affiliation(s)
- Janna Kiselar
- Center for Proteomics and Bioinformatics, and Department of Nutrition, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Mark R. Chance
- Center for Proteomics and Bioinformatics, and Department of Nutrition, Case Western Reserve University, Cleveland, Ohio 44106, USA
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35
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Mehaffey MR, Cammarata MB, Brodbelt JS. Tracking the Catalytic Cycle of Adenylate Kinase by Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2018; 90:839-846. [PMID: 29188992 PMCID: PMC5750083 DOI: 10.1021/acs.analchem.7b03591] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The complex interplay of dynamic protein plasticity and specific side-chain interactions with substrate molecules that allows enzymes to catalyze reactions has yet to be fully unraveled. Top-down ultraviolet photodissociation (UVPD) mass spectrometry is used to track snapshots of conformational fluctuations in the phosphotransferase adenylate kinase (AK) throughout its active reaction cycle by characterization of complexes containing AK and each of four different adenosine phosphate ligands. Variations in efficiencies of UVPD backbone cleavages were consistently observed for three α-helices and the adenosine binding regions for AK complexes representing different steps of the catalytic cycle, implying that these stretches of the protein sample various structural microstates as the enzyme undergoes global open-to-closed transitions. Focusing on the conformational impact of recruiting or releasing the Mg2+ cofactor highlights two loop regions for which fragmentation increases upon UVPD, signaling an increase in loop flexibility as the metal cation disrupts the loop interactions with the substrate ligands. Additionally, the observation of holo ions and variations in UVPD backbone cleavage efficiency at R138 implicate this conserved active site residue in stabilizing the donor phosphoryl group during catalysis. This study showcases the utility of UVPD-MS to provide insight into conformational fluctuations of single residues for active enzymes.
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Affiliation(s)
- M. Rachel Mehaffey
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712
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36
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Claesen J, Burzykowski T. Computational methods and challenges in hydrogen/deuterium exchange mass spectrometry. MASS SPECTROMETRY REVIEWS 2017; 36:649-667. [PMID: 27602546 DOI: 10.1002/mas.21519] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 05/08/2016] [Accepted: 08/18/2016] [Indexed: 06/06/2023]
Abstract
Hydrogen/Deuterium exchange (HDX) has been applied, since the 1930s, as an analytical tool to study the structure and dynamics of (small) biomolecules. The popularity of using HDX to study proteins increased drastically in the last two decades due to the successful combination with mass spectrometry (MS). Together with this growth in popularity, several technological advances have been made, such as improved quenching and fragmentation. As a consequence of these experimental improvements and the increased use of protein-HDXMS, large amounts of complex data are generated, which require appropriate analysis. Computational analysis of HDXMS requires several steps. A typical workflow for proteins consists of identification of (non-)deuterated peptides or fragments of the protein under study (local analysis), or identification of the deuterated protein as a whole (global analysis); determination of the deuteration level; estimation of the protection extent or exchange rates of the labile backbone amide hydrogen atoms; and a statistically sound interpretation of the estimated protection extent or exchange rates. Several algorithms, specifically designed for HDX analysis, have been proposed. They range from procedures that focus on one specific step in the analysis of HDX data to complete HDX workflow analysis tools. In this review, we provide an overview of the computational methods and discuss outstanding challenges. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:649-667, 2017.
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Affiliation(s)
- Jürgen Claesen
- I-BioStat, Hasselt University, Campus Diepenbeek, Agoralaan Gebouw D, Diepenbeek 3590, Belgium
| | - Tomasz Burzykowski
- I-BioStat, Hasselt University, Campus Diepenbeek, Agoralaan Gebouw D, Diepenbeek 3590, Belgium
- Statistics and Medical informatics Unit, Medical University of Bialystok, Białystok, Poland
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37
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Quantitative Protein Topography Measurements by High Resolution Hydroxyl Radical Protein Footprinting Enable Accurate Molecular Model Selection. Sci Rep 2017; 7:4552. [PMID: 28674401 PMCID: PMC5495787 DOI: 10.1038/s41598-017-04689-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/18/2017] [Indexed: 11/23/2022] Open
Abstract
We report an integrated workflow that allows mass spectrometry-based high-resolution hydroxyl radical protein footprinting (HR-HRPF) measurements to accurately measure the absolute average solvent accessible surface area (<SASA>) of amino acid side chains. This approach is based on application of multi-point HR-HRPF, electron-transfer dissociation (ETD) tandem MS (MS/MS) acquisition, measurement of effective radical doses by radical dosimetry, and proper normalization of the inherent reactivity of the amino acids. The accuracy of the resulting <SASA> measurements was tested by using well-characterized protein models. Moreover, we demonstrated the ability to use <SASA> measurements from HR-HRPF to differentiate molecular models of high accuracy (<3 Å backbone RMSD) from models of lower accuracy (>4 Å backbone RMSD). The ability of <SASA> data from HR-HRPF to differentiate molecular model quality was found to be comparable to that of <SASA> data obtained from X-ray crystal structures, indicating the accuracy and utility of HR-HRPF for evaluating the accuracy of computational models.
