1
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Shepherd SO, Green AW, Resendiz ES, Newton KR, Kurulugama RT, Prell JS. Effects of Nano-Electrospray Ionization Emitter Position on Unintentional In-Source Activation of Peptide and Protein Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:498-507. [PMID: 38374644 PMCID: PMC11315166 DOI: 10.1021/jasms.3c00371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Native ion mobility-mass spectrometry (IM-MS) typically introduces protein ions into the gas phase through nano-electrospray ionization (nESI). Many nESI setups have mobile stages for tuning the ion signal and extent of co-solute and salt adduction. However, tuning the position of the emitter capillary in nESI can have unintended downstream consequences for collision-induced unfolding or collision-induced dissociation (CIU/D) experiments. Here, we show that relatively small variations in the nESI emitter position can shift the midpoint (commonly called the "CID50" or "CIU50") potential of CID breakdown curves and CIU transitions by as much as 8 V on commercial instruments. A spatial "map" of the shift in CID50 for the loss of heme from holomyoglobin onto the emitter position on a Waters Synapt G2-Si mass spectrometer shows that emitter positions closer to the instrument inlet can result in significantly greater in-source activation, whereas different effects are found on an Agilent 6545XT instrument for the ions studied. A similar effect is observed for CID of the singly protonated leucine enkephalin peptide and Shiga toxin 1 subunit B homopentamer on the Waters Synapt G2-Si instrument. In-source activation effects on a Waters Synapt G2-Si are also investigated by examining the RMSD between CIU fingerprints acquired at different emitter positions and the shifts in CIU50 for structural transitions of bovine serum albumin and NIST monoclonal antibody.
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Affiliation(s)
- Samantha O. Shepherd
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA, 97403-1253
| | - Austin W. Green
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA, 97403-1253
| | - Elizabeth S. Resendiz
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA, 97403-1253
| | - Kenneth R. Newton
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA, 97403-1253
- 5301 Stevens Creek Blvd, Agilent Technologies, Santa Clara, 95051, CA, USA
| | | | - James S. Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA, 97403-1253
- Materials Science Institute, 1252 University of Oregon, Eugene, OR, USA, 97403-1252
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2
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Aliyari E, Konermann L. Atomistic Insights into the Formation of Nonspecific Protein Complexes during Electrospray Ionization. Anal Chem 2021; 93:12748-12757. [PMID: 34494821 DOI: 10.1021/acs.analchem.1c02836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Native electrospray ionization (ESI)-mass spectrometry (MS) is widely used for the detection and characterization of multi-protein complexes. A well-known problem with this approach is the possible occurrence of nonspecific protein clustering in the ESI plume. This effect can distort the results of binding affinity measurements, and it can even generate gas-phase complexes from proteins that are strictly monomeric in bulk solution. By combining experiments and molecular dynamics (MD) simulations, the current work for the first time provides detailed insights into the ESI clustering of proteins. Using ubiquitin as a model system, we demonstrate how the entrapment of more than one protein molecule in an ESI droplet can generate nonspecific clusters (e.g., dimers or trimers) via solvent evaporation to dryness. These events are in line with earlier proposals, according to which protein clustering is associated with the charged residue model (CRM). MD simulations on cytochrome c (which carries a large intrinsic positive charge) confirmed the viability of this CRM avenue. In addition, the cytochrome c data uncovered an alternative mechanism where protein-protein contacts were formed early within ESI droplets, followed by cluster ejection from the droplet surface. This second pathway is consistent with the ion evaporation model (IEM). The observation of these IEM events for large protein clusters is unexpected because the IEM has been thought to be associated primarily with low-molecular-weight analytes. In all cases, our MD simulations produced protein clusters that were stabilized by intermolecular salt bridges. The MD-generated charge states agreed with experiments. Overall, this work reveals that ESI-induced protein clustering does not follow a tightly orchestrated pathway but can proceed along different avenues.
