1
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Gorshkov V, Kjeldsen F. Exploiting Charge State Distribution To Probe Intramolecular Interactions in Gas-Phase Phosphopeptides and Enhance Proteomics Analyses. Anal Chem 2024; 96:1167-1177. [PMID: 38183295 DOI: 10.1021/acs.analchem.3c04270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2024]
Abstract
Charging of analytes is a prerequisite for performing mass spectrometry analysis. In proteomics, electrospray ionization is the dominant technique for this process. Although the observation of differences in the peptide charge state distribution (CSD) is well-known among experimentalists, its analytical value remains underexplored. To investigate the utility of this dimension, we analyzed several public data sets, comprising over 250,000 peptide CSD profiles from the human proteome. We found that the dimensions of the CSD demonstrate high reproducibility across multiple laboratories, mass analyzers, and extensive time intervals. The general observation was that the CSD enabled effective partitioning of the peptide property space, resulting in enhanced discrimination between sequence and constitutional peptide isomers. Next, by evaluating the CSD values of phosphorylated peptides, we were able to differentiate between phosphopeptides that indicate the formation of intramolecular structures in the gas phase and those that do not. The reproducibility of the CSD values (mean cosine similarity above 0.97 for most of the experiments) qualified CSD data suitable to train a deep-learning model capable of accurately predicting CSD values (mean cosine similarity - 0.98). When we applied the CSD dimension to MS1- and MS2-based proteomics experiments, we consistently observed around a 5% increase in protein and peptide identification rate. Even though the CSD dimension is not as effective a discriminator as the widely used retention time dimension, it still holds the potential for application in direct infusion proteomics.
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Affiliation(s)
- Vladimir Gorshkov
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Frank Kjeldsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
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2
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Cheung See Kit M, Cropley TC, Bleiholder C, Chouinard CD, Sobott F, Webb IK. The role of solvation on the conformational landscape of α-synuclein. Analyst 2023; 149:125-136. [PMID: 37982746 PMCID: PMC10760066 DOI: 10.1039/d3an01680c] [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: 11/21/2023]
Abstract
Native ion mobility mass spectrometry has been used extensively to characterize ensembles of intrinsically disordered protein (IDP) conformers, but the extent to which the gaseous measurements provide realistic pictures of the solution conformations for such flexible proteins remains unclear. Therefore, we systematically studied the relationship between the solution and gaseous structural ensembles by measuring electrospray charge state and collision cross section (CCS) distributions for cationic and anionic forms of α-synuclein (αSN), an anionic protein in solution, as well as directly probed gas phase residue to residue distances via ion/ion reactions between gaseous α-synuclein cations and disulfonic acid linkers that form strong electrostatic bonds. We also combined results from in-solution protein crosslinking identified from native tandem mass spectrometry (MS/MS) with an initial αSN ensemble generated computationally by IDPConformerGenerator to generate an experimentally restrained solution ensemble of αSN. CCS distributions were directly calculated for the solution ensembles determined by NMR and compared to predicted gaseous conformers. While charge state and collision cross section distributions are useful for qualitatively describing the relative structural dynamics of proteins and major conformational changes induced by changes to solution states, the predicted and measured gas phase conformers include subpopulations that are significantly different than those expected from completely "freezing" solution conformations and preserving them in the gas phase. However, insights were gained on the various roles of solvent in stabilizing various conformers for extremely dynamic proteins like α-synuclein.
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Affiliation(s)
- Melanie Cheung See Kit
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, USA.
| | - Tyler C Cropley
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
| | | | - Frank Sobott
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Ian K Webb
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, USA.
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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3
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Hua Y, Strauss M, Fisher S, Mauser MFX, Manchet P, Smacchia M, Geyer P, Shayeghi A, Pfeffer M, Eggenweiler TH, Daly S, Commandeur J, Mayor M, Arndt M, Šolomek T, Köhler V. Giving the Green Light to Photochemical Uncaging of Large Biomolecules in High Vacuum. JACS AU 2023; 3:2790-2799. [PMID: 37885583 PMCID: PMC10598566 DOI: 10.1021/jacsau.3c00351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
The isolation of biomolecules in a high vacuum enables experiments on fragile species in the absence of a perturbing environment. Since many molecular properties are influenced by local electric fields, here we seek to gain control over the number of charges on a biopolymer by photochemical uncaging. We present the design, modeling, and synthesis of photoactive molecular tags, their labeling to peptides and proteins as well as their photochemical validation in solution and in the gas phase. The tailored tags can be selectively cleaved off at a well-defined time and without the need for any external charge-transferring agents. The energy of a single or two green photons can already trigger the process, and it is soft enough to ensure the integrity of the released biomolecular cargo. We exploit differences in the cleavage pathways in solution and in vacuum and observe a surprising robustness in upscaling the approach from a model system to genuine proteins. The interaction wavelength of 532 nm is compatible with various biomolecular entities, such as oligonucleotides or oligosaccharides.
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Affiliation(s)
- Yong Hua
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
| | - Marcel Strauss
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Sergey Fisher
- Van’t
Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, PO Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Martin F. X. Mauser
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Pierre Manchet
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Martina Smacchia
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Philipp Geyer
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Armin Shayeghi
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Michael Pfeffer
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
| | - Tim Henri Eggenweiler
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
| | - Steven Daly
- MS
Vision, Televisieweg
40, 1322 AM Almere, The Netherlands
| | - Jan Commandeur
- MS
Vision, Televisieweg
40, 1322 AM Almere, The Netherlands
| | - Marcel Mayor
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
- Institute
for Nanotechnology (INT), Karlsruhe Institute
of Technology (KIT), P.O. Box 3640, DE-76021 Karlsruhe Eggenstein-Leopoldshafen, Germany
- Lehn Institute
of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou 510274, P. R. China
| | - Markus Arndt
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Tomáš Šolomek
- Van’t
Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, PO Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Valentin Köhler
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
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4
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Shoff TA, Julian RR. Fragment Ion Abundance Reveals Information about Structure and Charge Localization in Highly Charged Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37477985 PMCID: PMC10401701 DOI: 10.1021/jasms.3c00196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Top-down mass spectrometry (MS) is a versatile tool that has been employed to investigate both protein sequence and structure. Although a variety of different fragmentation methods are available in top-down MS that can potentially yield structural information, quantifying differences between spectra remains challenging. Herein, we show that subtle differences in spectra produced by a variety of fragmentation methods are surprisingly sensitive to protein structure and/or charge localization, even in highly unfolded proteins observed in high charge states. In addition to exposing information about the protein structure, differences in fragmentation also reveal insight into the mechanisms underlying the dissociation methods themselves. The results further reveal that small changes in experimental parameters (such as the addition of methanol instead of acetonitrile) lead to changes in structure that are reflected in statistically reproducible differences in dissociation. Collisional annealing of structurally dissimilar ions in the gas phase eventually leads to dissociation spectra that are indistinguishable, suggesting that structural differences can be erased by sufficient thermal activation. Additional experiments illustrate that identical charge states of the same protein can be distinguished if those produced directly by electrospray are compared to ions manipulated by in vacuo proton-transfer charge reduction. Overall, the results show that subtle differences in both three-dimensional structure and charge-site localization can influence the abundance of fragment ions produced by top-down MS, including dissociation methods not typically thought to be structurally sensitive.