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38
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Lu Y, Liu H, Saer R, Li VL, Zhang H, Shi L, Goodson C, Gross ML, Blankenship RE. A Molecular Mechanism for Nonphotochemical Quenching in Cyanobacteria. Biochemistry 2017; 56:2812-2823. [PMID: 28513152 DOI: 10.1021/acs.biochem.7b00202] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cyanobacterial orange carotenoid protein (OCP) protects photosynthetic cyanobacteria from photodamage by dissipating excess excitation energy collected by phycobilisomes (PBS) as heat. Dissociation of the PBS-OCP complex in vivo is facilitated by another protein known as the fluorescence recovery protein (FRP), which primarily exists as a dimeric complex. We used various mass spectrometry (MS)-based techniques to investigate the molecular mechanism of this FRP-mediated process. FRP in the dimeric state (dFRP) retains its high affinity for the C-terminal domain (CTD) of OCP in the red state (OCPr). Site-directed mutagenesis and native MS suggest the head region on FRP is a candidate to bind OCP. After attachment to the CTD, the conformational changes of dFRP allow it to bridge the two domains, facilitating the reversion of OCPr into the orange state (OCPo) accompanied by a structural rearrangement of dFRP. Interestingly, we found a mutual response between FRP and OCP; that is, FRP and OCPr destabilize each other, whereas FRP and OCPo stabilize each other. A detailed mechanism of FRP function is proposed on the basis of the experimental results.
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Affiliation(s)
- Yue Lu
- Department of Chemistry, Washington University in St. Louis , St. Louis, Missouri 63130, United States.,Photosynthetic Antenna Research Center, Washington University in St. Louis , St. Louis, Missouri 63130, United States
| | - Haijun Liu
- Photosynthetic Antenna Research Center, Washington University in St. Louis , St. Louis, Missouri 63130, United States.,Department of Biology, Washington University in St. Louis , St. Louis, Missouri 63130, United States
| | - Rafael Saer
- Photosynthetic Antenna Research Center, Washington University in St. Louis , St. Louis, Missouri 63130, United States.,Department of Biology, Washington University in St. Louis , St. Louis, Missouri 63130, United States
| | - Veronica L Li
- Department of Chemistry, Washington University in St. Louis , St. Louis, Missouri 63130, United States.,Photosynthetic Antenna Research Center, Washington University in St. Louis , St. Louis, Missouri 63130, United States
| | - Hao Zhang
- Department of Chemistry, Washington University in St. Louis , St. Louis, Missouri 63130, United States.,Photosynthetic Antenna Research Center, Washington University in St. Louis , St. Louis, Missouri 63130, United States
| | - Liuqing Shi
- Department of Chemistry, Washington University in St. Louis , St. Louis, Missouri 63130, United States
| | - Carrie Goodson
- Photosynthetic Antenna Research Center, Washington University in St. Louis , St. Louis, Missouri 63130, United States.,Department of Biology, Washington University in St. Louis , St. Louis, Missouri 63130, United States
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis , St. Louis, Missouri 63130, United States.,Photosynthetic Antenna Research Center, Washington University in St. Louis , St. Louis, Missouri 63130, United States
| | - Robert E Blankenship
- Department of Chemistry, Washington University in St. Louis , St. Louis, Missouri 63130, United States.,Photosynthetic Antenna Research Center, Washington University in St. Louis , St. Louis, Missouri 63130, United States.,Department of Biology, Washington University in St. Louis , St. Louis, Missouri 63130, United States
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39
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Mandacaru SC, do Vale LHF, Vahidi S, Xiao Y, Skinner OS, Ricart CAO, Kelleher NL, de Sousa MV, Konermann L. Characterizing the Structure and Oligomerization of Major Royal Jelly Protein 1 (MRJP1) by Mass Spectrometry and Complementary Biophysical Tools. Biochemistry 2017; 56:1645-1655. [PMID: 28252287 DOI: 10.1021/acs.biochem.7b00020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Royal jelly (RJ) triggers the development of female honeybee larvae into queens. This effect has been attributed to the presence of major royal jelly protein 1 (MRJP1) in RJ. MRJP1 isolated from royal jelly is tightly associated with apisimin, a 54-residue α-helical peptide that promotes the noncovalent assembly of MRJP1 into multimers. No high-resolution structural data are available for these complexes, and their binding stoichiometry remains uncertain. We examined MRJP1/apisimin using a range of biophysical techniques. We also investigated the behavior of deglycosylated