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Affiliation(s)
- Elnaz Aliyari
- 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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3
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Albuquerque ADO, da Silva Junior HC, Sartori GR, Martins da Silva JH. Computationally-obtained structural insights into the molecular interactions between Pidilizumab and binding partners DLL1 and PD-1. J Biomol Struct Dyn 2021; 40:6450-6462. [PMID: 33559526 DOI: 10.1080/07391102.2021.1885492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Pidilizumab is a monoclonal antibody tested against several types of malignancies, such as lymphoma and metastatic melanoma, showing promising results. In 2016, the FDA put Pidilizumab's clinical studies on partial hold due to emerging evidence pointing to the antibody target uncertainty. Although initial studies indicated an interaction with the PD-1 checkpoint receptor, recent updates assert that Pidilizumab binds primarily to Notch ligand DLL1. However, a detailed description of which interactions coordinate antibody-antigen complex formation is lacking. Therefore, this study uses computational tools to identify molecular interactions between Pidilizumab and its reported targets PD-1 and DLL1. A docking methodology was validated and applied to determine the binding modes between modeled Pidilizumab scFvs and the two antigens. We used Molecular Dynamics (MD) simulations to verify the complexes' stability and submitted the resulting trajectory files to MM/PBSA and Principal Component Analysis. A set of different prediction tools determined scFv interface hot-spots. Whereas docking and MD simulations revealed that the antibody fragments do not interact straightforwardly with PD-1, ten scFv hot-spots, including Met93 and Leu112, mediated the interaction with the DLL1 C2 domain. The interaction triggered a conformational selection-like effect on DLL1, allowing new hydrogen bonds on the β3-β4 interface loop. The unprecedented structural data on Pidilizumab's interactions provided novel evidence that its legitimate target is the DLL1 protein and offered structural insight on how these molecules interact, shedding light on the pathways that could be affected by the use of this essential immunobiological.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Geraldo Rodrigues Sartori
- Grupo para Modelagem, Simulação e Evolução, in sílico, de Biomoléculas, Fiocruz-Ceará, Eusébio, Brazil
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4
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Yu Y, Liu H, Yu Z, Witkowska HE, Cheng Y. Stoichiometry of Nucleotide Binding to Proteasome AAA+ ATPase Hexamer Established by Native Mass Spectrometry. Mol Cell Proteomics 2020; 19:1997-2015. [PMID: 32883800 PMCID: PMC7710143 DOI: 10.1074/mcp.ra120.002067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 08/04/2020] [Indexed: 11/06/2022] Open
Abstract
AAA+ ATPases constitute a large family of proteins that are involved in a plethora of cellular processes including DNA disassembly, protein degradation and protein complex disassembly. They typically form a hexametric ring-shaped structure with six subunits in a (pseudo) 6-fold symmetry. In a subset of AAA+ ATPases that facilitate protein unfolding and degradation, six subunits cooperate to translocate protein substrates through a central pore in the ring. The number and type of nucleotides in an AAA+ ATPase hexamer is inherently linked to the mechanism that underlies cooperation among subunits and couples ATP hydrolysis with substrate translocation. We conducted a native MS study of a monodispersed form of PAN, an archaeal proteasome AAA+ ATPase, to determine the number of nucleotides bound to each hexamer of the WT protein. We utilized ADP and its analogs (TNP-ADP and mant-ADP), and a nonhydrolyzable ATP analog (AMP-PNP) to study nucleotide site occupancy within the PAN hexamer in ADP- and ATP-binding states, respectively. Throughout all experiments we used a Walker A mutant (PANK217A) that is impaired in nucleotide binding as an internal standard to mitigate the effects of residual solvation on mass measurement accuracy and to serve as a reference protein to control for nonspecific nucleotide binding. This approach led to the unambiguous finding that a WT PAN hexamer carried - from expression host - six tightly bound ADP molecules that could be exchanged for ADP and ATP analogs. Although the Walker A mutant did not bind ADP analogs, it did bind AMP-PNP, albeit at multiple stoichiometries. We observed variable levels of hexamer dissociation and an appearance of multimeric species with the over-charged molecular ion distributions across repeated experiments. We posit that these phenomena originated during ESI process at the final stages of ESI droplet evolution.
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Affiliation(s)
- Yadong Yu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Haichuan Liu
- Department of OBGYN & Reproductive Sci, Sandler-Moore MS Core Facility, University of California San Francisco, San Francisco, California, USA
| | - Zanlin Yu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - H Ewa Witkowska
- Department of OBGYN & Reproductive Sci, Sandler-Moore MS Core Facility, University of California San Francisco, San Francisco, California, USA.
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA; Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California, USA.
