1
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Favell JW, Bui DT, Li J, Han L, Kitova EN, Schmidt EN, Brassard R, Kitov PI, St-Pierre Y, Mahal LK, Lemieux MJ, Macauley MS, Klassen JS. Elusive Protein-Glycosphingolipid Interactions Revealed by Membrane Anchor-Assisted Native Mass Spectrometry. J Am Chem Soc 2024; 146:21700-21709. [PMID: 39052014 DOI: 10.1021/jacs.4c05805] [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: 07/27/2024]
Abstract
Interactions between glycan-binding proteins (GBPs) and glycosphingolipids (GSLs) present in cell membranes are implicated in a wide range of biological processes. However, studying GSL binding is hindered by the paucity of purified GSLs and the weak affinities typical of monovalent GBP-GSL interactions. Native mass spectrometry (nMS) performed using soluble model membranes is a promising approach for the discovery of GBP ligands, but the detection of weak interactions remains challenging. The present work introduces MEmbrane ANchor-assisted nMS (MEAN-nMS) for the detection of low-affinity GBP-GSL complexes. The assay utilizes a membrane anchor, produced by covalent cross-linking of the GBP and a lipid in the membrane, to localize the GBP on the surface and promote GSL binding. Ligands are identified by nMS detection of intact GBP-GSL complexes (MEAN-nMS) or using a catch-and-release (CaR) strategy, wherein GSLs are released from GBP-GSL complexes upon collisional activation and detected (MEAN-CaR-nMS). To establish reliability, a library of purified gangliosides incorporated into nanodiscs was screened against human immune lectins, and the results compared with affinities of the corresponding ganglioside oligosaccharides. Without a membrane anchor, nMS analysis yielded predominantly false negatives. In contrast, all ligands were identified by MEAN-(CaR)-nMS, with no false positives. To highlight the potential of MEAN-CaR-nMS for ligand discovery, a natural library of GSLs was incorporated into nanodiscs and screened against human and viral proteins to uncover elusive ligands. Finally, nMS-based detection of GSL ligands directly from cells is demonstrated. This breakthrough paves the way for shotgun glycomics screening using intact cells.
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Affiliation(s)
- James W Favell
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Duong T Bui
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Jianing Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Ling Han
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Elena N Kitova
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Edward N Schmidt
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Raelynn Brassard
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Pavel I Kitov
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Yves St-Pierre
- INRS-Institut Armand-Frappier, Laval, Québec H7V 1B7, Canada
| | - Lara K Mahal
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Matthew S Macauley
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - John S Klassen
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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2
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Jayasekera HS, Mohona FA, Ewbank M, Marty MT. Simultaneous Native Mass Spectrometry Analysis of Single and Double Mutants To Probe Lipid Binding to Membrane Proteins. Anal Chem 2024; 96:10426-10433. [PMID: 38859611 PMCID: PMC11215972 DOI: 10.1021/acs.analchem.4c01704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Lipids are critical modulators of membrane protein structure and function. However, it is challenging to investigate the thermodynamics of protein-lipid interactions because lipids can simultaneously bind membrane proteins at different sites with different specificities. Here, we developed a native mass spectrometry (MS) approach using single and double mutants to measure the relative energetic contributions of specific residues on Aquaporin Z (AqpZ) toward cardiolipin (CL) binding. We first mutated potential lipid-binding residues on AqpZ, and mixed mutant and wild-type proteins together with CL. By using native MS to simultaneously resolve lipid binding to the mutant and wild-type proteins in a single spectrum, we directly determined the relative affinities of CL binding, thereby revealing the relative Gibbs free energy change for lipid binding caused by the mutation. Comparing different mutants revealed that W14 contributes to the tightest CL binding site, with R224 contributing to a lower affinity site. Using double mutant cycling, we investigated the synergy between W14 and R224 sites on CL binding. Overall, this novel native MS approach provides unique insights into the binding of lipids to specific sites on membrane proteins.
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Affiliation(s)
- Hiruni S. Jayasekera
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721
| | - Farhana Afrin Mohona
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721
| | - Megan Ewbank
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721
| | - Michael T. Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721
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3
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Suzuki N, Konuma T, Ikegami T, Akashi S. Biophysical insights into the dimer formation of human Sirtuin 2. Protein Sci 2024; 33:e4994. [PMID: 38647411 PMCID: PMC11034489 DOI: 10.1002/pro.4994] [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: 12/27/2023] [Revised: 03/16/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
Sirtuin 2 (SIRT2) is a class III histone deacetylase that is highly conserved from bacteria to mammals. We prepared and characterized the wild-type (WT) and mutant forms of the histone deacetylase (HDAC) domain of human SIRT2 (hSIRT2) using various biophysical methods and evaluated their deacetylation activity. We found that WT hSIRT2 HDAC (residues 52-357) forms a homodimer in a concentration-dependent manner with a dimer-monomer dissociation constant of 8.3 ± 0.5 μM, which was determined by mass spectrometry. The dimer was disrupted into two monomers by binding to the HDAC inhibitors SirReal1 and SirReal2. We also confirmed dimer formation of hSIRT2 HDAC in living cells using a NanoLuc complementation reporter system. Examination of the relationship between dimer formation and deacetylation activity using several mutants of hSIRT2 HDAC revealed that some non-dimerizing mutants exhibited deacetylation activity for the N-terminal peptide of histone H3, similar to the wild type. The hSIRT2 HDAC mutant Δ292-306, which lacks a SIRT2-specific disordered loop region, was identified to exist as a monomer with slightly reduced deacetylation activity; the X-ray structure of the mutant Δ292-306 was almost identical to that of the WT hSIRT2 HDAC bound to an inhibitor. These results indicate that hSIRT2 HDAC forms a dimer, but this is independent of deacetylation activity. Herein, we discuss insights into the dimer formation of hSIRT2 based on our biophysical experimental results.
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Affiliation(s)
- Noa Suzuki
- Graduate School of Medical Life Science, Yokohama City UniversityYokohamaKanagawaJapan
| | - Tsuyoshi Konuma
- Graduate School of Medical Life Science, Yokohama City UniversityYokohamaKanagawaJapan
| | - Takahisa Ikegami
- Graduate School of Medical Life Science, Yokohama City UniversityYokohamaKanagawaJapan
| | - Satoko Akashi
- Graduate School of Medical Life Science, Yokohama City UniversityYokohamaKanagawaJapan
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4
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Photenhauer AL, Villafuerte-Vega RC, Cerqueira FM, Armbruster KM, Mareček F, Chen T, Wawrzak Z, Hopkins JB, Vander Kooi CW, Janeček Š, Ruotolo BT, Koropatkin NM. The Ruminococcus bromii amylosome protein Sas6 binds single and double helical α-glucan structures in starch. Nat Struct Mol Biol 2024; 31:255-265. [PMID: 38177679 PMCID: PMC11081458 DOI: 10.1038/s41594-023-01166-6] [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: 11/20/2022] [Accepted: 10/27/2023] [Indexed: 01/06/2024]
Abstract
Resistant starch is a prebiotic accessed by gut bacteria with specialized amylases and starch-binding proteins. The human gut symbiont Ruminococcus bromii expresses Sas6 (Starch Adherence System member 6), which consists of two starch-specific carbohydrate-binding modules from family 26 (RbCBM26) and family 74 (RbCBM74). Here, we present the crystal structures of Sas6 and of RbCBM74 bound with a double helical dimer of maltodecaose. The RbCBM74 starch-binding groove complements the double helical α-glucan geometry of amylopectin, suggesting that this module selects this feature in starch granules. Isothermal titration calorimetry and native mass spectrometry demonstrate that RbCBM74 recognizes longer single and double helical α-glucans, while RbCBM26 binds short maltooligosaccharides. Bioinformatic analysis supports the conservation of the amylopectin-targeting platform in CBM74s from resistant-starch degrading bacteria. Our results suggest that RbCBM74 and RbCBM26 within Sas6 recognize discrete aspects of the starch granule, providing molecular insight into how this structure is accommodated by gut bacteria.
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Affiliation(s)
- Amanda L Photenhauer
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Filipe M Cerqueira
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Krista M Armbruster
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Filip Mareček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Tiantian Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Zdzislaw Wawrzak
- Northwestern Synchrotron Research Center-LS-CAT, Northwestern University, Argonne, IL, USA
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological, Chemical, and Physical Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - Craig W Vander Kooi
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Nicole M Koropatkin
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
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5
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Jayasekera HS, Mohona FA, Ewbank M, Marty MT. SIMULTANEOUS NATIVE MASS SPECTROMETRY ANALYSIS OF SINGLE AND DOUBLE MUTANTS TO PROBE LIPID BINDING TO MEMBRANE PROTEINS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558516. [PMID: 37781586 PMCID: PMC10541089 DOI: 10.1101/2023.09.19.558516] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Lipids are critical modulators of membrane protein structure and function. However, it is challenging to investigate the thermodynamics of protein-lipid interactions because lipids can simultaneously bind membrane proteins at different sites with different specificities. Here, we developed a native mass spectrometry (MS) approach using single and double mutants to measure the relative energetic contributions of specific residues on Aquaporin Z (AqpZ) toward cardiolipin (CL) binding. We first mutated potential lipid-binding residues on AqpZ, and mixed mutant and wild-type proteins together with CL. By using native MS to simultaneously resolve lipid binding to the mutant and wild-type proteins in a single spectrum, we directly determined the relative affinities of CL binding, thereby revealing the relative Gibbs free energy change for lipid binding caused by the mutation. Comparing different mutants revealed that the W14 contributes to the tightest CL binding site, with R224 contributing to a lower affinity site. Using double mutant cycling, we investigated the synergy between W14 and R224 sites on CL binding. Overall, this novel native MS approach provides unique insights into lipid binding to specific sites on membrane proteins.
