1
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Lantz C, Rider RL, Yun SD, Laganowsky A, Russell DH. Water Plays Key Roles in Stabilities of Wild Type and Mutant Transthyretin Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1854-1864. [PMID: 39057193 PMCID: PMC11311534 DOI: 10.1021/jasms.4c00170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 07/01/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024]
Abstract
Transthyretin (TTR), a 56 kDa homotetramer that is involved in the transport of thyroxine and retinol, has been linked to amyloidosis through disassembly of tetramers to form monomers, dimers, and trimers that then reassemble into higher order oligomers and/or fibrils. Hybrid TTR (hTTR) tetramers are found in heterozygous individuals that express both wild type TTR (wt-TTR) and mutant TTR (mTTR) forms of the protein, and these states display increased rates of amyloidosis. Here we monitor subunit exchange (SUE) reactions involving homomeric and mixed tetramers using high resolution native mass spectrometry (nMS). Our results show evidence that differences in TTR primary structure alter tetramer stabilities, and hTTR products can form spontaneously by SUE reactions. In addition, we find that solution temperature has strong effects on TTR tetramer stabilities and formation of SUE products. Lower temperatures promote formation of hTTR tetramers containing L55P and V30M subunits, whereas small effects on the formation of hTTR tetramers containing F87A and T119M subunits are observed. We hypothesize that the observed temperature dependent stabilities and subsequent SUE behavior are a result of perturbations to the network of "two kinds of water": hydrating and structure stabilizing water molecules (Spyrakis et al. J. Med. Chem. 2017, 60 (16), 6781-6827; Xu et al. Soft Matter 2012, 8, 324-336) that stabilize wt-TTR and mTTR tetramers. The results presented in this work illustrate the utility of high resolution nMS for studies of the structures, stabilities, and dynamics of protein complexes that directly influence SUE reactions.
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Affiliation(s)
- Carter Lantz
- Department of Chemistry, Texas A&M University, College
Station, Texas 77843, United States
| | - Robert L. Rider
- Department of Chemistry, Texas A&M University, College
Station, Texas 77843, United States
| | - Sangho D. Yun
- 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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2
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Lutomski CA, El-Baba TJ, Clemmer DE, Jarrold MF. Thermal Remodeling of Human HDL Particles Reveals Diverse Subspecies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:2002-2007. [PMID: 39051481 PMCID: PMC11311237 DOI: 10.1021/jasms.4c00228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/14/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
High-density lipoproteins (HDL) are micelle-like particles consisting of a core of triglycerides and cholesteryl esters surrounded by a shell of phospholipid, cholesterol, and apolipoproteins. HDL is considered "good" cholesterol, and its concentration in plasma is used clinically in assessing cardiovascular health. However, these particles vary in structure, composition, and therefore function, and thus can be resolved into subpopulations, some of which have specific cardioprotective properties. Mass measurements of HDL by charge detection mass spectrometry (CD-MS) previously revealed seven distinct subpopulations which could be delineated by mass and charge [Lutomski, C. A. et al. Anal. Chem. 2018]. Here, we investigate the thermal stabilities of these subpopulations; upon heating, the particles within each subpopulation undergo structural rearrangements with distinct transition temperatures. In addition, we find evidence for many new families of structures within each subpopulation; at least 15 subspecies of HDL are resolved. These subspecies vary in size, charge, and thermal stability. While this suggests that these new subspecies have unique molecular compositions, we cannot rule out the possibility that we have found evidence for new structural forms within the known subpopulations. The ability to resolve new subspecies of HDL particles may be important in understanding and delineating the role of unique particles in cardiovascular health and disease.