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5
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Oh MI, Consta S. General solvation motifs of a charged linear macroion in an aqueous droplet. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1596326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Myong In Oh
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
| | - Styliani Consta
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
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6
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Beveridge R, Migas LG, Das RK, Pappu RV, Kriwacki RW, Barran PE. Ion Mobility Mass Spectrometry Uncovers the Impact of the Patterning of Oppositely Charged Residues on the Conformational Distributions of Intrinsically Disordered Proteins. J Am Chem Soc 2019; 141:4908-4918. [PMID: 30823702 PMCID: PMC6488185 DOI: 10.1021/jacs.8b13483] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The
global dimensions and amplitudes of conformational fluctuations
of intrinsically disordered proteins are governed, in part, by the
linear segregation versus clustering of oppositely charged residues
within the primary sequence. Ion mobility-mass spectrometry (IM-MS)
affords unique advantages for probing the conformational consequences
of the linear patterning of oppositely charged residues because it
measures and separates proteins electrosprayed from solution on the
basis of charge and shape. Here, we use IM-MS to measure the conformational
consequences of charge patterning on the C-terminal intrinsically
disordered region (p27 IDR) of the cell cycle inhibitory protein p27Kip1. We report the range of charge states and accompanying
collisional cross section distributions for wild-type p27 IDR and
two variants with identical amino acid compositions, κ14 and
κ56, distinguished by the extent of linear mixing versus segregation
of oppositely charged residues. Wild-type p27 IDR (κ31) and
κ14, where the oppositely charged residues are more evenly distributed,
exhibit a broad distribution of charge states. This is concordant
with high degrees of conformational heterogeneity in solution. By
contrast, κ56 with linear segregation of oppositely charged
residues leads to limited conformational heterogeneity and a narrow
distribution of charged states. Gas-phase molecular dynamics simulations
demonstrate that the interplay between chain solvation and intrachain
interactions (self-solvation) leads to conformational distributions
that are modulated by salt concentration, with the wild-type sequence
showing the most sensitivity to changes in salt concentration. These
results suggest that the charge patterning within the wild-type p27
IDR may be optimized to sample both highly solvated and self-solvated
conformational states.
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Affiliation(s)
- Rebecca Beveridge
- The Michael Barber Centre for Collaborative Mass Spectrometry, The School of Chemistry, Manchester Institute for Biotechnology , University of Manchester , Manchester M13 9PL , U.K
| | - Lukasz G Migas
- The Michael Barber Centre for Collaborative Mass Spectrometry, The School of Chemistry, Manchester Institute for Biotechnology , University of Manchester , Manchester M13 9PL , U.K
| | - Rahul K Das
- Department of Biomedical Engineering and Center for Biological Systems Engineering , Washington University in St. Louis , Campus Box 1097, One Brookings Drive , St. Louis , Missouri 63130 , United States
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering , Washington University in St. Louis , Campus Box 1097, One Brookings Drive , St. Louis , Missouri 63130 , United States
| | - Richard W Kriwacki
- Structural Biology, MS 311, Room D1024F , St. Jude Children's Research Hospital , 262 Danny Thomas Place , Memphis , Tennessee 38105-3678 , United States
| | - Perdita E Barran
- The Michael Barber Centre for Collaborative Mass Spectrometry, The School of Chemistry, Manchester Institute for Biotechnology , University of Manchester , Manchester M13 9PL , U.K
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7
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Consta S, In Oh M, Kwan V, Malevanets A. Strengths and Weaknesses of Molecular Simulations of Electrosprayed Droplets. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2287-2296. [PMID: 30259408 DOI: 10.1007/s13361-018-2039-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 07/05/2018] [Accepted: 07/13/2018] [Indexed: 06/08/2023]
Abstract
The origin and the magnitude of the charge in a macroion are critical questions in mass spectrometry analysis coupled to electrospray and other ionization techniques that transfer analytes from the bulk solution into the gaseous phase via droplets. In many circumstances, it is the later stages of the existence of a macroion in the containing solvent drop before the detection that determines the final charge state. Experimental characterization of small (with linear dimensions of several nanometers) and short-lived droplets is quite challenging. Molecular simulations in principle may provide insight exactly in this challenging for experiments regime. We discuss the strengths and weaknesses of the molecular modeling of electrosprayed droplets using molecular dynamics. We illustrate the limitations of the molecular modeling in the analysis of large macroions and specifically proteins away from their native states. Graphical Abstract ᅟ.