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Affiliation(s)
- Hiruni S. Jayasekera
- [a] Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721
| | - Farhana Afrin Mohona
- [a] Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721
| | - Megan Ewbank
- [a] Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721
| | - Michael T. Marty
- [a] Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721
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6
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Kundlacz T, Schmidt C. Deciphering Solution and Gas-Phase Interactions between Peptides and Lipids by Native Mass Spectrometry. Anal Chem 2023; 95:17292-17299. [PMID: 37956985 PMCID: PMC10688224 DOI: 10.1021/acs.analchem.3c03428] [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: 08/01/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 11/21/2023]
Abstract
Many biological processes depend on the interactions between proteins and lipids. Accordingly, the analysis of protein-lipid complexes has become increasingly important. Native mass spectrometry is often used to identify and characterize specific protein-lipid interactions. However, it requires the transfer of the analytes into the gas phase, where electrostatic interactions are enhanced and hydrophobic interactions do not exist. Accordingly, the question remains whether interactions that are observed in the gas phase accurately reflect interactions that are formed in solution. Here, we systematically explore noncovalent interactions between the antimicrobial peptide LL-37 and glycerophospholipids containing different headgroups or varying in fatty acyl chain length. We observe differences in peak intensities for different peptide-lipid complexes, as well as their relative binding strength in the gas phase. Accordingly, we found that ion intensities and gas-phase stability correlate well for complexes formed by electrostatic interactions. Probing hydrophobic interactions by varying the length of fatty acyl chains, we detected differences in ion intensities based on hydrophobic interactions formed in solution. The relative binding strength of these peptide-lipid complexes revealed only minor differences originating from van der Waals interactions and different binding modes of lipid headgroups in solution. In summary, our results demonstrate that hydrophobic interactions are reflected by ion intensities, while electrostatic interactions, including van der Waals interactions, determine the gas-phase stability of complexes.
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Affiliation(s)
- Til Kundlacz
- Interdisciplinary
Research Centre HALOmem, Institute of Biochemistry and Biotechnology,
Charles Tanford Protein Centre, Martin Luther
University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle, Germany
- Institute
of Chemistry, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 4, 06120 Halle, Germany
| | - Carla Schmidt
- Interdisciplinary
Research Centre HALOmem, Institute of Biochemistry and Biotechnology,
Charles Tanford Protein Centre, Martin Luther
University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle, Germany
- Department
of Chemistry—Biochemistry, Johannes
Gutenberg University Mainz, Biocenter II, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany
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7
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Edwards AN, Blue AJ, Conforti JM, Cordes MS, Trakselis MA, Gallagher ES. Gas-phase stability and thermodynamics of ligand-bound, binary complexes of chloramphenicol acetyltransferase reveal negative cooperativity. Anal Bioanal Chem 2023; 415:6201-6212. [PMID: 37542535 DOI: 10.1007/s00216-023-04891-5] [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: 05/12/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/07/2023]
Abstract
The biological role of the bacterial chloramphenicol (Chl)-resistance enzyme, chloramphenicol acetyltransferase (CAT), has seen renewed interest due to the resurgent use of Chl against multi-drug-resistant microbes. This looming threat calls for more rationally designed antibiotic derivatives that have improved antimicrobial properties and reduced toxicity in humans. Herein, we utilize native ion mobility spectrometry-mass spectrometry (IMS-MS) to investigate the gas-phase structure and thermodynamic stability of the type I variant of CAT from Escherichia coli (EcCATI) and several EcCATI:ligand-bound complexes. EcCATI readily binds multiple Chl without incurring significant changes to its gas-phase structure or stability. A non-hydrolyzable acetyl-CoA derivative (S-ethyl-CoA, S-Et-CoA) was used to kinetically trap EcCATI and Chl in a ternary, ligand-bound state (EcCATI:S-Et-CoA:Chl). Using collision-induced unfolding (CIU)-IMS-MS, we find that Chl dissociates from EcCATI:S-Et-CoA:Chl complexes at low collision energies, while S-Et-CoA remains bound to EcCATI even as protein unfolding occurs. Gas-phase binding constants further suggest that EcCATI binds S-Et-CoA more tightly than Chl. Both ligands exhibit negative cooperativity of subsequent ligand binding in their respective binary complexes. While we observe no significant change in structure or stability to EcCATI when bound to either or both ligands, we have elucidated novel gas-phase unfolding and dissociation behavior and provided a foundation for further characterization of alternative substrates and/or inhibitors of EcCATI.
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Affiliation(s)
- Alexis N Edwards
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Anthony J Blue
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Jessica M Conforti
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Michael S Cordes
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Elyssia S Gallagher
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA.
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8
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Heel SV, Bartosik K, Juen F, Kreutz C, Micura R, Breuker K. Native Top-Down Mass Spectrometry Uncovers Two Distinct Binding Motifs of a Functional Neomycin-Sensing Riboswitch Aptamer. J Am Chem Soc 2023. [PMID: 37420313 PMCID: PMC10360057 DOI: 10.1021/jacs.3c02774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
Understanding how ligands bind to ribonucleic acids (RNA) is important for understanding RNA recognition in biological processes and drug development. Here, we have studied neomycin B binding to neomycin-sensing riboswitch aptamer constructs by native top-down mass spectrometry (MS) using electrospray ionization (ESI) and collisionally activated dissociation (CAD). Our MS data for a 27 nt aptamer construct reveal the binding site and ligand interactions, in excellent agreement with the structure derived from nuclear magnetic resonance (NMR) studies. Strikingly, for an extended 40 nt aptamer construct, which represents the sequence with the highest regulatory factor for riboswitch function, we identified two binding motifs for neomycin B binding, one corresponding to the bulge-loop motif of the 27 nt construct and the other one in the minor groove of the lower stem, which according to the MS data are equally populated. By replacing a noncanonical with a canonical base pair in the lower stem of the 40 nt aptamer, we can reduce binding to the minor groove motif from ∼50 to ∼30%. Conversely, the introduction of a CUG/CUG motif in the lower stem shifts the binding equilibrium in favor of minor groove binding. The MS data reveal site-specific and stoichiometry-resolved information on aminoglycoside binding to RNA that is not directly accessible by other methods and underscore the role of noncanonical base pairs in RNA recognition by aminoglycosides.
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Affiliation(s)
- Sarah Viola Heel
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Karolina Bartosik
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Fabian Juen
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
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9
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Liu S, Abboud M, Mikhailov V, Liu X, Reinbold R, Schofield CJ. Differentiating Inhibition Selectivity and Binding Affinity of Isocitrate Dehydrogenase 1 Variant Inhibitors. J Med Chem 2023; 66:5279-5288. [PMID: 36952395 PMCID: PMC10108345 DOI: 10.1021/acs.jmedchem.3c00203] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Indexed: 03/25/2023]
Abstract
Isocitrate dehydrogenase (IDH) 1/2 gain-of-function variants catalyze the production of the oncometabolite 2-hydroxyglutarate and are validated targets for leukemia treatment. We report binding and inhibition studies on 13 IDH1/2 variant inhibitors, including clinical candidates and drugs, with wild-type (wt) IDH1 and its cancer-associated variant, IDH1 R132H. Interestingly, all the variant inhibitors bind wt IDH1 despite not, or only weakly, inhibiting it. Selective inhibition of the IDH1 R132H variant over wt IDH1 does not principally relate to the affinities of the inhibitors for the resting forms of the enzymes. Rather, the independent binding of Mg2+ and 2-oxoglutarate to the IDH1 variant makes the variant more susceptible to allosteric inhibition, compared to the tighter binding of the isocitrate-Mg2+ complex substrate to wt IDH1. The results highlight that binding affinity need not correlate with inhibition selectivity and have implications for interpretation of inhibitor screening results with IDH and related enzymes using turnover versus binding assays.
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Affiliation(s)
| | | | - Victor Mikhailov
- Chemistry Research Laboratory, Department
of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Xiao Liu
- Chemistry Research Laboratory, Department
of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Raphael Reinbold
- Chemistry Research Laboratory, Department
of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department
of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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10
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Fiorentino F, Rotili D, Mai A. Native mass spectrometry-directed drug discovery: Recent advances in investigating protein function and modulation. Drug Discov Today 2023; 28:103548. [PMID: 36871843 DOI: 10.1016/j.drudis.2023.103548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/15/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
Native mass spectrometry (nMS) is a biophysical method for studying protein complexes and can provide insights into subunit stoichiometry and composition, protein-ligand, and protein-protein interactions (PPIs). These analyses are made possible by preserving non-covalent interactions in the gas phase, thereby allowing the analysis of proteins in their native state. Consequently, nMS has been increasingly applied in early drug discovery campaigns for the characterization of protein-drug interactions and the evaluation of PPI modulators. Here, we discuss recent developments in nMS-directed drug discovery and provide a timely perspective on the possible applications of this technology in drug discovery.
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Affiliation(s)
- Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
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11
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Gheorghita AA, Li YE, Kitova EN, Bui DT, Pfoh R, Low KE, Whitfield GB, Walvoort MTC, Zhang Q, Codée JDC, Klassen JS, Howell PL. Structure of the AlgKX modification and secretion complex required for alginate production and biofilm attachment in Pseudomonas aeruginosa. Nat Commun 2022; 13:7631. [PMID: 36494359 PMCID: PMC9734138 DOI: 10.1038/s41467-022-35131-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
Synthase-dependent secretion systems are a conserved mechanism for producing exopolysaccharides in Gram-negative bacteria. Although widely studied, it is not well understood how these systems are organized to coordinate polymer biosynthesis, modification, and export across both membranes and the peptidoglycan. To investigate how synthase-dependent secretion systems produce polymer at a molecular level, we determined the crystal structure of the AlgK-AlgX (AlgKX) complex involved in Pseudomonas aeruginosa alginate exopolysaccharide acetylation and export. We demonstrate that AlgKX directly binds alginate oligosaccharides and that formation of the complex is vital for polymer production and biofilm attachment. Finally, we propose a structural model for the AlgEKX outer membrane modification and secretion complex. Together, our study provides insight into how alginate biosynthesis proteins coordinate production of a key exopolysaccharide involved in establishing persistent Pseudomonas lung infections.
