1
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Long P, Su S, Wen M, Ho CT, Han Z, Zuo X, Jiang Y, Ke JP, Lai G, Zhu M, Wan X, Zhang L. Novel Pink Pigments Produced by Thermal Interaction of Theaflavins, Theanine, and Glucose: Color Formation, Isolation, and Structural Characterization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39324431 DOI: 10.1021/acs.jafc.4c07072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
A color-deepening effect of theaflavins on the theanine-glucose thermal reaction model was revealed. Generated chromogenic intermediates in the initial stage and an accelerated browning rate through the promoted degradation of theanine-glucose Amadori rearrangement product in the intermediate and final stages are responsible for the color-deepening effect. Four pink-to-red theaflavin-theanine intermediates were verified as theaflavinies referencing the nuclear magnetic resonance and liquid chromatography-mass spectrometry information on theaflavins and l-theanine, including one accurately identified as theaflavinie 4. Theaflavinie 4 showed two maximum absorption peaks at 401 and 506 nm with parallel intensities, which resulted in a significant dichromic color change from pale pink to orange and red. Theaflavinies also could undergo further thermal reactions to yield brown polymers under higher temperatures (130 and 140 °C). This research provided new insight into realizing thermally formed polymers during black tea processing, which may be formed by oxidation products and amino acids or proteins through non-enzymatic thermal reactions.
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Affiliation(s)
- Piaopiao Long
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Shengxiao Su
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Mingchun Wen
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Chi-Tang Ho
- Department of Food Science, Rutgers University, New Brunswick, New Jersey 08901, United States
| | - Zisheng Han
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Xiaobo Zuo
- Zhejiang Key Laboratory of Transboundary Applied Technology for Tea Resources, Hangzhou Tea Research Institute, CHINA COOP, Hangzhou 310016, China
| | - Yulan Jiang
- Zhejiang Key Laboratory of Transboundary Applied Technology for Tea Resources, Hangzhou Tea Research Institute, CHINA COOP, Hangzhou 310016, China
| | - Jia-Ping Ke
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Guoping Lai
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Mengting Zhu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Liang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
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2
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Niphakis MJ, Cravatt BF. Ligand discovery by activity-based protein profiling. Cell Chem Biol 2024; 31:1636-1651. [PMID: 39303700 DOI: 10.1016/j.chembiol.2024.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/15/2024] [Accepted: 08/19/2024] [Indexed: 09/22/2024]
Abstract
Genomic technologies have led to massive gains in our understanding of human gene function and disease relevance. Chemical biologists are a primary beneficiary of this information, which can guide the prioritization of proteins for chemical probe and drug development. The vast functional and structural diversity of disease-relevant proteins, however, presents challenges for conventional small molecule screening libraries and assay development that in turn raise questions about the broader "druggability" of the human proteome. Here, we posit that activity-based protein profiling (ABPP), by generating global maps of small molecule-protein interactions in native biological systems, is well positioned to address major obstacles in human biology-guided chemical probe and drug discovery. We will support this viewpoint with case studies highlighting a range of small molecule mechanisms illuminated by ABPP that include the disruption and stabilization of biomolecular (protein-protein/nucleic acid) interactions and underscore allostery as a rich source of chemical tools for historically "undruggable" protein classes.
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3
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Jeanne Dit Fouque K, Fernandez-Rojas M, Roque AE, Fernandez-Lima F. Top-Down Structural Characterization of Native Ubiquitin Combining Solution-Stable Isotope Labeling, Trapped Ion Mobility Spectrometry, and Tandem Electron Capture Dissociation Mass Spectrometry. Anal Chem 2024; 96:14963-14970. [PMID: 39214608 DOI: 10.1021/acs.analchem.4c03070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Solution-phase hydrogen/deuterium exchange (HDX) coupled to native ion mobility spectrometry mass spectrometry (IMS-MS) can provide complementary structural information about the conformational dynamics of biological molecules. In the present work, the solution-stable isotope labeling (SIL) combined with trapped ion mobility spectrometry (TIMS) in tandem with top-down electron capture dissociation (ECD) is illustrated for the structural characterization of the solution native states of ubiquitin. Four different ubiquitin electrospray solution conditions: (i) single-tip nondeuterated, (ii) theta tip for online SIL HDX, (iii) single-tip SIL-deuterated, and (iv) theta tip for online SIL H/D back exchange (HDbX), were investigated to assess the H/D exchange reactivities of native ubiquitin. The combination of TIMS and ECD in a q-ToF MS instrument allowed for additional inspection of gas-phase HDbX added by top-down fragmentation, revealing the exposed and protected residues with limited scrambling effects (e.g., intramolecular H/D migration). A native charge state distribution (5+ to 7+) and TIMS profiles were observed under the single-tip nondeuterated solution conditions. Mass shift distributions of ∼40, ∼104, and ∼87D were observed when incorporating deuterium for online SIL HDX, SIL HDX, and online SIL HDbX, respectively, while retaining similar conformational states. ECD fragmentation allowed for the localization of the deuterated labeled residues of the peptide fragments, with a sequence coverage of ∼90%, for each of the ubiquitin solution condition. Changes in the TIMS trapping time settings (∼70 to ∼795 ms) were used to determine the H/D back exchange dynamics of native ubiquitin. HDbX-TIMS-q-ECD-MS/MS exhibited H/D back exchanges in the six-residue C-terminal tail as well as around Lys6, Lys11, Lys33, Lys48, and Lys63 residues, indicating that these regions are the most exposed area (less protected hydrogens) of ubiquitin as compared to the rest of the core residues that adopt a compact β-grasp fold (protected hydrogens), which was consistent with the accessible surface area of ubiquitin. The present data highlight for the first time consistency between the solution HDX and gas-phase HDbX-TIMS data for native studies.
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Meiby Fernandez-Rojas
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Anelis E Roque
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
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4
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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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5
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Kihn KC, Purdy O, Lowe V, Slachtova L, Smith AK, Shapiro P, Deredge DJ. Integration of Hydrogen-Deuterium Exchange Mass Spectrometry with Molecular Dynamics Simulations and Ensemble Reweighting Enables High Resolution Protein-Ligand Modeling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39254669 DOI: 10.1021/jasms.4c00202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Hydrogen-Deuterium exchange mass spectrometry's (HDX-MS) utility in identifying and characterizing protein-small molecule interaction sites has been established. The regions that are seen to be protected from exchange upon ligand binding indicate regions that may be interacting with the ligand, giving a qualitative understanding of the ligand binding pocket. However, quantitatively deriving an accurate high-resolution structure of the protein-ligand complex from the HDX-MS data remains a challenge, often limiting its use in applications such as small molecule drug design. Recent efforts have focused on the development of methods to quantitatively model Hydrogen-Deuterium exchange (HDX) data from computationally modeled structures to garner atomic level insights from peptide-level resolution HDX-MS. One such method, HDX ensemble reweighting (HDXer), employs maximum entropy reweighting of simulated HDX data to experimental HDX-MS to model structural ensembles. In this study, we implement and validate a workflow which quantitatively leverages HDX-MS data to accurately model protein-small molecule ligand interactions. To that end, we employ a strategy combining computational protein-ligand docking, molecular dynamics simulations, HDXer, and dimensional reduction and clustering approaches to extract high-resolution drug binding poses that most accurately conform with HDX-MS data. We apply this workflow to model the interaction of ERK2 and FosA with small molecule compounds and inhibitors they are known to bind. In five out of six of the protein-ligand pairs tested, the HDX derived protein-ligand complexes result in a ligand root-mean-square deviation (RMSD) within 2.5 Å of the known crystal structure ligand.
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Affiliation(s)
- Kyle C Kihn
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Olivia Purdy
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Vincent Lowe
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Lenka Slachtova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague 116 36, Czech Republic
| | - Ally K Smith
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Paul Shapiro
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Daniel J Deredge
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
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6
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Morstein J, Bowcut V, Fernando M, Yang Y, Zhu L, Jenkins ML, Evans JT, Guiley KZ, Peacock DM, Krahnke S, Lin Z, Taran KA, Huang BJ, Stephen AG, Burke JE, Lightstone FC, Shokat KM. Targeting Ras-, Rho-, and Rab-family GTPases via a conserved cryptic pocket. Cell 2024:S0092-8674(24)00908-5. [PMID: 39255801 DOI: 10.1016/j.cell.2024.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 05/07/2024] [Accepted: 08/08/2024] [Indexed: 09/12/2024]
Abstract
The family of Ras-like GTPases consists of over 150 different members, regulated by an even larger number of guanine exchange factors (GEFs) and GTPase-activating proteins (GAPs) that comprise cellular switch networks that govern cell motility, growth, polarity, protein trafficking, and gene expression. Efforts to develop selective small molecule probes and drugs for these proteins have been hampered by the high affinity of guanosine triphosphate (GTP) and lack of allosteric regulatory sites. This paradigm was recently challenged by the discovery of a cryptic allosteric pocket in the switch II region of K-Ras. Here, we ask whether similar pockets are present in GTPases beyond K-Ras. We systematically surveyed members of the Ras, Rho, and Rab family of GTPases and found that many GTPases exhibit targetable switch II pockets. Notable differences in the composition and conservation of key residues offer potential for the development of optimized inhibitors for many members of this previously undruggable family.
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Affiliation(s)
- Johannes Morstein
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Victoria Bowcut
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Micah Fernando
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Yue Yang
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Lab, Livermore, CA 94550, USA
| | - Lawrence Zhu
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - John T Evans
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Keelan Z Guiley
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - D Matthew Peacock
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Sophie Krahnke
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Zhi Lin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Katrine A Taran
- Department of Pediatrics, University of California, San Francisco, CA 94158, USA
| | - Benjamin J Huang
- Department of Pediatrics, University of California, San Francisco, CA 94158, USA
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Felice C Lightstone
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Lab, Livermore, CA 94550, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA.
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7
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Eisinger M, Rahn H, Chen Y, Fernandes M, Lin Z, Hentze N, Tavella D, Moussa EM. Elucidation of the Reversible Self-Association Interface of a Diabody-Interleukin Fusion Protein Using Hydrogen-Exchange Mass Spectrometry and In Silico Modeling. Mol Pharm 2024; 21:4285-4296. [PMID: 38922328 DOI: 10.1021/acs.molpharmaceut.4c00169] [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] [Indexed: 06/27/2024]
Abstract
Reversible self-association (RSA) of therapeutic proteins presents major challenges in the development of high-concentration formulations, especially those intended for subcutaneous administration. Understanding self-association mechanisms is therefore critical to the design and selection of candidates with acceptable developability to advance to clinical trials. The combination of experiments and in silico modeling presents a powerful tool to elucidate the interface of self-association. RSA of monoclonal antibodies has been studied extensively under different solution conditions and have been shown to involve interactions for both the antigen-binding fragment and the crystallizable fragment. Novel modalities such as bispecific antibodies, antigen-binding fragments, single-chain-variable fragments, and diabodies constitute a fast-growing class of antibody-based therapeutics that have unique physiochemical properties compared to monoclonal antibodies. In this study, the RSA interface of a diabody-interleukin 22 fusion protein (FP-1) was studied using hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS) in combination with in silico modeling. Taken together, the results show that a complex solution behavior underlies the self-association of FP-1 and that the interface thereof can be attributed to a specific segment in the variable light chain of the diabody. These findings also demonstrate that the combination of HDX-MS with in silico modeling is a powerful tool to guide the design and candidate selection of novel biotherapeutic modalities.