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Affiliation(s)
- Corinne A. Lutomski
- Department
of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, Indiana 47405, United States
| | - Tarick J. El-Baba
- Department
of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, Indiana 47405, United States
| | - David E. Clemmer
- Department
of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, Indiana 47405, United States
| | - Martin F. Jarrold
- Department
of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, Indiana 47405, United States
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3
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Jordan JS, Lee KJ, Williams ER. Overcoming aggregation with laser heated nanoelectrospray mass spectrometry: thermal stability and pathways for loss of bicarbonate from carbonic anhydrase II. Analyst 2024; 149:2281-2290. [PMID: 38497240 DOI: 10.1039/d4an00229f] [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: 03/19/2024]
Abstract
Variable temperature electrospray mass spectrometry is useful for multiplexed measurements of the thermal stabilities of biomolecules, but the ionization process can be disrupted by aggregation-prone proteins/complexes that have irreversible unfolding transitions. Resistively heating solutions containing a mixture of bovine carbonic anhydrase II (BCAII), a CO2 fixing enzyme involved in many biochemical pathways, and cytochrome c leads to complete loss of carbonic anhydrase signal and a significant reduction in cytochrome c signal above ∼72 °C due to aggregation. In contrast, when the tips of borosilicate glass nanoelectrospray emitters are heated with a laser, complete thermal denaturation curves for both proteins are obtained in <1 minute. The simultaneous measurements of the melting temperature of BCAII and BCAII bound to bicarbonate reveal that the bicarbonate stabilizes the folded form of this protein by ∼6.4 °C. Moreover, the temperature dependences of different bicarbonate loss pathways are obtained. Although protein analytes are directly heated by the laser for only 140 ms, heat conduction further up the emitter leads to a total analyte heating time of ∼41 s. Pulsed laser heating experiments could reduce this time to ∼0.5 s for protein aggregation that occurs on a faster time scale. Laser heating provides a powerful method for studying the detailed mechanisms of cofactor/ligand loss with increasing temperature and promises a new tool for studying the effect of ligands, drugs, growth conditions, buffer additives, or other treatments on the stabilities of aggregation-prone biomolecules.
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Affiliation(s)
- Jacob S Jordan
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, USA.
| | - Katherine J Lee
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, USA.
| | - Evan R Williams
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, USA.
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4
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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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5
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Pan H, Raab SA, El-Baba TJ, Schrecke SR, Laganowsky A, Russell DH, Clemmer DE. Variation of CI-2 Conformers upon Addition of Methanol to Water: An IMS-MS-Based Thermodynamic Analysis. J Phys Chem A 2023; 127:9399-9408. [PMID: 37934510 PMCID: PMC11212803 DOI: 10.1021/acs.jpca.3c03651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Chymotrypsin inhibitor 2 (CI-2) is a well-studied, textbook example of a cooperative, two-state, native ↔ denatured folding transition. A recent hybrid ion mobility spectrometry (IMS)/mass spectrometry (MS) thermal denaturation study of CI-2 (the well-studied truncated 64-residue model) in water reported evidence that this two-state transition involves numerous (∼41) unique native and non-native (denatured) solution conformations. The characterization of so many, often low-abundance, states is possible because of the very high dynamic range of IMS-MS measurements of ionic species that are produced upon electrospraying CI-2 solutions from a variable temperature electrospray ionization source. A thermodynamic analysis of these states revealed large changes in enthalpy (ΔH) and entropy (ΔS) at different temperatures, and it was suggested that such variation might arise because of temperature-dependent conformational changes of the protein in response to changes in the conformational entropy and the dielectric permeability of water, which drops from a value of ε ∼ 79 at 24 °C to ∼ 60 at 82 °C. Herein, we examine how adding methanol to water influences the distributions of CI-2 conformers and their ensuing stabilities. The dielectric constant of a 60:40 water:methanol (MeOH) drops from ε ∼ 60 at 24 °C to ∼ 51 at 64 °C. Although the same set of conformers observed in water appears to be present in 60:40 water:MeOH, the abundance of each is substantially altered by the presence of methanol. Relative free energy values (ΔG) and thermodynamic values [ΔH and ΔS and heat capacities (ΔCp)] are derived from a Gibbs-Helmholtz analysis. A comparison of these data from water and water:MeOH systems allows rare insight into how variations in solvation and temperature affect many-state protein equilibria. While these studies confirm that variations in solvent dielectric constant with temperature affect the distributions of conformers that are observed, our findings suggest that other solvent differences may also affect abundances.