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Affiliation(s)
- Andreea A. Gheorghita
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Biochemistry, University of Toronto, Toronto, ON Canada
| | - Yancheng E. Li
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Biochemistry, University of Toronto, Toronto, ON Canada ,grid.20861.3d0000000107068890Present Address: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA USA
| | - Elena N. Kitova
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, Edmonton, AB Canada
| | - Duong T. Bui
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, Edmonton, AB Canada
| | - Roland Pfoh
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada
| | - Kristin E. Low
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada ,grid.55614.330000 0001 1302 4958Present Address: Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB Canada
| | - Gregory B. Whitfield
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Biochemistry, University of Toronto, Toronto, ON Canada ,grid.14848.310000 0001 2292 3357Present Address: Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC Canada
| | - Marthe T. C. Walvoort
- grid.5132.50000 0001 2312 1970Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands ,grid.4830.f0000 0004 0407 1981Present Address: Department of Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Groningen, The Netherlands
| | - Qingju Zhang
- grid.5132.50000 0001 2312 1970Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands ,grid.411862.80000 0000 8732 9757Present Address: National Research Centre for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang, China
| | - Jeroen D. C. Codée
- grid.5132.50000 0001 2312 1970Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - John S. Klassen
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, Edmonton, AB Canada
| | - P. Lynne Howell
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Biochemistry, University of Toronto, Toronto, ON Canada
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12
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Bui D, Li Z, Kitov PI, Han L, Kitova EN, Fortier M, Fuselier C, Granger Joly de Boissel P, Chatenet D, Doucet N, Tompkins SM, St-Pierre Y, Mahal LK, Klassen JS. Quantifying Biomolecular Interactions Using Slow Mixing Mode (SLOMO) Nanoflow ESI-MS. ACS CENTRAL SCIENCE 2022; 8:963-974. [PMID: 35912341 PMCID: PMC9335916 DOI: 10.1021/acscentsci.2c00215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) is a powerful label-free assay for detecting noncovalent biomolecular complexes in vitro and is increasingly used to quantify binding thermochemistry. A common assumption made in ESI-MS affinity measurements is that the relative ion signals of free and bound species quantitatively reflect their relative concentrations in solution. However, this is valid only when the interacting species and their complexes have similar ESI-MS response factors (RFs). For many biomolecular complexes, such as protein-protein interactions, this condition is not satisfied. Existing strategies to correct for nonuniform RFs are generally incompatible with static nanoflow ESI (nanoESI) sources, which are typically used for biomolecular interaction studies, thereby significantly limiting the utility of ESI-MS. Here, we introduce slow mixing mode (SLOMO) nanoESI-MS, a direct technique that allows both the RF and affinity (K d) for a biomolecular interaction to be determined from a single measurement using static nanoESI. The approach relies on the continuous monitoring of interacting species and their complexes under nonhomogeneous solution conditions. Changes in ion signals of free and bound species as the system approaches or moves away from a steady-state condition allow the relative RFs of the free and bound species to be determined. Combining the relative RF and the relative abundances measured under equilibrium conditions enables the K d to be calculated. The reliability of SLOMO and its ease of use is demonstrated through affinity measurements performed on peptide-antibiotic, protease-protein inhibitor, and protein oligomerization systems. Finally, affinities measured for the binding of human and bacterial lectins to a nanobody, a viral glycoprotein, and glycolipids displayed within a model membrane highlight the tremendous power and versatility of SLOMO for accurately quantifying a wide range of biomolecular interactions important to human health and disease.
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Affiliation(s)
- Duong
T. Bui
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Zhixiong Li
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Pavel I. Kitov
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Ling Han
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Elena N. Kitova
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Marlène Fortier
- Centre
Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université
du Québec, Laval, Québec H7V 1B7, Canada
| | - Camille Fuselier
- Centre
Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université
du Québec, Laval, Québec H7V 1B7, Canada
| | - Philippine Granger Joly de Boissel
- Centre
Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université
du Québec, Laval, Québec H7V 1B7, Canada
| | - David Chatenet
- Centre
Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université
du Québec, Laval, Québec H7V 1B7, Canada
| | - Nicolas Doucet
- Centre
Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université
du Québec, Laval, Québec H7V 1B7, Canada
| | - Stephen M. Tompkins
- Center
for Vaccines and Immunology, University
of Georgia, Athens, Georgia 30605, United States
- Emory-UGA
Centers of Excellence for Influenza Research and Surveillance (CEIRS), Emory University School of Medicine, Athens, Georgia 30322, United States
| | - Yves St-Pierre
- Centre
Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université
du Québec, Laval, Québec H7V 1B7, Canada
| | - Lara K. Mahal
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - John S. Klassen
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
- . Telephone: (780) 492-3501. Fax: (780) 492-8231
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13
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Abstract
Native mass spectrometry (MS) involves the analysis and characterization of macromolecules, predominantly intact proteins and protein complexes, whereby as much as possible the native structural features of the analytes are retained. As such, native MS enables the study of secondary, tertiary, and even quaternary structure of proteins and other biomolecules. Native MS represents a relatively recent addition to the analytical toolbox of mass spectrometry and has over the past decade experienced immense growth, especially in enhancing sensitivity and resolving power but also in ease of use. With the advent of dedicated mass analyzers, sample preparation and separation approaches, targeted fragmentation techniques, and software solutions, the number of practitioners and novel applications has risen in both academia and industry. This review focuses on recent developments, particularly in high-resolution native MS, describing applications in the structural analysis of protein assemblies, proteoform profiling of─among others─biopharmaceuticals and plasma proteins, and quantitative and qualitative analysis of protein-ligand interactions, with the latter covering lipid, drug, and carbohydrate molecules, to name a few.
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Affiliation(s)
- Sem Tamara
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Maurits A. den Boer
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
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14
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Peters T, Creutznacher R, Maass T, Mallagaray A, Ogrissek P, Taube S, Thiede L, Uetrecht C. Norovirus-glycan interactions - how strong are they really? Biochem Soc Trans 2022; 50:347-359. [PMID: 34940787 PMCID: PMC9022987 DOI: 10.1042/bst20210526] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 12/25/2022]
Abstract
Infection with human noroviruses requires attachment to histo blood group antigens (HBGAs) via the major capsid protein VP1 as a primary step. Several crystal structures of VP1 protruding domain dimers, so called P-dimers, complexed with different HBGAs have been solved to atomic resolution. Corresponding binding affinities have been determined for HBGAs and other glycans exploiting different biophysical techniques, with mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy being most widely used. However, reported binding affinities are inconsistent. At the extreme, for the same system MS detects binding whereas NMR spectroscopy does not, suggesting a fundamental source of error. In this short essay, we will explain the reason for the observed differences and compile reliable and reproducible binding affinities. We will then highlight how a combination of MS techniques and NMR experiments affords unique insights into the process of HBGA binding by norovirus capsid proteins.
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Affiliation(s)
- Thomas Peters
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany
| | - Robert Creutznacher
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany
| | - Thorben Maass
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany
| | - Alvaro Mallagaray
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany
| | - Patrick Ogrissek
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany
| | - Stefan Taube
- Institute of Virology and Cell Biology, University of Lübeck, 23562 Lübeck, Germany
| | - Lars Thiede
- Centre for Structural Systems Biology (CSSB), 22607 Hamburg & Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany
| | - Charlotte Uetrecht
- Centre for Structural Systems Biology (CSSB), 22607 Hamburg & Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany
- School of Life Sciences, University of Siegen, 57076 Siegen & Deutsches Elektronensynchrotron (DESY), 22607 Hamburg & European XFEL GmbH, 22869 Schenefeld, Germany
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15
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Li Z, Kitov PI, Kitova EN, Bui DT, Moremen KW, Wakarchuk WW, Mahal LK, Macauley MS, Klassen JS. Quantifying Carbohydrate-Active Enzyme Activity with Glycoprotein Substrates Using Electrospray Ionization Mass Spectrometry and Center-of-Mass Monitoring. Anal Chem 2021; 93:15262-15270. [PMID: 34752696 DOI: 10.1021/acs.analchem.1c02089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Carbohydrate-active enzymes (CAZymes) play critical roles in diverse physiological and pathophysiological processes and are important for a wide range of biotechnology applications. Kinetic measurements offer insight into the activity and substrate specificity of CAZymes, information that is of fundamental interest and supports diverse applications. However, robust and versatile kinetic assays for monitoring the kinetics of intact glycoprotein and glycolipid substrates are lacking. Here, we introduce a simple but quantitative electrospray ionization mass spectrometry (ESI-MS) method for measuring the kinetics of CAZyme reactions involving glycoprotein substrates. The assay, referred to as center-of-mass (CoM) monitoring (CoMMon), relies on continuous (real-time) monitoring of the CoM of an ensemble of glycoprotein substrates and their corresponding CAZyme products. Notably, there is no requirement for calibration curves, internal standards, labeling, or mass spectrum deconvolution. To demonstrate the reliability of CoMMon, we applied the method to the neuraminidase-catalyzed cleavage of N-acetylneuraminic acid (Neu5Ac) residues from a series of glycoproteins of varying molecular weights and degrees of glycosylation. Reaction progress curves and initial rates determined with CoMMon are in good agreement (initial rates within ≤5%) with results obtained, simultaneously, using an isotopically labeled Neu5Ac internal standard, which enabled the time-dependent concentration of released Neu5Ac to be precisely measured. To illustrate the applicability of CoMMon to glycosyltransferase reactions, the assay was used to measure the kinetics of sialylation of a series of asialo-glycoproteins by a human sialyltransferase. Finally, we show how combining CoMMon and the competitive universal proxy receptor assay enables the relative reactivity of glycoprotein substrates to be quantitatively established.
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Affiliation(s)
- Zhixiong Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Pavel I Kitov
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Elena N Kitova
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Duong T Bui
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Warren W Wakarchuk
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Lara K Mahal
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Matthew S Macauley
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.,Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - John S Klassen
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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16
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Liu S, Abboud MI, John T, Mikhailov V, Hvinden I, Walsby-Tickle J, Liu X, Pettinati I, Cadoux-Hudson T, McCullagh JSO, Schofield CJ. Roles of metal ions in the selective inhibition of oncogenic variants of isocitrate dehydrogenase 1. Commun Biol 2021; 4:1243. [PMID: 34725432 PMCID: PMC8560763 DOI: 10.1038/s42003-021-02743-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 10/04/2021] [Indexed: 12/29/2022] Open
Abstract
Cancer linked isocitrate dehydrogenase (IDH) 1 variants, notably R132H IDH1, manifest a 'gain-of-function' to reduce 2-oxoglutarate to 2-hydroxyglutarate. High-throughput screens have enabled clinically useful R132H IDH1 inhibitors, mostly allosteric binders at the dimer interface. We report investigations on roles of divalent metal ions in IDH substrate and inhibitor binding that rationalise this observation. Mg2+/Mn2+ ions enhance substrate binding to wt IDH1 and R132H IDH1, but with the former manifesting lower Mg2+/Mn2+ KMs. The isocitrate-Mg2+ complex is the preferred wt IDH1 substrate; with R132H IDH1, separate and weaker binding of 2-oxoglutarate and Mg2+ is preferred. Binding of R132H IDH1 inhibitors at the dimer interface weakens binding of active site Mg2+ complexes; their potency is affected by the Mg2+ concentration. Inhibitor selectivity for R132H IDH1 over wt IDH1 substantially arises from different stabilities of wt and R132H IDH1 substrate-Mg2+ complexes. The results reveal the importance of substrate-metal ion complexes in wt and R132H IDH1 catalysis and the basis for selective R132H IDH1 inhibition. Further studies on roles of metal ion complexes in TCA cycle and related metabolism, including from an evolutionary perspective, are of interest.