samples, as well as samples with reduced apisimin content. Our mass spectrometry (MS) data demonstrate that the native complexes predominantly exist in a (MRJP14 apisimin4) stoichiometry. Hydrogen/deuterium exchange MS reveals that MRJP1 within these complexes is extensively disordered in the range of residues 20-265. Marginally stable secondary structure (likely antiparallel β-sheet) exists around residues 266-432. These weakly structured regions interchange with conformers that are extensively unfolded, giving rise to bimodal (EX1) isotope distributions. We propose that the native complexes have a "dimer of dimers" quaternary structure in which MRJP1 chains are bridged by apisimin. Specifically, our data suggest that apisimin acts as a linker that forms hydrophobic contacts involving the MRJP1 segment 316VLFFGLV322. Deglycosylation produces large soluble aggregates, highlighting the role of glycans as aggregation inhibitors. Samples with reduced apisimin content form dimeric complexes with a (MRJP12 apisimin1) stoichiometry. The information uncovered in this work will help pave the way toward a better understanding of the unique physiological role played by MRJP1 during queen differentiation.
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Affiliation(s)
- Samuel C Mandacaru
- Department of Chemistry, Western University , London, Ontario, Canada N6A 5B7.,Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, University of Brasilia , Brasilia, Brazil
| | - Luis H F do Vale
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, University of Brasilia , Brasilia, Brazil.,Proteomics Center of Excellence, Departments of Chemistry and Molecular Biosciences, Northwestern University , Evanston, Illinois 60611, United States
| | - Siavash Vahidi
- Department of Chemistry, Western University , London, Ontario, Canada N6A 5B7
| | - Yiming Xiao
- Department of Chemistry, Western University , London, Ontario, Canada N6A 5B7
| | - Owen S Skinner
- Proteomics Center of Excellence, Departments of Chemistry and Molecular Biosciences, Northwestern University , Evanston, Illinois 60611, United States
| | - Carlos A O Ricart
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, University of Brasilia , Brasilia, Brazil
| | - Neil L Kelleher
- Proteomics Center of Excellence, Departments of Chemistry and Molecular Biosciences, Northwestern University , Evanston, Illinois 60611, United States
| | - Marcelo Valle de Sousa
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, University of Brasilia , Brasilia, Brazil
| | - Lars Konermann
- Department of Chemistry, Western University , London, Ontario, Canada N6A 5B7
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40
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Mohler K, Aerni HR, Gassaway B, Ling J, Ibba M, Rinehart J. MS-READ: Quantitative measurement of amino acid incorporation. Biochim Biophys Acta Gen Subj 2017; 1861:3081-3088. [PMID: 28130155 DOI: 10.1016/j.bbagen.2017.01.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/18/2017] [Indexed: 10/20/2022]
Abstract
Ribosomal protein synthesis results in the genetically programmed incorporation of amino acids into a growing polypeptide chain. Faithful amino acid incorporation that accurately reflects the genetic code is critical to the structure and function of proteins as well as overall proteome integrity. Errors in protein synthesis are generally detrimental to cellular processes yet emerging evidence suggest that proteome diversity generated through mistranslation may be beneficial under certain conditions. Cumulative translational error rates have been determined at the organismal level, however codon specific error rates and the spectrum of misincorporation errors from system to system remain largely unexplored. In particular, until recently technical challenges have limited the ability to detect and quantify comparatively rare amino acid misincorporation events, which occur orders of magnitude less frequently than canonical amino acid incorporation events. We now describe a technique for the quantitative analysis of amino acid incorporation that provides the sensitivity necessary to detect mistranslation events during translation of a single codon at frequencies as low as 1 in 10,000 for all 20 proteinogenic amino acids, as well as non-proteinogenic and modified amino acids. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Affiliation(s)
- Kyle Mohler
- Department of Microbiology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Hans-Rudolf Aerni
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Brandon Gassaway
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Michael Ibba
- Department of Microbiology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Jesse Rinehart
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA.