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Affiliation(s)
- Martin Eisinger
- Biologics Analytical Research and Development, AbbVie Deutschland GmbH & Co. KG, Ludwigshafen 67061, Germany
| | - Harri Rahn
- Biologics Analytical Research and Development, AbbVie Deutschland GmbH & Co. KG, Ludwigshafen 67061, Germany
| | - Yong Chen
- Biologics Analytical Research and Development, AbbVie Inc., North Chicago, Illinois 60061, United States
| | - Melissa Fernandes
- Biologics Drug Product Development, AbbVie Inc., North Chicago, Illinois 60061, United States
| | - Zhiyi Lin
- Biologics Drug Product Development, AbbVie Inc., North Chicago, Illinois 60061, United States
| | - Nikolai Hentze
- Biologics Analytical Research and Development, AbbVie Deutschland GmbH & Co. KG, Ludwigshafen 67061, Germany
| | - Davide Tavella
- Biotherapeutics and Genetic Medicine, AbbVie Inc., Worcester, Massachusetts 01604, United States
| | - Ehab M Moussa
- Biologics Drug Product Development, AbbVie Inc., North Chicago, Illinois 60061, United States
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8
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Kirsch ZJ, Ashby J, Vachet RW. Investigating Protein-Nucleic Acid Binding Interactions with Diethylpyrocarbonate Covalent Labeling-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39208253 DOI: 10.1021/jasms.4c00285] [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
Nucleic acids are important biomolecules that facilitate numerous cellular functions and have in recent years become promising candidates for treating disease. Consequently, there is a need for methods to characterize protein interactions with these molecules. Here, we demonstrate that diethylpyrocarbonate (DEPC) covalent labeling-mass spectrometry (CL-MS) can provide structural information for protein-nucleic acid binding by characterizing the binding sites of two DNA aptamers specific to thrombin. Reductions in thrombin labeling are observed at the pair's binding interfaces. Furthermore, we find that binding of the aptamers causes changes in labeling at residues in the thrombin active site and known exosites for each aptamer, showcasing the sensitivity of DEPC CL-MS to significant allosteric changes.
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Affiliation(s)
- Zachary J Kirsch
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Jonathan Ashby
- Department of Chemistry, Trinity College, Hartford, Connecticut 06106, United States
| | - Richard W Vachet
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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9
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Kawashima F, Okutsu K, Kohno JY. Hydrogen/Deuterium Exchange Reaction Rate of Cytochrome c Determined by Droplet Collision Atmospheric Pressure Infrared Laser Ablation Mass Spectrometry. J Phys Chem A 2024; 128:7208-7213. [PMID: 39141611 DOI: 10.1021/acs.jpca.4c03597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
The hydrogen/deuterium (H/D) exchange rate is an optimal measure for studying the structures and dynamics of hydrogen bonding systems, as it reflects the molecular contact environment and the strength of the hydrogen bonds. A method for rapid measurement of the H/D exchange reaction rates is required to examine the intermolecular environments of molecules in solutions. We developed a droplet collision atmospheric pressure infrared laser ablation mass spectrometry technique for this purpose. We obtained the H/D exchange reaction rate of cytochrome c in a methanol/H2O·D2O solution. We revealed that the first hydration shell of the cytochrome c molecule hinders the penetration of D2O to the surface of the molecule from the rates, which provides a novel method to investigate solution structures by a mass-spectrometric method. The droplet-collision mass spectrometry method developed in the present study can be extended to research on the molecular interactions in solutions, such as the mutual interactions of protein molecules, which are of importance in living cells.
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Affiliation(s)
- Fusae Kawashima
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
| | - Kenichi Okutsu
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
| | - Jun-Ya Kohno
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
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10
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Wang CR, McFarlane LO, Pukala TL. Exploring snake venoms beyond the primary sequence: From proteoforms to protein-protein interactions. Toxicon 2024; 247:107841. [PMID: 38950738 DOI: 10.1016/j.toxicon.2024.107841] [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: 04/22/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/03/2024]
Abstract
Snakebite envenomation has been a long-standing global issue that is difficult to treat, largely owing to the flawed nature of current immunoglobulin-based antivenom therapy and the complexity of snake venoms as sophisticated mixtures of bioactive proteins and peptides. Comprehensive characterisation of venom compositions is essential to better understanding snake venom toxicity and inform effective and rationally designed antivenoms. Additionally, a greater understanding of snake venom composition will likely unearth novel biologically active proteins and peptides that have promising therapeutic or biotechnological applications. While a bottom-up proteomic workflow has been the main approach for cataloguing snake venom compositions at the toxin family level, it is unable to capture snake venom heterogeneity in the form of protein isoforms and higher-order protein interactions that are important in driving venom toxicity but remain underexplored. This review aims to highlight the importance of understanding snake venom heterogeneity beyond the primary sequence, in the form of post-translational modifications that give rise to different proteoforms and the myriad of higher-order protein complexes in snake venoms. We focus on current top-down proteomic workflows to identify snake venom proteoforms and further discuss alternative or novel separation, instrumentation, and data processing strategies that may improve proteoform identification. The current higher-order structural characterisation techniques implemented for snake venom proteins are also discussed; we emphasise the need for complementary and higher resolution structural bioanalytical techniques such as mass spectrometry-based approaches, X-ray crystallography and cryogenic electron microscopy, to elucidate poorly characterised tertiary and quaternary protein structures. We envisage that the expansion of the snake venom characterisation "toolbox" with top-down proteomics and high-resolution protein structure determination techniques will be pivotal in advancing structural understanding of snake venoms towards the development of improved therapeutic and biotechnology applications.
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Affiliation(s)
- C Ruth Wang
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Lewis O McFarlane
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Tara L Pukala
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia.
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11
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Quintero AV, Liyanage OT, Kim HJ, Gallagher ES. Characterizing the Dynamics of Solvated Disaccharides with In-Electrospray Ionization Hydrogen/Deuterium Exchange-Mass Spectrometry. Anal Chem 2024; 96:12649-12657. [PMID: 39061116 DOI: 10.1021/acs.analchem.4c01136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Carbohydrates have various biological functions that are based on their structures. However, the composition and the glycosidic-bond linkage and configuration of carbohydrates present challenges for their characterization. Furthermore, isomeric features contribute to the formation of intramolecular hydrogen bonds, which influence the flexibility and dynamics of carbohydrates. Hydrogen/deuterium exchange-mass spectrometry (HDX-MS) enables the analysis of protein dynamics by monitoring deuterium labeling after HDX for different lengths of time. In-electrospray ionization (in-ESI) HDX-MS has been used to rapidly label solvated carbohydrates with labeling occurring during desolvation of ESI droplets. Therefore, HDX-labeling times can be altered by changing the spray-solvent conductivity, which changes the initial size of ESI droplets and their resulting lifetimes. Here, we utilize in-ESI HDX-MS to characterize nine isomeric disaccharides with different monosaccharide compositions and glycosidic-bond linkages and configurations. We compared both the relative D-uptake of isomers at individual conductivities, or HDX-labeling times, and the trends associated with labeling at multiple conductivities. Interestingly, the relative D-uptake trends were correlated to isomeric features that affect disaccharide flexibility, including formation of intramolecular hydrogen bonds. Among the isomeric features studied, linkage was observed to have a significant influence on relative D-uptake with (1-3)-linked disaccharides having more change in relative D-uptake with changing conductivity compared to other linkages. Overall, this research illustrates how in-ESI HDX-MS can be applied to structurally characterize disaccharides with distinct isomeric features. Furthermore, this work shows that in-ESI HDX-MS can be used to monitor the dynamics of solvated molecules with rapidly exchanging functional groups.
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Affiliation(s)
- Ana V Quintero
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
| | - O Tara Liyanage
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
| | - H Jamie Kim
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
| | - Elyssia S Gallagher
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
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12
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Matsuzaka Y, Yashiro R. Therapeutic Application and Structural Features of Adeno-Associated Virus Vector. Curr Issues Mol Biol 2024; 46:8464-8498. [PMID: 39194716 DOI: 10.3390/cimb46080499] [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: 06/10/2024] [Revised: 07/02/2024] [Accepted: 07/12/2024] [Indexed: 08/29/2024] Open
Abstract
Adeno-associated virus (AAV) is characterized by non-pathogenicity, long-term infection, and broad tropism and is actively developed as a vector virus for gene therapy products. AAV is classified into more than 100 serotypes based on differences in the amino acid sequence of the capsid protein. Endocytosis involves the uptake of viral particles by AAV and accessory receptors during AAV infection. After entry into the cell, they are transported to the nucleus through the nuclear pore complex. AAVs mainly use proteoglycans as receptors to enter cells, but the types of sugar chains in proteoglycans that have binding ability are different. Therefore, it is necessary to properly evaluate the primary structure of receptor proteins, such as amino acid sequences and post-translational modifications, including glycosylation, and the higher-order structure of proteins, such as the folding of the entire capsid structure and the three-dimensional (3D) structure of functional domains, to ensure the efficacy and safety of biopharmaceuticals. To further enhance safety, it is necessary to further improve the efficiency of gene transfer into target cells, reduce the amount of vector administered, and prevent infection of non-target cells.
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Affiliation(s)
- Yasunari Matsuzaka
- Division of Molecular and Medical Genetics, Center for Gene and Cell Therapy, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
- Administrative Section of Radiation Protection, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira 187-8551, Japan
| | - Ryu Yashiro
- Administrative Section of Radiation Protection, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira 187-8551, Japan
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
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13
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Janowska MK, Reiter K, Magala P, Guttman M, Klevit RE. HDXBoxeR: an R package for statistical analysis and visualization of multiple Hydrogen-Deuterium Exchange Mass-Spectrometry datasets of different protein states. Bioinformatics 2024; 40:btae479. [PMID: 39078213 PMCID: PMC11310453 DOI: 10.1093/bioinformatics/btae479] [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: 04/19/2024] [Revised: 07/18/2024] [Accepted: 07/29/2024] [Indexed: 07/31/2024] Open
Abstract
SUMMARY Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) is a powerful protein characterization technique that provides insights into protein dynamics and flexibility at the peptide level. However, analyzing HDX-MS data presents a significant challenge due to the wealth of information it generates. Each experiment produces data for hundreds of peptides, often measured in triplicate across multiple time points. Comparisons between different protein states create distinct datasets containing thousands of peptides that require matching, rigorous statistical evaluation, and visualization. Our open-source R package, HDXBoxeR, is a comprehensive tool designed to facilitate statistical analysis and comparison of multiple sets among samples and time points for different protein states, along with data visualization. AVAILABILITY AND IMPLEMENTATION HDXBoxeR is accessible as the R package (https://cran.r-project.org/web//packages/HDXBoxeR) and GitHub: mkajano/HDXBoxeR.
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Affiliation(s)
- Maria K Janowska
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, United States
| | - Katherine Reiter
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, United States
- Lyterian Therapeutics, South San Francisco, CA, 94080, United States
| | - Pearl Magala
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, United States
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, United States
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14
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Kephart SM, Hom N, Lee KK. Visualizing intermediate stages of viral membrane fusion by cryo-electron tomography. Trends Biochem Sci 2024:S0968-0004(24)00160-9. [PMID: 39054240 DOI: 10.1016/j.tibs.2024.06.012] [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: 03/06/2024] [Revised: 06/07/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024]
Abstract
Protein-mediated membrane fusion is the dynamic process where specialized protein machinery undergoes dramatic conformational changes that drive two membrane bilayers together, leading to lipid mixing and opening of a fusion pore between previously separate membrane-bound compartments. Membrane fusion is an essential stage of enveloped virus entry that results in viral genome delivery into host cells. Recent studies applying cryo-electron microscopy techniques in a time-resolved fashion provide unprecedented glimpses into the interaction of viral fusion proteins and membranes, revealing fusion intermediate states from the initiation of fusion to release of the viral genome. In combination with complementary structural, biophysical, and computation modeling approaches, these advances are shedding new light on the mechanics and dynamics of protein-mediated membrane fusion.
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Affiliation(s)
- Sally M Kephart
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Nancy Hom
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA; Biological Structure Physics and Design Graduate Program, University of Washington, Seattle, WA, USA.
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15
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Lai Y, Koelmel JP, Walker DI, Price EJ, Papazian S, Manz KE, Castilla-Fernández D, Bowden JA, Nikiforov V, David A, Bessonneau V, Amer B, Seethapathy S, Hu X, Lin EZ, Jbebli A, McNeil BR, Barupal D, Cerasa M, Xie H, Kalia V, Nandakumar R, Singh R, Tian Z, Gao P, Zhao Y, Froment J, Rostkowski P, Dubey S, Coufalíková K, Seličová H, Hecht H, Liu S, Udhani HH, Restituito S, Tchou-Wong KM, Lu K, Martin JW, Warth B, Godri Pollitt KJ, Klánová J, Fiehn O, Metz TO, Pennell KD, Jones DP, Miller GW. High-Resolution Mass Spectrometry for Human Exposomics: Expanding Chemical Space Coverage. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:12784-12822. [PMID: 38984754 PMCID: PMC11271014 DOI: 10.1021/acs.est.4c01156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024]
Abstract
In the modern "omics" era, measurement of the human exposome is a critical missing link between genetic drivers and disease outcomes. High-resolution mass spectrometry (HRMS), routinely used in proteomics and metabolomics, has emerged as a leading technology to broadly profile chemical exposure agents and related biomolecules for accurate mass measurement, high sensitivity, rapid data acquisition, and increased resolution of chemical space. Non-targeted approaches are increasingly accessible, supporting a shift from conventional hypothesis-driven, quantitation-centric targeted analyses toward data-driven, hypothesis-generating chemical exposome-wide profiling. However, HRMS-based exposomics encounters unique challenges. New analytical and computational infrastructures are needed to expand the analysis coverage through streamlined, scalable, and harmonized workflows and data pipelines that permit longitudinal chemical exposome tracking, retrospective validation, and multi-omics integration for meaningful health-oriented inferences. In this article, we survey the literature on state-of-the-art HRMS-based technologies, review current analytical workflows and informatic pipelines, and provide an up-to-date reference on exposomic approaches for chemists, toxicologists, epidemiologists, care providers, and stakeholders in health sciences and medicine. We propose efforts to benchmark fit-for-purpose platforms for expanding coverage of chemical space, including gas/liquid chromatography-HRMS (GC-HRMS and LC-HRMS), and discuss opportunities, challenges, and strategies to advance the burgeoning field of the exposome.
