1
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Thibert S, Reid DJ, Wilson JW, Varikoti R, Maltseva N, Schultz KJ, Kruel A, Babnigg G, Joachimiak A, Kumar N, Zhou M. Native Mass Spectrometry Dissects the Structural Dynamics of an Allosteric Heterodimer of SARS-CoV-2 Nonstructural Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:912-921. [PMID: 38535992 PMCID: PMC11066969 DOI: 10.1021/jasms.3c00453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 05/02/2024]
Abstract
Structure-based drug design, which relies on precise understanding of the target protein and its interaction with the drug candidate, is dramatically expedited by advances in computational methods for candidate prediction. Yet, the accuracy needs to be improved with more structural data from high throughput experiments, which are challenging to generate, especially for dynamic and weak associations. Herein, we applied native mass spectrometry (native MS) to rapidly characterize ligand binding of an allosteric heterodimeric complex of SARS-CoV-2 nonstructural proteins (nsp) nsp10 and nsp16 (nsp10/16), a complex essential for virus survival in the host and thus a desirable drug target. Native MS showed that the dimer is in equilibrium with monomeric states in solution. Consistent with the literature, well characterized small cosubstrate, RNA substrate, and product bind with high specificity and affinity to the dimer but not the free monomers. Unsuccessfully designed ligands bind indiscriminately to all forms. Using neutral gas collision, the nsp16 monomer with bound cosubstrate can be released from the holo dimer complex, confirming the binding to nsp16 as revealed by the crystal structure. However, we observed an unusual migration of the endogenous zinc ions bound to nsp10 to nsp16 after collisional dissociation. The metal migration can be suppressed by using surface collision with reduced precursor charge states, which presumably resulted in minimal gas-phase structural rearrangement and highlighted the importance of complementary techniques. With minimal sample input (∼μg), native MS can rapidly detect ligand binding affinities and locations in dynamic multisubunit protein complexes, demonstrating the potential of an "all-in-one" native MS assay for rapid structural profiling of protein-to-AI-based compound systems to expedite drug discovery.
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Affiliation(s)
- Stephanie
M. Thibert
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Deseree J. Reid
- Chemical
and Biological Signature Sciences, Pacific
Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jesse W. Wilson
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Rohith Varikoti
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Natalia Maltseva
- Center
for Structural Biology of Infectious Diseases, Consortium for Advanced
Science and Engineering, University of Chicago, Chicago, Illinois 60637, United States
- Structural
Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Katherine J. Schultz
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Agustin Kruel
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Gyorgy Babnigg
- Center
for Structural Biology of Infectious Diseases, Consortium for Advanced
Science and Engineering, University of Chicago, Chicago, Illinois 60637, United States
- Biosciences
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Andrzej Joachimiak
- Center
for Structural Biology of Infectious Diseases, Consortium for Advanced
Science and Engineering, University of Chicago, Chicago, Illinois 60637, United States
- Structural
Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Neeraj Kumar
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Mowei Zhou
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
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2
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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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3
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Zhuang X, Li X, Zhao B, Liu Z, Song F, Lu J. Native Mass Spectrometry Based Method for Studying the Interactions between Superoxide Dismutase 1 and Stilbenoids. ACS Chem Neurosci 2020; 11:184-190. [PMID: 31820923 DOI: 10.1021/acschemneuro.9b00574] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
To inhibit the abnormal aggregation of Cu, Zn-superoxide dismutase (SOD1) is regarded as a potential therapeutic strategy of SOD1-linked amyotrophic lateral sclerosis (ALS). Herein the interactions between SOD1 and four stilbene-based polyphenols, namely, resveratrol, oxyresveratrol, polydatin, and 2,3,4',5-tetrahydroxystilbene-2-O-β-d-glycoside (THSG), were investigated using electrospray ionization mass spectrometry (ESI-MS) combined with ion mobility (IM) spectrometry. The addition of tandem MS to the study of SOD1-ligand complexes provides further insight into their gas-phase stability. Monitoring the unfolding of SOD1-ligand complexes using IM-MS allows observation of subtle changes in the protein stability upon ligand binding. From the MS/MS and IM-MS measurements, polydatin and THSG were highlighted as the strongest bound compounds in the gas phase, and both of them appear to provide a stabilizing effect on the SOD1 dimer conformation. In addition, the data of fluorescence assays clearly show the ability of the ligands to inhibit apoSOD1 from aggregation, and polydatin was found to have the strongest inhibitory effect. Overall, the method described here can be an effective approach to investigate the interactions between SOD1 and other drug-like molecules.