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Affiliation(s)
- Hua Pan
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Shannon A Raab
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Tarick J El-Baba
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Samantha R Schrecke
- 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
| | - David E Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
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6
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Kodikara S, Gyawali P, Gleeson JT, Jakli A, Sprunt S, Balci H. Stability of End-to-End Base Stacking Interactions in Highly Concentrated DNA Solutions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4838-4846. [PMID: 36952670 PMCID: PMC10078606 DOI: 10.1021/acs.langmuir.3c00318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Positionally ordered bilayer liquid crystalline nanostructures formed by gapped DNA (GDNA) constructs provide a practical window into DNA-DNA interactions at physiologically relevant DNA concentrations; concentrations several orders of magnitude greater than those in commonly used biophysical assays. The bilayer structure of these states of matter is stabilized by end-to-end base stacking interactions; moreover, such interactions also promote in-plane positional ordering of duplexes that are separated from each other by less than twice the duplex diameter. The end-to-end stacked as well as in-plane ordered duplexes exhibit distinct signatures when studied via small-angle X-ray scattering (SAXS). This enables analysis of the thermal stability of both the end-to-end and side-by-side interactions. We performed synchrotron SAXS experiments over a temperature range of 5-65 °C on GDNA constructs that differ only by the terminal base-pairs at the blunt duplex ends, resulting in identical side-by-side interactions, while end-to-end base stacking interactions are varied. Our key finding is that bilayers formed by constructs with GC termination transition into the monolayer state at temperatures as much as 30 °C higher than for those with AT termination, while mixed (AT/GC) terminations have intermediate stability. By modeling the bilayer melting in terms of a temperature-dependent reduction in the average fraction of end-to-end paired duplexes, we estimate the stacking free energies in DNA solutions of physiologically relevant concentrations. The free-energies thereby determined are generally smaller than those reported in single-molecule studies, which might reflect the elevated DNA concentrations in our studies.
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Affiliation(s)
- Sineth
G. Kodikara
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
| | - Prabesh Gyawali
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
| | - James T. Gleeson
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
| | - Antal Jakli
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
- Advanced
Materials and Liquid Crystals Institute, Kent State University, Kent, Ohio 44242, United States
| | - Samuel Sprunt
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
- Advanced
Materials and Liquid Crystals Institute, Kent State University, Kent, Ohio 44242, United States
| | - Hamza Balci
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
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7
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Walker T, Sun HM, Gunnels T, Wysocki V, Laganowsky A, Rye H, Russell D. Dissecting the Thermodynamics of ATP Binding to GroEL One Nucleotide at a Time. ACS CENTRAL SCIENCE 2023; 9:466-475. [PMID: 36968544 PMCID: PMC10037461 DOI: 10.1021/acscentsci.2c01065] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Indexed: 06/18/2023]
Abstract
Variable-temperature electrospray ionization (vT-ESI) native mass spectrometry (nMS) is used to determine the thermodynamics for stepwise binding of up to 14 ATP molecules to the 801 kDa GroEL tetradecamer chaperonin complex. Detailed analysis reveals strong enthalpy-entropy compensation (EEC) for the ATP binding events leading to formation of GroEL-ATP7 and GroEL-ATP14 complexes. The observed variations in EEC and stepwise free energy changes of specific ATP binding are consistent with the well-established nested cooperativity model describing GroEL-ATP interactions, viz., intraring positive cooperativity and inter-ring negative cooperativity (Dyachenko A.; Proc. Natl. Acad. Sci. U.S.A.2013, 110, 7235-7239). Entropy-driven ATP binding is to be expected for ligand-induced conformational changes of the GroEL tetradecamer, though the magnitude of the entropy change suggests that reorganization of GroEL-hydrating water molecules and/or expulsion of water from the GroEL cavity may also play key roles. The capability for determining complete thermodynamic signatures (ΔG, ΔH, and -TΔS) for individual ligand binding reactions for the large, nearly megadalton GroEL complex expands our fundamental view of chaperonin functional chemistry. Moreover, this work and related studies of protein-ligand interactions illustrate important new capabilities of vT-ESI-nMS for thermodynamic studies of protein interactions with ligands and other molecules such as proteins and drugs.