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Affiliation(s)
- Thomas A Shoff
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, California 92521, United States
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5
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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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6
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Haidar Y, Konermann L. Effects of Hydrogen/Deuterium Exchange on Protein Stability in Solution and in the Gas Phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37314114 DOI: 10.1021/jasms.3c00130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mass spectrometry (MS)-based techniques are widely used for probing protein structure and dynamics in solution. H/D exchange (HDX)-MS is one of the most common approaches in this context. HDX is often considered to be a "benign" labeling method, in that it does not perturb protein behavior in solution. However, several studies have reported that D2O pushes unfolding equilibria toward the native state. The origin, and even the existence of this protein stabilization remain controversial. Here we conducted thermal unfolding assays in solution to confirm that deuterated proteins in D2O are more stable, with 2-4 K higher melting temperatures than unlabeled proteins in H2O. Previous studies tentatively attributed this phenomenon to strengthened H-bonds after deuteration, an effect that may arise from the lower zero-point vibrational energy of the deuterated species. Specifically, it was proposed that strengthened water-water bonds (W···W) in D2O lower the solubility of nonpolar side chains. The current work takes a broader view by noting that protein stability in solution also depends on water-protein (W···P) and protein-protein (P···P) H-bonds. To help unravel these contributions, we performed collision-induced unfolding (CIU) experiments on gaseous proteins generated by native electrospray ionization. CIU profiles of deuterated and unlabeled proteins were indistinguishable, implying that P···P contacts are insensitive to deuteration. Thus, protein stabilization in D2O is attributable to solvent effects, rather than alterations of intraprotein H-bonds. Strengthening of W···W contacts represents one possible explanation, but the stabilizing effect of D2O can also originate from weakened W···P bonds. Future work will be required to elucidate which of these two scenarios is correct, or if both contribute to protein stabilization in D2O. In any case, the often-repeated adage that "D-bonds are more stable than H-bonds" does not apply to intramolecular contacts in native proteins.
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Affiliation(s)
- Yousef Haidar
- 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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7
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Moore CC, Staroverov VN, Konermann L. Using Density Functional Theory for Testing the Robustness of Mobile-Proton Molecular Dynamics Simulations on Electrosprayed Ions: Structural Implications for Gaseous Proteins. J Phys Chem B 2023; 127:4061-4071. [PMID: 37116098 DOI: 10.1021/acs.jpcb.3c01581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Current experiments only provide low-resolution information on gaseous protein ions generated by electrospray ionization (ESI). Molecular dynamics (MD) simulations can yield complementary insights. Unfortunately, conventional MD does not capture the mobile nature of protons in gaseous proteins. Mobile-proton MD (MPMD) overcomes this limitation. Earlier MPMD data at 300 K indicated that protein ions generated by "native" ESI retain solution-like structures with a hydrophobic core and zwitterionic exterior [Bakhtiari, M.; Konermann, L. J. Phys. Chem. B 2019, 123, 1784-1796]. MPMD redistributes protons using electrostatic and proton affinity calculations. The robustness of this approach has never been scrutinized. Here, we close this gap by benchmarking MPMD against density functional theory (DFT) at the B3LYP/6-31G* level, which is well suited for predicting proton affinities. The computational cost of DFT necessitated the use of small peptides. The MPMD energetic ranking of proton configurations was found to be consistent with DFT single-point energies, implying that MPMD can reliably identify favorable protonation sites. Peptide MPMD runs converged to DFT-optimized structures only when applying 300-500 K temperature cycling, which was necessary to prevent trapping in local minima. Temperature cycling MPMD was then applied to gaseous protein ions. Native ubiquitin converted to slightly expanded structures with a zwitterionic core and a nonpolar exterior. Our data suggest that such inside-out protein structures are intrinsically preferred in the gas phase, and that they form in ESI experiments after moderate collisional excitation. This is in contrast to native ESI (with minimal collisional excitation, simulated by MPMD at 300 K), where kinetic trapping promotes the survival of solution-like structures. In summary, this work validates the MPMD approach for simulations on gaseous peptides and proteins.
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Affiliation(s)
- Conrad C Moore
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Viktor N Staroverov
- 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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8
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Christofi E, Barran P. Ion Mobility Mass Spectrometry (IM-MS) for Structural Biology: Insights Gained by Measuring Mass, Charge, and Collision Cross Section. Chem Rev 2023; 123:2902-2949. [PMID: 36827511 PMCID: PMC10037255 DOI: 10.1021/acs.chemrev.2c00600] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
The investigation of macromolecular biomolecules with ion mobility mass spectrometry (IM-MS) techniques has provided substantial insights into the field of structural biology over the past two decades. An IM-MS workflow applied to a given target analyte provides mass, charge, and conformation, and all three of these can be used to discern structural information. While mass and charge are determined in mass spectrometry (MS), it is the addition of ion mobility that enables the separation of isomeric and isobaric ions and the direct elucidation of conformation, which has reaped huge benefits for structural biology. In this review, where we focus on the analysis of proteins and their complexes, we outline the typical features of an IM-MS experiment from the preparation of samples, the creation of ions, and their separation in different mobility and mass spectrometers. We describe the interpretation of ion mobility data in terms of protein conformation and how the data can be compared with data from other sources with the use of computational tools. The benefit of coupling mobility analysis to activation via collisions with gas or surfaces or photons photoactivation is detailed with reference to recent examples. And finally, we focus on insights afforded by IM-MS experiments when applied to the study of conformationally dynamic and intrinsically disordered proteins.
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Affiliation(s)
- Emilia Christofi
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
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9
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Reid DJ, Thibert S, Zhou M. Dissecting the structural heterogeneity of proteins by native mass spectrometry. Protein Sci 2023; 32:e4612. [PMID: 36851867 PMCID: PMC10031758 DOI: 10.1002/pro.4612] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/01/2023]
Abstract
A single gene yields many forms of proteins via combinations of post-transcriptional/post-translational modifications. Proteins also fold into higher-order structures and interact with other molecules. The combined molecular diversity leads to the heterogeneity of proteins that manifests as distinct phenotypes. Structural biology has generated vast amounts of data, effectively enabling accurate structural prediction by computational methods. However, structures are often obtained heterologously under homogeneous states in vitro. The lack of native heterogeneity under cellular context creates challenges in precisely connecting the structural data to phenotypes. Mass spectrometry (MS) based proteomics methods can profile proteome composition of complex biological samples. Most MS methods follow the "bottom-up" approach, which denatures and digests proteins into short peptide fragments for ease of detection. Coupled with chemical biology approaches, higher-order structures can be probed via incorporation of covalent labels on native proteins that are maintained at the peptide level. Alternatively, native MS follows the "top-down" approach and directly analyzes intact proteins under nondenaturing conditions. Various tandem MS activation methods can dissect the intact proteins for in-depth structural elucidation. Herein, we review recent native MS applications for characterizing heterogeneous samples, including proteins binding to mixtures of ligands, homo/hetero-complexes with varying stoichiometry, intrinsically disordered proteins with dynamic conformations, glycoprotein complexes with mixed modification states, and active membrane protein complexes in near-native membrane environments. We summarize the benefits, challenges, and ongoing developments in native MS, with the hope to demonstrate an emerging technology that complements other tools by filling the knowledge gaps in understanding molecular heterogeneity of proteins. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Deseree J Reid
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Stephanie Thibert
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
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10
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Liu R, Xia S, Li H. Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes. MASS SPECTROMETRY REVIEWS 2022:e21793. [PMID: 35757976 DOI: 10.1002/mas.21793] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Progress in structural biology research has led to a high demand for powerful and yet complementary analytical tools for structural characterization of proteins and protein complexes. This demand has significantly increased interest in native mass spectrometry (nMS), particularly native top-down mass spectrometry (nTDMS) in the past decade. This review highlights recent advances in nTDMS for structural research of biological assemblies, with a particular focus on the extra multi-layers of information enabled by TDMS. We include a short introduction of sample preparation and ionization to nMS, tandem fragmentation techniques as well as mass analyzers and software/analysis pipelines used for nTDMS. We highlight unique structural information offered by nTDMS and examples of its broad range of applications in proteins, protein-ligand interactions (metal, cofactor/drug, DNA/RNA, and protein), therapeutic antibodies and antigen-antibody complexes, membrane proteins, macromolecular machineries (ribosome, nucleosome, proteosome, and viruses), to endogenous protein complexes. The challenges, potential, along with perspectives of nTDMS methods for the analysis of proteins and protein assemblies in recombinant and biological samples are discussed.