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Affiliation(s)
- Xiaoyu Zhuang
- School of Phamacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
- Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Xiuxiu Li
- School of Phamacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Bing Zhao
- National Center of Mass Spectrometry in Changchun & Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Zhiqiang Liu
- National Center of Mass Spectrometry in Changchun & Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Fengrui Song
- National Center of Mass Spectrometry in Changchun & Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Jianzhong Lu
- School of Phamacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
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4
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Hong S, Bush MF. Collision-Induced Unfolding Is Sensitive to the Polarity of Proteins and Protein Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2430-2437. [PMID: 31502225 DOI: 10.1007/s13361-019-02326-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 08/11/2019] [Accepted: 08/16/2019] [Indexed: 06/10/2023]
Abstract
Collision-induced unfolding (CIU) uses ion mobility to probe the structures of ions of proteins and noncovalent complexes as a function of the extent of gas-phase activation prior to analysis. CIU can be sensitive to domain structures, isoform identities, and binding partners, which makes it appealing for many applications. Almost all previous applications of CIU have probed cations. Here, we evaluate the application of CIU to anions and compare the results for anions with those for cations. Towards that end, we developed a "similarity score" that we used to quantify the differences between the results of different CIU experiments and evaluate the significance of those differences relative to the variance of the underlying measurements. Many of the differences between anions and cations that were identified can be attributed to the lower absolute charge states of anions. For example, the extents of the increase in collision cross section over the full range of energies depended strongly on absolute charge state. However, over intermediate energies, there are significant difference between anions and cations with the same absolute charge state. Therefore, CIU is sensitive to the polarity of protein ions. Based on these results, we propose that the utility of CIU to differentiate similar proteins or noncovalent complexes may also depend on polarity. More generally, these results indicate that the relationship between the structures and dynamics of native-like cations and anions deserve further attention and that future studies may benefit from integrating results from ions of both polarities.
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Affiliation(s)
- Seoyeon Hong
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA.
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5
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Lermyte F, Everett J, Lam YPY, Wootton CA, Brooks J, Barrow MP, Telling ND, Sadler PJ, O'Connor PB, Collingwood JF. Metal Ion Binding to the Amyloid β Monomer Studied by Native Top-Down FTICR Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2123-2134. [PMID: 31350722 PMCID: PMC6805827 DOI: 10.1007/s13361-019-02283-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/01/2019] [Accepted: 07/01/2019] [Indexed: 05/22/2023]
Abstract
Native top-down mass spectrometry is a fast, robust biophysical technique that can provide molecular-scale information on the interaction between proteins or peptides and ligands, including metal cations. Here we have analyzed complexes of the full-length amyloid β (1-42) monomer with a range of (patho)physiologically relevant metal cations using native Fourier transform ion cyclotron resonance mass spectrometry and three different fragmentation methods-collision-induced dissociation, electron capture dissociation, and infrared multiphoton dissociation-all yielding consistent results. Amyloid β is of particular interest as its oligomerization and aggregation are major events in the etiology of Alzheimer's disease, and it is known that interactions between the peptide and bioavailable metal cations have the potential to significantly damage neurons. Those metals which exhibited the strongest binding to the peptide (Cu2+, Co2+, Ni2+) all shared a very similar binding region containing two of the histidine residues near the N-terminus (His6, His13). Notably, Fe3+ bound to the peptide only when stabilized toward hydrolysis, aggregation, and precipitation by a chelating ligand, binding in the region between Ser8 and Gly25. We also identified two additional binding regions near the flexible, hydrophobic C-terminus, where other metals (Mg2+, Ca2+, Mn2+, Na+, and K+) bound more weakly-one centered on Leu34, and one on Gly38. Unexpectedly, collisional activation of the complex formed between the peptide and [CoIII(NH3)6]3+ induced gas-phase reduction of the metal to CoII, allowing the peptide to fragment via radical-based dissociation pathways. This work demonstrates how native mass spectrometry can provide new insights into the interactions between amyloid β and metal cations.
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Affiliation(s)
- Frederik Lermyte
- School of Engineering, University of Warwick, Coventry, CV4 7AL, UK.