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Affiliation(s)
- Shuang Liu
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Martine I Abboud
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Department of Natural Sciences, Lebanese American University, Byblos/Beirut, Lebanon
| | - Tobias John
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Victor Mikhailov
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Ingvild Hvinden
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - John Walsby-Tickle
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Xiao Liu
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Ilaria Pettinati
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Tom Cadoux-Hudson
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - James S O McCullagh
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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17
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Bennett JL, Nguyen GTH, Donald WA. Protein-Small Molecule Interactions in Native Mass Spectrometry. Chem Rev 2021; 122:7327-7385. [PMID: 34449207 DOI: 10.1021/acs.chemrev.1c00293] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Small molecule drug discovery has been propelled by the continual development of novel scientific methodologies to occasion therapeutic advances. Although established biophysical methods can be used to obtain information regarding the molecular mechanisms underlying drug action, these approaches are often inefficient, low throughput, and ineffective in the analysis of heterogeneous systems including dynamic oligomeric assemblies and proteins that have undergone extensive post-translational modification. Native mass spectrometry can be used to probe protein-small molecule interactions with unprecedented speed and sensitivity, providing unique insights into polydisperse biomolecular systems that are commonly encountered during the drug discovery process. In this review, we describe potential and proven applications of native MS in the study of interactions between small, drug-like molecules and proteins, including large multiprotein complexes and membrane proteins. Approaches to quantify the thermodynamic and kinetic properties of ligand binding are discussed, alongside a summary of gas-phase ion activation techniques that have been used to interrogate the structure of protein-small molecule complexes. We additionally highlight some of the key areas in modern drug design for which native mass spectrometry has elicited significant advances. Future developments and applications of native mass spectrometry in drug discovery workflows are identified, including potential pathways toward studying protein-small molecule interactions on a whole-proteome scale.
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Affiliation(s)
- Jack L Bennett
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Giang T H Nguyen
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
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18
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Báez Bolivar EG, Bui DT, Kitova EN, Han L, Zheng RB, Luber EJ, Sayed SY, Mahal LK, Klassen JS. Submicron Emitters Enable Reliable Quantification of Weak Protein-Glycan Interactions by ESI-MS. Anal Chem 2021; 93:4231-4239. [PMID: 33630563 DOI: 10.1021/acs.analchem.0c05003] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Interactions between carbohydrates (glycans) and glycan-binding proteins (GBPs) regulate a wide variety of important biological processes. However, the affinities of most monovalent glycan-GBP complexes are typically weak (dissociation constant (Kd) > μM) and difficult to reliably measure with conventional assays; consequently, the glycan specificities of most GBPs are not well established. Here, we demonstrate how electrospray ionization mass spectrometry (ESI-MS), implemented with nanoflow ESI emitters with inner diameters of ∼50 nm, allows for the facile quantification of low-affinity glycan-GBP interactions. The small size of the droplets produced from these submicron emitters effectively eliminates the formation of nonspecific glycan-GBP binding (false positives) during the ESI process up to ∼mM glycan concentrations. Thus, interactions with affinities as low as ∼5 mM can be measured directly from the mass spectrum. The general suppression of nonspecific adducts (including nonvolatile buffers and salts) achieved with these tips enables ESI-MS glycan affinity measurements to be performed on C-type lectins, a class of GBPs that bind glycans in a calcium-dependent manner and are important regulators of immune response. At physiologically relevant calcium ion concentrations (2-3 mM), the extent of Ca2+ nonspecific adduct formation observed using the submicron emitters is dramatically suppressed, allowing glycan affinities, and the influence of Ca2+ thereon, to be measured. Finally, we show how the use of submicron emitters and suppression of nonspecific binding enable the quantification of labile (prone to in-source dissociation) glycan-GBP interactions.
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Affiliation(s)
- Erick G Báez Bolivar
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Duong T Bui
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Elena N Kitova
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Ling Han
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Ruixiang B Zheng
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Erik J Luber
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Sayed Youssef Sayed
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Lara K Mahal
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - John S Klassen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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19
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Chen Y, Yuan S, Liu Y, Huang G. Rapid desalting during electrospray ionization mass spectrometry for investigating protein-ligand interactions in the presence of concentrated salts. Anal Chim Acta 2021; 1141:120-126. [PMID: 33248644 DOI: 10.1016/j.aca.2020.10.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/10/2020] [Accepted: 10/19/2020] [Indexed: 11/18/2022]
Abstract
Investigation of protein-ligand interactions in physiological conditions is crucial for better understanding of biochemistry because the binding stoichiometry and conformations of complexes in biological processes, such as various types of regulation and transportation, could reveal key pathways in organisms. Nanoelectrospray ionization mass spectrometry is widely used in studies of biological processes and systems biology. However, non-volatile salts in biological fluid may adversely interfere with nanoelectrospray ionization mass spectrometry. In this study, the previously developed method of induced nanoelectrospray ionization was used to facilitate in situ desalting of protein in solutions with high concentrations of non-volatile salts, and direct investigation of protein-ligand interactions for the first time. In situ desalting occurred at the tip of emitters within a short period lasting for a few to tens of milliseconds, enabling the maintenance of nativelike conditions compatible with mass spectrometry measurements. Induced nanoelectrospray ionization was driven by pulsed potential and exhibited microelectrophoresis effect in each spray cycle, which is not observed in conventional nanoelectrospray ionization because the continuous spray procedure is driven by direct current. Microelectrophoresis caused desalting through micron-sized spray emitters (1-20 μm), as confirmed experimentally with proteins in 100 mM NaCl solution. The method developed in this study has been further illustrated as a potential option for fast and direct identification of protein-ligand (small molecules or metal ions) interactions in complex samples. The results of this study demonstrate that the newly developed method may represent a reliable approach for investigations of proteins and protein complexes in biological samples.
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Affiliation(s)
- Yuting Chen
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, China
| | - Siming Yuan
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, China
| | - Yangzhong Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, China
| | - Guangming Huang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, China; National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, 230029, PR China.
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20
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Filandrová R, Vališ K, Černý J, Chmelík J, Slavata L, Fiala J, Rosůlek M, Kavan D, Man P, Chum T, Cebecauer M, Fabris D, Novák P. Motif orientation matters: Structural characterization of TEAD1 recognition of genomic DNA. Structure 2020; 29:345-356.e8. [PMID: 33333006 DOI: 10.1016/j.str.2020.11.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/09/2020] [Accepted: 11/24/2020] [Indexed: 11/29/2022]
Abstract
TEAD transcription factors regulate gene expression through interactions with DNA and other proteins. They are crucial for the development of eukaryotic organisms and to control the expression of genes involved mostly in cell proliferation and differentiation; however, their deregulation can lead to tumorigenesis. To study the interactions of TEAD1 with M-CAT motifs and their inverted versions, the KD of each complex was determined, and H/D exchange, quantitative chemical cross-linking, molecular docking, and smFRET were utilized for structural characterization. ChIP-qPCR was employed to correlate the results with a cell line model. The results obtained showed that although the inverted motif has 10× higher KD, the same residues were affected by the presence of M-CAT in both orientations. Molecular docking and smFRET revealed that TEAD1 binds the inverted motif rotated 180°. In addition, the inverted motif was proven to be occupied by TEAD1 in Jurkat cells, suggesting that the low-affinity binding sites present in the human genome may possess biological relevance.
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Affiliation(s)
- Růžena Filandrová
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Karel Vališ
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic
| | - Jiří Černý
- Institute of Biotechnology, Czech Academy of Sciences, Vestec 252 50, Czech Republic
| | - Josef Chmelík
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Lukáš Slavata
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Jan Fiala
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Michal Rosůlek
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Daniel Kavan
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Petr Man
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Tomáš Chum
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague 182 00, Czech Republic
| | - Marek Cebecauer
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague 182 00, Czech Republic
| | - Daniele Fabris
- University of Connecticut, Department of Chemistry, 55 N. Eagleville Road, Storrs, CT 06269, USA
| | - Petr Novák
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic.
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21
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Paraskevopoulou V, Schimpl M, Overman RC, Stolnik S, Chen Y, Nguyen L, Winkler GS, Gellert P, Klassen JS, Falcone FH. Structural and binding characterization of the LacdiNAc-specific adhesin (LabA; HopD) exodomain from Helicobacter pylori. Curr Res Struct Biol 2020; 3:19-29. [PMID: 34235483 PMCID: PMC8244420 DOI: 10.1016/j.crstbi.2020.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/31/2020] [Accepted: 12/10/2020] [Indexed: 01/02/2023] Open
Abstract
Helicobacter pylori (H. pylori) uses several outer membrane proteins for adhering to its host's gastric mucosa, an important step in establishing and preserving colonization. Several adhesins (SabA, BabA, HopQ) have been characterized in terms of their three-dimensional structure. A recent addition to the growing list of outer membrane porins is LabA (LacdiNAc-binding adhesin), which is thought to bind specifically to GalNAcβ1-4GlcNAc, occurring in the gastric mucosa. LabA47-496 protein expressed as His-tagged protein in the periplasm of E. coli and purified via subtractive IMAC after TEV cleavage and subsequent size exclusion chromatography, resulted in bipyramidal crystals with good diffraction properties. Here, we describe the 2.06 Å resolution structure of the exodomain of LabA from H. pylori strain J99 (PDB ID: 6GMM). Strikingly, despite the relatively low levels of sequence identity with the other three structurally characterized adhesins (20-49%), LabA shares an L-shaped fold with SabA and BabA. The 'head' region contains a 4 + 3 α-helix bundle, with a small insertion domain consisting of a short antiparallel beta sheet and an unstructured region, not resolved in the crystal structure. Sequence alignment of LabA from different strains shows a high level of conservation in the N- and C-termini, and identifies two main types based on the length of the insertion domain ('crown' region), the 'J99-type' (insertion ~31 amino acids), and the H. pylori '26695 type' (insertion ~46 amino acids). Analysis of ligand binding using Native Electrospray Ionization Mass Spectrometry (ESI-MS) together with solid phase-bound, ELISA-type assays could not confirm the originally described binding of GalNAcβ1-4GlcNAc-containing oligosaccharides, in line with other recent reports, which also failed to confirm LacdiNAc binding.