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Affiliation(s)
- Ruijie Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shujun Xia
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
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11
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Norgate EL, Upton R, Hansen K, Bellina B, Brookes C, Politis A, Barran PE. Cold Denaturation of Proteins in the Absence of Solvent: Implications for Protein Storage. Angew Chem Int Ed Engl 2022; 61:e202115047. [PMID: 35313047 PMCID: PMC9325448 DOI: 10.1002/anie.202115047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Indexed: 12/12/2022]
Abstract
The effect of temperature on the stability of proteins is well explored above 298 K, but harder to track experimentally below 273 K. Variable-temperature ion mobility mass spectrometry (VT IM-MS) allows us to measure the structure of molecules at sub-ambient temperatures. Here we monitor conformational changes that occur to two isotypes of monoclonal antibodies (mAbs) on cooling by measuring their collision cross sections (CCS) at discrete drift gas temperatures from 295 to 160 K. The CCS at 250 K is larger than predicted from collisional theory and experimental data at 295 K. This restructure is attributed to change in the strength of stabilizing intermolecular interactions. Below 250 K the CCS of the mAbs increases in line with prediction implying no rearrangement. Comparing data from isotypes suggest disulfide bridging influences thermal structural rearrangement. These findings indicate that in vacuo deep-freezing minimizes denaturation and maintains the native fold and VT IM-MS measurements at sub ambient temperatures provide new insights to the phenomenon of cold denaturation.
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Affiliation(s)
- Emma L Norgate
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester, M1 7DN, UK
| | - Rosie Upton
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester, M1 7DN, UK
| | - Kjetil Hansen
- Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK
| | - Bruno Bellina
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester, M1 7DN, UK
| | - C Brookes
- Bristol-Myers Squibb, Moreton, Wirral, CH46 1QW, UK
| | - Argyris Politis
- Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK
| | - Perdita E Barran
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester, M1 7DN, UK
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12
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Norgate EL, Upton R, Hansen K, Bellina B, Brookes C, Politis A, Barran PE. Cold Denaturation of Proteins in the Absence of Solvent: Implications for Protein Storage. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202115047. [PMID: 38505418 PMCID: PMC10947158 DOI: 10.1002/ange.202115047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Indexed: 11/07/2022]
Abstract
The effect of temperature on the stability of proteins is well explored above 298 K, but harder to track experimentally below 273 K. Variable-temperature ion mobility mass spectrometry (VT IM-MS) allows us to measure the structure of molecules at sub-ambient temperatures. Here we monitor conformational changes that occur to two isotypes of monoclonal antibodies (mAbs) on cooling by measuring their collision cross sections (CCS) at discrete drift gas temperatures from 295 to 160 K. The CCS at 250 K is larger than predicted from collisional theory and experimental data at 295 K. This restructure is attributed to change in the strength of stabilizing intermolecular interactions. Below 250 K the CCS of the mAbs increases in line with prediction implying no rearrangement. Comparing data from isotypes suggest disulfide bridging influences thermal structural rearrangement. These findings indicate that in vacuo deep-freezing minimizes denaturation and maintains the native fold and VT IM-MS measurements at sub ambient temperatures provide new insights to the phenomenon of cold denaturation.
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Affiliation(s)
- Emma L. Norgate
- Manchester Institute of BiotechnologyUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
| | - Rosie Upton
- Manchester Institute of BiotechnologyUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
| | - Kjetil Hansen
- Department of ChemistryKing's College London7 Trinity StreetLondonSE1 1DBUK
| | - Bruno Bellina
- Manchester Institute of BiotechnologyUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
| | - C. Brookes
- Bristol-Myers SquibbMoretonWirralCH46 1QWUK
| | - Argyris Politis
- Department of ChemistryKing's College London7 Trinity StreetLondonSE1 1DBUK
| | - Perdita E. Barran
- Manchester Institute of BiotechnologyUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
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13
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Gavriilidou AFM, Sokratous K, Yen HY, De Colibus L. High-Throughput Native Mass Spectrometry Screening in Drug Discovery. Front Mol Biosci 2022; 9:837901. [PMID: 35495635 PMCID: PMC9047894 DOI: 10.3389/fmolb.2022.837901] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/15/2022] [Indexed: 12/15/2022] Open
Abstract
The design of new therapeutic molecules can be significantly informed by studying protein-ligand interactions using biophysical approaches directly after purification of the protein-ligand complex. Well-established techniques utilized in drug discovery include isothermal titration calorimetry, surface plasmon resonance, nuclear magnetic resonance spectroscopy, and structure-based drug discovery which mainly rely on protein crystallography and, more recently, cryo-electron microscopy. Protein-ligand complexes are dynamic, heterogeneous, and challenging systems that are best studied with several complementary techniques. Native mass spectrometry (MS) is a versatile method used to study proteins and their non-covalently driven assemblies in a native-like folded state, providing information on binding thermodynamics and stoichiometry as well as insights on ternary and quaternary protein structure. Here, we discuss the basic principles of native mass spectrometry, the field’s recent progress, how native MS is integrated into a drug discovery pipeline, and its future developments in drug discovery.
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14
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Vallejo DD, Rojas Ramírez C, Parson KF, Han Y, Gadkari VV, Ruotolo BT. Mass Spectrometry Methods for Measuring Protein Stability. Chem Rev 2022; 122:7690-7719. [PMID: 35316030 DOI: 10.1021/acs.chemrev.1c00857] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mass spectrometry is a central technology in the life sciences, providing our most comprehensive account of the molecular inventory of the cell. In parallel with developments in mass spectrometry technologies targeting such assessments of cellular composition, mass spectrometry tools have emerged as versatile probes of biomolecular stability. In this review, we cover recent advancements in this branch of mass spectrometry that target proteins, a centrally important class of macromolecules that accounts for most biochemical functions and drug targets. Our efforts cover tools such as hydrogen-deuterium exchange, chemical cross-linking, ion mobility, collision induced unfolding, and other techniques capable of stability assessments on a proteomic scale. In addition, we focus on a range of application areas where mass spectrometry-driven protein stability measurements have made notable impacts, including studies of membrane proteins, heat shock proteins, amyloidogenic proteins, and biotherapeutics. We conclude by briefly discussing the future of this vibrant and fast-moving area of research.
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Affiliation(s)
- Daniel D Vallejo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Carolina Rojas Ramírez
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kristine F Parson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yilin Han
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Varun V Gadkari
- 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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15
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Crilly CJ, Brom JA, Warmuth O, Esterly HJ, Pielak GJ. Protection by desiccation-tolerance proteins probed at the residue level. Protein Sci 2022; 31:396-406. [PMID: 34766407 PMCID: PMC8819849 DOI: 10.1002/pro.4231] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 02/03/2023]
Abstract
Extremotolerant organisms from all domains of life produce protective intrinsically disordered proteins (IDPs) in response to desiccation stress. In vitro, many of these IDPs protect enzymes from dehydration stress better than U.S. Food and Drug Administration-approved excipients. However, as with most excipients, their protective mechanism is poorly understood. Here, we apply thermogravimetric analysis, differential scanning calorimetry, and liquid-observed vapor exchange (LOVE) NMR to study the protection of two model globular proteins (the B1 domain of staphylococcal protein G [GB1] and chymotrypsin inhibitor 2 [CI2]) by two desiccation-tolerance proteins (CAHS D from tardigrades and PvLEA4 from an anhydrobiotic midge), as well as by disordered and globular protein controls. We find that all protein samples retain similar amounts of water and possess similar glass transition temperatures, suggesting that neither enhanced water retention nor vitrification is responsible for protection. LOVE NMR reveals that IDPs protect against dehydration-induced unfolding better than the globular protein control, generally protect the same regions of GB1 and CI2, and protect GB1 better than CI2. These observations suggest that electrostatic interactions, charge patterning, and expanded conformations are key to protection. Further application of LOVE NMR to additional client proteins and protectants will deepen our understanding of dehydration protection, enabling the streamlined production of dehydrated proteins for expanded use in the medical, biotechnology, and chemical industries.