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Affiliation(s)
- Thomas Walker
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - He Mirabel Sun
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Tiffany Gunnels
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | - Vicki Wysocki
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Arthur Laganowsky
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Hays Rye
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | - David Russell
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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8
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Fiorentino F, Rotili D, Mai A. Native mass spectrometry-directed drug discovery: Recent advances in investigating protein function and modulation. Drug Discov Today 2023; 28:103548. [PMID: 36871843 DOI: 10.1016/j.drudis.2023.103548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/15/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
Native mass spectrometry (nMS) is a biophysical method for studying protein complexes and can provide insights into subunit stoichiometry and composition, protein-ligand, and protein-protein interactions (PPIs). These analyses are made possible by preserving non-covalent interactions in the gas phase, thereby allowing the analysis of proteins in their native state. Consequently, nMS has been increasingly applied in early drug discovery campaigns for the characterization of protein-drug interactions and the evaluation of PPI modulators. Here, we discuss recent developments in nMS-directed drug discovery and provide a timely perspective on the possible applications of this technology in drug discovery.
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Affiliation(s)
- Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
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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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Fan L, Russell DH. An ion mobility-mass spectrometry study of copper-metallothionein-2A: binding sites and stabilities of Cu-MT and mixed metal Cu-Ag and Cu-Cd complexes. Analyst 2023; 148:546-555. [PMID: 36545796 PMCID: PMC9904198 DOI: 10.1039/d2an01556k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The presence of Cu, a highly redox active metal, is known to damage DNA as well as other cellular components, but the adverse effects of cellular Cu can be mitigated by metallothioneins (MT), small cysteine rich proteins that are known to bind to a broad range of metal ions. While metal ion binding has been shown to involve the cysteine thiol groups, the specific ion binding sites are controversial as are the overall structure and stability of the Cu-MT complexes. Here, we report results obtained using nano-electrospray ionization mass spectrometry and ion mobility-mass spectrometry for several Cu-MT complexes and compare our results with those previously reported for Ag-MT complexes. The data include determination of the stoichiometries of the complex (Cui-MT, i = 1-19), and Cu+ ion binding sites for complexes where i = 4, 6, and 10 using bottom-up and top-down proteomics. The results show that Cu+ ions first bind to the β-domain to form Cu4MT then Cu6MT, followed by addition of four Cu+ ions to the α-domain to form a Cu10-MT complex. Stabilities of the Cui-MT (i = 4, 6 and 10) obtained using collision-induced unfolding (CIU) are reported and compared with previously reported CIU data for Ag-MT complexes. We also compare CIU data for mixed metal complexes (CuiAgj-MT, where i + j = 4 and 6 and CuiCdj, where i + j = 4 and 7). Lastly, higher order Cui-MT complexes, where i = 11-19, were also detected at higher concentrations of Cu+ ions, and the metalated product distributions observed are compared to previously reported results for Cu-MT-1A (Scheller et al., Metallomics, 2017, 9, 447-462).
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Affiliation(s)
- Liqi Fan
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA.
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA.