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Affiliation(s)
| | - Marianne Schimpl
- Structure, Biophysics and Fragment-based Lead Generation, Discovery Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Ross C. Overman
- Protein Science, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Snow Stolnik
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Yajie Chen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Canada
| | - Linh Nguyen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Canada
| | | | - Paul Gellert
- Innovation Strategy & External Liaison, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, United Kingdom
| | - John S. Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Canada
| | - Franco H. Falcone
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
- Institute for Parasitology, Justus-Liebig-University Gießen, Schubertstr. 81, D-35392, Gießen, Germany
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22
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Du Y, Zhao F, Xing J, Cui M, Liu Z. Investigation of interactions between cytochrome c and ginsenosides by native mass spectrometry and molecular docking simulations. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8853. [PMID: 32511843 DOI: 10.1002/rcm.8853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 05/22/2020] [Accepted: 06/03/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Ginsenosides are considered to be the main functional components in ginseng and possess various important pharmacological activities. The study of the interactions between ginsenosides and proteins is indispensable for understanding the pharmacological activities of ginsenosides. In this work, the interactions of ginsenosides with cytochrome c (cyt c) were investigated by native mass spectrometry and molecular docking simulations. METHODS The interactions of four ginsenosides (Rb1 , Rb3 , Rf, Rg1 ) and cyt c in NH4 OAc solution were investigated by electrospray ionization linear ion trap mass spectrometry (ESI-LTQ-MS). Molecular docking simulations of cyt c complexes were carried out by AutoDock. RESULTS The native mass spectrometry results showed that the four ginsenosides were directly bound to cyt c, with stoichiometric ratios of 1:1 and 2:1 in NH4 OAc. The order of relative binding abilities of ginsenosides to cyt c obtained by ESI-MS was Rb1 > Rb3 > Rf > Rg1 , which was consistent with the docking results. Moreover, molecular docking simulations also indicated potential binding sites of cyt c and ginsenosides. Hydrogen-bond interaction played a very important role in cyt c binding with ginsenosides. CONCLUSIONS It has been demonstrated that native MS is a useful tool to investigate the interactions of ginsenosides with cyt c. Molecular docking is a good complement to ESI analysis, and can provide information on potential binding sites of cyt c-ginsenoside complexess. This strategy will be helpful to further understand the interactions of proteins and small molecules.
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Affiliation(s)
- Yang Du
- National Center for Mass Spectrometry in Changchun, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- University of Science and Technology of China, Hefei, Anhui, 230029, China
| | - Fengjiao Zhao
- National Center for Mass Spectrometry in Changchun, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- University of Science and Technology of China, Hefei, Anhui, 230029, China
| | - Junpeng Xing
- National Center for Mass Spectrometry in Changchun, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Meng Cui
- National Center for Mass Spectrometry in Changchun, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- University of Science and Technology of China, Hefei, Anhui, 230029, China
| | - Zhiqiang Liu
- National Center for Mass Spectrometry in Changchun, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
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23
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Liu T, Marcinko TM, Vachet RW. Protein-Ligand Affinity Determinations Using Covalent Labeling-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1544-1553. [PMID: 32501685 PMCID: PMC7332385 DOI: 10.1021/jasms.0c00131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Determining the binding affinity is an important aspect of characterizing protein-ligand complexes. Here, we describe an approach based on covalent labeling (CL)-mass spectrometry (MS) that can accurately provide protein-ligand dissociation constants (Kd values) using diethylpyrocarbonate (DEPC) as the labeling reagent. Even though DEPC labeling reactions occur on a time scale that is similar to the dissociation/reassociation rates of many protein-ligand complexes, we demonstrate that relatively accurate binding constants can still be obtained as long as the extent of protein labeling is kept below 30%. Using two well-established model systems and one insufficiently characterized system, we find that Kd values can be determined that are close to values obtained in previous measurements. The CL-MS-based strategy that is described here should serve as an alternative for characterizing protein-ligand complexes that are challenging to measure by other methods. Moreover, this method has the potential to provide, simultaneously, the affinity and binding site information.
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Affiliation(s)
| | | | - Richard W. Vachet
- Corresponding author: Prof. Richard W. Vachet, Department of Chemistry, University of Massachusetts, Amherst, MA 01003, , Phone: (413) 545-2733
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24
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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25
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Structural and biochemical characterization of the exopolysaccharide deacetylase Agd3 required for Aspergillus fumigatus biofilm formation. Nat Commun 2020; 11:2450. [PMID: 32415073 PMCID: PMC7229062 DOI: 10.1038/s41467-020-16144-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/16/2020] [Indexed: 01/14/2023] Open
Abstract
The exopolysaccharide galactosaminogalactan (GAG) is an important virulence factor of the fungal pathogen Aspergillus fumigatus. Deletion of a gene encoding a putative deacetylase, Agd3, leads to defects in GAG deacetylation, biofilm formation, and virulence. Here, we show that Agd3 deacetylates GAG in a metal-dependent manner, and is the founding member of carbohydrate esterase family CE18. The active site is formed by four catalytic motifs that are essential for activity. The structure of Agd3 includes an elongated substrate-binding cleft formed by a carbohydrate binding module (CBM) that is the founding member of CBM family 87. Agd3 homologues are encoded in previously unidentified putative bacterial exopolysaccharide biosynthetic operons and in other fungal genomes.
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26
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Chen S, Gong X, Tan H, Liu Y, He L, Ouyang J. Study of the noncovalent interactions between phenolic acid and lysozyme by cold spray ionization mass spectrometry (CSI-MS), multi-spectroscopic and molecular docking approaches. Talanta 2020; 211:120762. [PMID: 32070628 DOI: 10.1016/j.talanta.2020.120762] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 01/16/2020] [Accepted: 01/17/2020] [Indexed: 12/29/2022]
Abstract
Elucidating the recognition mechanisms of the noncovalent interactions between pharmaceutical molecules and proteins is important for understanding drug delivery in vivo, and for the further rapid screening of clinical drug candidates and biomarkers. In this work, a strategy based on cold spray ionization mass spectrometry (CSI-MS), combined with fluorescence, circular dichroism (CD), Fourier transform infrared spectroscopy (FTIR), and molecular docking methods, was developed and applied to the study of the noncovalent interactions between phenolic acid and lysozyme (Lys). Based on the real characterization of noncovalent complex, the detailed binding parameters, as well as the protein conformational changes and specific binding sites could be obtained. CSI-MS and tandem mass spectrometry (MS/MS) technique were used to investigate the phenolic acid-Lys complexes and the structure-affinity relationship, and to assess their structural composition and gas phase stability. The binding affinity was obtained by direct and indirect MS methods. The fluorescence spectra showed that the intrinsic fluorescence quenching of Lys in solution was a static quenching mechanism caused by complex formation, which supported the MS results. The CD and FTIR spectra revealed that phenolic acid changed the secondary structure of Lys and increased the α-helix content, indicating an increase in the tryptophan (W) hydrophobicity near the protein binding site resulting in a conformational alteration of the protein. In addition, molecular docking studies were performed to investigate the binding sites and binding modes of phenolic acid on Lys. This strategy can more comprehensively and truly characterize the noncovalent interactions and can guide further research on the interactions of phenolic acid with other proteins.
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Affiliation(s)
- Su Chen
- National Institutes for Food and Drug Control, Beijing, 102629, China; College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Xin Gong
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Hongwei Tan
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Yang Liu
- National Institutes for Food and Drug Control, Beijing, 102629, China
| | - Lan He
- National Institutes for Food and Drug Control, Beijing, 102629, China.
| | - Jin Ouyang
- College of Chemistry, Beijing Normal University, Beijing, 100875, China.
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27
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Zhou Y, Chen S, Qiao J, Cui Y, Yuan C, He L, Ouyang J. Study of the noncovalent interactions of ginsenosides and amyloid-β-peptide by CSI-MS and molecular docking. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4463. [PMID: 31671229 DOI: 10.1002/jms.4463] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 10/07/2019] [Accepted: 10/22/2019] [Indexed: 06/10/2023]
Abstract
Noncovalent interactions between drugs and proteins play significant roles for drug metabolisms and drug discoveries. Mass spectrometry has been a commonly used method for studying noncovalent interactions. However, the harsh ionization process in electrospray ionization mass spectrometry (ESI-MS) is not conducive to the preservation of noncovalent and unstable biomolecular complexes compared with the cold spray ionization mass spectrometry (CSI-MS). A cold spray ionization providing a stable solvation-ionization at low temperature is milder than ESI, which was more suitable for studying noncovalent drug-protein complexes with exact stoichiometries. In this paper, we apply CSI-MS to explore the interactions of ginsenosides toward amyloid-β-peptide (Aβ) and clarify the therapeutic effect of ginsenosides on Alzheimer's disease (AD) at the molecular level for the first time. The interactions of ginsenosides with Aβ were performed by CSI-MS and ESI-MS, respectively. The ginsenosides Rg1 bounded to Aβ at the stoichiometries of 1:1 to 5:1 could be characterized by CSI-MS, while dehydration products are more readily available by ESI-MS. The binding force depends on the number of glycosyls and the type of ginsenosides. The relative binding affinities were sorted in order as follows: Rg1 ≈ Re > Rd ≈ Rg2 > Rh2, protopanaxatriol by competition experiments, which were supported by molecular docking experiment. CSI-MS is expected to be a more appropriate approach to determine the weak but specific interactions of proteins with other natural products especially polyhydroxy compounds.
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Affiliation(s)
- Yanan Zhou
- National Institutes for Food and Drug Control, Beijing, 102629, China
| | - Su Chen
- National Institutes for Food and Drug Control, Beijing, 102629, China
| | - Jinping Qiao
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Yanyun Cui
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
- School of Science, Beijing Technology and Business University, Beijing, 100048, China
| | - Chang Yuan
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Lan He
- National Institutes for Food and Drug Control, Beijing, 102629, China
| | - Jin Ouyang
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
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28
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Kleiner D, Shmulevich F, Zarivach R, Shahar A, Sharon M, Ben-Nissan G, Bershtein S. The interdimeric interface controls function and stability of Ureaplasma urealiticum methionine S-adenosyltransferase. J Mol Biol 2019; 431:4796-4816. [PMID: 31520601 DOI: 10.1016/j.jmb.2019.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/20/2019] [Accepted: 09/04/2019] [Indexed: 10/26/2022]
Abstract
Methionine S-adenosyltransferases (MATs) are predominantly homotetramers, comprised of dimers of dimers. The larger, highly conserved intradimeric interface harbors two active sites, making the dimer the obligatory functional unit. However, functionality of the smaller, more diverged, and recently evolved interdimeric interface is largely unknown. Here, we show that the interdimeric interface of Ureaplasmaurealiticum MAT has evolved to control the catalytic activity and structural integrity of the homotetramer in response to product accumulation. When all four active sites are occupied with the product, S-adenosylmethionine (SAM), binding of four additional SAM molecules to the interdimeric interface prompts a ∼45° shift in the dimer orientation and a concomitant ∼60% increase in the interface area. This rearrangement inhibits the enzymatic activity by locking the flexible active site loops in a closed state and renders the tetramer resistant to proteolytic degradation. Our findings suggest that the interdimeric interface of MATs is subject to rapid evolutionary changes that tailor the molecular properties of the entire homotetramer to the specific needs of the organism.