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Affiliation(s)
- Yunjia Lai
- Department
of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
| | - Jeremy P. Koelmel
- Department
of Environmental Health Sciences, Yale School
of Public Health, New Haven, Connecticut 06520, United States
| | - Douglas I. Walker
- Gangarosa
Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, United States
| | - Elliott J. Price
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Stefano Papazian
- Department
of Environmental Science, Science for Life Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
- National
Facility for Exposomics, Metabolomics Platform, Science for Life Laboratory, Stockholm University, Solna 171 65, Sweden
| | - Katherine E. Manz
- Department
of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Delia Castilla-Fernández
- Department
of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, 1010 Vienna, Austria
| | - John A. Bowden
- Center for
Environmental and Human Toxicology, Department of Physiological Sciences,
College of Veterinary Medicine, University
of Florida, Gainesville, Florida 32611, United States
| | | | - Arthur David
- Univ Rennes,
Inserm, EHESP, Irset (Institut de recherche en santé, environnement
et travail) − UMR_S, 1085 Rennes, France
| | - Vincent Bessonneau
- Univ Rennes,
Inserm, EHESP, Irset (Institut de recherche en santé, environnement
et travail) − UMR_S, 1085 Rennes, France
| | - Bashar Amer
- Thermo
Fisher Scientific, San Jose, California 95134, United States
| | | | - Xin Hu
- Gangarosa
Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, United States
| | - Elizabeth Z. Lin
- Department
of Environmental Health Sciences, Yale School
of Public Health, New Haven, Connecticut 06520, United States
| | - Akrem Jbebli
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Brooklynn R. McNeil
- Biomarkers
Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Dinesh Barupal
- Department
of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Marina Cerasa
- Institute
of Atmospheric Pollution Research, Italian National Research Council, 00015 Monterotondo, Rome, Italy
| | - Hongyu Xie
- Department
of Environmental Science, Science for Life Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Vrinda Kalia
- Department
of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
| | - Renu Nandakumar
- Biomarkers
Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Randolph Singh
- Department
of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
| | - Zhenyu Tian
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Peng Gao
- Department
of Environmental and Occupational Health, and Department of Civil
and Environmental Engineering, University
of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- UPMC Hillman
Cancer Center, Pittsburgh, Pennsylvania 15232, United States
| | - Yujia Zhao
- Institute
for Risk Assessment Sciences, Utrecht University, Utrecht 3584CM, The Netherlands
| | | | | | - Saurabh Dubey
- Biomarkers
Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Kateřina Coufalíková
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Hana Seličová
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Helge Hecht
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Sheng Liu
- Department
of Environmental Health Sciences, Yale School
of Public Health, New Haven, Connecticut 06520, United States
| | - Hanisha H. Udhani
- Biomarkers
Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Sophie Restituito
- Department
of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
| | - Kam-Meng Tchou-Wong
- Department
of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
| | - Kun Lu
- Department
of Environmental Sciences and Engineering, Gillings School of Global
Public Health, The University of North Carolina
at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jonathan W. Martin
- Department
of Environmental Science, Science for Life Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
- National
Facility for Exposomics, Metabolomics Platform, Science for Life Laboratory, Stockholm University, Solna 171 65, Sweden
| | - Benedikt Warth
- Department
of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, 1010 Vienna, Austria
| | - Krystal J. Godri Pollitt
- Department
of Environmental Health Sciences, Yale School
of Public Health, New Haven, Connecticut 06520, United States
| | - Jana Klánová
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Oliver Fiehn
- West Coast
Metabolomics Center, University of California−Davis, Davis, California 95616, United States
| | - Thomas O. Metz
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Kurt D. Pennell
- School
of Engineering, Brown University, Providence, Rhode Island 02912, United States
| | - Dean P. Jones
- Department
of Medicine, School of Medicine, Emory University, Atlanta, Georgia 30322, United States
| | - Gary W. Miller
- Department
of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
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16
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Otun O, Aljamous C, Del Nero E, Arimont-Segura M, Bosma R, Zarzycka B, Girbau T, Leyrat C, de Graaf C, Leurs R, Durroux T, Granier S, Cong X, Bechara C. Conformational dynamics underlying atypical chemokine receptor 3 activation. Proc Natl Acad Sci U S A 2024; 121:e2404000121. [PMID: 39008676 PMCID: PMC11287255 DOI: 10.1073/pnas.2404000121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/28/2024] [Indexed: 07/17/2024] Open
Abstract
Atypical Chemokine Receptor 3 (ACKR3) belongs to the G protein-coupled receptor family but it does not signal through G proteins. The structural properties that govern the functional selectivity and the conformational dynamics of ACKR3 activation are poorly understood. Here, we combined hydrogen/deuterium exchange mass spectrometry, site-directed mutagenesis, and molecular dynamics simulations to examine the binding mode and mechanism of action of ACKR3 ligands of different efficacies. Our results show that activation or inhibition of ACKR3 is governed by intracellular conformational changes of helix 6, intracellular loop 2, and helix 7, while the DRY motif becomes protected during both processes. Moreover, we identified the binding sites and the allosteric modulation of ACKR3 upon β-arrestin 1 binding. In summary, this study highlights the structure-function relationship of small ligands, the binding mode of β-arrestin 1, the activation dynamics, and the atypical dynamic features in ACKR3 that may contribute to its inability to activate G proteins.
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Affiliation(s)
- Omolade Otun
- Institut de Génomique Fonctionnelle, University of Montpellier, CNRS, INSERM, Montpellier Cedex 534094, France
| | - Christelle Aljamous
- Institut de Génomique Fonctionnelle, University of Montpellier, CNRS, INSERM, Montpellier Cedex 534094, France
| | - Elise Del Nero
- Institut de Génomique Fonctionnelle, University of Montpellier, CNRS, INSERM, Montpellier Cedex 534094, France
| | - Marta Arimont-Segura
- Department of Medicinal Chemistry, Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam1081 HV, The Netherlands
| | - Reggie Bosma
- Department of Medicinal Chemistry, Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam1081 HV, The Netherlands
| | - Barbara Zarzycka
- Department of Medicinal Chemistry, Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam1081 HV, The Netherlands
| | - Tristan Girbau
- Institut de Génomique Fonctionnelle, University of Montpellier, CNRS, INSERM, Montpellier Cedex 534094, France
| | - Cédric Leyrat
- Institut de Génomique Fonctionnelle, University of Montpellier, CNRS, INSERM, Montpellier Cedex 534094, France
| | - Chris de Graaf
- Department of Medicinal Chemistry, Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam1081 HV, The Netherlands
| | - Rob Leurs
- Department of Medicinal Chemistry, Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam1081 HV, The Netherlands
| | - Thierry Durroux
- Institut de Génomique Fonctionnelle, University of Montpellier, CNRS, INSERM, Montpellier Cedex 534094, France
| | - Sébastien Granier
- Institut de Génomique Fonctionnelle, University of Montpellier, CNRS, INSERM, Montpellier Cedex 534094, France
| | - Xiaojing Cong
- Institut de Génomique Fonctionnelle, University of Montpellier, CNRS, INSERM, Montpellier Cedex 534094, France
| | - Cherine Bechara
- Institut de Génomique Fonctionnelle, University of Montpellier, CNRS, INSERM, Montpellier Cedex 534094, France
- Institut Universitaire de France, Paris75005, France
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17
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Suresh S, Shaw AL, Pemberton JG, Scott MK, Harris NJ, Parson MAH, Jenkins ML, Rohilla P, Alvarez-Prats A, Balla T, Yip CK, Burke JE. Molecular basis for plasma membrane recruitment of PI4KA by EFR3. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.587787. [PMID: 38746453 PMCID: PMC11092606 DOI: 10.1101/2024.04.30.587787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The lipid kinase phosphatidylinositol 4 kinase III alpha (PI4KIIIa/PI4KA) is a master regulator of the lipid composition and asymmetry of the plasma membrane. PI4KA exists primarily in a heterotrimeric complex with its regulatory proteins TTC7 and FAM126. Fundamental to PI4KA activity is its targeted recruitment to the plasma membrane by the lipidated proteins EFR3A and EFR3B. Here, we report a cryo-EM structure of the C-terminus of EFR3A bound to the PI4KA-TTC7B-FAM126A complex, with extensive validation using both hydrogen deuterium exchange mass spectrometry (HDX-MS), and mutational analysis. The EFR3A C-terminus undergoes a disorder-order transition upon binding to the PI4KA complex, with an unexpected direct interaction with both TTC7B and FAM126A. Complex disrupting mutations in TTC7B, FAM126A, and EFR3 decrease PI4KA recruitment to the plasma membrane. Multiple post-translational modifications and disease linked mutations map to this site, providing insight into how PI4KA membrane recruitment can be regulated and disrupted in human disease.
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Affiliation(s)
- Sushant Suresh
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Alexandria L Shaw
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
- Current address: Department of Biology, Western University, London, ON, N6A 3K7 Canada
| | - Mackenzie K Scott
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Noah J Harris
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Matthew AH Parson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Pooja Rohilla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Alejandro Alvarez-Prats
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
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18
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Bimai O, Banerjee I, Rozman Grinberg I, Huang P, Hultgren L, Ekström S, Lundin D, Sjöberg BM, Logan DT. Nucleotide binding to the ATP-cone in anaerobic ribonucleotide reductases allosterically regulates activity by modulating substrate binding. eLife 2024; 12:RP89292. [PMID: 38968292 PMCID: PMC11226230 DOI: 10.7554/elife.89292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2024] Open
Abstract
A small, nucleotide-binding domain, the ATP-cone, is found at the N-terminus of most ribonucleotide reductase (RNR) catalytic subunits. By binding adenosine triphosphate (ATP) or deoxyadenosine triphosphate (dATP) it regulates the enzyme activity of all classes of RNR. Functional and structural work on aerobic RNRs has revealed a plethora of ways in which dATP inhibits activity by inducing oligomerisation and preventing a productive radical transfer from one subunit to the active site in the other. Anaerobic RNRs, on the other hand, store a stable glycyl radical next to the active site and the basis for their dATP-dependent inhibition is completely unknown. We present biochemical, biophysical, and structural information on the effects of ATP and dATP binding to the anaerobic RNR from Prevotella copri. The enzyme exists in a dimer-tetramer equilibrium biased towards dimers when two ATP molecules are bound to the ATP-cone and tetramers when two dATP molecules are bound. In the presence of ATP, P. copri NrdD is active and has a fully ordered glycyl radical domain (GRD) in one monomer of the dimer. Binding of dATP to the ATP-cone results in loss of activity and increased dynamics of the GRD, such that it cannot be detected in the cryo-EM structures. The glycyl radical is formed even in the dATP-bound form, but the substrate does not bind. The structures implicate a complex network of interactions in activity regulation that involve the GRD more than 30 Å away from the dATP molecules, the allosteric substrate specificity site and a conserved but previously unseen flap over the active site. Taken together, the results suggest that dATP inhibition in anaerobic RNRs acts by increasing the flexibility of the flap and GRD, thereby preventing both substrate binding and radical mobilisation.