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Affiliation(s)
- Styliani Consta
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada.
| | - Myong In Oh
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Victor Kwan
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Anatoly Malevanets
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
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8
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Consta S, Oh MI, Sharawy M, Malevanets A. Macroion–Solvent Interactions in Charged Droplets. J Phys Chem A 2018; 122:5239-5250. [DOI: 10.1021/acs.jpca.8b01404] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Styliani Consta
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7
| | - Myong In Oh
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7
| | - Mahmoud Sharawy
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7
| | - Anatoly Malevanets
- Department of Electrical and Computer Engineering, The University of University of Western Ontario, London, Ontario, Canada N6A 5B9
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9
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Oh MI, Consta S. What factors determine the stability of a weak protein-protein interaction in a charged aqueous droplet? Phys Chem Chem Phys 2018; 19:31965-31981. [PMID: 29177351 DOI: 10.1039/c7cp05043g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Maintaining the interface of a weak transient protein complex transferred from bulk solution to the gaseous state via evaporating droplets is a critical question in the detection of the complex association (dissociation) constant by using electrospray ionization mass spectrometry (ESI-MS). Here we explore the factors that may affect the stability of a protein-protein interaction (PPI) using atomistic molecular dynamics (MD) modelling of a complex of ubiquitin (Ub) and the ubiquitin-associated domain (UbA) (RCSB PDB code ) and a non-covalent complex of diubiquitin (RCSB PDB code ) in aqueous droplets. A general method is presented to determine the protonation states of the complexes we investigate in particular, and that of a protein in general, under various pH conditions that an evaporating droplet acquires due to its change in size. We find that the combination of high temperature and high charge states of the protein complexes may destabilize the interface by creating new interfaces instead of a direct rupture of the initial stable interface. We provide evidence that highly charged protein complexes are found in droplets that form conical extrusions of the solvent on the surface due to charge-induced instability. This distinct droplet morphology leads to a higher solvent evaporation rate that assists in transferring the complex in the gaseous state without dissociation. The conical solvent protrusions expose on the droplet surface certain amino acids that otherwise would be solvated in a droplet with the protein complex of low charge states. The new vapor-protein interface does not have a direct effect on the stability of the PPI. A common way in experiments to stabilize the protein complexes in droplets is to reduce the protonation state of the proteins. Here we find that weakly bound protein complexes even at high protonation states can be stabilized by the presence of a small number of counterions, without affecting the protonation state of the protein. Our findings may provide guiding principles in ESI-MS experiments to stabilize weak transient PPIs.
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Affiliation(s)
- Myong In Oh
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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10
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Oh MI, Malevanets A, Paliy M, Frenkel D, Consta S. When droplets become stars: charged dielectric droplets beyond the Rayleigh limit. SOFT MATTER 2017; 13:8781-8795. [PMID: 29139530 DOI: 10.1039/c7sm02017a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
When a nano-drop comprising a single spherical central ion and dielectric solvent is charged above a well-defined threshold, it acquires a stable star morphology. In contrast, conducting droplets, will undergo fission. Here we report combined atomistic molecular dynamics and continuum modelling study of star formation of droplets that contain a highly charged ion. We assume that in the continuum model the dielectric response is linear. In this linear continuum model, which is an extension of Rayleigh model, the energy of the drop is comprised of terms analogous to those in Rayleigh model, which are surface energy and electrostatic energy of dielectric droplet charged by a central point charge. We present the stability analysis of the continuum model to determine the threshold of instability. Indeed we find that the model accounts well for the onset of the instabilities. Molecular dynamics show that the number of points of the star-shaped nano-drops depends only on the surface tension, dielectric constant and size of the droplet, and on the magnitude of the charge of the central ion, but not on its sign. Intuitively, it is expected that when a spherical dielectric drop becomes unstable it would transform into a non-spherical finite shape of the same volume as the initial spherical shape with the point charge located in the drop interior. To test whether the extended Rayleigh model can account for the observed droplet shapes, we performed numerical simulations of the linear continuum model. Contrary to the expectations, the simulations of the extended Rayleigh model does not reproduce the stable star shapes found in the atomistic simulations, not even when we account for the bending rigidity and spontaneous curvature of the surface. We argue that the assumption that the dielectric response is linear breaks down if the droplet surface approaches the central macro-ion, where the electric field strength is such that dielectric saturation sets in. We envisage that for certain solvents, these stars could be made permanent by cross-linking, opening the way to the production of a novel class of highly-non-convex colloids.