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11
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Lin CW, Oney-Hawthorne SD, Kuo ST, Barondeau DP, Russell DH. Mechanistic Insights into IscU Conformation Regulation for Fe-S Cluster Biogenesis Revealed by Variable Temperature Electrospray Ionization Native Ion Mobility Mass Spectrometry. Biochemistry 2022; 61:2733-2741. [PMID: 36351081 PMCID: PMC10009881 DOI: 10.1021/acs.biochem.2c00429] [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: 11/10/2022]
Abstract
Iron-sulfur (Fe-S) cluster (ISC) cofactors are required for the function of many critical cellular processes. In the ISC Fe-S cluster biosynthetic pathway, IscU assembles Fe-S cluster intermediates from iron, electrons, and inorganic sulfur, which is provided by the cysteine desulfurase enzyme IscS. IscU also binds to Zn, which mimics and competes for binding with the Fe-S cluster. Crystallographic and nuclear magnetic resonance spectroscopic studies reveal that IscU is a metamorphic protein that exists in multiple conformational states, which include at least a structured form and a disordered form. The structured form of IscU is favored by metal binding and is stable in a narrow temperature range, undergoing both cold and hot denaturation. Interestingly, the form of IscU that binds IscS and functions in Fe-S cluster assembly remains controversial. Here, results from variable temperature electrospray ionization (vT-ESI) native ion mobility mass spectrometry (nIM-MS) establish that IscU exists in structured, intermediate, and disordered forms that rearrange to more extended conformations at higher temperatures. A comparison of Zn-IscU and apo-IscU reveals that Zn(II) binding attenuates the cold/heat denaturation of IscU, promotes refolding of IscU, favors the structured and intermediate conformations, and inhibits the disordered high charge states. Overall, these findings provide a structural rationalization for the role of Zn(II) in stabilizing IscU conformations and IscS in altering the IscU active site to prepare for Zn(II) release and cluster synthesis. This work highlights how vT-ESI-nIM-MS can be applied as a powerful tool in mechanistic enzymology by providing details of relationships among temperature, protein conformations, and ligand/protein binding.
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Affiliation(s)
- Cheng-Wei Lin
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - Shelby D Oney-Hawthorne
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - Syuan-Ting Kuo
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - David P Barondeau
- 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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12
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Parvate AD, Powell SM, Brookreson JT, Moser TH, Novikova IV, Zhou M, Evans JE. Cryo-EM structure of the diapause chaperone artemin. Front Mol Biosci 2022; 9:998562. [DOI: 10.3389/fmolb.2022.998562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/01/2022] [Indexed: 11/29/2022] Open
Abstract
The protein artemin acts as both an RNA and protein chaperone and constitutes over 10% of all protein in Artemia cysts during diapause. However, its mechanistic details remain elusive since no high-resolution structure of artemin exists. Here we report the full-length structure of artemin at 2.04 Å resolution. The cryo-EM map contains density for an intramolecular disulfide bond between Cys22-Cys61 and resolves the entire C-terminus extending into the core of the assembled protein cage but in a different configuration than previously hypothesized with molecular modeling. We also provide data supporting the role of C-terminal helix F towards stabilizing the dimer form that is believed to be important for its chaperoning activity. We were able to destabilize this effect by placing a tag at the C-terminus to fully pack the internal cavity and cause limited steric hindrance.
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13
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Instability Challenges and Stabilization Strategies of Pharmaceutical Proteins. Pharmaceutics 2022; 14:pharmaceutics14112533. [PMID: 36432723 PMCID: PMC9699111 DOI: 10.3390/pharmaceutics14112533] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/13/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Maintaining the structure of protein and peptide drugs has become one of the most important goals of scientists in recent decades. Cold and thermal denaturation conditions, lyophilization and freeze drying, different pH conditions, concentrations, ionic strength, environmental agitation, the interaction between the surface of liquid and air as well as liquid and solid, and even the architectural structure of storage containers are among the factors that affect the stability of these therapeutic biomacromolecules. The use of genetic engineering, side-directed mutagenesis, fusion strategies, solvent engineering, the addition of various preservatives, surfactants, and additives are some of the solutions to overcome these problems. This article will discuss the types of stress that lead to instabilities of different proteins used in pharmaceutics including regulatory proteins, antibodies, and antibody-drug conjugates, and then all the methods for fighting these stresses will be reviewed. New and existing analytical methods that are used to detect the instabilities, mainly changes in their primary and higher order structures, are briefly summarized.