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Affiliation(s)
- Ornella Bimai
- Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | - Ipsita Banerjee
- Section for Biochemistry and Structural Biology, Centre for Molecular Protein Science, Department of Chemistry, Lund UniversityLundSweden
| | | | - Ping Huang
- Department of Chemistry - Ångström Laboratory, Uppsala UniversityUppsalaSweden
| | - Lucas Hultgren
- Structural Proteomics, SciLifeLab, Lund UniversityLundSweden
| | - Simon Ekström
- Structural Proteomics, SciLifeLab, Lund UniversityLundSweden
| | - Daniel Lundin
- Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | - Britt-Marie Sjöberg
- Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | - Derek T Logan
- Section for Biochemistry and Structural Biology, Centre for Molecular Protein Science, Department of Chemistry, Lund UniversityLundSweden
- Cryo-EM for Life Science, SciLifeLab, Lund UniversityLundSweden
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19
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Nie DY, Tabor JR, Li J, Kutera M, St-Germain J, Hanley RP, Wolf E, Paulakonis E, Kenney TMG, Duan S, Shrestha S, Owens DDG, Maitland MER, Pon A, Szewczyk M, Lamberto AJ, Menes M, Li F, Penn LZ, Barsyte-Lovejoy D, Brown NG, Barsotti AM, Stamford AW, Collins JL, Wilson DJ, Raught B, Licht JD, James LI, Arrowsmith CH. Recruitment of FBXO22 for targeted degradation of NSD2. Nat Chem Biol 2024:10.1038/s41589-024-01660-y. [PMID: 38965384 DOI: 10.1038/s41589-024-01660-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 05/31/2024] [Indexed: 07/06/2024]
Abstract
Targeted protein degradation (TPD) is an emerging therapeutic strategy that would benefit from new chemical entities with which to recruit a wider variety of ubiquitin E3 ligases to target proteins for proteasomal degradation. Here we describe a TPD strategy involving the recruitment of FBXO22 to induce degradation of the histone methyltransferase and oncogene NSD2. UNC8732 facilitates FBXO22-mediated degradation of NSD2 in acute lymphoblastic leukemia cells harboring the NSD2 gain-of-function mutation p.E1099K, resulting in growth suppression, apoptosis and reversal of drug resistance. The primary amine of UNC8732 is metabolized to an aldehyde species, which engages C326 of FBXO22 to recruit the SCFFBXO22 Cullin complex. We further demonstrate that a previously reported alkyl amine-containing degrader targeting XIAP is similarly dependent on SCFFBXO22. Overall, we present a potent NSD2 degrader for the exploration of NSD2 disease phenotypes and a new FBXO22-recruitment strategy for TPD.
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Affiliation(s)
- David Y Nie
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John R Tabor
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jianping Li
- University of Florida Health Cancer Center, Gainesville, FL, USA
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Maria Kutera
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ronan P Hanley
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- C4 Therapeutics, Watertown, MA, USA
| | - Esther Wolf
- Department of Chemistry, York University, Toronto, Ontario, Canada
| | - Ethan Paulakonis
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Tristan M G Kenney
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Shili Duan
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Suman Shrestha
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Dominic D G Owens
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Amphista Therapeutics, Cambridge, UK
| | | | - Ailing Pon
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Magdalena Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | - Michael Menes
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Linda Z Penn
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas G Brown
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anthony M Barsotti
- Deerfield Discovery and Development, Deerfield Management, New York, NY, USA
| | - Andrew W Stamford
- Deerfield Discovery and Development, Deerfield Management, New York, NY, USA
| | - Jon L Collins
- Office of the Vice Chancellor for Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, Ontario, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan D Licht
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Lindsey I James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
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20
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Rincon Pabon JP, Akbar Z, Politis A. MSe Collision Energy Optimization for the Analysis of Membrane Proteins Using HDX-cIMS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1383-1389. [PMID: 38842540 PMCID: PMC11228973 DOI: 10.1021/jasms.4c00093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/09/2024] [Accepted: 06/05/2024] [Indexed: 06/07/2024]
Abstract
Hydrogen/deuterium exchange mass spectrometry (HDX-MS) has evolved as an essential technique in structural proteomics. The use of ion mobility separation (IMS) coupled to HDX-MS has increased the applicability of the technique to more complex systems and has been shown to improve data quality and robustness. The first step when running any HDX-MS workflow is to confirm the sequence and retention time of the peptides resulting from the proteolytic digestion of the nondeuterated protein. Here, we optimized the collision energy ramp of HDMSE experiments for membrane proteins using a Waters SELECT SERIES cIMS-QTOF system following an HDX workflow using Phosphorylase B, XylE transporter, and Smoothened receptor (SMO) as model systems. Although collision energy (CE) ramp 10-50 eV gave the highest amount of positive identified peptides when using Phosphorylase B, XylE, and SMO, results suggest optimal CE ramps are protein specific, and different ramps can produce a unique set of peptides. We recommend cIMS users use different CE ramps in their HDMSE experiments and pool the results to ensure maximum peptide identifications. The results show how selecting an appropriate CE ramp can change the sequence coverage of proteins ranging from 4 to 94%.
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Affiliation(s)
- Juan Pablo Rincon Pabon
- Faculty of Biology, Medicine and Health, Division of Molecular and Cellular Function, The University of Manchester, Manchester M13 9PT, U.K
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, U.K
| | - Zulaikha Akbar
- Faculty of Biology, Medicine and Health, Division of Molecular and Cellular Function, The University of Manchester, Manchester M13 9PT, U.K
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, U.K
| | - Argyris Politis
- Faculty of Biology, Medicine and Health, Division of Molecular and Cellular Function, The University of Manchester, Manchester M13 9PT, U.K
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, U.K
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21
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Borotto NB. The path forward for protein footprinting, covalent labeling, and mass spectrometry-based protein conformational analyses. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5064. [PMID: 38873895 PMCID: PMC11210343 DOI: 10.1002/jms.5064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/15/2024]
Abstract
Mass spectrometry-based approaches to assess protein conformation have become widely utilized due to their sensitivity, low sample requirements, and broad applicability to proteins regardless of size and environment. Their wide applicability and sensitivity also make these techniques suitable for the analysis of complex mixtures of proteins, and thus, they have been applied at the cell and even the simple organism levels. These works are impressive, but they predominately employ "bottom-up" workflows and require proteolytic digestion prior to analysis. Once digested, it is not possible to distinguish the proteoform from which any single peptide is derived and therefore, one cannot associate distal-in primary structure-concurrent post-translational modifications (PTMs) or covalent labels, as they would be found on separate peptides. Thus, analyses via bottom-up proteomics report the average PTM status and higher-order structure (HOS) of all existing proteoforms. Second, these works predominately employ promiscuous reagents to probe protein HOS. While this does lead to improved conformational resolution, the formation of many products can divide the signal associated with low-copy number proteins below signal-to-noise thresholds and complicate the bioinformatic analysis of these already challenging systems. In this perspective, I further detail these limitations and discuss the positives and negatives of top-down proteomics as an alternative.
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22
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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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23
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Ye X, Hu Y, Qiu H, Li N. Probe capsid structure stability and dynamics of adeno-associated virus as an important viral vector for gene therapy by hydrogen-deuterium exchange-mass spectrometry. Protein Sci 2024; 33:e5074. [PMID: 38888268 PMCID: PMC11184576 DOI: 10.1002/pro.5074] [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: 01/08/2024] [Revised: 04/14/2024] [Accepted: 05/25/2024] [Indexed: 06/20/2024]
Abstract
Adeno-associated virus (AAV), a widely used gene therapy vector, is a small, nonenveloped virus that contains a single-stranded DNA genome with a maximum length of 4.7 kb. Despite extensive biophysical and structural characterization, many aspects of AAV functions remain elusive. This knowledge gap is primarily due to a lack of structurally resolved dynamic information and the absence of structural coverage of functionally critical segments on the AAV capsid. Here, we developed a protocol to study AAV structural dynamics by hydrogen-deuterium exchange mass spectrometry (HDX-MS), a powerful method for monitoring protein structure stability and dynamics in solution. We performed HDX-MS measurements on AAVs without or with different DNA payloads of different sizes, and obtained detailed dynamic information on the entire AAV sequence including the two functionally important segments not previously structurally characterized. The unique N terminus of the capsid protein VP1 (VP1u) was found to adopt a highly dynamic and unstable conformation with low HDX protection across the entire region, whereas the presence of a DNA payload increased its protection. The VP1 and VP2 shared region (VP1/2) showed no measurable protection, with or without DNA. Differential HDX between empty and full capsid samples allowed us to identify potential new DNA-capsid interaction sites located primarily around the five-fold channel, which differ from the three-fold pocket binding site previously identified. Our HDX-MS method for characterizing AAV structural dynamics opens a new way for future efforts to understand AAV structure-function relationships and engineer next-generation AAV vectors with improved gene delivery properties.
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Affiliation(s)
- Xiang Ye
- Regeneron Pharmaceuticals, Inc.TarrytownNew YorkUSA
| | - Yunli Hu
- Regeneron Pharmaceuticals, Inc.TarrytownNew YorkUSA
| | - Haibo Qiu
- Regeneron Pharmaceuticals, Inc.TarrytownNew YorkUSA
| | - Ning Li
- Regeneron Pharmaceuticals, Inc.TarrytownNew YorkUSA
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24
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Jakobowski A, Hill SG, Guy SW, Offenbacher AR. Substitution of the mononuclear, non-heme iron cofactor in lipoxygenases for structural studies. Methods Enzymol 2024; 704:59-87. [PMID: 39300657 DOI: 10.1016/bs.mie.2024.05.011] [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] [Indexed: 09/22/2024]
Abstract
This Chapter describes methods for the biosynthetic substitution of the mononuclear, non-heme iron in plant and animal lipoxygenases (LOXs). Substitution of this iron center for a manganese ion results in an inactive, yet faithful structural surrogate of the LOX enzymes. This metal ion substitution permits structural and dynamical studies of enzyme-substrate complexes in solution and immobilized on lipid membrane surfaces. Representative procedures for two LOXs, soybean lipoxygenase (SLO) from plants and human epithelial 15-lipoxygenase-2 (15-LOX-2) from mammals, are described as examples.
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Affiliation(s)
- Andrew Jakobowski
- Department of Chemistry, East Carolina University, Greenville, NC, United States
| | - S Gage Hill
- Department of Chemistry, East Carolina University, Greenville, NC, United States
| | - S Wyatt Guy
- Department of Chemistry, East Carolina University, Greenville, NC, United States
| | - Adam R Offenbacher
- Department of Chemistry, East Carolina University, Greenville, NC, United States.
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25
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Wang GQ, Zhang Y, Zhou YX, Yang D, Han P, Jing LH, Tang K. Photoredox Synthesis of Silicon-Containing Isoindolin-1-ones and Deuterated Analogues Through Hydrosilylation and Deuterium-silylation. J Org Chem 2024. [PMID: 38728220 DOI: 10.1021/acs.joc.4c00576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
An efficient, practical, and metal-free protocol for the synthesis of silicon-containing isoindolin-1-ones and deuterated analogues via the synergistic combination of an organic photoredox and hydrogen atom transfer process is described. This strategy features mild reaction conditions, high atom economy, and excellent functional group compatibility, delivering a myriad of structurally diverse and valuable products with good to excellent yields.
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Affiliation(s)
- Guo-Qin Wang
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637002, China
| | - Yue Zhang
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637002, China
| | - Yuan-Xia Zhou
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637002, China
| | - Dan Yang
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637002, China
| | - Pan Han
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637002, China
| | - Lin-Hai Jing
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637002, China
| | - Kai Tang
- Key Laboratories of Fine Chemicals and Surfactants in Sichuan Provincial Universities, School of Chemical Engineering, Sichuan University of Science and Engineering, Zigong 643000, China
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26
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Attanayake K, Mahmud S, Banerjee C, Sharif D, Rahman M, Majuta S, DeBastiani A, Sultana MN, Foroushani SH, Li C, Li P, Valentine SJ. Examining DNA Structures with In-droplet Hydrogen/Deuterium Exchange Mass Spectrometry. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2024; 499:117231. [PMID: 38854816 PMCID: PMC11156224 DOI: 10.1016/j.ijms.2024.117231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Capillary vibrating sharp-edge spray ionization (cVSSI) combined with hydrogen/deuterium exchange-mass spectrometry (HDX-MS) has been utilized to characterize different solution-phase DNA conformers including DNA G-quadruplex topologies as well as triplex DNA and duplex DNA. In general, G-quadruplex DNA shows a wide range of protection of hydrogens extending from ~12% to ~21% deuterium incorporation. Additionally, the DNA sequences selected to represent parallel, antiparallel, and hybrid G-quadruplex topologies exhibit slight differences in deuterium uptake levels which appear to loosely relate to overall conformer stability. Notably, the exchange level for one of the hybrid sequence sub topologies of G-quadruplex DNA (24 TTG) is significantly different (compared with the others studied here) despite the DNA sequences being highly comparable. For the quadruplex-forming sequences, correlation analysis suggests protection of base hydrogens involved in tetrad hydrogen bonding. For duplex DNA ~19% deuterium incorporation is observed while only ~16% is observed for triplex DNA. This increased protection of hydrogens may be due to the added backbone scaffolding and Hoogsteen base pairing of the latter species. These experiments lay the groundwork for future studies aimed at determining the structural source of this protection as well as the applicability of the approach for ascertaining different oligonucleotide folds, co-existing conformations, and/or overall conformer flexibility.