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Affiliation(s)
- Candice J. Crilly
- Department of ChemistryUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA
| | - Julia A. Brom
- Department of ChemistryUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA
| | - Owen Warmuth
- Department of ChemistryUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA
| | - Harrison J. Esterly
- Department of ChemistryUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA
| | - Gary J. Pielak
- Department of ChemistryUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA,Department of Biochemistry & BiophysicsUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA,Lineberger Cancer CenterUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA,Integrative Program for Biological and Genome SciencesUniversity of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNorth CarolinaUSA
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16
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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: 31] [Impact Index Per Article: 10.3] [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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17
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Konermann L, Aliyari E, Lee JH. Mobile Protons Limit the Stability of Salt Bridges in the Gas Phase: Implications for the Structures of Electrosprayed Protein Ions. J Phys Chem B 2021; 125:3803-3814. [PMID: 33848419 DOI: 10.1021/acs.jpcb.1c00944] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Electrosprayed protein ions can retain native-like conformations. The intramolecular contacts that stabilize these compact gas-phase structures remain poorly understood. Recent work has uncovered abundant salt bridges in electrosprayed proteins. Salt bridges are zwitterionic BH+/A- contacts. The low dielectric constant in the vacuum strengthens electrostatic interactions, suggesting that salt bridges could be a key contributor to the retention of compact protein structures. A problem with this assertion is that H+ are mobile, such that H+ transfer can convert salt bridges into neutral B0/HA0 contacts. This possible salt bridge annihilation puts into question the role of zwitterionic motifs in the gas phase, and it calls for a detailed analysis of BH+/A- versus B0/HA0 interactions. Here, we investigate this issue using molecular dynamics (MD) simulations and electrospray experiments. MD data for short model peptides revealed that salt bridges with static H+ have dissociation energies around 700 kJ mol-1. The corresponding B0/HA0 contacts are 1 order of magnitude weaker. When considering the effects of mobile H+, BH+/A- bond energies were found to be between these two extremes, confirming that H+ migration can significantly weaken salt bridges. Next, we examined the protein ubiquitin under collision-induced unfolding (CIU) conditions. CIU simulations were conducted using three different MD models: (i) Positive-only runs with static H+ did not allow for salt bridge formation and produced highly expanded CIU structures. (ii) Zwitterionic runs with static H+ resulted in abundant salt bridges, culminating in much more compact CIU structures. (iii) Mobile H+ simulations allowed for the dynamic formation/annihilation of salt bridges, generating CIU structures intermediate between scenarios (i) and (ii). Our results uncover that mobile H+ limit the stabilizing effects of salt bridges in the gas phase. Failure to consider the effects of mobile H+ in MD simulations will result in unrealistic outcomes under CIU conditions.
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Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Elnaz Aliyari
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Justin H Lee
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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18
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Bellamy‐Carter J, O'Grady L, Passmore M, Jenner M, Oldham NJ. Decoding Protein Gas‐Phase Stability with Alanine Scanning and Collision‐Induced Unfolding Ion Mobility Mass Spectrometry. ACTA ACUST UNITED AC 2020. [DOI: 10.1002/anse.202000019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Louisa O'Grady
- School of Chemistry University of Nottingham University Park Nottingham NG7 2RD UK
| | - Munro Passmore
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
| | - Matthew Jenner
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
- Warwick Integrative Synthetic Biology Centre University of Warwick Coventry CV4 7AL UK
| | - Neil J. Oldham
- School of Chemistry University of Nottingham University Park Nottingham NG7 2RD UK
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19
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Crittenden CM, Novelli ET, Mehaffey MR, Xu GN, Giles DH, Fies WA, Dalby KN, Webb LJ, Brodbelt JS. Structural Evaluation of Protein/Metal Complexes via Native Electrospray Ultraviolet Photodissociation Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1140-1150. [PMID: 32275426 PMCID: PMC7386362 DOI: 10.1021/jasms.0c00066] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Ultraviolet photodissociation (UVPD) has emerged as a promising tool to characterize proteins with regard to not only their primary sequences and post-translational modifications, but also their tertiary structures. In this study, three metal-binding proteins, Staphylococcal nuclease, azurin, and calmodulin, are used to demonstrate the use of UVPD to elucidate metal-binding regions via comparisons between the fragmentation patterns of apo (metal-free) and holo (metal-bound) proteins. The binding of staphylococcal nuclease to calcium was evaluated, in addition to a series of lanthanide(III) ions which are expected to bind in a similar manner as calcium. On the basis of comparative analysis of the UVPD spectra, the binding region for calcium and the lanthanide ions was determined to extend from residues 40-50, aligning with the known crystal structure. Similar analysis was performed for both azurin (interrogating copper and silver binding) and calmodulin (four calcium binding sites). This work demonstrates the utility of UVPD methods for determining and analyzing the metal binding sites of a variety of classes of proteins.
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Affiliation(s)
| | - Elisa T Novelli
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - M Rachel Mehaffey
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Gulan N Xu
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - David H Giles
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Whitney A Fies
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas 78712, United States
- Graduate Program in Cell and Molecular Biology, University of Texas, Austin, Texas 78712, United States
| | - Lauren J Webb
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
- Institute for Cell and Molecular Biology, University of Texas, Austin, Texas 78712, United States
- Texas Materials Institute, University of Texas, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
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20
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Polasky DA, Dixit SM, Keating MF, Gadkari VV, Andrews PC, Ruotolo BT. Pervasive Charge Solvation Permeates Native-like Protein Ions and Dramatically Influences Top-down Sequencing Data. J Am Chem Soc 2020; 142:6750-6760. [DOI: 10.1021/jacs.0c01076] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Daniel A. Polasky
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Sugyan M. Dixit
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Michael F. Keating
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Varun V. Gadkari
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Philip C. Andrews
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
- Department of Biological Chemistry, University of Michigan, 1150 West Medical Center Drive, Ann Arbor Michigan 48109, United States
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
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21
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Shirzadeh M, Poltash ML, Laganowsky A, Russell DH. Structural Analysis of the Effect of a Dual-FLAG Tag on Transthyretin. Biochemistry 2020; 59:1013-1022. [PMID: 32101399 DOI: 10.1021/acs.biochem.0c00105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recombinant proteins have increased our knowledge regarding the physiological role of proteins; however, affinity purification tags are often not cleaved prior to analysis, and their effects on protein structure, stability and assembly are often overlooked. In this study, the stabilizing effects of an N-terminus dual-FLAG (FT2) tag fusion to transthyretin (TTR), a construct used in previous studies, are investigated using native ion mobility-mass spectrometry (IM-MS). A combination of collision-induced unfolding and variable-temperature electrospray ionization is used to compare gas- and solution-phase stabilities of FT2-TTR to wild-type and C-terminal tagged TTR. Despite an increased stability of both gas- and solution-phase FT2-TTR, thermal degradation of FT2-TTR was observed at elevated temperatures, viz., backbone cleavage occurring between Lys9 and Cys10. This cleavage reaction is consistent with previously reported metalloprotease activity of TTR [Liz et al. 2009] and is suppressed by either metal chelation or excess zinc. This study brings to the fore the effect of affinity tag stabilization of TTR and emphasizes unprecedented detail afforded by native IM-MS to assess structural discrepancies of recombinant proteins from their wild-type counterparts.
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Affiliation(s)
- Mehdi Shirzadeh
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - Michael L Poltash
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
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22
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Simmonds AL, Lopez-Clavijo AF, Winn PJ, Russell DH, Styles IB, Cooper HJ. Structural Analysis of 14-3-3-ζ-Derived Phosphopeptides Using Electron Capture Dissociation Mass Spectrometry, Traveling Wave Ion Mobility Spectrometry, and Molecular Modeling. J Phys Chem B 2020; 124:461-469. [PMID: 31859508 DOI: 10.1021/acs.jpcb.9b08506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Previously, we have demonstrated the effect of salt bridges on the electron capture dissociation mass spectrometry behavior of synthetic model phosphopeptides and applied an ion mobility spectrometry/molecular modeling approach to rationalize the findings in terms of peptide ion structure. Here, we develop and apply the approach to a biologically derived phosphopeptide. Specifically, we have investigated variants of a 15-mer phosphopeptide VVGARRSsWRVVSSI (s denotes phosphorylated Ser) derived from Akt1 substrate 14-3-3-ζ, which contains the phosphorylation motif RRSsWR. Variants were generated by successive arginine-to-leucine substitutions within the phosphorylation motif. ECD fragmentation patterns for the eight phosphopeptide variants show greater sequence coverage with successive R → L substitutions. Peptides with two or more basic residues had regions with no sequence coverage, while full sequence coverage was observed for peptides with one or no basic residues. For three of the peptide variants, low-abundance fragments were observed between the phosphoserine and a basic residue, possibly due to the presence of multiple conformers with and without noncovalent interactions between these residues. For the five variants whose dissociation behavior suggested the presence of intramolecular noncovalent interactions, we employed ion mobility spectrometry and molecular modeling to probe the nature of these interactions. Our workflow allowed us to propose candidate structures whose noncovalent interactions were consistent with the ECD data for all of the peptides modeled. Additionally, the AMBER parameter sets created for and validated by this work are presented and made available online ( http://www.biosciences-labs.bham.ac.uk/cooper/datasets.php ).