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Affiliation(s)
- Myong In Oh
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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11
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Liigand P, Heering Suu A, Kaupmees K, Leito I, Girod M, Antoine R, Kruve A. The Evolution of Electrospray Generated Droplets is Not Affected by Ionization Mode. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2124-2131. [PMID: 28744770 DOI: 10.1007/s13361-017-1737-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/22/2017] [Accepted: 06/11/2017] [Indexed: 06/07/2023]
Abstract
Ionization efficiency and mechanism in ESI is strongly affected by the properties of mobile phase. The use of mobile-phase properties to accurately describe droplets in ESI source is convenient but may be inadequate as the composition of the droplets is changing in the plume due to electrochemical reactions occurring in the needle tip as well as continuous drying and fission of droplets. Presently, there is paucity of research on the effect of the polarity of the ESI mode on mobile phase composition in the droplets. In this paper, the change in the organic solvent content, pH, and droplet size are studied in the ESI plume in both ESI+ and ESI- ionization mode. We introduce a rigorous way - the absolute pH (pHabsH2O) - to describe pH change in the plume that takes into account organic solvent content in the mobile phase. pHabsH2O enables comparing acidities of ESI droplets with different organic solvent contents. The results are surprisingly similar for both ionization modes, indicating that the dynamics of the change of mobile-phase properties is independent from the ESI mode used. This allows us to conclude that the evolution of ESI droplets first of all proceeds via the evaporation of the organic modifier and to a lesser extent via fission of smaller droplets from parent droplets. Secondly, our study shows that qualitative findings related to the ESI process obtained on the ESI+ mode can almost directly be applied also in the ESI- mode. Graphical Abstract ᅟ.
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Affiliation(s)
- Piia Liigand
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411, Tartu, Estonia.
| | - Agnes Heering Suu
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411, Tartu, Estonia
| | - Karl Kaupmees
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411, Tartu, Estonia
| | - Ivo Leito
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411, Tartu, Estonia
| | - Marion Girod
- CNRS, Université Claude Bernard Lyon 1, Ens de Lyon, Institut des Sciences Analytiques, University of Lyon, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Rodolphe Antoine
- Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, University of Lyon, UMR 5306, F-69622, Lyon, France
| | - Anneli Kruve
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411, Tartu, Estonia
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Technion City, Haifa, 3200008, Israel
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12
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Konermann L. Addressing a Common Misconception: Ammonium Acetate as Neutral pH "Buffer" for Native Electrospray Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1827-1835. [PMID: 28710594 DOI: 10.1007/s13361-017-1739-3] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 06/14/2017] [Accepted: 06/15/2017] [Indexed: 05/12/2023]
Abstract
Native ESI-MS involves the transfer of intact proteins and biomolecular complexes from solution into the gas phase. One potential pitfall is the occurrence of pH-induced changes that can affect the analyte while it is still surrounded by solvent. Most native ESI-MS studies employ neutral aqueous ammonium acetate solutions. It is a widely perpetuated misconception that ammonium acetate buffers the analyte solution at neutral pH. By definition, a buffer consists of a weak acid and its conjugate weak base. The buffering range covers the weak acid pKa ± 1 pH unit. NH4+ and CH3-COO- are not a conjugate acid/base pair, which means that they do not constitute a buffer at pH 7. Dissolution of ammonium acetate salt in water results in pH 7, but this pH is highly labile. Ammonium acetate does provide buffering around pH 4.75 (the pKa of acetic acid) and around pH 9.25 (the pKa of ammonium). This implies that neutral ammonium acetate solutions electrosprayed in positive ion mode will likely undergo acidification down to pH 4.75 ± 1 in the ESI plume. Ammonium acetate nonetheless remains a useful additive for native ESI-MS. It is a volatile electrolyte that can mimic the solvation properties experienced by proteins under physiological conditions. Also, a drop from pH 7 to around pH 4.75 is less dramatic than the acidification that would take place in pure water. It is hoped that the habit of referring to pH 7 solutions as ammonium acetate "buffer" will disappear from the literature. Ammonium acetate "solution" should be used instead. Graphical Abstract ᅟ.
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Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada.
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13
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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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14
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Consta S, Sharawy M, Oh MI, Malevanets A. Advances in Modeling the Stability of Noncovalent Complexes in Charged Droplets with Applications in Electrospray Ionization-MS Experiments. Anal Chem 2017; 89:8192-8202. [DOI: 10.1021/acs.analchem.7b01941] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Styliani Consta
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Mahmoud Sharawy
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Myong In Oh
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Anatoly Malevanets
- Department
of Electrical and Computer Engineering, The University of Western Ontario, London, Ontario N6A 5B9, Canada
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