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41
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Pan LY, Salas-Solano O, Valliere-Douglass JF. Localized conformational interrogation of antibody and antibody-drug conjugates by site-specific carboxyl group footprinting. MAbs 2016; 9:307-318. [PMID: 27929747 DOI: 10.1080/19420862.2016.1268306] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Establishing and maintaining conformational integrity of monoclonal antibodies (mAbs) and antibody-drug conjugates (ADCs) during development and manufacturing is critical for ensuring their clinical efficacy. As presented here, we applied site-specific carboxyl group footprinting (CGF) for localized conformational interrogation of mAbs. The approach relies on covalent labeling that introduces glycine ethyl ester tags onto solvent-accessible side chains of protein carboxylates. Peptide mapping is used to monitor the labeling kinetics of carboxyl residues and the labeling kinetics reflects the conformation or solvent-accessibility of side chains. Our results for two case studies are shown here. The first study was aimed at defining the conformational changes of mAbs induced by deglycosylation. We found that two residues in CH2 domain (D268 and E297) show significantly enhanced side chain accessibility upon deglycosylation. This site-specific result highlighted the advantage of monitoring the labeling kinetics at the amino acid level as opposed to the peptide level, which would result in averaging out of highly localized conformational differences. The second study was designed to assess conformational effects brought on by conjugation of mAbs with drug-linkers. All 59 monitored carboxyl residues displayed similar solvent-accessibility between the ADC and mAb under native conditions, which suggests the ADC and mAb share similar side chain conformation. The findings are well correlated and complementary with results from other assays. This work illustrated that site-specific CGF is capable of pinpointing local conformational changes in mAbs or ADCs that might arise during development and manufacturing. The methodology can be readily implemented within the industry to provide comprehensive conformational assessment of these molecules.
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42
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Elviri L, Bergonzi C, Bianchera A, Bettini R. Mapping insulin non-covalent interactions with natural polysaccharides by hydrogen/deuterium exchange mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:2323-2330. [PMID: 27495851 DOI: 10.1002/rcm.7708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/01/2016] [Accepted: 07/29/2016] [Indexed: 06/06/2023]
Abstract
RATIONALE Drug development efforts involving therapeutic peptides or proteins strongly lead optimization of drug delivery, drug stability, solubility and functionality. The key feature of controlled drug delivery is the use of biocompatible polymers able to interact via non-covalent bonds with an active principle through multiple functional groups. Here amide hydrogen/deuterium exchange (HDX) mass spectrometry was employed to localize insulin dynamics induced by interactions with three natural polysaccharides, i.e. chitosan (CH), sodium alginate (ALG) and chondroitin sulfate (CS). METHODS LTQ-Orbitap continuous-labelling mass spectra were collected by diluting insulin stock solution (10 mM in 0.1% formic acid) to a final concentration of 0.1 mM in D2 O containing 1 mM deuterated ammonium acetate (final pH .6) (insulin:polysaccharide ratio 1:2, w/w). For peptide mapping, deuterated samples were quenched after 0.5, 30, 60, 120 minutes exchange by adding HCl (pH ) and digested with pepsin before LC-MS/MS analysis. RESULTS Differences in the insulin backbone dynamics in the presence of the three polysaccharides were highlighted by monitoring peptic peptides at different time points. No significant differences were observed in the presence of CH, whereas the negatively charged ALG and CS were able to induce significant conformational variations at the B-chain level resulting in more protection against H/D exchange. The A-chain interacted only with CS reducing the protein mobility on a long time scale (120 min). HDX data evidenced heterogeneous insulin dynamics in the presence of ALG and CS. CONCLUSIONS The studies reported here demonstrated the capabilities of mass spectrometry techniques and HDX methods to obtain useful information toward the flexibility and the behavior of native insulin in the presence of natural polysaccharides, and could provide insights to study the behavior of pharmaceutical formulations. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Lisa Elviri
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 27/A, 43124, Parma, Italy.