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Affiliation(s)
| | | | | | - David H Russell
- Texas A&M University , College Station , Texas 77843 , United States
| | - Iain B Styles
- Centre of Membrane Proteins and Receptors (COMPARE) , Universities of Birmingham and Nottingham , Midlands , U.K
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23
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Hu J, Lei W, Wang J, Chen HY, Xu JJ. Preservation of Protein Zwitterionic States in the Transition from Solution to Gas Phase Revealed by Sodium Adduction Mass Spectrometry. Anal Chem 2019; 91:7858-7863. [PMID: 31134800 DOI: 10.1021/acs.analchem.9b01602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structural characterization of proteins and their interaction network mapping in the gas phase highlights the need to preserve their most nativelike conformers in the transition from the solution to gas phase. Zwitterionic interactions in a protein are weak bonds between oppositely charged residues, which make an important contribution to protein stability. However, it is still not clear whether the native zwitterionic states of proteins can be retained or not when it is transferred from the solution to gas phase. Using the nonspecific Na+ adduction as a novel signature, here we show that the zwitterionic states of proteins can be preserved when a moderated droplet desolvation condition (temperature <30 °C) is used in native electrospray ionization mass spectrometry. The very low-level nonspecific metal adduction to proteins under such conditions also enables rapid and direct determination of the binding states of metal-binding proteins and sensitive detection of proteins from solutions containing highly concentrated involatile salts (e.g., 50 mM NaCl). We believe that our findings can be instructive for performing mass spectrometric analysis of proteins and useful for protein ions desalting which simply involves altering the temperature and flow rate of drying gas in the desolvation region.
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Affiliation(s)
- Jun Hu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , P. R. China
| | - Wen Lei
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , P. R. China
| | - Jiang Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , P. R. China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , P. R. China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , P. R. China
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24
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Wootton CA, Millett AJ, Lopez-Clavijo AF, Chiu CKC, Barrow MP, Clarkson GJ, Sadler PJ, O'Connor PB. Structural analysis of peptides modified with organo-iridium complexes, opportunities from multi-mode fragmentation. Analyst 2019; 144:1575-1581. [PMID: 30663751 DOI: 10.1039/c8an02094a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The most widely used anticancer drugs are platinum complexes, but complexes of other transition metals also show promise and may widen the spectrum of activity, reduce side-effects, and overcome resistance. The latter include organo-iridium(iii) 'piano-stool' complexes. To understand their mechanism of action, it is important to discover how they bind to biomolecules and how binding is affected by functionalisation of the ligands bound to iridium. We have characterised, by MS and MS/MS techniques, unusual adducts from reactions between 3 novel iridium(iii) anti-cancer complexes each possessing reactive sites both at the metal (coordination by substitution of a labile chlorido ligand) and on the ligand (covalent bond formation involving imine formation by one or two aldehyde functions). Peptide modification by the metal complex had a drastic effect on both Collisonally Activated Dissociation (CAD) and Electron Capture Dissociation (ECD) MS/MS behaviour, tuning requirements, and fragmentation channels. CAD MS/MS was effective only when studying the covalent condensation products. ECD MS/MS, although hindered by electron-quenching at the Iridium complex site, was suitable for studying many of the species observed, locating the modification sites, and often identifying them to within a single amino acid residue.
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25
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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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26
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Rabuck-Gibbons JN, Lodge JM, Mapp AK, Ruotolo BT. Collision-Induced Unfolding Reveals Unique Fingerprints for Remote Protein Interaction Sites in the KIX Regulation Domain. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:94-102. [PMID: 30136215 PMCID: PMC6320266 DOI: 10.1007/s13361-018-2043-6] [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: 04/09/2018] [Revised: 07/24/2018] [Accepted: 07/28/2018] [Indexed: 06/08/2023]
Abstract
The kinase-inducible domain (KIX) of the transcriptional coactivator CBP binds multiple transcriptional regulators through two allosterically connected sites. Establishing a method for observing activator-specific KIX conformations would facilitate the discovery of drug-like molecules that capture specific conformations and further elucidate how distinct activator-KIX complexes produce differential transcriptional effects. However, the transient and low to moderate affinity interactions between activators and KIX are difficult to capture using traditional biophysical assays. Here, we describe a collision-induced unfolding-based approach that produces unique fingerprints for peptides bound to each of the two available sites within KIX, as well as a third fingerprint for ternary KIX complexes. Furthermore, we evaluate the analytical utility of unfolding fingerprints for KIX complexes using CIUSuite, and conclude by speculating as to the structural origins of the conformational families created from KIX:peptide complexes following collisional activation. Graphical Abstract ᅟ.
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Affiliation(s)
- Jessica N Rabuck-Gibbons
- Department of Chemistry, University of Michigan, 930 N University, Ann Arbor, MI, 48109, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Jean M Lodge
- Department of Chemistry, University of Michigan, 930 N University, Ann Arbor, MI, 48109, USA
- Life Science Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI, 48109, USA
- University of Wisconsin, Genome Center, 425 Henry Mall, Madison, WI, 53706, USA
| | - Anna K Mapp
- Department of Chemistry, University of Michigan, 930 N University, Ann Arbor, MI, 48109, USA
- Life Science Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI, 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, 930 N University, Ann Arbor, MI, 48109, USA.
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27
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Theisen A, Black R, Corinti D, Brown JM, Bellina B, Barran PE. Initial Protein Unfolding Events in Ubiquitin, Cytochrome c and Myoglobin Are Revealed with the Use of 213 nm UVPD Coupled to IM-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:24-33. [PMID: 29949061 PMCID: PMC6318241 DOI: 10.1007/s13361-018-1992-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 05/11/2023]
Abstract
The initial stages of protein unfolding may reflect the stability of the entire fold and can also reveal which parts of a protein can be perturbed, without restructuring the rest. In this work, we couple UVPD with activated ion mobility mass spectrometry to measure how three model proteins start to unfold. Ubiquitin, cytochrome c and myoglobin ions produced via nESI from salty solutions are subjected to UV irradiation pre-mobility separation; experiments are conducted with a range of source conditions which alter the conformation of the precursor ion as shown by the drift time profiles. For all three proteins, the compact structures result in less fragmentation than more extended structures which emerge following progressive in-source activation. Cleavage sites are found to differ between conformational ensembles, for example, for the dominant charge state of cytochrome c [M + 7H]7+, cleavage at Phe10, Thr19 and Val20 was only observed in activating conditions whilst cleavage at Ala43 is dramatically enhanced. Mapping the photo-cleaved fragments onto crystallographic structures provides insight into the local structural changes that occur as protein unfolding progresses, which is coupled to global restructuring observed in the drift time profiles. Graphical Abstract.
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Affiliation(s)
- Alina Theisen
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Rachelle Black
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", 00185, Rome, Italy
| | - Jeffery M Brown
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, UK
| | - Bruno Bellina
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Perdita E Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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28
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Abstract
A sizeable proportion of active protein sequences lack structural motifs making them irresolvable by NMR and crystallography. Such intrinsically disordered proteins (IDPs) or regions (IDRs) play a major role in biological mechanisms. They are often involved in cell regulation processes, and by extension can be the perpetrator or signifier of disease. In light of their importance and the shortcomings of conventional methods of biophysical analysis to identify them and to describe their conformational variance, IDPs and IDRs have been termed "the dark proteome." In this chapter we describe the use of ion mobility-mass spectrometry (IM-MS) coupled with electrospray ionization to analyze the conformational diversity of IDPs. Using the LEA protein COR15A as an exemplar system and contrasting it with the behavior of myoglobin, we outline the methods for analyzing an IDP using nanoelectrospray ionization coupled with IM-MS, covering sample preparation, purification; optimization of mass spectrometry conditions and tuning parameters; data collection and analysis. Following this, we detail the use of a "toy" model that provides a predictive framework for the study of all proteins with ESI-IM-MS.