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Affiliation(s)
- Daniel Kleiner
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, Beer-Sheva, 84105, Israel
| | - Fannia Shmulevich
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, Beer-Sheva, 84105, Israel
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, Beer-Sheva, 84105, Israel; Macromolecular Crystallography Research Center (MCRC), The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Anat Shahar
- Macromolecular Crystallography Research Center (MCRC), The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shimon Bershtein
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, Beer-Sheva, 84105, Israel.
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29
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Fu H, Qian C, Tong W, Li H, Chen DD. Mass spectrometry and affinity capillary electrophoresis for characterization of host-guest interactions. J Chromatogr A 2019; 1589:182-190. [DOI: 10.1016/j.chroma.2019.01.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 01/02/2019] [Accepted: 01/08/2019] [Indexed: 12/14/2022]
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30
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Bakhtiari M, Konermann L. Protein Ions Generated by Native Electrospray Ionization: Comparison of Gas Phase, Solution, and Crystal Structures. J Phys Chem B 2019; 123:1784-1796. [DOI: 10.1021/acs.jpcb.8b12173] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Maryam Bakhtiari
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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31
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Liu XR, Zhang MM, Rempel DL, Gross ML. Protein-Ligand Interaction by Ligand Titration, Fast Photochemical Oxidation of Proteins and Mass Spectrometry: LITPOMS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:213-217. [PMID: 30484077 PMCID: PMC6438201 DOI: 10.1007/s13361-018-2076-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 09/19/2018] [Accepted: 09/23/2018] [Indexed: 05/03/2023]
Abstract
We report a novel method named LITPOMS (ligand titration, fast photochemical oxidation of proteins and mass spectrometry) to characterize protein-ligand binding stoichiometry, binding sites, and site-specific binding constants. The system used to test the method is melittin-calmodulin, in which the peptide melittin binds to calcium-bound calmodulin. Global-level measurements reveal the binding stoichiometry of 1:1 whereas peptide-level data coupled with fitting reveal the binding sites and the site-specific binding affinity. Moreover, we extended the analysis to the residue level and identified six critical binding residues. The results show that melittin binds to the N-terminal, central linker, and C-terminal regions of holo-calmodulin with an affinity of 4.6 nM, in agreement with results of previous studies. LITPOMS, for the first time, brings high residue-level resolution to affinity measurements, providing simultaneously qualitative and quantitative understanding of protein-ligand binding. The approach can be expanded to other binding systems without tagging the protein to give high spatial resolution. Graphical Abstract.
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Affiliation(s)
- Xiaoran Roger Liu
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Mengru Mira Zhang
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Don L Rempel
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA.
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32
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El-Hawiet A, Chen Y, Shams-Ud-Doha K, Kitova EN, Kitov PI, Bode L, Hage N, Falcone FH, Klassen JS. Screening natural libraries of human milk oligosaccharides against lectins using CaR-ESI-MS. Analyst 2018; 143:536-548. [PMID: 29239412 DOI: 10.1039/c7an01397c] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Human milk oligosaccharides (HMOs) afford many health benefits to breast-fed infants, such as protection against infection and regulation of the immune system, through the formation of non-covalent interactions with protein receptors. However, the molecular details of these interactions are poorly understood. Here, we describe the application of catch-and-release electrospray ionization mass spectrometry (CaR-ESI-MS) for screening natural libraries of HMOs against lectins. The HMOs in the libraries were first identified based on molecular weights (MWs), ion mobility separation arrival times (IMS-ATs) and collision-induced dissociation (CID) fingerprints of their deprotonated anions. The libraries were then screened against lectins and the ligands identified from the MWs, IMS-ATs and CID fingerprints of HMOs released from the lectin in the gas phase. To demonstrate the assay, four fractions, extracted from pooled human milk and containing ≥35 different HMOs, were screened against a C-terminal fragment of human galectin-3 (hGal-3C), for which the HMOs specificities have been previously investigated, and a fragment of the blood group antigen-binding adhesin (BabA) from Helicobacter pylori, for which the HMO specificities have not been previously established. The structures of twenty-one ligands, corresponding to both neutral and acidic HMOs, of hGal-3C were identified; all twenty-one were previously shown to be ligands for this lectin. The presence of HMO ligands at six other MWs was also ascertained. Application of the assay to BabA revealed nineteen specific HMO structures that are recognized by the protein and HMO ligands at two other MWs. Notably, it was found that BabA exhibits broad specificity for HMOs, and recognizes both neutral HMOs, including non-fucosylated ones, and acidic HMOs. The results of competitive binding experiments indicate that HMOs can interact with BabA at previously unknown binding sites. The affinities of eight purified HMOs for BabA were measured by ESI-MS and found to be in the 103 M-1 to 104 M-1 range.
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Affiliation(s)
- Amr El-Hawiet
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2.
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Patterson A, Tokmina-Lukaszewska M, Bothner B. Probing Cascade complex composition and stability using native mass spectrometry techniques. Methods Enzymol 2018; 616:87-116. [PMID: 30691656 DOI: 10.1016/bs.mie.2018.10.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Adaptive prokaryotic immune systems rely on clustered regularly interspaced short palindromic repeats and their associated genes to provide the components necessary to clear infection by foreign genetic elements. These immune systems are based on highly specific nucleases that bind DNA or RNA and, upon sequence recognition, degrade the bound nucleic acid. Because of their specificity, CRISPR-Cas systems are being co-opted to edit genes in eukaryotic cells. While the general function of these systems is well understood, an understanding of mechanistic details to facilitate engineering and application to this new arena remains a topic of intense study. Here, we present two methods that have been successfully used to study the structure and mechanism of the Type IE CRISPR system, Cascade, from Escherichia coli. We provide the protocol for a typical native mass spectrometry experiment which, because it allows for analysis of a protein complex without disruption of the noncovalent interactions within the complex, can be used to determine complex composition, architecture, and relative affinity between subunits. We, also, provide the protocol for intact protein hydrogen-deuterium exchange mass spectrometry, which provides insight into the overall conformational stability of the complex and changes in complex stability based on conditions such as substrate binding. Investigating the solution-phase structure, stability, and dynamics of these complexes improves the overall understanding of the mechanism facilitating engineered adjustments to function or utility.
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Affiliation(s)
- Angela Patterson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | | | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States.
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34
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Garabedian A, Bolufer A, Leng F, Fernandez-Lima F. Peptide Sequence Influence on the Conformational Dynamics and DNA binding of the Intrinsically Disordered AT-Hook 3 Peptide. Sci Rep 2018; 8:10783. [PMID: 30018295 PMCID: PMC6050235 DOI: 10.1038/s41598-018-28956-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/28/2018] [Indexed: 11/09/2022] Open
Abstract
The intrinsically disordered ATHP3 was studied at native conditions and in complex with DNA using single amino acid substitutions and high-resolution ion mobility spectrometry coupled to mass spectrometry (trapped IMS-MS). Results showed that ATHP3 can exist in multiple conformations at native conditions (at least 10 conformers were separated), with a variety of proline cis/trans orientations, side chain orientations and protonation sites. When in complex with AT rich DNA hairpins, the -RGRP- core is essential for stabilizing the ATHP3: DNA complex. In particular, the arginine in the sixth position plays an important role during binding to AT-rich regions of hairpin DNA, in good agreement with previous NMR and X-ray data. Mobility based correlation matrices are proposed as a way to reveal differences in structural motifs across the peptide mutants based on the conformational space and relative conformer abundance.
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Affiliation(s)
- Alyssa Garabedian
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, United States
| | - Alexander Bolufer
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, United States
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, United States.,Biomolecular Sciences Institute, Florida International University, Miami, Florida, 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, United States. .,Biomolecular Sciences Institute, Florida International University, Miami, Florida, 33199, United States.
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35
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How can native mass spectrometry contribute to characterization of biomacromolecular higher-order structure and interactions? Methods 2018; 144:3-13. [PMID: 29704661 DOI: 10.1016/j.ymeth.2018.04.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/03/2018] [Accepted: 04/21/2018] [Indexed: 01/16/2023] Open
Abstract
Native mass spectrometry (MS) is an emerging approach for characterizing biomacromolecular structure and interactions under physiologically relevant conditions. In native MS measurement, intact macromolecules or macromolecular complexes are directly ionized from a non-denaturing solvent, and key noncovalent interactions that hold the complexes together can be preserved for MS analysis in the gas phase. This technique provides unique multi-level structural information such as conformational changes, stoichiometry, topology and dynamics, complementing conventional biophysical techniques. Despite the maturation of native MS and greatly expanded range of applications in recent decades, further dissemination is needed to make the community aware of such a technique. In this review, we attempt to provide an overview of the current body of knowledge regarding major aspects of native MS and explain how such technique contributes to the characterization of biomacromolecular higher-order structure and interactions.
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36
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Haramija M, Peter-Katalinić J. Quantitative characterization of galectin-3-C affinity mass spectrometry measurements: Comprehensive data analysis, obstacles, shortcuts and robustness. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:1709-1719. [PMID: 28805274 DOI: 10.1002/rcm.7956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/14/2017] [Accepted: 08/06/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Affinity mass spectrometry (AMS) is an emerging tool in the field of the study of protein•carbohydrate complexes. However, experimental obstacles and data analysis are preventing faster integration of AMS methods into the glycoscience field. Here we show how analysis of direct electrospray ionization mass spectrometry (ESI-MS) AMS data can be simplified for screening purposes, even for complex AMS spectra. METHODS A direct ESI-MS assay was tested in this study and binding data for the galectin-3C•lactose complex were analyzed using a comprehensive and simplified data analysis approach. In the comprehensive data analysis approach, noise, all protein charge states, alkali ion adducts and signal overlap were taken into account. In a simplified approach, only the intensities of the fully protonated free protein and the protein•carbohydrate complex for the main protein charge state were taken into account. RESULTS In our study, for high intensity signals, noise was negligible, sodiated protein and sodiated complex signals cancelled each other out when calculating the Kd value, and signal overlap influenced the Kd value only to a minor extent. Influence of these parameters on low intensity signals was much higher. However, low intensity protein charge states should be avoided in quantitative AMS analyses due to poor ion statistics. CONCLUSIONS The results indicate that noise, alkali ion adducts, signal overlap, as well as low intensity protein charge states, can be neglected for preliminary experiments, as well as in screening assays. One comprehensive data analysis performed as a control should be sufficient to validate this hypothesis for other binding systems as well.