| | - Carlo Bergonzi
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 27/A, 43124, Parma, Italy
| | - Annalisa Bianchera
- Interdepartmental Centre Biopharmanet-Tec, University of Parma, Parco Area delle Scienze 27/A, 43124, Parma, Italy
| | - Ruggero Bettini
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 27/A, 43124, Parma, Italy
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Structural and dynamic insights into the subtype-specific IP3-binding mechanism of the IP3 receptor. Biochem J 2016; 473:3533-3543. [DOI: 10.1042/bcj20160539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/21/2016] [Indexed: 11/17/2022]
Abstract
There are three subtypes of vertebrate inositol 1,4,5-trisphosphate (IP3) receptor (IP3R), a Ca2+-release channel on the ER membrane — IP3R1, IP3R2, and IP3R3 — each of which has a distinctive role in disease development. To determine the subtype-specific IP3-binding mechanism, we compared the thermodynamics, thermal stability, and conformational dynamics between the N-terminal regions of IP3R1 (IP3R1-NT) and IP3R3 (IP3R3-NT) by performing circular dichroism (CD), isothermal titration calorimetry (ITC), and hydrogen–deuterium exchange mass spectrometry (HDX-MS). Previously determined crystal structures of IP3R1-NT and HDX-MS results from this study revealed that both IP3R1 and IP3R3 adopt a similar IP3-binding mechanism. However, several regions, including the α- and β-interfaces, of IP3R1-NT and IP3R3-NT show significantly different conformational dynamics upon IP3 binding, which may explain the different IP3-binding affinities between the subtypes. The importance of the interfaces for subtype-specific IP3 binding is also supported by the different dynamic conformations of the two subtypes in the apo-states. Furthermore, IP3R1-NT and IP3R3-NT show different IP3-binding affinities and thermal stabilities, but share similar thermodynamic properties for IP3 binding. These results collectively provide new insights into the mechanism underlying IP3 binding to IP3Rs and the subtype-specific regulatory mechanism.
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44
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Wessels HJCT, de Almeida NM, Kartal B, Keltjens JT. Bacterial Electron Transfer Chains Primed by Proteomics. Adv Microb Physiol 2016; 68:219-352. [PMID: 27134025 DOI: 10.1016/bs.ampbs.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.
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Affiliation(s)
- H J C T Wessels
- Nijmegen Center for Mitochondrial Disorders, Radboud Proteomics Centre, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N M de Almeida
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - B Kartal
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands; Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - J T Keltjens
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.
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45
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Kaur P, Tomechko SE, Kiselar J, Shi W, Deperalta G, Wecksler AT, Gokulrangan G, Ling V, Chance MR. Characterizing monoclonal antibody structure by carboxyl group footprinting. MAbs 2016; 7:540-52. [PMID: 25933350 DOI: 10.1080/19420862.2015.1023683] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Structural characterization of proteins and their antigen complexes is essential to the development of new biologic-based medicines. Amino acid-specific covalent labeling (CL) is well suited to probe such structures, especially for cases that are difficult to examine by alternative means due to size, complexity, or instability. We present here a detailed account of carboxyl group labeling (with glycine ethyl ester (GEE) tagging) applied to a glycosylated monoclonal antibody therapeutic (mAb). The experiments were optimized to preserve the structural integrity of the mAb, and experimental conditions were varied and replicated to establish the reproducibility of the technique. Homology-based models were generated and used to compare the solvent accessibility of the labeled residues, which include aspartic acid (D), glutamic acid (E), and the C-terminus (i.e., the target probes), with the experimental data in order to understand the accuracy of the approach. Data from the mAb were compared to reactivity measures of several model peptides to explain observed variations in reactivity. Attenuation of reactivity in otherwise solvent accessible probes is documented as arising from the effects of positive charge or bond formation between adjacent amine and carboxyl groups, the latter accompanied by observed water loss. A comparison of results with previously published data by Deperalta et al using hydroxyl radical footprinting showed that 55% (32/58) of target residues were GEE labeled in this study whereas the previous study reported 21% of the targets were labeled. Although the number of target residues in GEE labeling is fewer, the two approaches provide complementary information. The results highlight advantages of this approach, such as the ease of use at the bench top, the linearity of the dose response plots at high levels of labeling, reproducibility of replicate experiments (<2% variation in modification extent), the similar reactivity of the three target probes, and significant correlation of reactivity and solvent accessible surface area.