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29
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Lermyte F, Valkenborg D, Loo JA, Sobott F. Radical solutions: Principles and application of electron-based dissociation in mass spectrometry-based analysis of protein structure. MASS SPECTROMETRY REVIEWS 2018; 37:750-771. [PMID: 29425406 PMCID: PMC6131092 DOI: 10.1002/mas.21560] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 01/19/2018] [Accepted: 01/19/2018] [Indexed: 05/11/2023]
Abstract
In recent years, electron capture (ECD) and electron transfer dissociation (ETD) have emerged as two of the most useful methods in mass spectrometry-based protein analysis, evidenced by a considerable and growing body of literature. In large part, the interest in these methods is due to their ability to induce backbone fragmentation with very little disruption of noncovalent interactions which allows inference of information regarding higher order structure from the observed fragmentation behavior. Here, we review the evolution of electron-based dissociation methods, and pay particular attention to their application in "native" mass spectrometry, their mechanism, determinants of fragmentation behavior, and recent developments in available instrumentation. Although we focus on the two most widely used methods-ECD and ETD-we also discuss the use of other ion/electron, ion/ion, and ion/neutral fragmentation methods, useful for interrogation of a range of classes of biomolecules in positive- and negative-ion mode, and speculate about how this exciting field might evolve in the coming years.
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Affiliation(s)
- Frederik Lermyte
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- School of Engineering, University of Warwick, Coventry, United Kingdom
| | - Dirk Valkenborg
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Agoralaan, Diepenbeek, Belgium
- Applied Bio and Molecular Systems, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Joseph A Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, California
- UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, California
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
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30
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Schneeberger EM, Breuker K. Replacing H + by Na + or K + in phosphopeptide anions and cations prevents electron capture dissociation. Chem Sci 2018; 9:7338-7353. [PMID: 30542537 PMCID: PMC6237128 DOI: 10.1039/c8sc02470g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/07/2018] [Indexed: 01/29/2023] Open
Abstract
By successively replacing H+ by Na+ or K+ in phosphopeptide anions and cations, we show that the efficiency of fragmentation into c and z˙ or c˙ and z fragments from N-Cα backbone bond cleavage by negative ion electron capture dissociation (niECD) and electron capture dissociation (ECD) substantially decreases with increasing number of alkali ions attached. In proton-deficient phosphopeptide ions with a net charge of 2-, we observed an exponential decrease in electron capture efficiency with increasing number of Na+ or K+ ions attached, suggesting that electrons are preferentially captured at protonated sites. In proton-abundant phosphopeptide ions with a net charge of 3+, the electron capture efficiency was not affected by replacing up to four H+ ions with Na+ or K+ ions, but the yield of c, z˙ and c˙, z fragments from N-Cα backbone bond cleavage generally decreased next to Na+ or K+ binding sites. We interpret the site-specific decrease in fragmentation efficiency as Na+ or K+ binding to backbone amide oxygen in competition with interactions of protonated sites that would otherwise lead to backbone cleavage into c, z˙ or c˙, z fragments. Our findings seriously challenge the hypothesis that the positive charge responsible for ECD into c, z˙ or c˙, z fragments can generally be a sodium or other metal ion instead of a proton.
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Affiliation(s)
- Eva-Maria Schneeberger
- Institute of Organic Chemistry , Center for Molecular Biosciences Innsbruck (CMBI) , University of Innsbruck , Innrain 80/82 , 6020 Innsbruck , Austria . ; http://www.bioms-breuker.at/
| | - Kathrin Breuker
- Institute of Organic Chemistry , Center for Molecular Biosciences Innsbruck (CMBI) , University of Innsbruck , Innrain 80/82 , 6020 Innsbruck , Austria . ; http://www.bioms-breuker.at/
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31
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Crittenden CM, Morrison LJ, Fitzpatrick MD, Myers AP, Novelli ET, Rosenberg J, Akin LD, Srinivasa S, Shear JB, Brodbelt JS. Towards mapping electrostatic interactions between Kdo 2-lipid A and cationic antimicrobial peptides via ultraviolet photodissociation mass spectrometry. Analyst 2018; 143:3607-3618. [PMID: 29968868 PMCID: PMC6056329 DOI: 10.1039/c8an00652k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cationic antimicrobial peptides (CAMPs) have been known to act as multi-modal weapons against Gram-negative bacteria. As a new approach to investigate the nature of the interactions between CAMPs and the surfaces of bacteria, native mass spectrometry and two MS/MS strategies (ultraviolet photodissociation (UVPD) and higher energy collisional activation (HCD)) are used to examine formation and disassembly of saccharolipid·peptide complexes. Kdo2-lipid A (KLA) is used as a model saccharolipid to evaluate complexation with a series of cationic peptides (melittin and three analogs). Collisional activation of the KLA·peptide complexes results in the disruption of electrostatic interactions, resulting in apo-sequence ions with shifts in the distribution of ions compared to the fragmentation patterns of the apo-peptides. UVPD of the KLA·peptide complexes results in both apo- and holo-sequence ions of the peptides, the latter in which the KLA remains bound to the truncated peptide fragment despite cleavage of a covalent bond of the peptide backbone. Mapping both the N- and C-terminal holo-product ions gives insight into the peptide motifs (specifically an electropositive KRKR segment and a proline residue) that are responsible for mediating the electrostatic interactions between the cationic peptides and saccharolipid.
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Affiliation(s)
| | - Lindsay J Morrison
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA.
| | - Mignon D Fitzpatrick
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA.
| | - Allison P Myers
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA.
| | - Elisa T Novelli
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA.
| | - Jake Rosenberg
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA.
| | - Lucas D Akin
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA.
| | - Sorin Srinivasa
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA.
| | - Jason B Shear
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA.
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA.
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32
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Konermann L, Metwally H, McAllister RG, Popa V. How to run molecular dynamics simulations on electrospray droplets and gas phase proteins: Basic guidelines and selected applications. Methods 2018; 144:104-112. [DOI: 10.1016/j.ymeth.2018.04.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/10/2018] [Accepted: 04/12/2018] [Indexed: 12/13/2022] Open
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33
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Morrison LJ, Chai W, Rosenberg JA, Henkelman G, Brodbelt JS. Characterization of hydrogen bonding motifs in proteins: hydrogen elimination monitoring by ultraviolet photodissociation mass spectrometry. Phys Chem Chem Phys 2018; 19:20057-20074. [PMID: 28722742 DOI: 10.1039/c7cp04073c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Determination of structure and folding of certain classes of proteins remains intractable by conventional structural characterization strategies and has spurred the development of alternative methodologies. Mass spectrometry-based approaches have a unique capacity to differentiate protein heterogeneity due to the ability to discriminate populations, whether minor or major, featuring modifications or complexation with non-covalent ligands on the basis of m/z. Cleavage of the peptide backbone can be further utilized to obtain residue-specific structural information. Here, hydrogen elimination monitoring (HEM) upon ultraviolet photodissociation (UVPD) of proteins transferred to the gas phase via nativespray ionization is introduced as an innovative approach to deduce backbone hydrogen bonding patterns. Using well-characterized peptides and a series of proteins, prediction of the engagement of the amide carbonyl oxygen of the protein backbone in hydrogen bonding using UVPD-HEM is demonstrated to show significant agreement with the hydrogen-bonding motifs derived from molecular dynamics simulations and X-ray crystal structures.
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34
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Torii H. Strategy for Modeling the Electrostatic Responses of the Spectroscopic Properties of Proteins. J Phys Chem B 2017; 122:154-164. [PMID: 29192780 DOI: 10.1021/acs.jpcb.7b10791] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For better understanding and more efficient use of the spectroscopic probes (vibrational and NMR) of the local electrostatic situations inside proteins, appropriate modeling of the properties of those probes is essential. The present study is devoted to examining the strategy for constructing such models. A more well-founded derivation than the ones in previous studies is given in constructing the models. Theoretical analyses are conducted on two representative example cases related to proteins, i.e., the peptide group of the main chains and the CO and NO ligands to the Fe2+ ion of heme, with careful treatment of the behavior of electrons in the electrostatic responses and with verification of consistency with observable quantities. It is shown that, for the stretching frequencies and NMR chemical shifts, it is possible to construct reasonable electrostatic interaction models that encompass the situations of hydration and uniform electric field environment and thus are applicable also to the cases of nonuniform electrostatic situations, which are highly expected for inside of proteins.