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - James Everett
- School of Engineering, University of Warwick, Coventry, CV4 7AL, UK
- Institute for Science and Technology in Medicine, Keele University, Stoke-on-Trent, Staffordshire, ST4 7QB, UK
| | - Yuko P Y Lam
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Jake Brooks
- School of Engineering, University of Warwick, Coventry, CV4 7AL, UK
| | - Mark P Barrow
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Neil D Telling
- Institute for Science and Technology in Medicine, Keele University, Stoke-on-Trent, Staffordshire, ST4 7QB, UK
| | - Peter J Sadler
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
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6
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Stiving AQ, VanAernum ZL, Busch F, Harvey SR, Sarni SH, Wysocki VH. Surface-Induced Dissociation: An Effective Method for Characterization of Protein Quaternary Structure. Anal Chem 2019; 91:190-209. [PMID: 30412666 PMCID: PMC6571034 DOI: 10.1021/acs.analchem.8b05071] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Alyssa Q. Stiving
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Zachary L. VanAernum
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Florian Busch
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
| | - Samantha H. Sarni
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210
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7
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Busch F, Van Aernum ZL, Ju Y, Yan J, Gilbert JD, Quintyn RS, Bern M, Wysocki VH. Localization of Protein Complex Bound Ligands by Surface-Induced Dissociation High-Resolution Mass Spectrometry. Anal Chem 2018; 90:12796-12801. [PMID: 30299922 PMCID: PMC7307135 DOI: 10.1021/acs.analchem.8b03263] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Surface-induced dissociation (SID) is a powerful means of deciphering protein complex quaternary structures due to its capability of yielding dissociation products that reflect the native structures of protein complexes in solution. Here we explore the suitability of SID to locate the ligand binding sites in protein complexes. We studied C-reactive protein (CRP) pentamer, which contains a ligand binding site within each subunit, and cholera toxin B (CTB) pentamer, which contains a ligand binding site between each adjacent subunit. SID dissects ligand-bound CRP into subcomplexes with each subunit carrying predominantly one ligand. In contrast, SID of ligand-bound CTB results in the generation of subcomplexes with a ligand distribution reflective of two subunits contributing to each ligand binding site. SID thus has potential application in localizing sites of small ligand binding for multisubunit protein-ligand complexes.
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Affiliation(s)
- Florian Busch
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Zachary L. Van Aernum
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Yue Ju
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jing Yan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Joshua D. Gilbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Royston S. Quintyn
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Marshall Bern
- Protein Metrics Inc., 20863 Stevens Creek Blvd., Suite 450, Cupertino, California 95014, USA
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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8
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Reid DJ, Keener JE, Wheeler AP, Zambrano DE, Diesing JM, Reinhardt-Szyba M, Makarov A, Marty MT. Engineering Nanodisc Scaffold Proteins for Native Mass Spectrometry. Anal Chem 2017; 89:11189-11192. [PMID: 29048874 DOI: 10.1021/acs.analchem.7b03569] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lipoprotein nanodiscs are ideally suited for native mass spectrometry because they provide a relatively monodisperse nanoscale lipid bilayer environment for delivering membrane proteins into the gas phase. However, native mass spectrometry of nanodiscs produces complex spectra that can be challenging to assign unambiguously. To simplify interpretation of nanodisc spectra, we engineered a series of mutant membrane scaffold proteins (MSP) that do not affect nanodisc formation but shift the masses of nanodiscs in a controllable way, eliminating isobaric interference from the lipids. Moreover, by mixing two different belts before assembly, the stoichiometry of MSP is encoded in the peak shape, which allows the stoichiometry to be assigned unambiguously from a single spectrum. Finally, we demonstrate the use of mixed belt nanodiscs with embedded membrane proteins to confirm the dissociation of MSP prior to desolvation.
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Affiliation(s)
- Deseree J Reid
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | - James E Keener
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | - Andrew P Wheeler
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | - Dane Evan Zambrano
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | - Jessica M Diesing
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | | | | | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
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9
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Jovanović M, Peter-Katalinić J. Preliminary mass spectrometry characterization studies of galectin-3 samples, prior to carbohydrate-binding studies using Affinity mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:129-136. [PMID: 27791284 DOI: 10.1002/rcm.7775] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 09/11/2016] [Accepted: 10/24/2016] [Indexed: 05/22/2023]
Abstract