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Affiliation(s)
- Kushani Attanayake
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Sultan Mahmud
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Chandrima Banerjee
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Daud Sharif
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Mohammad Rahman
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Sandra Majuta
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Anthony DeBastiani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Mst Nigar Sultana
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | | | - Chong Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
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27
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Jia Z, Yu W, Li J, Zhang M, Zhan B, Yan L, Ming Z, Cheng Y, Tian X, Shao S, Huang J, Zhu X. Crystal structure of Trichinella spiralis calreticulin and the structural basis of its complement evasion mechanism involving C1q. Front Immunol 2024; 15:1404752. [PMID: 38690267 PMCID: PMC11059001 DOI: 10.3389/fimmu.2024.1404752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 05/02/2024] Open
Abstract
Helminths produce calreticulin (CRT) to immunomodulate the host immune system as a survival strategy. However, the structure of helminth-derived CRT and the structural basis of the immune evasion process remains unclarified. Previous study found that the tissue-dwelling helminth Trichinella spiralis produces calreticulin (TsCRT), which binds C1q to inhibit activation of the complement classical pathway. Here, we used x-ray crystallography to resolve the structure of truncated TsCRT (TsCRTΔ), the first structure of helminth-derived CRT. TsCRTΔ was observed to share the same binding region on C1q with IgG based on the structure and molecular docking, which explains the inhibitory effect of TsCRT on C1q-IgG-initiated classical complement activation. Based on the key residues in TsCRTΔ involved in the binding activity to C1q, a 24 amino acid peptide called PTsCRT was constructed that displayed strong C1q-binding activity and inhibited C1q-IgG-initiated classical complement activation. This study is the first to elucidate the structural basis of the role of TsCRT in immune evasion, providing an approach to develop helminth-derived bifunctional peptides as vaccine target to prevent parasite infections or as a therapeutic agent to treat complement-related autoimmune diseases.
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Affiliation(s)
- Zhihui Jia
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Wen Yu
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Jingmo Li
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Mingming Zhang
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Bin Zhan
- Departments of Pediatrics and Molecular Virology and Microbiology, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Liming Yan
- Ministry of Education Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China
| | - Zhenhua Ming
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Yuli Cheng
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xiaolin Tian
- Ministry of Education Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shuai Shao
- Beijing institute of Clinical Medicine, Capital Medical University Affiliated Beijing Friendship Hospital, Beijing, China
| | - Jingjing Huang
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xinping Zhu
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
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28
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Gao S, Wu XT, Zhang W, Richardson T, Barrow SL, Thompson-Kucera CA, Iavarone AT, Klinman JP. Temporal Resolution of Activity-Related Solvation Dynamics in the TIM Barrel Enzyme Murine Adenosine Deaminase. ACS Catal 2024; 14:4554-4567. [PMID: 39099600 PMCID: PMC11296675 DOI: 10.1021/acscatal.3c02687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
Murine adenosine deaminase (mADA) is a prototypic system for studying the thermal activation of active site chemistry within the TIM barrel family of enzyme reactions. Previous temperature-dependent hydrogen deuterium exchange studies under various conditions have identified interconnected thermal networks for heat transfer from opposing protein-solvent interfaces to active site residues in mADA. One of these interfaces contains a solvent exposed helix-loop-helix moiety that presents the hydrophobic face of its long α-helix to the backside of bound substrate. Herein we pursue the time and temperature dependence of solvation dynamics at the surface of mADA, for comparison to established kinetic parameters that represent active site chemistry. We first created a modified protein devoid of native tryptophans with close to native kinetic behavior. Single site-specific tryptophan mutants were back inserted into each of the four positions where native tryptophans reside. Measurements of nanosecond fluorescence relaxation lifetimes and Stokes shift decays, that reflect time dependent environmental reoroganization around the photo-excited state of Trp*, display minimal temperature dependences. These regions serve as controls for the behavior of a new single tryptophan inserted into a solvent exposed region near the helix-loop-helix moiety located behind the bound substrate, Lys54Trp. This installed Trp displays a significantly elevated value for Ea ( k Stokes shift ) ; further, when Phe61 within the long helix positioned behind bound substrate is replaced by a series of aliphatic hydrophobic side chains, the trends in Ea ( k Stokes shift ) mirror the earlier reported impact of the same series of function-altering hydrophobic side chains on the activation energy of catalysis, Ea ( k cat ) .The reported experimental findings implicate a solvent initiated and rapid (>ns) protein restructuring that contributes to the enthalpic activation barrier to catalysis in mADA.
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Affiliation(s)
- Shuaihua Gao
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
- California Institute for Quantitative Biosciences, and University of California, Berkeley, Berkeley, California, 94720, United States
| | - Xin Ting Wu
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
- California Institute for Quantitative Biosciences, and University of California, Berkeley, Berkeley, California, 94720, United States
| | - Wenju Zhang
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Tyre Richardson
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
- California Institute for Quantitative Biosciences, and University of California, Berkeley, Berkeley, California, 94720, United States
| | - Samuel L. Barrow
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
| | - Christian A. Thompson-Kucera
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
- California Institute for Quantitative Biosciences, and University of California, Berkeley, Berkeley, California, 94720, United States
| | - Anthony T. Iavarone
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
- California Institute for Quantitative Biosciences, and University of California, Berkeley, Berkeley, California, 94720, United States
| | - Judith P. Klinman
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
- California Institute for Quantitative Biosciences, and University of California, Berkeley, Berkeley, California, 94720, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, United States
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29
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Ohler A, Taylor PE, Bledsoe JA, Iavarone AT, Gilbert NC, Offenbacher AR. Identification of the Thermal Activation Network in Human 15-Lipoxygenase-2: Divergence from Plant Orthologs and Its Relationship to Hydrogen Tunneling Activation Barriers. ACS Catal 2024; 14:5444-5457. [PMID: 38601784 PMCID: PMC11003420 DOI: 10.1021/acscatal.4c00439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/05/2024] [Accepted: 03/13/2024] [Indexed: 04/12/2024]
Abstract
The oxidation of polyunsaturated fatty acids by lipoxygenases (LOXs) is initiated by a C-H cleavage step in which the hydrogen atom is transferred quantum mechanically (i.e., via tunneling). In these reactions, protein thermal motions facilitate the conversion of ground-state enzyme-substrate complexes to tunneling-ready configurations and are thus important for transferring energy from the solvent to the active site for the activation of catalysis. In this report, we employed temperature-dependent hydrogen-deuterium exchange mass spectrometry (TDHDX-MS) to identify catalytically linked, thermally activated peptides in a representative animal LOX, human epithelial 15-LOX-2. TDHDX-MS of wild-type 15-LOX-2 was compared to two active site mutations that retain structural stability but have increased activation energies (Ea) of catalysis. The Ea value of one variant, V427L, is implicated to arise from suboptimal substrate positioning by increased active-site side chain rotamer dynamics, as determined by X-ray crystallography and ensemble refinement. The resolved thermal network from the comparative Eas of TDHDX-MS between wild-type and V426A is localized along the front face of the 15-LOX-2 catalytic domain. The network contains a clustering of isoleucine, leucine, and valine side chains within the helical peptides. This thermal network of 15-LOX-2 is different in location, area, and backbone structure compared to a model plant lipoxygenase from soybean that exhibits a low Ea value of catalysis compared to the human ortholog. The presented data provide insights into the divergence of thermally activated protein motions in plant and animal LOXs and their relationships to the enthalpic barriers for facilitating hydrogen tunneling.
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Affiliation(s)
- Amanda Ohler
- Department
of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
| | - Paris E. Taylor
- Department
of Biological Sciences, Louisiana State
University, Baton
Rouge, Louisiana 70803, United States
| | - Jasmine A. Bledsoe
- Department
of Biological Sciences, Louisiana State
University, Baton
Rouge, Louisiana 70803, United States
| | - Anthony T. Iavarone
- QB3/Chemistry
Mass Spectrometry Facility, University of
California, Berkeley, Berkeley, California 94720, United States
| | - Nathaniel C. Gilbert
- Department
of Biological Sciences, Louisiana State
University, Baton
Rouge, Louisiana 70803, United States
| | - Adam R. Offenbacher
- Department
of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
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30
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Lawrence RE, Shoemaker SR, Deal A, Sangwan S, Anand AA, Wang L, Marqusee S, Walter P. A helical fulcrum in eIF2B coordinates allosteric regulation of stress signaling. Nat Chem Biol 2024; 20:422-431. [PMID: 37945896 PMCID: PMC10972756 DOI: 10.1038/s41589-023-01453-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 09/17/2023] [Indexed: 11/12/2023]
Abstract
The integrated stress response (ISR) enables cells to survive a variety of acute stresses, but chronic activation of the ISR underlies age-related diseases. ISR signaling downregulates translation and activates expression of stress-responsive factors that promote return to homeostasis and is initiated by inhibition of the decameric guanine nucleotide exchange factor eIF2B. Conformational and assembly transitions regulate eIF2B activity, but the allosteric mechanisms controlling these dynamic transitions and mediating the therapeutic effects of the small-molecule ISR inhibitor ISRIB are unknown. Using hydrogen-deuterium exchange-mass spectrometry and cryo-electron microscopy, we identified a central α-helix whose orientation allosterically coordinates eIF2B conformation and assembly. Biochemical and cellular signaling assays show that this 'switch-helix' controls eIF2B activity and signaling. In sum, the switch-helix acts as a fulcrum of eIF2B conformational regulation and is a highly conserved actuator of ISR signal transduction. This work uncovers a conserved allosteric mechanism and unlocks new therapeutic possibilities for ISR-linked diseases.
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Affiliation(s)
- Rosalie E Lawrence
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Sophie R Shoemaker
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Aniliese Deal
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- Altos Laboratories, Bay Area Institute of Science, Redwood City, CA, USA
| | - Smriti Sangwan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Aditya A Anand
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- Genentech, Inc., South San Francisco, CA, USA
| | - Lan Wang
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
- The Hong Kong University of Science and Technology, Hong Kong, Hong Kong.
| | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
| | - Peter Walter
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
- Altos Laboratories, Bay Area Institute of Science, Redwood City, CA, USA.
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31
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Filandr F, Sarpe V, Raval S, Crowder DA, Khan MF, Douglas P, Coales S, Viner R, Syed A, Tainer JA, Lees-Miller SP, Schriemer DC. Automating data analysis for hydrogen/deuterium exchange mass spectrometry using data-independent acquisition methodology. Nat Commun 2024; 15:2200. [PMID: 38467655 PMCID: PMC10928179 DOI: 10.1038/s41467-024-46610-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Abstract
We present a hydrogen/deuterium exchange workflow coupled to tandem mass spectrometry (HX-MS2) that supports the acquisition of peptide fragment ions alongside their peptide precursors. The approach enables true auto-curation of HX data by mining a rich set of deuterated fragments, generated by collisional-induced dissociation (CID), to simultaneously confirm the peptide ID and authenticate MS1-based deuteration calculations. The high redundancy provided by the fragments supports a confidence assessment of deuterium calculations using a combinatorial strategy. The approach requires data-independent acquisition (DIA) methods that are available on most MS platforms, making the switch to HX-MS2 straightforward. Importantly, we find that HX-DIA enables a proteomics-grade approach and wide-spread applications. Considerable time is saved through auto-curation and complex samples can now be characterized and at higher throughput. We illustrate these advantages in a drug binding analysis of the ultra-large protein kinase DNA-PKcs, isolated directly from mammalian cells.
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Affiliation(s)
- Frantisek Filandr
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Vladimir Sarpe
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Shaunak Raval
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada
- Department of Chemistry, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - D Alex Crowder
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Morgan F Khan
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Pauline Douglas
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Stephen Coales
- Trajan Scientific & Medical - Raleigh, Morrisville, NC, USA
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, CA, USA
| | - Aleem Syed
- Division of Radiation and Genome Instability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Susan P Lees-Miller
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada.