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Affiliation(s)
- Marko Haramija
- Institute of Medical Physics and Biophysics, University of Münster, Robert-Koch-Strasse 31, D-48149, Münster, Germany
| | - Jasna Peter-Katalinić
- Institute of Medical Physics and Biophysics, University of Münster, Robert-Koch-Strasse 31, D-48149, Münster, Germany
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Konermann L. Addressing a Common Misconception: Ammonium Acetate as Neutral pH "Buffer" for Native Electrospray Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1827-1835. [PMID: 28710594 DOI: 10.1007/s13361-017-1739-3] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 06/14/2017] [Accepted: 06/15/2017] [Indexed: 05/12/2023]
Abstract
Native ESI-MS involves the transfer of intact proteins and biomolecular complexes from solution into the gas phase. One potential pitfall is the occurrence of pH-induced changes that can affect the analyte while it is still surrounded by solvent. Most native ESI-MS studies employ neutral aqueous ammonium acetate solutions. It is a widely perpetuated misconception that ammonium acetate buffers the analyte solution at neutral pH. By definition, a buffer consists of a weak acid and its conjugate weak base. The buffering range covers the weak acid pKa ± 1 pH unit. NH4+ and CH3-COO- are not a conjugate acid/base pair, which means that they do not constitute a buffer at pH 7. Dissolution of ammonium acetate salt in water results in pH 7, but this pH is highly labile. Ammonium acetate does provide buffering around pH 4.75 (the pKa of acetic acid) and around pH 9.25 (the pKa of ammonium). This implies that neutral ammonium acetate solutions electrosprayed in positive ion mode will likely undergo acidification down to pH 4.75 ± 1 in the ESI plume. Ammonium acetate nonetheless remains a useful additive for native ESI-MS. It is a volatile electrolyte that can mimic the solvation properties experienced by proteins under physiological conditions. Also, a drop from pH 7 to around pH 4.75 is less dramatic than the acidification that would take place in pure water. It is hoped that the habit of referring to pH 7 solutions as ammonium acetate "buffer" will disappear from the literature. Ammonium acetate "solution" should be used instead. Graphical Abstract ᅟ.
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Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada.
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Niu S, Kim BC, Fierke CA, Ruotolo BT. Ion Mobility-Mass Spectrometry Reveals Evidence of Specific Complex Formation between Human Histone Deacetylase 8 and Poly-r(C)-binding Protein 1. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2017; 420:9-15. [PMID: 28983190 PMCID: PMC5624731 DOI: 10.1016/j.ijms.2016.12.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Histone deacetylase 8, part of a broad class of proteins responsible for regulating transcription and many other cellular processes and directly linked to a host of human disease through its mis-function, has been canonically described as a zinc-based mettalo-enzyme for many years. Recent evidence, however, has linked this protein to iron incorporation, loaded through transient interactions with the poly r(C)-binding protein 1, a metallo-chaperone and storage protein. In this report, we construct and deploy an electrospray-mass spectrometry based assay aimed at quantifying the interaction strength between these two weakly-associated proteins, as well as the zinc and iron associated form of the histone deacetylase. Despite challenges derived from artifact protein complexes derived from the electrospray process, we use carefully-constructed positive and negative control experiments, along with detailed measurements of protein ionization efficiency to validate our dissociation constant measurements for protein dimers in this size range. Furthermore, our data strongly support that complexes between histone deacetylase 8 and poly r(C)-binding protein 1 are specific, and that they are equally strong when both zinc and iron-loaded proteins are involved, or perhaps mildly promoted in the latter case, suggesting an in vivo role for the non-canonical, iron-incorporated histone deacetylase.
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Landreh M, Costeira-Paulo J, Gault J, Marklund EG, Robinson CV. Effects of Detergent Micelles on Lipid Binding to Proteins in Electrospray Ionization Mass Spectrometry. Anal Chem 2017. [PMID: 28627869 PMCID: PMC5559180 DOI: 10.1021/acs.analchem.7b00922] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
A wide
variety of biological processes rely upon interactions between
proteins and lipids, ranging from molecular transport to the organization
of the cell membrane. It was recently established that electrospray
ionization mass spectrometry (ESI-MS) is capable of capturing transient
interactions between membrane proteins and their lipid environment,
and a detailed understanding of the underlying processes is therefore
of high importance. Here, we apply ESI-MS to investigate the factors
that govern complex formation in solution and gas phases by comparing
nonselective lipid binding with soluble and membrane proteins. We
find that exogenously added lipids did not bind to soluble proteins,
suggesting that lipids have a low propensity to form electrospray
ionization adducts. The presence of detergents at increasing micelle
concentrations, on the other hand, resulted in moderate lipid binding
to soluble proteins. A direct ESI-MS comparison of lipid binding to
the soluble protein serum albumin and to the integral membrane protein
NapA shows that soluble proteins acquire fewer lipid adducts. Our
results suggest that protein–lipid complexes form via contacts
between proteins and mixed lipid/detergent micelles. For soluble proteins,
these complexes arise from nonspecific contacts between the protein
and detergent/lipid micelles in the electrospray droplet. For membrane
proteins, lipids are incorporated into the surrounding micelle in
solution, and complex formation occurs independently of the ESI process.
We conclude that the lipids in the resulting complexes interact predominantly
with sites located in the transmembrane segments, resulting in nativelike
complexes that can be interrogated by MS.
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Affiliation(s)
- Michael Landreh
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, Oxfordshire OX1 3QZ, United Kingdom
| | - Joana Costeira-Paulo
- Department of Chemistry, Uppsala Biomedical Centre, Uppsala University , Box 576, SE-751 23 Uppsala, Sweden
| | - Joseph Gault
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, Oxfordshire OX1 3QZ, United Kingdom
| | - Erik G Marklund
- Department of Chemistry, Uppsala Biomedical Centre, Uppsala University , Box 576, SE-751 23 Uppsala, Sweden
| | - Carol V Robinson
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, Oxfordshire OX1 3QZ, United Kingdom
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Eschweiler JD, Kerr R, Rabuck-Gibbons J, Ruotolo BT. Sizing Up Protein-Ligand Complexes: The Rise of Structural Mass Spectrometry Approaches in the Pharmaceutical Sciences. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:25-44. [PMID: 28301749 DOI: 10.1146/annurev-anchem-061516-045414] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Capturing the dynamic interplay between proteins and their myriad interaction partners is critically important for advancing our understanding of almost every biochemical process and human disease. The importance of this general area has spawned many measurement methods capable of assaying such protein complexes, and the mass spectrometry-based structural biology methods described in this review form an important part of that analytical arsenal. Here, we survey the basic principles of such measurements, cover recent applications of the technology that have focused on protein-small-molecule complexes, and discuss the bright future awaiting this group of technologies.
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Affiliation(s)
| | - Richard Kerr
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109;
| | | | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109;
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Soper-Hopper MT, Eschweiler JD, Ruotolo BT. Ion Mobility-Mass Spectrometry Reveals a Dipeptide That Acts as a Molecular Chaperone for Amyloid β. ACS Chem Biol 2017; 12:1113-1120. [PMID: 28240851 DOI: 10.1021/acschembio.7b00045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Previously, we discovered and structurally characterized a complex between amyloid β 1-40 and the neuropeptide leucine enkephalin. This work identified leucine enkephalin as a potentially useful starting point for the discovery of peptide-related biotherapeutics for Alzheimer's disease. In order to better understand such complexes that are formed in vitro, we describe here the analysis of a series of site-directed amino acid substitution variants of both peptides, covering the leucine enkephalin sequence in its entirety and a large number of selected residues of amyloid β 1-40 (residues: D1, E3, F4, R5, H6, Y10, E11, H13, H14, Q15, K16, E22, K28, and V40). Ion mobility-mass spectrometry measurements and molecular dynamics simulations reveal that the hydrophobic C-terminus of leucine enkephalin (Phe-Leu, FL) is crucial for the formation of peptide complexes. As such, we explore here the interaction of the dipeptide FL with both wildtype and variant forms of amyloid β in order to structurally characterize the complexes formed. We find that FL binds preferentially to amyloid β oligomers and attaches to amyloid β within the region between its N-terminus and its hydrophobic core, most specifically at residues Y10 and Q15. We further show that FL is able to prevent fibril formation.
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Affiliation(s)
- Molly T. Soper-Hopper
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Joseph D. Eschweiler
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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Shams-Ud-Doha K, Kitova EN, Kitov PI, St-Pierre Y, Klassen JS. Human Milk Oligosaccharide Specificities of Human Galectins. Comparison of Electrospray Ionization Mass Spectrometry and Glycan Microarray Screening Results. Anal Chem 2017; 89:4914-4921. [PMID: 28345865 DOI: 10.1021/acs.analchem.6b05169] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The affinities of thirty-two free human milk oligosaccharides (HMOs) for four human galectin proteins, a stable mutant of hGal1 (hGal-1), a C-terminal fragment of hGal-3 (hGal-3C), hGal-7, and an N-terminal fragment of hGal-9 (hGal-9N), were measured using electrospray ionization mass spectrometry (ESI-MS). The binding data show that each of the four galectins recognize the majority of the HMOs tested (hGal-1 binds thirty-two HMOs, hGal-3C binds twenty-six, hGal-7 binds thirty-one, and hGal-9N binds twenty-six). Twenty-five of the HMOs tested bind all four galectins, with affinities ranging from 103 to 105 M-1. The reliability of the ESI-MS assay for quantifying the affinities of HMOs for lectins was established from the agreement found between the ESI-MS data and affinities of a small number of HMOs for hGal-1, hGal-3C, and hGal-7 measured by isothermal titration calorimetry (ITC). Comparison of the relative affinities (of 14 HMOs) measured by ESI-MS with the reported specificities of hGal-1, hGal-3, hGal-7, and hGal-9 for these same HMOs established using the shotgun human milk glycan microarray (HM-SGM-v2) showed fair-to-poor correlation, with evidence of false positives and false negatives in the microarray data. The results of this study suggest that HMO specificities of lectins established using microarrays may not accurately reflect their true HMO-binding properties and that the use of "in solution" assays such as ESI-MS and ITC is to be preferred.