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Affiliation(s)
- Hajime Torii
- Department of Chemistry, Faculty of Education and Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University , 836 Ohya, Shizuoka 422-8529, Japan
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35
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Vušurović J, Schneeberger E, Breuker K. Interactions of Protonated Guanidine and Guanidine Derivatives with Multiply Deprotonated RNA Probed by Electrospray Ionization and Collisionally Activated Dissociation. ChemistryOpen 2017; 6:739-750. [PMID: 29226062 PMCID: PMC5715244 DOI: 10.1002/open.201700143] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/06/2017] [Indexed: 11/25/2022] Open
Abstract
Interactions of ribonucleic acid (RNA) with guanidine and guanidine derivatives are important features in RNA-protein and RNA-drug binding. Here we have investigated noncovalently bound complexes of an 8-nucleotide RNA and six different ligands, all of which have a guanidinium moiety, by using electrospray ionization (ESI) and collisionally activated dissociation (CAD) mass spectrometry (MS). The order of complex stability correlated almost linearly with the number of ligand atoms that can potentially be involved in hydrogen-bond or salt-bridge interactions with the RNA, but not with the proton affinity of the ligands. However, ligand dissociation of the complex ions in CAD was generally accompanied by proton transfer from ligand to RNA, which indicated conversion of salt-bridge into hydrogen-bond interactions. The relative stabilities and dissociation pathways of [RNA+m L-n H] n- complexes with different stoichiometries (m=1-5) and net charge (n= 2-5) revealed both specific and unspecific ligand binding to the RNA.
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Affiliation(s)
- Jovana Vušurović
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Eva‐Maria Schneeberger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
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36
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Zhang Z, Vachet RW. Gas-Phase Protein Salt Bridge Stabilities from Collisional Activation and Electron Transfer Dissociation. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2017; 420:51-56. [PMID: 29056866 PMCID: PMC5646825 DOI: 10.1016/j.ijms.2016.09.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The gas phase structures of several proteins have been studied by electron transfer dissociation (ETD) with and without prior collisional heating after electrospraying these proteins from native-like solutions into a quadrupole ion trap mass spectrometer. Without prior collisional heating, we find that ETD fragmentation is mostly limited to regions of the protein that are not spanned by the salt bridges known to form in solution. When protein ions are collisionally heated before ETD, new product ions are observed, and in almost all cases, these new ions arise from protein regions that are spanned by the salt bridges. Together these results confirm the existence of salt bridges in protein ions and demonstrate that a sufficient amount energy is required to disrupt these salt bridges in the gas phase. More interestingly, we also show that different salt bridges require different collisional activation voltages to be disrupted, suggesting that they have variable stabilities in the gas phase. These stabilities appear to be influenced by the gas-phase basicities of the involved residues and the presence of nearby charged residues. We also find that higher collisional activation voltages are needed to enable the formation of new product from sites spanned by multiple salt bridges.
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Affiliation(s)
| | - Richard W. Vachet
- Address: Department of Chemistry, LGRT 104, 710 N. Pleasant St., University of Massachusetts, Amherst, MA 01003,
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37
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Konermann L. Molecular Dynamics Simulations on Gas-Phase Proteins with Mobile Protons: Inclusion of All-Atom Charge Solvation. J Phys Chem B 2017; 121:8102-8112. [DOI: 10.1021/acs.jpcb.7b05703] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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38
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Lyon YA, Beran G, Julian RR. Leveraging Electron Transfer Dissociation for Site Selective Radical Generation: Applications for Peptide Epimer Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1365-1373. [PMID: 28374314 PMCID: PMC5497491 DOI: 10.1007/s13361-017-1627-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 02/07/2017] [Accepted: 02/08/2017] [Indexed: 06/07/2023]
Abstract
Traditional electron-transfer dissociation (ETD) experiments operate through a complex combination of hydrogen abundant and hydrogen deficient fragmentation pathways, yielding c and z ions, side-chain losses, and disulfide bond scission. Herein, a novel dissociation pathway is reported, yielding homolytic cleavage of carbon-iodine bonds via electronic excitation. This observation is very similar to photodissociation experiments where homolytic cleavage of carbon-iodine bonds has been utilized previously, but ETD activation can be performed without addition of a laser to the mass spectrometer. Both loss of iodine and loss of hydrogen iodide are observed, with the abundance of the latter product being greatly enhanced for some peptides after additional collisional activation. These observations suggest a novel ETD fragmentation pathway involving temporary storage of the electron in a charge-reduced arginine side chain. Subsequent collisional activation of the peptide radical produced by loss of HI yields spectra dominated by radical-directed dissociation, which can be usefully employed for identification of peptide isomers, including epimers. Graphical Abstract ᅟ.
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Affiliation(s)
- Yana A Lyon
- Department of Chemistry, University of California-Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Gregory Beran
- Department of Chemistry, University of California-Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Ryan R Julian
- Department of Chemistry, University of California-Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA.
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39
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Schneeberger E, Breuker K. Native Top-Down Mass Spectrometry of TAR RNA in Complexes with a Wild-Type tat Peptide for Binding Site Mapping. Angew Chem Int Ed Engl 2017; 56:1254-1258. [PMID: 28000363 PMCID: PMC5299493 DOI: 10.1002/anie.201610836] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Indexed: 12/18/2022]
Abstract
Ribonucleic acids (RNA) frequently associate with proteins in many biological processes to form more or less stable complex structures. The characterization of RNA-protein complex structures and binding interfaces by nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography, or strategies based on chemical crosslinking, however, can be quite challenging. Herein, we have explored the use of an alternative method, native top-down mass spectrometry (MS), for probing of complex stoichiometry and protein binding sites at the single-residue level of RNA. Our data show that the electrostatic interactions between HIV-1 TAR RNA and a peptide comprising the arginine-rich binding region of tat protein are sufficiently strong in the gas phase to survive phosphodiester backbone cleavage of RNA by collisionally activated dissociation (CAD), thus allowing its use for probing tat binding sites in TAR RNA by top-down MS. Moreover, the MS data reveal time-dependent 1:2 and 1:1 stoichiometries of the TAR-tat complexes and suggest structural rearrangements of TAR RNA induced by binding of tat peptide.
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Affiliation(s)
- Eva‐Maria Schneeberger
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität InnsbruckInnrain 80-826020InnsbruckAustria
| | - Kathrin Breuker
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität InnsbruckInnrain 80-826020InnsbruckAustria
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40
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Schneeberger E, Breuker K. Native Top‐Down Mass Spectrometry of TAR RNA in Complexes with a Wild‐Type tat Peptide for Binding Site Mapping. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201610836] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Eva‐Maria Schneeberger
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI) Universität Innsbruck Innrain 80-82 6020 Innsbruck Austria
| | - Kathrin Breuker
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI) Universität Innsbruck Innrain 80-82 6020 Innsbruck Austria
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41
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Holden DD, Brodbelt JS. Ultraviolet Photodissociation of Native Proteins Following Proton Transfer Reactions in the Gas Phase. Anal Chem 2016; 88:12354-12362. [PMID: 28193062 DOI: 10.1021/acs.analchem.6b03565] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The growing use of mass spectrometry in the field of structural biology has catalyzed the development of many new strategies to examine intact proteins in the gas phase. Native mass spectrometry methods have further accelerated the need for methods that can manipulate proteins and protein complexes while minimizing disruption of noncovalent interactions critical for stabilizing conformations. Proton-transfer reactions (PTR) in the gas phase offer the ability to effectively modulate the charge states of proteins, allowing decongestion of mass spectra through separation of overlapping species. PTR was combined with ultraviolet photodissociation (UVPD) to probe the degree of structural changes that occur upon charge reduction reactions in the gas phase. For protein complexes myoglobin·heme (17.6 kDa) and dihydrofolate reductase·methotrexate (19.4 kDa), minor changes were found in the fragmentation patterns aside from some enhancement of fragmentation near the N- and C-terminal regions consistent with slight fraying. After finding little perturbation was caused by charge reduction using PTR, homodimeric superoxide dismutase/CuZn (31.4 kDa) was subjected to PTR in order to separate overlapping monomer and dimer species of the protein that were observed at identical m/z values.