RATIONALE Investigation of non-covalent complexes of proteins using Affinity Mass Spectrometry (AMS) represents a major challenge in modern biomedical research. However, many experimental obstacles can make AMS data analysis complex. Additionally, sample purity and size of the protein may still pose significant challenges. METHODS Matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry (MS) was used for initial mapping of protein samples. nanoESI (electrospray ionization) quadrupole-time-of-flight (QTOF) MS was used for mapping of protein samples under native conditions and subsequent AMS studies. The human galectin-3 protein sample was expressed in E. coli. RESULTS Full length galectin-3 was difficult to work with, due to several truncated forms observed after the purification procedures. On the other hand, galectin-3C produced excellent quality nanoESI-MS spectra. A covalent adduct of lactose was found to be located on residue Lys 176. Functional AMS control studies indicated that galectin-3 interactions with oligosaccharides may be dependent on its charge. CONCLUSIONS Mass spectrometry represents a valuable tool that can be efficiently used for structural characterization of protein samples prior to functional analyses. By means of accurate mass measurements, many protein truncations can be identified based on mass alone. Analysis of covalent adducts is more challenging. Finally, for AMS studies, careful use of controls may reveal charge-dependence of protein-oligosaccharide interactions. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Marko Jovanović
- Institute of Medical Physics and Biophysics, University of Münster, Robert-Koch-Strasse 31, D-48149, Münster, Germany
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, 51 000, Rijeka, Croatia
| | - Jasna Peter-Katalinić
- Institute of Medical Physics and Biophysics, University of Münster, Robert-Koch-Strasse 31, D-48149, Münster, Germany
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10
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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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11
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Sharon M, Horovitz A. Probing allosteric mechanisms using native mass spectrometry. Curr Opin Struct Biol 2015; 34:7-16. [PMID: 26005781 DOI: 10.1016/j.sbi.2015.05.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 05/01/2015] [Accepted: 05/04/2015] [Indexed: 11/16/2022]
Abstract
Native mass spectrometry (MS) and ion mobility MS provide a way to discriminate between various allosteric mechanisms that cannot be distinguished using ensemble measurements of ligand binding in bulk protein solutions. Native MS, which yields mass measurements of intact assemblies, can be used to determine the values of ligand binding constants of multimeric allosteric proteins, thereby providing a way to distinguish, for example, between concerted and sequential allosteric models. Native MS can also be employed to study cooperativity owing to ligand-modulated protein oligomerization. The rotationally averaged cross-section areas of complexes obtained by ion mobility MS can be used to distinguish between induced fit and conformational selection. Native MS and its allied techniques are, therefore, becoming increasingly powerful tools for dissecting allosteric mechanisms.
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Affiliation(s)
- Michal Sharon
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Amnon Horovitz
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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12
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Han L, Tan M, Xia M, Kitova EN, Jiang X, Klassen JS. Gangliosides are ligands for human noroviruses. J Am Chem Soc 2014; 136:12631-7. [PMID: 25105447 PMCID: PMC4160279 DOI: 10.1021/ja505272n] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
![]()
Human
noroviruses (NoVs) are known to recognize histo-blood group
antigens (HBGAs) as attachment factors. We report the first experimental
evidence that sialic acid-containing glycosphingolipids (gangliosides)
are also ligands for human NoVs. Electrospray ionization mass spectrometry-based
carbohydrate binding measurements performed on assemblies (P dimer,
P particle, and virus-like particle) of recombinant viral capsid proteins
of two NoV strains, VA387 (GII.4) and VA115 (GI.3), identified binding
to the oligosaccharides of mono-, di-, and trisialylated gangliosides.
The intrinsic (per binding site) affinities measured for these ligands
are similar in magnitude (102–103 M–1) to those of human HBGAs. Binding of NoV VLPs, P
particles, and glutathione S-transferase (GST)-P domain fusion proteins
to sialic acid-containing glycoconjugates, observed in enzyme-linked
immunosorbent assays, provided additional confirmation of the NoV–ganglioside
interactions.
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Affiliation(s)
- Ling Han
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
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13
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Lössl P, Snijder J, Heck AJR. Boundaries of mass resolution in native mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:906-17. [PMID: 24700121 DOI: 10.1007/s13361-014-0874-3] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 02/18/2014] [Accepted: 02/28/2014] [Indexed: 05/10/2023]
Abstract
Over the last two decades, native mass spectrometry (MS) has emerged as a valuable tool to study intact proteins and noncovalent protein complexes. Studied experimental systems range from small-molecule (drug)-protein interactions, to nanomachineries such as the proteasome and ribosome, to even virus assembly. In native MS, ions attain high m/z values, requiring special mass analyzers for their detection. Depending on the particular mass analyzer used, instrumental mass resolution does often decrease at higher m/z but can still be above a couple of thousand at m/z 5000. However, the mass resolving power obtained on charge states of protein complexes in this m/z region is experimentally found to remain well below the inherent instrument resolution of the mass analyzers employed. Here, we inquire into reasons for this discrepancy and ask how native MS would benefit from higher instrumental mass resolution. To answer this question, we discuss advantages and shortcomings of mass analyzers used to study intact biomolecules and biomolecular complexes in their native state, and we review which other factors determine mass resolving power in native MS analyses. Recent examples from the literature are given to illustrate the current status and limitations.