- Department of Chemistry, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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32
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Di Ianni A, Di Ianni A, Cowan K, Barbero LM, Sirtori FR. Leveraging Cross-Linking Mass Spectrometry for Modeling Antibody-Antigen Complexes. J Proteome Res 2024; 23:1049-1061. [PMID: 38372774 DOI: 10.1021/acs.jproteome.3c00816] [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] [Indexed: 02/20/2024]
Abstract
Elucidating antibody-antigen complexes at the atomic level is of utmost interest for understanding immune responses and designing better therapies. Cross-linking mass spectrometry (XL-MS) has emerged as a powerful tool for mapping protein-protein interactions, suggesting valuable structural insights. However, the use of XL-MS studies to enable epitope/paratope mapping of antibody-antigen complexes is still limited up to now. XL-MS data can be used to drive integrative modeling of antibody-antigen complexes, where cross-links information serves as distance restraints for the precise determination of binding interfaces. In this approach, XL-MS data are employed to identify connections between binding interfaces of the antibody and the antigen, thus informing molecular modeling. Current literature provides minimal input about the impact of XL-MS data on the integrative modeling of antibody-antigen complexes. Here, we applied XL-MS to retrieve information about binding interfaces of three antibody-antigen complexes. We leveraged XL-MS data to perform integrative modeling using HADDOCK (active-passive residues and distance restraints strategies) and AlphaLink2. We then compared these three approaches with initial predictions of investigated antibody-antigen complexes by AlphaFold Multimer. This work emphasizes the importance of cross-linking data in resolving conformational dynamics of antibody-antigen complexes, ultimately enhancing the design of better protein therapeutics and vaccines.
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Affiliation(s)
- Andrea Di Ianni
- NBE-DMPK Innovative BioAnalytics, Merck Serono RBM S.p.A., an Affiliate of Merck KGaA, Darmstadt, Germany, Via Ribes 1, Colleretto Giacosa (TO) 10010, Italy
- University of Turin, Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin 10126, Italy
| | - Alessio Di Ianni
- Martin Luther University Halle-Wittenberg, Department of Pharmaceutical Chemistry and Bioanalytics, Center for Structural Mass Spectrometry, Institute of Pharmacy, Kurt-Mothes-Str. 3, Halle/Saale D-06120, Germany
| | - Kyra Cowan
- New Biological Entities, Drug Metabolism and Pharmacokinetics (NBE-DMPK), Research and Development, Merck KGaA, Frankfurterstrasse 250, Darmstadt 64293, Germany
| | - Luca M Barbero
- NBE-DMPK Innovative BioAnalytics, Merck Serono RBM S.p.A., an Affiliate of Merck KGaA, Darmstadt, Germany, Via Ribes 1, Colleretto Giacosa (TO) 10010, Italy
| | - Federico Riccardi Sirtori
- NBE-DMPK Innovative BioAnalytics, Merck Serono RBM S.p.A., an Affiliate of Merck KGaA, Darmstadt, Germany, Via Ribes 1, Colleretto Giacosa (TO) 10010, Italy
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33
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Narjes F, Edfeldt F, Petersen J, Öster L, Hamblet C, Bird J, Bold P, Rae R, Bäck E, Stomilovic S, Zlatoidsky P, Svensson T, Hidestål L, Kunalingam L, Shamovsky I, De Maria L, Gordon E, Lewis RJ, Watcham S, van Rietschoten K, Mudd GE, Harrison H, Chen L, Skynner MJ. Discovery and Characterization of a Bicyclic Peptide (Bicycle) Binder to Thymic Stromal Lymphopoietin. J Med Chem 2024; 67:2220-2235. [PMID: 38284169 DOI: 10.1021/acs.jmedchem.3c02163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Thymic stromal lymphopoietin (TSLP) is an epithelial-derived pro-inflammatory cytokine involved in the development of asthma and other atopic diseases. We used Bicycle Therapeutics' proprietary phage display platform to identify bicyclic peptides (Bicycles) with high affinity for TSLP, a target that is difficult to drug with conventional small molecules due to the extended protein-protein interactions it forms with both receptors. The hit series was shown to bind to TSLP in a hotspot, that is also used by IL-7Rα. Guided by the first X-ray crystal structure of a small peptide binding to TSLP and the identification of key metabolites, we were able to improve the proteolytic stability of this series in lung S9 fractions without sacrificing binding affinity. This resulted in the potent Bicycle 46 with nanomolar affinity to TSLP (KD = 13 nM), low plasma clearance of 6.4 mL/min/kg, and an effective half-life of 46 min after intravenous dosing to rats.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Sophie Watcham
- BicycleTx Limited, Portway Building, Granta Park, Cambridge CB21 6GS, U.K
| | | | - Gemma E Mudd
- BicycleTx Limited, Portway Building, Granta Park, Cambridge CB21 6GS, U.K
| | - Helen Harrison
- BicycleTx Limited, Portway Building, Granta Park, Cambridge CB21 6GS, U.K
| | - Liuhong Chen
- BicycleTx Limited, Portway Building, Granta Park, Cambridge CB21 6GS, U.K
| | - Michael J Skynner
- BicycleTx Limited, Portway Building, Granta Park, Cambridge CB21 6GS, U.K
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34
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Nguyen HMH, Thomas DC, Hart MA, Steenback KR, Levy JN, McNally A. Synthesis of 15N-Pyridines and Higher Mass Isotopologs via Zincke Imine Intermediates. J Am Chem Soc 2024; 146:2944-2949. [PMID: 38227776 DOI: 10.1021/jacs.3c12445] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Methods to incorporate stable radioisotopes are integral to pharmaceutical and agrochemical development. However, despite the prevalence of pyridines in candidate compounds, methods to incorporate 15N atoms within their structures are limited. Here, we present a general approach to pyridine 15N-labeling that proceeds via ring-opening to NTf-Zincke imines and then ring-closure with commercially available 15NH4Cl salts. This process functions on a range of substituted pyridines, from simple building block-type compounds to late-stage labeling of complex pharmaceuticals, and 15N-incorporation is >95% in most cases. The reactivity of the Zincke imine intermediates also enables deuteration of the pyridine C3- and C5-positions, resulting in higher mass isotopologs required for LCMS analysis of biological fluids during drug development.
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Affiliation(s)
- Hillary M H Nguyen
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - David C Thomas
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Marie A Hart
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Kaila R Steenback
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Jeffrey N Levy
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Andrew McNally
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
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35
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James EI, Baggett DW, Chang E, Schachter J, Nixey T, Choi K, Guttman M, Nath A. Tryptanthrin Analogs Substoichiometrically Inhibit Seeded and Unseeded Tau4RD Aggregation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.02.578649. [PMID: 38352474 PMCID: PMC10862865 DOI: 10.1101/2024.02.02.578649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Microtubule-associated protein tau is an intrinsically disordered protein (IDP) that forms characteristic fibrillar aggregates in several diseases, the most well-known of which is Alzheimer's disease (AD). Despite keen interest in disrupting or inhibiting tau aggregation to treat AD and related dementias, there are currently no FDA-approved tau-targeting drugs. This is due, in part, to the fact that tau and other IDPs do not exhibit a single well-defined conformation but instead populate a fluctuating conformational ensemble that precludes finding a stable "druggable" pocket. Despite this challenge, we previously reported the discovery of two novel families of tau ligands, including a class of aggregation inhibitors, identified through a protocol that combines molecular dynamics, structural analysis, and machine learning. Here we extend our exploration of tau druggability with the identification of tryptanthrin and its analogs as potent, substoichiometric aggregation inhibitors, with the best compounds showing potencies in the low nanomolar range even at a ~100-fold molar excess of tau4RD. Moreover, conservative changes in small molecule structure can have large impacts on inhibitory potency, demonstrating that similar structure-activity relationship (SAR) principles as used for traditional drug development also apply to tau and potentially to other IDPs.
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Affiliation(s)
- Ellie I. James
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA
| | - David W. Baggett
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
- Current address: Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Edcon Chang
- Takeda Development Center Americas, San Diego, CA
| | | | - Thomas Nixey
- Takeda Development Center Americas, San Diego, CA
| | | | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA
| | - Abhinav Nath
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA
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36
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Wu R, Svingou D, Metternich JB, Benzenberg LR, Zenobi R. Transition Metal Ion FRET-Based Probe to Study Cu(II)-Mediated Amyloid- β Ligand Binding. J Am Chem Soc 2024; 146:2102-2112. [PMID: 38225538 DOI: 10.1021/jacs.3c11533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Recent therapeutic strategies suggest that small peptides can act as aggregation inhibitors of monomeric amyloid-β (Αβ) by inducing structural rearrangements upon complexation. However, characterizing the binding events in such dynamic and transient noncovalent complexes, especially in the presence of natively occurring metal ions, remains a challenge. Here, we deploy a combined transition metal ion Förster resonance energy transfer (tmFRET) and native ion mobility-mass spectrometry (IM-MS) approach to characterize the structure of mass- and charge-selected Aβ complexes with Cu(II) ions (a quencher) and a potential aggregation inhibitor, a small neuropeptide named leucine enkephalin (LE). We show conformational changes of monomeric Αβ species upon Cu(II)-binding, indicating an uncoiled N-terminus and a close interaction between the C-terminus and the central hydrophobic region. Furthermore, we introduce LE labeled at the N-terminus with a metal-chelating agent, nitrilotriacetic acid (NTA). This allows us to employ tmFRET to probe the binding even in low-abundance and transient Aβ-inhibitor-metal ion complexes. Complementary intramolecular distance and global shape information from tmFRET and native IM-MS, respectively, confirmed Cu(II) displacement toward the N-terminus of Αβ, which discloses the binding region and the inhibitor's orientation.
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Affiliation(s)
- Ri Wu
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Despoina Svingou
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Jonas B Metternich
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Lukas R Benzenberg
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Renato Zenobi
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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37
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Li Y, Lyu J, Wang Y, Ye M, Wang H. Ligand Modification-Free Methods for the Profiling of Protein-Environmental Chemical Interactions. Chem Res Toxicol 2024; 37:1-15. [PMID: 38146056 DOI: 10.1021/acs.chemrestox.3c00282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Adverse health outcomes caused by environmental chemicals are often initiated via their interactions with proteins. Essentially, one environmental chemical may interact with a number of proteins and/or a protein may interact with a multitude of environmental chemicals, forming an intricate interaction network. Omics-wide protein-environmental chemical interaction profiling (PECI) is of prominent importance for comprehensive understanding of these interaction networks, including the toxicity mechanisms of action (MoA), and for providing systematic chemical safety assessment. However, such information remains unknown for most environmental chemicals, partly due to their vast chemical diversity. In recent years, with the continuous efforts afforded, especially in mass spectrometry (MS) based omics technologies, several ligand modification-free methods have been developed, and new attention for systematic PECI profiling was gained. In this Review, we provide a comprehensive overview on these methodologies for the identification of ligand-protein interactions, including affinity interaction-based methods of affinity-driven purification, covalent modification profiling, and activity-based protein profiling (ABPP) in a competitive mode, physicochemical property changes assessment methods of ligand-directed nuclear magnetic resonance (ligand-directed NMR), MS integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS), thermal proteome profiling (TPP), limited proteolysis-coupled mass spectrometry (LiP-MS), stability of proteins from rates of oxidation (SPROX), and several intracellular downstream response characterization methods. We expect that the applications of these ligand modification-free technologies will drive a considerable increase in the number of PECI identified, facilitate unveiling the toxicological mechanisms, and ultimately contribute to systematic health risk assessment of environmental chemicals.
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Affiliation(s)
- Yanan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jiawen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Yan Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
- State Key Laboratory of Medical Proteomics, Beijing, 102206, China
| | - Hailin Wang
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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38
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Kish M, Ivory DP, Phillips JJ. Transient Structural Dynamics of Glycogen Phosphorylase from Nonequilibrium Hydrogen/Deuterium-Exchange Mass Spectrometry. J Am Chem Soc 2024; 146:298-307. [PMID: 38158228 PMCID: PMC10786028 DOI: 10.1021/jacs.3c08934] [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: 08/16/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024]
Abstract
It remains a major challenge to ascertain the specific structurally dynamic changes that underpin protein functional switching. There is a growing need in molecular biology and drug discovery to complement structural models with the ability to determine the dynamic structural changes that occur as these proteins are regulated and function. The archetypal allosteric enzyme glycogen phosphorylase is a clinical target of great interest to treat type II diabetes and metastatic cancers. Here, we developed a time-resolved nonequilibrium millisecond hydrogen/deuterium-exchange mass spectrometry (HDX-MS) approach capable of precisely locating dynamic structural changes during allosteric activation and inhibition of glycogen phosphorylase. We resolved obligate transient changes in the localized structure that are absent when directly comparing active/inactive states of the enzyme and show that they are common to allosteric activation by AMP and inhibition by caffeine, operating at different sites. This indicates that opposing allosteric regulation by inhibitor and activator ligands is mediated by pathways that intersect with a common structurally dynamic motif. This mass spectrometry approach uniquely stands to discover local transient structural dynamics and could be used broadly to identify features that influence the structural transitions of proteins.