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Affiliation(s)
- Km Shams-Ud-Doha
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta , Edmonton, Alberta Canada T6G 2G2
| | - Elena N Kitova
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta , Edmonton, Alberta Canada T6G 2G2
| | - Pavel I Kitov
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta , Edmonton, Alberta Canada T6G 2G2
| | - Yves St-Pierre
- INRS-Institut Armand-Frappier , Laval, Québec Canada H7 V 1B7
| | - John S Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta , Edmonton, Alberta Canada T6G 2G2
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43
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Jovanović M, Peter-Katalinić J. Preliminary mass spectrometry characterization studies of galectin-3 samples, prior to carbohydrate-binding studies using Affinity mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:129-136. [PMID: 27791284 DOI: 10.1002/rcm.7775] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 09/11/2016] [Accepted: 10/24/2016] [Indexed: 05/22/2023]
Abstract
RATIONALE Investigation of non-covalent complexes of proteins using Affinity Mass Spectrometry (AMS) represents a major challenge in modern biomedical research. However, many experimental obstacles can make AMS data analysis complex. Additionally, sample purity and size of the protein may still pose significant challenges. METHODS Matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry (MS) was used for initial mapping of protein samples. nanoESI (electrospray ionization) quadrupole-time-of-flight (QTOF) MS was used for mapping of protein samples under native conditions and subsequent AMS studies. The human galectin-3 protein sample was expressed in E. coli. RESULTS Full length galectin-3 was difficult to work with, due to several truncated forms observed after the purification procedures. On the other hand, galectin-3C produced excellent quality nanoESI-MS spectra. A covalent adduct of lactose was found to be located on residue Lys 176. Functional AMS control studies indicated that galectin-3 interactions with oligosaccharides may be dependent on its charge. CONCLUSIONS Mass spectrometry represents a valuable tool that can be efficiently used for structural characterization of protein samples prior to functional analyses. By means of accurate mass measurements, many protein truncations can be identified based on mass alone. Analysis of covalent adducts is more challenging. Finally, for AMS studies, careful use of controls may reveal charge-dependence of protein-oligosaccharide interactions. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Marko Jovanović
- Institute of Medical Physics and Biophysics, University of Münster, Robert-Koch-Strasse 31, D-48149, Münster, Germany
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, 51 000, Rijeka, Croatia
| | - Jasna Peter-Katalinić
- Institute of Medical Physics and Biophysics, University of Münster, Robert-Koch-Strasse 31, D-48149, Münster, Germany
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44
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Lössl P, van de Waterbeemd M, Heck AJ. The diverse and expanding role of mass spectrometry in structural and molecular biology. EMBO J 2016; 35:2634-2657. [PMID: 27797822 PMCID: PMC5167345 DOI: 10.15252/embj.201694818] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/25/2016] [Accepted: 10/07/2016] [Indexed: 12/20/2022] Open
Abstract
The emergence of proteomics has led to major technological advances in mass spectrometry (MS). These advancements not only benefitted MS-based high-throughput proteomics but also increased the impact of mass spectrometry on the field of structural and molecular biology. Here, we review how state-of-the-art MS methods, including native MS, top-down protein sequencing, cross-linking-MS, and hydrogen-deuterium exchange-MS, nowadays enable the characterization of biomolecular structures, functions, and interactions. In particular, we focus on the role of mass spectrometry in integrated structural and molecular biology investigations of biological macromolecular complexes and cellular machineries, highlighting work on CRISPR-Cas systems and eukaryotic transcription complexes.
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Affiliation(s)
- Philip Lössl
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Michiel van de Waterbeemd
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Albert Jr Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
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45
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Pedro L, Van Voorhis WC, Quinn RJ. Optimization of Electrospray Ionization by Statistical Design of Experiments and Response Surface Methodology: Protein-Ligand Equilibrium Dissociation Constant Determinations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1520-30. [PMID: 27225419 PMCID: PMC4972871 DOI: 10.1007/s13361-016-1417-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 04/29/2016] [Accepted: 05/04/2016] [Indexed: 05/28/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) binding studies between proteins and ligands under native conditions require that instrumental ESI source conditions are optimized if relative solution-phase equilibrium concentrations between the protein-ligand complex and free protein are to be retained. Instrumental ESI source conditions that simultaneously maximize the relative ionization efficiency of the protein-ligand complex over free protein and minimize the protein-ligand complex dissociation during the ESI process and the transfer from atmospheric pressure to vacuum are generally specific for each protein-ligand system and should be established when an accurate equilibrium dissociation constant (KD) is to be determined via titration. In this paper, a straightforward and systematic approach for ESI source optimization is presented. The method uses statistical design of experiments (DOE) in conjunction with response surface methodology (RSM) and is demonstrated for the complexes between Plasmodium vivax guanylate kinase (PvGK) and two ligands: 5'-guanosine monophosphate (GMP) and 5'-guanosine diphosphate (GDP). It was verified that even though the ligands are structurally similar, the most appropriate ESI conditions for KD determination by titration are different for each. Graphical Abstract ᅟ.
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Affiliation(s)
- Liliana Pedro
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | | | - Ronald J Quinn
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia.
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46
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Native Mass Spectrometry in Fragment-Based Drug Discovery. Molecules 2016; 21:molecules21080984. [PMID: 27483215 PMCID: PMC6274484 DOI: 10.3390/molecules21080984] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 07/14/2016] [Accepted: 07/23/2016] [Indexed: 11/17/2022] Open
Abstract
The advent of native mass spectrometry (MS) in 1990 led to the development of new mass spectrometry instrumentation and methodologies for the analysis of noncovalent protein-ligand complexes. Native MS has matured to become a fast, simple, highly sensitive and automatable technique with well-established utility for fragment-based drug discovery (FBDD). Native MS has the capability to directly detect weak ligand binding to proteins, to determine stoichiometry, relative or absolute binding affinities and specificities. Native MS can be used to delineate ligand-binding sites, to elucidate mechanisms of cooperativity and to study the thermodynamics of binding. This review highlights key attributes of native MS for FBDD campaigns.
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47
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Syntheses and complexing ability of α-d-gluco- and α-d-xylofuranoside-based lariat ethers. J INCL PHENOM MACRO 2016. [DOI: 10.1007/s10847-016-0601-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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48
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Yao Y, Richards MR, Kitova EN, Klassen JS. Influence of Sulfolane on ESI-MS Measurements of Protein-Ligand Affinities. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:498-506. [PMID: 26667179 DOI: 10.1007/s13361-015-1312-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 11/22/2015] [Accepted: 11/24/2015] [Indexed: 06/05/2023]
Abstract
The results of an investigation into the influence of sulfolane, a commonly used supercharging agent, on electrospray ionization mass spectrometry (ESI-MS) measurements of protein-ligand affinities are described. Binding measurements carried out on four protein-carbohydrate complexes, lysozyme with β-D-GlcNAc-(1→4)-β-D-GlcNAc-(1→4)-β-D-GlcNAc-(1→4)-D-GlcNAc, a single chain variable fragment and α-D-Gal-(1→2)-[α-D-Abe-(1→3)]-α-D-Man-OCH3, cholera toxin B subunit homopentamer with β-D-Gal-(1→3)-β-D-GalNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Gal-(1→4)-β-D-Glc, and a fragment of galectin 3 and α-L-Fuc-(1→2)-β-D-Gal-(1→3)-β-D-GlcNAc-(1→3)-β-D-Gal-(1→4)-β-D-Glc, revealed that sulfolane generally reduces the apparent (as measured by ESI-MS) protein-ligand affinities. To establish the origin of this effect, a detailed study was undertaken using the lysozyme-tetrasaccharide interaction as a model system. Measurements carried out using isothermal titration calorimetry (ITC), circular dichroism, and nuclear magnetic resonance spectroscopies reveal that sulfolane reduces the binding affinity in solution but does not cause any significant change in the higher order structure of lysozyme or to the intermolecular interactions. These observations confirm that changes to the structure of lysozyme in bulk solution are not responsible for the supercharging effect induced by sulfolane. Moreover, the agreement between the ESI-MS and ITC-derived affinities indicates that there is no dissociation of the complex during ESI or in the gas phase (i.e., in-source dissociation). This finding suggests that supercharging of lysozyme by sulfolane is not related to protein unfolding during the ESI process. Binding measurements performed using liquid sample desorption ESI-MS revealed that protein supercharging with sulfolane can be achieved without a reduction in affinity.
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Affiliation(s)
- Yuyu Yao
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Michele R Richards
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Elena N Kitova
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - John S Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.
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49
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Young LM, Saunders JC, Mahood RA, Revill CH, Foster RJ, Ashcroft AE, Radford SE. ESI-IMS-MS: A method for rapid analysis of protein aggregation and its inhibition by small molecules. Methods 2016; 95:62-9. [PMID: 26007606 PMCID: PMC4769093 DOI: 10.1016/j.ymeth.2015.05.017] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 03/26/2015] [Accepted: 05/07/2015] [Indexed: 11/21/2022] Open
Abstract
Electrospray ionisation-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) is a powerful method for the study of conformational changes in protein complexes, including oligomeric species populated during protein self-aggregation into amyloid fibrils. Information on the mass, stability, cross-sectional area and ligand binding capability of each transiently populated intermediate, present in the heterogeneous mixture of assembling species, can be determined individually in a single experiment in real-time. Determining the structural characterisation of oligomeric species and alterations in self-assembly pathways observed in the presence of small molecule inhibitors is of great importance, given the urgent demand for effective therapeutics. Recent studies have demonstrated the capability of ESI-IMS-MS to identify small molecule modulators of amyloid assembly and to determine the mechanism by which they interact (positive, negative, non-specific binding, or colloidal) in a high-throughput format. Here, we demonstrate these advances using self-assembly of Aβ40 as an example, and reveal two new inhibitors of Aβ40 fibrillation.
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Affiliation(s)
- Lydia M Young
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, United Kingdom.
| | - Janet C Saunders
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, United Kingdom.
| | - Rachel A Mahood
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, United Kingdom.
| | - Charlotte H Revill
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; School of Chemistry, University of Leeds, LS2 9JT, United Kingdom.
| | - Richard J Foster
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; School of Chemistry, University of Leeds, LS2 9JT, United Kingdom.
| | - Alison E Ashcroft
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, United Kingdom.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, United Kingdom.
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Lee HJ, Kerr RA, Korshavn KJ, Lee J, Kang J, Ramamoorthy A, Ruotolo BT, Lim MH. Effects of hydroxyl group variations on a flavonoid backbone toward modulation of metal-free and metal-induced amyloid-β aggregation. Inorg Chem Front 2016. [DOI: 10.1039/c5qi00219b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural variations of a flavonoid framework noticeably tune the interaction and reactivity of flavonoids with metals, Aβ, and metal–Aβ.
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Affiliation(s)
- Hyuck Jin Lee
- Department of Chemistry
- Ulsan National Institute of Science and Technology (UNIST)
- Ulsan 44919
- Korea
- Department of Chemistry
| | | | | | - Jeeyeon Lee
- Department of Chemistry
- Ulsan National Institute of Science and Technology (UNIST)
- Ulsan 44919
- Korea
| | - Juhye Kang
- Department of Chemistry
- Ulsan National Institute of Science and Technology (UNIST)
- Ulsan 44919
- Korea
| | | | | | - Mi Hee Lim
- Department of Chemistry
- Ulsan National Institute of Science and Technology (UNIST)
- Ulsan 44919
- Korea
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