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Key Words
- 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide
- ACN, acetonitrile
- CD, circular dichroism
- CL, covalent labeling
- DR, dose response
- EDC, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide
- EIC, extracted ion chromatogram
- GEE, glycine ethyl ester
- HC, heavy chain
- HDX, hydrogen-deuterium exchange
- HRF, hydroxyl radical footprinting
- IT, ion trap
- IgG, immunoglobulin gamma
- LC, light chain
- Lys-C, lysyl endopeptidase
- MS, mass spectrometry
- RC, rate constant
- SASA, solvent accessible surface area
- SEC, size-exclusion chromatography
- acetonitrile
- circular dichroism
- covalent labeling
- dose response
- extracted ion chromatogram
- glycine ethyl ester
- heavy chain
- hydrogen-deuterium exchange
- hydroxyl radical footprinting
- immunoglobulin gamma
- ion trap
- light chain
- lysyl endopeptidase
- mAb, monoclonal antibody
- mass spectrometry
- monoclonal antibody
- rate constant
- size-exclusion chromatography
- solvent accessible surface area
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Affiliation(s)
- Parminder Kaur
- a Center for Proteomics and Bioinformatics; School of Medicine; Case Western Reserve University ; Cleveland , OH , USA
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Shi Y, Chen X, Elsasser S, Stocks BB, Tian G, Lee BH, Shi Y, Zhang N, de Poot SAH, Tuebing F, Sun S, Vannoy J, Tarasov SG, Engen JR, Finley D, Walters KJ. Rpn1 provides adjacent receptor sites for substrate binding and deubiquitination by the proteasome. Science 2016; 351:351/6275/aad9421. [PMID: 26912900 DOI: 10.1126/science.aad9421] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Hundreds of pathways for degradation converge at ubiquitin recognition by a proteasome. Here, we found that the five known proteasomal ubiquitin receptors in yeast are collectively nonessential for ubiquitin recognition and identified a sixth receptor, Rpn1. A site ( T1: ) in the Rpn1 toroid recognized ubiquitin and ubiquitin-like ( UBL: ) domains of substrate shuttling factors. T1 structures with monoubiquitin or lysine 48 diubiquitin show three neighboring outer helices engaging two ubiquitins. T1 contributes a distinct substrate-binding pathway with preference for lysine 48-linked chains. Proximal to T1 within the Rpn1 toroid is a second UBL-binding site ( T2: ) that assists in ubiquitin chain disassembly, by binding the UBL of deubiquitinating enzyme Ubp6. Thus, a two-site recognition domain intrinsic to the proteasome uses distinct ubiquitin-fold ligands to assemble substrates, shuttling factors, and a deubiquitinating enzyme.
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Affiliation(s)
- Yuan Shi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Xiang Chen
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Suzanne Elsasser
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Bradley B Stocks
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Geng Tian
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Byung-Hoon Lee
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Yanhong Shi
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA. Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
| | - Naixia Zhang
- Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
| | - Stefanie A H de Poot
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Fabian Tuebing
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Shuangwu Sun
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Jacob Vannoy
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA. Linganore High School, Frederick, MD 21701, USA
| | - Sergey G Tarasov
- Biophysics Resource, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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Hellwig P, Kriegel S, Friedrich T. Infrared spectroscopic studies on reaction induced conformational changes in the NADH ubiquinone oxidoreductase (complex I). BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:922-7. [PMID: 26702948 DOI: 10.1016/j.bbabio.2015.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 12/08/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
Abstract
Redox-dependent conformational changes are currently discussed to be a crucial part of the reaction mechanism of the respiratory complex I. Specialized difference Fourier transform infrared techniques allow the detection of side-chain movements and minute secondary structure changes. For complex I, (1)H/(2)H exchange kinetics of the amide modes revealed a better accessibility of the backbone in the presence of NADH and quinone. Interestingly, the presence of phospholipids, that is crucial for the catalytic activity of the isolated enzyme complex, changes the overall conformation. When comparing complex I samples from different species, very similar electrochemically induced FTIR difference spectra and very similar rearrangements are reported. Finally, the information obtained with variants and from Zn(2+) inhibited samples for the conformational reorganization of complex I upon electron transfer are discussed in this review. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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Affiliation(s)
- Petra Hellwig
- Laboratoire de bioelectrochimie et spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, Strasbourg, France
| | - Sébastien Kriegel
- Laboratoire de bioelectrochimie et spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, Strasbourg, France