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14
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Kostelic MM, Ryan JP, Brown LS, Jackson TW, Hsieh CC, Zak CK, Sanders HM, Liu Y, Chen VS, Byrne M, Aspinwall CA, Baker ES, Marty MT. Stability and Dissociation of Adeno-Associated Viral Capsids by Variable Temperature-Charge Detection-Mass Spectrometry. Anal Chem 2022; 94:11723-11727. [PMID: 35981215 DOI: 10.1021/acs.analchem.2c02378] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Adeno-associated viral (AAV) vectors have emerged as gene therapy and vaccine delivery systems. Differential scanning fluorimetry or differential scanning calorimetry is commonly used to measure the thermal stability of AAVs, but these global methods are unable to distinguish the stabilities of different AAV subpopulations in the same sample. To address this challenge, we combined charge detection-mass spectrometry (CD-MS) with a variable temperature (VT) electrospray source that controls the temperature of the solution prior to electrospray. Using VT-CD-MS, we measured the thermal stabilities of empty and filled capsids. We found that filled AAVs ejected their cargo first and formed intermediate empty capsids before completely dissociating. Finally, we observed that pH stress caused a major decrease in thermal stability. This new approach better characterizes the thermal dissociation of AAVs, providing the simultaneous measurement of the stabilities and dissociation pathways of different subpopulations.
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Affiliation(s)
- Marius M Kostelic
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Jack P Ryan
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Levi S Brown
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Tyler W Jackson
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Chih-Chieh Hsieh
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Ciara K Zak
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Henry M Sanders
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Yang Liu
- REGENXBIO Inc., 9804 Medical Center Dr., Rockville, Maryland 20850, United States
| | - Victor Shugui Chen
- REGENXBIO Inc., 9804 Medical Center Dr., Rockville, Maryland 20850, United States
| | - Michael Byrne
- REGENXBIO Inc., 9804 Medical Center Dr., Rockville, Maryland 20850, United States
| | - Craig A Aspinwall
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
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15
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Abstract
Native mass spectrometry (nMS) has emerged as an important tool in studying the structure and function of macromolecules and their complexes in the gas phase. In this review, we cover recent advances in nMS and related techniques including sample preparation, instrumentation, activation methods, and data analysis software. These advances have enabled nMS-based techniques to address a variety of challenging questions in structural biology. The second half of this review highlights recent applications of these technologies and surveys the classes of complexes that can be studied with nMS. Complementarity of nMS to existing structural biology techniques and current challenges in nMS are also addressed.
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Affiliation(s)
- Kelly R Karch
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA;
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
| | - Dalton T Snyder
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA;
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA;
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
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16
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Zhu Y, Schrecke S, Tang S, Odenkirk MT, Walker T, Stover L, Lyu J, Zhang T, Russell D, Baker ES, Yan X, Laganowsky A. Cupric Ions Selectively Modulate TRAAK-Phosphatidylserine Interactions. J Am Chem Soc 2022; 144:7048-7053. [PMID: 35421309 DOI: 10.1021/jacs.2c00612] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
TRAAK and TREK2 are two-pore domain K+ (K2P) channels and are modulated by diverse factors including temperature, membrane stretching, and lipids, such as phosphatidic acid. In addition, copper and zinc, both of which are essential for life, are known to regulate TREK2 and a number of other ion channels. However, the role of ions in the association of lipids with integral membrane proteins is poorly understood. Here, we discover cupric ions selectively modulate the binding of phosphatidylserine (PS) to TRAAK but not TREK2. Other divalent cations (Ca2+, Mg2+, and Zn2+) bind both channels but have no impact on binding PS and other lipids. Additionally, TRAAK binds more avidly to Cu2+ and Zn2+ than TREK2. In the presence of Cu2+, TRAAK binds similarly to PS with different acyl chains, indicating a crucial role of the serine headgroup in coordinating Cu2+. High-resolution native mass spectrometry (MS) enables the determination of equilibrium binding constants for distinct Cu2+-bound stoichiometries and uncovered the highest coupling factor corresponds to a 1:1 PS-to-Cu2+ ratio. Interestingly, the next three highest coupling factors had a ∼1.5:1 PS-to-Cu2+ ratio. Our findings bring forth the role of cupric ions as an essential cofactor in selective TRAAK-PS interactions.
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Affiliation(s)
- Yun Zhu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Samantha Schrecke
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Shuli Tang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Melanie T Odenkirk
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Thomas Walker
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lauren Stover
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Tianqi Zhang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States.,Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Xin Yan
- 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
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