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Affiliation(s)
- Philip Lössl
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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Leney AC, Fan X, Kitova EN, Klassen JS. Nanodiscs and Electrospray Ionization Mass Spectrometry: A Tool for Screening Glycolipids Against Proteins. Anal Chem 2014; 86:5271-7. [DOI: 10.1021/ac4041179] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aneika C. Leney
- Alberta Glycomics Centre
and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Xuxin Fan
- Alberta Glycomics Centre
and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Elena N. Kitova
- Alberta Glycomics Centre
and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - John S. Klassen
- Alberta Glycomics Centre
and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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15
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Liu J, Konermann L. Cation-induced stabilization of protein complexes in the gas phase: mechanistic insights from hemoglobin dissociation studies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:595-603. [PMID: 24452299 DOI: 10.1007/s13361-013-0814-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/13/2013] [Accepted: 12/14/2013] [Indexed: 06/03/2023]
Abstract
Collision-induced dissociation (CID) of electrosprayed protein complexes usually involves asymmetric charge partitioning, where a single unfolded chain gets ejected that carries a disproportionately large fraction of charge. Using hemoglobin (Hb) tetramers as model system, we confirm earlier reports that bound metal ions can stabilize protein complexes under CID conditions. We examine the mechanism underlying this effect. Nonvolatile salts cause extensive adduct formation. Significant stabilization was observed for Mg(2+) and Ca(2+), whereas K(+), Rb(+), and Cs(+) had no effect. Precursor ion selection was used to examine Hb subpopulations with well-defined metal binding levels. K(+), Rb(+), and Cs(+)-adducted tetramers eject monomers that carry roughly one-quarter of the metal ions that were bound to the precursor. This demonstrates that charge migration during CID is exclusively due to proton transfer, not metal ion transfer. Also, replacement of highly mobile charge carriers (protons) with less mobile species (metal ions) does not exert a stabilizing influence under the conditions used here. Interestingly, Hb carrying stabilizing ions (Mg(2+) and Ca(2+)) generates monomeric CID products that are metal depleted. This effect is attributed to a combination of two factors: (1) Me(2+) binding stabilizes Hb via formation of chelation bridges (e.g., R-COO(-) Me(2+) (-)OOC-R); the more Me(2+) a subunit contains the more stable it is. (2) More than ~90% of the tetramers contain at least one subunit with a below-average number of Me(2+). The prevalence of monomeric CID products with depleted Me(2+) levels is caused by the tendency of these low metal-containing subunits to undergo preferential unfolding/ejection.
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Affiliation(s)
- JiangJiang Liu
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
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Marty MT, Zhang H, Cui W, Gross ML, Sligar SG. Interpretation and deconvolution of nanodisc native mass spectra. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:269-77. [PMID: 24353133 PMCID: PMC3918181 DOI: 10.1007/s13361-013-0782-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 10/27/2013] [Accepted: 11/08/2013] [Indexed: 05/11/2023]
Abstract
Nanodiscs are a promising system for studying gas-phase and solution complexes of membrane proteins and lipids. We previously demonstrated that native electrospray ionization allows mass spectral analysis of intact Nanodisc complexes at single lipid resolution. This report details an improved theoretical framework for interpreting and deconvoluting native mass spectra of Nanodisc lipoprotein complexes. In addition to the intrinsic lipid count and charge distributions, Nanodisc mass spectra are significantly shaped by constructive overlap of adjacent charge states at integer multiples of the lipid mass. We describe the mathematical basis for this effect and develop a probability-based algorithm to deconvolute the underlying mass and charge distributions. The probability-based deconvolution algorithm is applied to a series of dimyristoylphosphatidylcholine Nanodisc native mass spectra and used to provide a quantitative picture of the lipid loss in gas-phase fragmentation.
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Affiliation(s)
- Michael T. Marty
- University of Illinois Urbana-Champaign, Department of Chemistry, Urbana, IL 61801
| | - Hao Zhang
- Washington University in St. Louis, Department of Chemistry, St. Louis, MO 63130
- Washington University in St. Louis, Photosynthetic Antenna Research Center (PARC), St. Louis, MO 63130
| | - Weidong Cui
- Washington University in St. Louis, Department of Chemistry, St. Louis, MO 63130
| | - Michael L. Gross
- Washington University in St. Louis, Department of Chemistry, St. Louis, MO 63130
| | - Stephen G. Sligar
- University of Illinois Urbana-Champaign, Department of Chemistry, Urbana, IL 61801
- University of Illinois Urbana-Champaign, Department of Biochemistry, Urbana, IL 61801
- Address reprint requests to: Stephen G. Sligar, 116 Morrill Hall, 505 S. Goodwin MC-119, Urbana, IL 61801, , Phone: 217-244-7395, Fax: 217-265-4073
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