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Affiliation(s)
- Monika Kish
- Living
Systems Institute, Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4
4QD, U.K.
| | - Dylan P. Ivory
- Living
Systems Institute, Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4
4QD, U.K.
| | - Jonathan J. Phillips
- Living
Systems Institute, Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4
4QD, U.K.
- Alan
Turing Institute, British Library, London NW1 2DB, U.K.
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39
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Mann M, Wolf E, Silva M, Kwak HA, Wilson B, Bolotokova A, Wilson DJ, Harding RJ, Schapira M. Small Molecule Screen Identifies Non-catalytic USP3 Chemical Handle. ACS OMEGA 2024; 9:917-924. [PMID: 38222562 PMCID: PMC10785082 DOI: 10.1021/acsomega.3c07070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 01/16/2024]
Abstract
Zinc-finger ubiquitin-binding domains (ZnF-UBDs) are noncatalytic domains mostly found in deubiquitylases (DUBs) such as USP3. They represent an underexplored opportunity for the development of deubiquitylase-targeting chimeras (DUBTACs) to pharmacologically induce the deubiquitylation of target proteins. We previously showed that ZnF-UBDs are ligandable domains. Here, a focused small molecule library screen against a panel of 11 ZnF-UBDs led to the identification of compound 59, a ligand engaging the ZnF-UBD of USP3 with a KD of 14 μM. The compound binds the expected C-terminal ubiquitin binding pocket of USP3 as shown by hydrogen-deuterium exchange mass spectrometry experiments and does not inhibit the cleavage of K48-linked diubiquitin by USP3. As such, this molecule is a chemical starting point toward chemical tools that could be used to interrogate the function of the USP3 Znf-UBD and the consequences of recruiting USP3 to ubiquitylated proteins.
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Affiliation(s)
- Mandeep
K. Mann
- Structural
Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower,
Suite 700, Toronto, Ontario M5G 1L7, Canada
- Department
of Pharmacology and Toxicology, University
of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Esther Wolf
- Department
of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Madhushika Silva
- Structural
Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower,
Suite 700, Toronto, Ontario M5G 1L7, Canada
| | - Haejin Angela Kwak
- Structural
Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower,
Suite 700, Toronto, Ontario M5G 1L7, Canada
- Department
of Pharmacology and Toxicology, University
of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Brian Wilson
- Drug
Discovery Program, Ontario Institute for
Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Albina Bolotokova
- Structural
Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower,
Suite 700, Toronto, Ontario M5G 1L7, Canada
| | - Derek J. Wilson
- Department
of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Rachel J. Harding
- Structural
Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower,
Suite 700, Toronto, Ontario M5G 1L7, Canada
- Department
of Pharmacology and Toxicology, University
of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Matthieu Schapira
- Structural
Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower,
Suite 700, Toronto, Ontario M5G 1L7, Canada
- Department
of Pharmacology and Toxicology, University
of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8, Canada
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40
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Miyagi M, Nakazawa T. Significance of Histidine Hydrogen-Deuterium Exchange Mass Spectrometry in Protein Structural Biology. BIOLOGY 2024; 13:37. [PMID: 38248468 PMCID: PMC10813008 DOI: 10.3390/biology13010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/23/2024]
Abstract
Histidine residues play crucial roles in shaping the function and structure of proteins due to their unique ability to act as both acids and bases. In other words, they can serve as proton donors and acceptors at physiological pH. This exceptional property is attributed to the side-chain imidazole ring of histidine residues. Consequently, determining the acid-base dissociation constant (Ka) of histidine imidazole rings in proteins often yields valuable insights into protein functions. Significant efforts have been dedicated to measuring the pKa values of histidine residues in various proteins, with nuclear magnetic resonance (NMR) spectroscopy being the most commonly used technique. However, NMR-based methods encounter challenges in assigning signals to individual imidazole rings and require a substantial amount of proteins. To address these issues associated with NMR-based approaches, a mass-spectrometry-based method known as histidine hydrogen-deuterium exchange mass spectrometry (His-HDX-MS) has been developed. This technique not only determines the pKa values of histidine imidazole groups but also quantifies their solvent accessibility. His-HDX-MS has proven effective across diverse proteins, showcasing its utility. This review aims to clarify the fundamental principles of His-HDX-MS, detail the experimental workflow, explain data analysis procedures and provide guidance for interpreting the obtained results.
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Affiliation(s)
- Masaru Miyagi
- Department of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-4988, USA
| | - Takashi Nakazawa
- Department of Chemistry, Nara Women’s University, Nara 630-8506, Japan
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41
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Cao JM, Liu XY, Rao W, Shen SS, Sheng D, Wang SY. Regioselective Thiol-yne Reaction of Thiol with ((Methyl-d 3)sulfonyl)ethyne: Synthesis of (2-((Methyl-d 3)sulfonyl)vinyl)sulfides. J Org Chem 2024; 89:363-372. [PMID: 38085815 DOI: 10.1021/acs.joc.3c02100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Herein, we have developed a new method for the synthesis of ((methyl-d3)sulfonyl)ethyne, which is cost-effective and environmentally friendly and can be synthesized at the gram level. As an ideal thiol-yne reagent, it can be reacted with various types of thiols to afford (Z)- and (E)-type vinyl sulfides under different conditions with high selectivity. In addition, it can complete the conformational transition from Z- to E-type products under suitable conditions, and can also carry out further derivatization smoothly. The deuterium content of all products was greater than 99%. The preliminary mechanistic studies support the visible light-mediated radical course, and herein provide a novel and efficient synthetic strategy for the direct introduction of deuterated methyl groups, enriching the methods for the construction of C-S bond-containing compounds.
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Affiliation(s)
- Ji-Min Cao
- Key Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry, Chemical Engineering and Materials Science & Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou 215123, P. R. China
| | - Xin-Yu Liu
- Key Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry, Chemical Engineering and Materials Science & Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou 215123, P. R. China
| | - Weidong Rao
- Key Laboratory of Biomass-based Green Fuels and Chemicals, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Shu-Su Shen
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No.99, Xuefu road, Huqiu district,Suzhou 215009, PR China
| | - Daopeng Sheng
- Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu 215123, China
| | - Shun-Yi Wang
- Key Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry, Chemical Engineering and Materials Science & Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou 215123, P. R. China
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42
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Luebbers A, Gonzalez-Hernandez AJ, Zhou M, Eyles SJ, Levitz J, Garcia-Marcos M. Dissecting the molecular basis for the modulation of neurotransmitter GPCR signaling by GINIP. Structure 2024; 32:47-59.e7. [PMID: 37989308 PMCID: PMC10872408 DOI: 10.1016/j.str.2023.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/23/2023] [Accepted: 10/25/2023] [Indexed: 11/23/2023]
Abstract
It is well established that G-protein-coupled receptors (GPCRs) stimulated by neurotransmitters are critical for neuromodulation. Much less is known about how heterotrimeric G-protein (Gαβγ) regulation after receptor-mediated activation contributes to neuromodulation. Recent evidence indicates that the neuronal protein GINIP shapes GPCR inhibitory neuromodulation via a unique mechanism of G-protein regulation that controls pain and seizure susceptibility. However, the molecular basis of this mechanism remains ill-defined because the structural determinants of GINIP responsible for binding and regulating G proteins are not known. Here, we combined hydrogen-deuterium exchange mass spectrometry, computational structure predictions, biochemistry, and cell-based biophysical assays to demonstrate an effector-like binding mode of GINIP to Gαi. Specific amino acids of GINIP's PHD domain first loop are essential for G-protein binding and subsequent regulation of Gαi-GTP and Gβγ signaling upon neurotransmitter GPCR stimulation. In summary, these findings shed light onto the molecular basis for a post-receptor mechanism of G-protein regulation that fine-tunes inhibitory neuromodulation.
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Affiliation(s)
- Alex Luebbers
- Department of Biochemistry & Cell Biology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
| | | | - Myles Zhou
- Department of Biochemistry & Cell Biology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
| | - Stephen J Eyles
- Mass Spectrometry Core Facility, Institute for Applied Life Sciences (IALS), University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10064, USA; Department of Psychiatry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Mikel Garcia-Marcos
- Department of Biochemistry & Cell Biology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; Department of Biology, College of Arts & Sciences, Boston University, Boston, MA 02115, USA.
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43
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Severt T, Weckwerth E, Kaderiya B, Feizollah P, Jochim B, Borne K, Ziaee F, P KR, Carnes KD, Dantus M, Rolles D, Rudenko A, Wells E, Ben-Itzhak I. Initial-site characterization of hydrogen migration following strong-field double-ionization of ethanol. Nat Commun 2024; 15:74. [PMID: 38168047 PMCID: PMC10761976 DOI: 10.1038/s41467-023-44311-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
An essential problem in photochemistry is understanding the coupling of electronic and nuclear dynamics in molecules, which manifests in processes such as hydrogen migration. Measurements of hydrogen migration in molecules that have more than two equivalent hydrogen sites, however, produce data that is difficult to compare with calculations because the initial hydrogen site is unknown. We demonstrate that coincidence ion-imaging measurements of a few deuterium-tagged isotopologues of ethanol can determine the contribution of each initial-site composition to hydrogen-rich fragments following strong-field double ionization. These site-specific probabilities produce benchmarks for calculations and answer outstanding questions about photofragmentation of ethanol dications; e.g., establishing that the central two hydrogen atoms are 15 times more likely to abstract the hydroxyl proton than a methyl-group proton to form H[Formula: see text] and that hydrogen scrambling, involving the exchange of hydrogen between different sites, is important in H2O+ formation. The technique extends to dynamic variables and could, in principle, be applied to larger non-cyclic hydrocarbons.
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Affiliation(s)
- Travis Severt
- J. R. Macdonald Laboratory, Physics Department, Kansas State University, Manhattan, KS, 66506, USA
| | - Eleanor Weckwerth
- Department of Physics, Augustana University, Sioux Falls, SD, 57108, USA
| | - Balram Kaderiya
- J. R. Macdonald Laboratory, Physics Department, Kansas State University, Manhattan, KS, 66506, USA
| | - Peyman Feizollah
- J. R. Macdonald Laboratory, Physics Department, Kansas State University, Manhattan, KS, 66506, USA
| | - Bethany Jochim
- J. R. Macdonald Laboratory, Physics Department, Kansas State University, Manhattan, KS, 66506, USA
| | - Kurtis Borne
- J. R. Macdonald Laboratory, Physics Department, Kansas State University, Manhattan, KS, 66506, USA
| | - Farzaneh Ziaee
- J. R. Macdonald Laboratory, Physics Department, Kansas State University, Manhattan, KS, 66506, USA
| | - Kanaka Raju P
- J. R. Macdonald Laboratory, Physics Department, Kansas State University, Manhattan, KS, 66506, USA
- School of Quantum Technology, DIAT (DU), Pune, Maharashtra, 411025, India
| | - Kevin D Carnes
- J. R. Macdonald Laboratory, Physics Department, Kansas State University, Manhattan, KS, 66506, USA
| | - Marcos Dantus
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Daniel Rolles
- J. R. Macdonald Laboratory, Physics Department, Kansas State University, Manhattan, KS, 66506, USA
| | - Artem Rudenko
- J. R. Macdonald Laboratory, Physics Department, Kansas State University, Manhattan, KS, 66506, USA
| | - Eric Wells
- Department of Physics, Augustana University, Sioux Falls, SD, 57108, USA.
| | - Itzik Ben-Itzhak
- J. R. Macdonald Laboratory, Physics Department, Kansas State University, Manhattan, KS, 66506, USA.