| | - Thorsten Friedrich
- Albert-Ludwigs-Universität Freiburg, Institut für Biochemie, Albertstr. 21, 79104 Freiburg i. Br., Germany
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48
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Kaur P, Tomechko S, Kiselar J, Shi W, Deperalta G, Wecksler AT, Gokulrangan G, Ling V, Chance MR. Characterizing monoclonal antibody structure by carbodiimide/GEE footprinting. MAbs 2015; 6:1486-99. [PMID: 25484052 DOI: 10.4161/19420862.2014.975096] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Amino acid-specific covalent labeling is well suited to probe protein structure and macromolecular interactions, especially for macromolecules and their complexes that are difficult to examine by alternative means, due to size, complexity, or instability. Here we present a detailed account of carbodiimide-based covalent labeling (with GEE tagging) applied to a glycosylated monoclonal antibody therapeutic, which represents an important class of biologic drugs. Characterization of such proteins and their antigen complexes is essential to development of new biologic-based medicines. In this study, the experiments were optimized to preserve the structural integrity of the protein, and experimental conditions were varied and replicated to establish the reproducibility and precision of the technique. Homology-based models were generated and used to compare the solvent accessibility of the labeled residues, which include D, E, and the C-terminus, against the experimental surface accessibility data in order to understand the accuracy of the approach in providing an unbiased assessment of structure. Data from the protein were also compared to reactivity measures of several model peptides to explain sequence or structure-based variations in reactivity. The results highlight several advantages of this approach. These include: the ease of use at the bench top, the linearity of the dose response plots at high levels of labeling (indicating that the label does not significantly perturb the structure of the protein), the high reproducibility of replicate experiments (<2 % variation in modification extent), the similar reactivity of the 3 target probe residues (as suggested by analysis of model peptides), and the overall positive and significant correlation of reactivity and solvent accessible surface area (the latter values predicted by the homology modeling). Attenuation of reactivity, in otherwise solvent accessible probes, is documented as arising from the effects of positive charge or bond formation between adjacent amine and carboxyl groups, the latter accompanied by observed water loss. The results are also compared with data from hydroxyl radical-mediated oxidative footprinting on the same protein, showing that complementary information is gained from the 2 approaches, although the number of target residues in carbodiimide/GEE labeling is fewer. Overall, this approach is an accurate and precise method for assessing protein structure of biologic drugs.
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Key Words
- ACN, acetonitrile
- CD, circular dichroism
- CL, covalent labeling
- DR, dose response
- EDC, 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide
- EIC, extracts the ion chromatogram
- FPOP, fast photochemical oxidation of proteins
- GEE
- GEE, glycine ethyl ester
- HC, heavy chain
- HDX, hydrogen-deuterium exchange
- HRF, hydroxyl radical footprinting
- IT, ion trap
- IgG, immunoglobulin gamma
- LC, light chain
- LysC, Lysyl endopeptidase
- MS, mass spectrometry
- NMR, nuclear magnetic resonance
- RC, rate constant
- SASA, solvent accessible surface area
- SEC, size-exclusion chromatography
- VEGF, vascular endothelial growth factor
- covalent labeling
- footprinting
- mAb, monoclonal antibody
- protein structure
- structural proteomics
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Affiliation(s)
- Parminder Kaur
- a Center for Proteomics and Bioinformatics ; Case Western Reserve University ; Cleveland , OH USA
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49
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Farrokhi V, Bajrami B, Nemati R, McShane AJ, Rueckert F, Wells B, Yao X. Development of Structural Marker Peptides for Cystic Fibrosis Transmembrane Conductance Regulator in Cell Plasma Membrane by Reversed-Footprinting Mass Spectrometry. Anal Chem 2015; 87:8603-7. [DOI: 10.1021/acs.analchem.5b01962] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | | | | | | | - Franz Rueckert
- Department
of Physics, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Barrett Wells
- Department
of Physics, University of Connecticut, Storrs, Connecticut 06269, United States
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50
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Abstract
Hydrogen exchange (HX) methods can reveal much about the structure, energetics, and dynamics of proteins. The addition of mass spectrometry (MS) to an earlier fragmentation-separation HX analysis now extends HX studies to larger proteins at high structural resolution and can provide information not available before. This chapter discusses experimental aspects of HX labeling, especially with respect to the use of MS and the analysis of MS data.
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Affiliation(s)
- Leland Mayne
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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