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Affiliation(s)
- Dustin D Holden
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
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42
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Cammarata MB, Schardon CL, Mehaffey MR, Rosenberg J, Singleton J, Fast W, Brodbelt JS. Impact of G12 Mutations on the Structure of K-Ras Probed by Ultraviolet Photodissociation Mass Spectrometry. J Am Chem Soc 2016; 138:13187-13196. [DOI: 10.1021/jacs.6b04474] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael B. Cammarata
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Christopher L. Schardon
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - M. Rachel Mehaffey
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Jake Rosenberg
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Jonathan Singleton
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Walter Fast
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
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43
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Morrison LJ, Brodbelt JS. 193 nm Ultraviolet Photodissociation Mass Spectrometry of Tetrameric Protein Complexes Provides Insight into Quaternary and Secondary Protein Topology. J Am Chem Soc 2016; 138:10849-59. [PMID: 27480400 DOI: 10.1021/jacs.6b03905] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein-protein interfaces and architecture are critical to the function of multiprotein complexes. Mass spectrometry-based techniques have emerged as powerful strategies for characterization of protein complexes, particularly for heterogeneous mixtures of structures. In the present study, activation and dissociation of three tetrameric protein complexes (streptavidin, transthyretin, and hemoglobin) in the gas phase was undertaken by 193 nm ultraviolet photodissociation (UVPD) for the characterization of higher order structure. High pulse energy UVPD resulted in the production of dimers and low charged monomers exhibiting symmetrical charge partitioning among the subunits (the so-called symmetrical dissociation pathways), consistent with the subunit organization of the complexes. In addition, UVPD promoted backbone cleavages of the monomeric subunits, the abundances of which corresponded to the more flexible loop regions of the proteins.
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Affiliation(s)
- Lindsay J Morrison
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
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44
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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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45
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Voronina L, Masson A, Kamrath M, Schubert F, Clemmer D, Baldauf C, Rizzo T. Conformations of Prolyl–Peptide Bonds in the Bradykinin 1–5 Fragment in Solution and in the Gas Phase. J Am Chem Soc 2016; 138:9224-33. [DOI: 10.1021/jacs.6b04550] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Liudmila Voronina
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Antoine Masson
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Michael Kamrath
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Franziska Schubert
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, D-14195 Berlin, Germany
| | - David Clemmer
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Carsten Baldauf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, D-14195 Berlin, Germany
| | - Thomas Rizzo
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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46
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Zhang Y, Cui W, Wecksler AT, Zhang H, Molina P, Deperalta G, Gross ML. Native MS and ECD Characterization of a Fab-Antigen Complex May Facilitate Crystallization for X-ray Diffraction. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1139-42. [PMID: 27103115 PMCID: PMC4899112 DOI: 10.1007/s13361-016-1398-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 05/11/2023]
Abstract
Native mass spectrometry (MS) and top-down electron-capture dissociation (ECD) combine as a powerful approach for characterizing large proteins and protein assemblies. Here, we report their use to study an antibody Fab (Fab-1)-VEGF complex in its near-native state. Native ESI with analysis by FTICR mass spectrometry confirms that VEGF is a dimer in solution and that its complex with Fab-1 has a binding stoichiometry of 2:2. Applying combinations of collisionally activated dissociation (CAD), ECD, and infrared multiphoton dissociation (IRMPD) allows identification of flexible regions of the complex, potentially serving as a guide for crystallization and X-ray diffraction analysis. Graphical Abstract ᅟ.
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Affiliation(s)
- Ying Zhang
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
- Analytical Research and Development, Pfizer Inc., Chesterfield, MO, 63017, USA
| | - Weidong Cui
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
| | - Aaron T Wecksler
- Protein Analytical Chemistry, Genentech, a Member of the Roche Group, South San Francisco, CA, 94080, USA
| | - Hao Zhang
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
| | - Patricia Molina
- Protein Analytical Chemistry, Genentech, a Member of the Roche Group, South San Francisco, CA, 94080, USA
| | - Galahad Deperalta
- Protein Analytical Chemistry, Genentech, a Member of the Roche Group, South San Francisco, CA, 94080, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA.
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Bartman CE, Metwally H, Konermann L. Effects of Multidentate Metal Interactions on the Structure of Collisionally Activated Proteins: Insights from Ion Mobility Spectrometry and Molecular Dynamics Simulations. Anal Chem 2016; 88:6905-13. [DOI: 10.1021/acs.analchem.6b01627] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Claire E. Bartman
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Haidy Metwally
- 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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48
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Loo RRO, Loo JA. Salt Bridge Rearrangement (SaBRe) Explains the Dissociation Behavior of Noncovalent Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:975-90. [PMID: 27052739 PMCID: PMC4865452 DOI: 10.1007/s13361-016-1375-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Revised: 02/28/2016] [Accepted: 03/01/2016] [Indexed: 05/11/2023]
Abstract
Native electrospray ionization-mass spectrometry, with gas-phase activation and solution compositions that partially release subcomplexes, can elucidate topologies of macromolecular assemblies. That so much complexity can be preserved in gas-phase assemblies is remarkable, although a long-standing conundrum has been the differences between their gas- and solution-phase decompositions. Collision-induced dissociation of multimeric noncovalent complexes typically distributes products asymmetrically (i.e., by ejecting a single subunit bearing a large percentage of the excess charge). That unexpected behavior has been rationalized as one subunit "unfolding" to depart with more charge. We present an alternative explanation based on heterolytic ion-pair scission and rearrangement, a mechanism that inherently partitions charge asymmetrically. Excessive barriers to dissociation are circumvented in this manner, when local charge rearrangements access a lower-barrier surface. An implication of this ion pair consideration is that stability differences between high- and low-charge state ions usually attributed to Coulomb repulsion may, alternatively, be conveyed by attractive forces from ion pairs (salt bridges) stabilizing low-charge state ions. Should the number of ion pairs be roughly inversely related to charge, symmetric dissociations would be favored from highly charged complexes, as observed. Correlations between a gas-phase protein's size and charge reflect the quantity of restraining ion pairs. Collisionally-facilitated salt bridge rearrangement (SaBRe) may explain unusual size "contractions" seen for some activated, low charge state complexes. That some low-charged multimers preferentially cleave covalent bonds or shed small ions to disrupting noncovalent associations is also explained by greater ion pairing in low charge state complexes. Graphical Abstract ᅟ.
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Affiliation(s)
- Rachel R Ogorzalek Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, 90095, USA.
| | - Joseph A Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, 90095, USA.
- UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA.
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49
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Schennach M, Schneeberger EM, Breuker K. Unfolding and Folding of the Three-Helix Bundle Protein KIX in the Absence of Solvent. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1079-88. [PMID: 26936183 PMCID: PMC4863917 DOI: 10.1007/s13361-016-1363-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 05/11/2023]
Abstract
Electron capture dissociation was used to probe the structure, unfolding, and folding of KIX ions in the gas phase. At energies for vibrational activation that were sufficiently high to cause loss of small molecules such as NH3 and H2O by breaking of covalent bonds in about 5% of the KIX (M + nH)(n+) ions with n = 7-9, only partial unfolding was observed, consistent with our previous hypothesis that salt bridges play an important role in stabilizing the native solution fold after transfer into the gas phase. Folding of the partially unfolded ions on a timescale of up to 10 s was observed only for (M + nH)(n+) ions with n = 9, but not n = 7 and n = 8, which we attribute to differences in the distribution of charges within the (M + nH)(n+) ions. Graphical Abstract ᅟ.
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Affiliation(s)
- Moritz Schennach
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Eva-Maria Schneeberger
- 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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50
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Affiliation(s)
- Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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