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44
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Largy E, Ranz M, Gabelica V. A General Framework to Interpret Hydrogen-Deuterium Exchange Native Mass Spectrometry of G-Quadruplex DNA. J Am Chem Soc 2023; 145:26843-26857. [PMID: 38044563 DOI: 10.1021/jacs.3c09365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
G-quadruplexes (G4s) are secondary structures formed by guanine-rich oligonucleotides involved in various biological processes. However, characterizing G4s is challenging, because of their structural polymorphism. Here, we establish how hydrogen-deuterium exchange native mass spectrometry (HDX/MS) can help to characterize the G4 structures and dynamics in solution. We correlated the time range of G4 exchange to the number of guanines involved in the inner and outer tetrads. We also established relationships among exchange rates, numbers of tetrads and bound cations, and stability. The use of HDX/native MS allows for the determination of tetrads formed and assessment of G4 stability at a constant temperature. A key finding is that stable G4s exchange through local fluctuations (EX2 exchange), whereas less stable G4s also undergo exchange through partial or complete unfolding (EX1 exchange). Deconvolution of the bimodal isotope distributions resulting from EX1 exchange provides valuable insight into the kinetics of folding and unfolding processes and allows one to detect and characterize transiently unfolded intermediates, even if scarcely populated. HDX/native MS thus represents a powerful tool for a more comprehensive exploration of the folding landscapes of G4s.
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Affiliation(s)
- Eric Largy
- Université de Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Matthieu Ranz
- Université de Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Valérie Gabelica
- Université de Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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45
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Kant R, Mishra N, Gross ML. Antibody Binding Captures High Energy State of an Antigen: The Case of Nsp1 SARS-CoV-2 as Revealed by Hydrogen-Deuterium Exchange Mass Spectrometry. Int J Mol Sci 2023; 24:17342. [PMID: 38139170 PMCID: PMC10743928 DOI: 10.3390/ijms242417342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/05/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
We describe an investigation using structural mass spectrometry (MS) of the impact of two antibodies, 15497 and 15498, binding the highly flexible SARS-CoV-2 Nsp1 protein. We determined the epitopes and paratopes involved in the antibody-protein interactions by using hydrogen-deuterium exchange MS (HDX-MS). Notably, the Fab (Fragment antigen binding) for antibody 15498 captured a high energy form of the antigen exhibiting significant conformational changes that added flexibility over most of the Nsp1 protein. The Fab for antibody 15497, however, showed usual antigen binding behavior, revealing local changes presumably including the binding site. These findings illustrate an unusual antibody effect on an antigen and are consistent with the dynamic nature of the Nsp1 protein. Our studies suggest that this interaction capitalizes on the high flexibility of Nsp1 to undergo conformational change and be trapped in a higher energy state by binding with a specific antibody.
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Affiliation(s)
- Ravi Kant
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA;
| | - Nawneet Mishra
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA;
| | - Michael L. Gross
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA;
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46
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Anderson KW, Hudgens JW. Hydrophilic Interaction Liquid Chromatography at Subzero Temperature for Hydrogen-Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2672-2679. [PMID: 37930109 PMCID: PMC10704588 DOI: 10.1021/jasms.3c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/26/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023]
Abstract
Chromatographic separations at subzero temperature significantly improve the precision of back-exchange-corrected hydrogen-deuterium exchange mass spectrometry (HDX-MS) determinations. Our previously reported dual-enzyme HDX-MS analysis instrument used reversed phase liquid chromatography (RPLC) at -30 °C, but high backpressures limited flow rates and required materials and equipment rated for very high pressures. Here, we report the design and performance of a dual-enzyme HDX-MS analysis instrument comprising a RPLC trap column and a hydrophilic interaction liquid chromatography (HILIC) analytical column in a two-dimensional RPLC-HILIC configuration at subzero temperature. During operation at -30 °C, the HILIC column manifests greatly reduced backpressure, which enables faster analytical flow rates and the use of materials rated for lower maximum pressures. The average peptide eluted from a HILIC column during a 40 min gradient at -30 °C contained ≈13% more deuterium than peptides eluted from a tandem RPLC-RPLC apparatus using a conventional 8 min gradient at 0 °C. A subset of peptides eluted from the HILIC apparatus contained ≈24% more deuterium.
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Affiliation(s)
- Kyle W. Anderson
- Bioprocess
Measurements Group, Biomolecular Measurement Division, National Institute of Standards and Technology, Rockville, Maryland 20850, United States
- Institute
for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
| | - Jeffrey W. Hudgens
- Bioprocess
Measurements Group, Biomolecular Measurement Division, National Institute of Standards and Technology, Rockville, Maryland 20850, United States
- Institute
for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
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47
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Nie DY, Tabor JR, Li J, Kutera M, St-Germain J, Hanley RP, Wolf E, Paulakonis E, Kenney TMG, Duan S, Shrestha S, Owens DDG, Pon A, Szewczyk M, Lamberto AJ, Menes M, Li F, Barsyte-Lovejoy D, Brown NG, Barsotti AM, Stamford AW, Collins JL, Wilson DJ, Raught B, Licht JD, James LI, Arrowsmith CH. Recruitment of FBXO22 for Targeted Degradation of NSD2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.01.564830. [PMID: 37961297 PMCID: PMC10635037 DOI: 10.1101/2023.11.01.564830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Targeted protein degradation (TPD) is an emerging therapeutic strategy that would benefit from new chemical entities with which to recruit a wider variety of ubiquitin E3 ligases to target proteins for proteasomal degradation. Here, we describe a TPD strategy involving the recruitment of FBXO22 to induce degradation of the histone methyltransferase and oncogene NSD2. UNC8732 facilitates FBXO22-mediated degradation of NSD2 in acute lymphoblastic leukemia cells harboring the NSD2 gain of function mutation p.E1099K, resulting in growth suppression, apoptosis, and reversal of drug resistance. The primary amine of UNC8732 is metabolized to an aldehyde species, which engages C326 of FBXO22 in a covalent and reversible manner to recruit the SCF FBXO22 Cullin complex. We further demonstrate that a previously reported alkyl amine-containing degrader targeting XIAP is similarly dependent on SCF FBXO22 . Overall, we present a highly potent NSD2 degrader for the exploration of NSD2 disease phenotypes and a novel FBXO22-dependent TPD strategy.
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48
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Lin Y, Moyle AB, Beaumont VA, Liu LL, Polleck S, Liu H, Shi H, Rouse JC, Kim HY, Zhang Y, Gross ML. Characterization of Higher Order Structural Changes of a Thermally Stressed Monoclonal Antibody via Mass Spectrometry Footprinting and Other Biophysical Approaches. Anal Chem 2023; 95:16840-16849. [PMID: 37933954 PMCID: PMC10909587 DOI: 10.1021/acs.analchem.3c02422] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Characterizing changes in the higher order structure (HOS) of monoclonal antibodies upon stressed conditions is critical to gaining a better understanding of the product and process. One single biophysical approach may not be best suited to assess HOS comprehensively; thus, the synergy from multiple, complementary approaches improves characterization accuracy and resolution. In this study, we employed two mass spectrometry (MS )-based footprinting techniques, namely, fast photochemical oxidation of proteins (FPOP)-MS and hydrogen-deuterium exchange (HDX)-MS, supported by dynamic light scattering (DLS), differential scanning calorimetry (DSC), circular dichroism (CD), and nuclear magnetic resonance (NMR) to study changes to the HOS of a mAb upon thermal stress. The biophysical techniques report a nuanced characterization of the HOS in which CD detects no changes to the secondary or tertiary structure, yet DLS measurements show an increase in the hydrodynamic radius. DSC indicates that the stability decreases, and chemical or conformational changes accumulate with incubation time according to NMR. Furthermore, whereas HDX-MS does not indicate HOS changes, FPOP-MS footprinting reveals conformational changes at residue resolution for some amino acids. The local phenomena observed with FPOP-MS indicate that several residues show various patterns of degradation during thermal stress: no change, an increase in solvent exposure, and a biphasic response to solvent exposure. All evidences show that FPOP-MS efficiently resolves subtle structural changes and novel degradation pathways upon thermal stress treatment at residue-level resolution.
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Affiliation(s)
- Yanchun Lin
- Department of Chemistry, Washington University in St Louis, St Louis, Missouri 63105, United States
| | - Austin B Moyle
- Department of Chemistry, Washington University in St Louis, St Louis, Missouri 63105, United States
| | - Victor A Beaumont
- Pharmaceutical Sciences Small Molecules, Analytical Research and Development, Pfizer, Inc., Sandwich CT13 9FF, U.K
| | - Lucy L Liu
- Biotherapeutics Pharmaceutical Sciences, Analytical Research and Development, Pfizer, Inc., Andover, Massachusetts 01810, United States
| | - Sharon Polleck
- Biotherapeutics Pharmaceutical Sciences, Analytical Research and Development, Pfizer, Inc., Andover, Massachusetts 01810, United States
| | - Haijun Liu
- Department of Chemistry, Washington University in St Louis, St Louis, Missouri 63105, United States
| | - Heliang Shi
- Global Product Development, Rare Disease Statistics, Pfizer, Inc., New York, New York 10017, United States
| | - Jason C Rouse
- Biotherapeutics Pharmaceutical Sciences, Analytical Research and Development, Pfizer, Inc., Andover, Massachusetts 01810, United States
| | - Hai-Young Kim
- Biotherapeutics Pharmaceutical Sciences, Analytical Research and Development, Pfizer, Inc., Andover, Massachusetts 01810, United States
| | - Ying Zhang
- Biotherapeutics Pharmaceutical Sciences, Analytical Research and Development, Pfizer, Inc., Andover, Massachusetts 01810, United States
| | - Michael L Gross
- Department of Chemistry, Washington University in St Louis, St Louis, Missouri 63105, United States
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49
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Bai Y, Zhang S, Dong H, Liu Y, Liu C, Zhang X. Advanced Techniques for Detecting Protein Misfolding and Aggregation in Cellular Environments. Chem Rev 2023; 123:12254-12311. [PMID: 37874548 DOI: 10.1021/acs.chemrev.3c00494] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Protein misfolding and aggregation, a key contributor to the progression of numerous neurodegenerative diseases, results in functional deficiencies and the creation of harmful intermediates. Detailed visualization of this misfolding process is of paramount importance for improving our understanding of disease mechanisms and for the development of potential therapeutic strategies. While in vitro studies using purified proteins have been instrumental in delivering significant insights into protein misfolding, the behavior of these proteins in the complex milieu of living cells often diverges significantly from such simplified environments. Biomedical imaging performed in cell provides cellular-level information with high physiological and pathological relevance, often surpassing the depth of information attainable through in vitro methods. This review highlights a variety of methodologies used to scrutinize protein misfolding within biological systems. This includes optical-based methods, strategies leaning on mass spectrometry, in-cell nuclear magnetic resonance, and cryo-electron microscopy. Recent advancements in these techniques have notably deepened our understanding of protein misfolding processes and the features of the resulting misfolded species within living cells. The progression in these fields promises to catalyze further breakthroughs in our comprehension of neurodegenerative disease mechanisms and potential therapeutic interventions.
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Affiliation(s)
- Yulong Bai
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Shengnan Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Hui Dong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Xin Zhang
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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50
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D’Ercole C, de Marco A. Native Agarose Gels and Contact Blotting as Means to Optimize the Protocols for the Formation of Antigen-Ligand Complexes. Bioengineering (Basel) 2023; 10:1111. [PMID: 37892841 PMCID: PMC10604731 DOI: 10.3390/bioengineering10101111] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Protein complexes provide valuable biological information, but can be difficult to handle. Therefore, technical advancements designed to improve their manipulation are always useful. METHODS We investigated the opportunity to exploit native agarose gels and the contact blot method for the transfer of native proteins to membranes as means for optimizing the conditions for obtaining stable complexes. As a simple model of protein-protein interactions, an antigen-ligand complex was used in which both proteins were fused to reporters. RESULTS At each step, it was possible to visualize both the antigen, fused to a fluorescent protein, and the ligand, fused to a monomeric ascorbate peroxidase (APEX) and, as such, a way to tune the protocol. The conditions for the complex formation were adapted by modifying the buffer conditions, the concentration of the proteins and of the cross-linkers. CONCLUSIONS The procedure is rapid, inexpensive, and the several detection opportunities allow for both the monitoring of complex stability and the preservation of the functionality of its components, which is critical for understanding their biomedical implications and supporting drug discovery. The overall protocol represents a handy alternative to gel filtration, uses very standard and ubiquitous equipment, and can be implemented rapidly and without specific training.
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Affiliation(s)
| | - Ario de Marco
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Vipavska Cesta 13, P.O. Box 301, SI-5000 Nova Gorica, Slovenia;
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