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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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Jordan JS, Williams ER. Laser Heating Nanoelectrospray Emitters for Fast Protein Melting Measurements with Mass Spectrometry. Anal Chem 2022; 94:16894-16900. [DOI: 10.1021/acs.analchem.2c04204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Jacob S. Jordan
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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Anichina J, Bohme DK. Mass-spectrometric studies of the interactions of selected metalloantibiotics and drugs with deprotonated hexadeoxynucleotide GCATGC. J Phys Chem B 2009; 113:328-35. [PMID: 19072169 DOI: 10.1021/jp807034v] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
ESI tandem mass spectrometry is employed in a detailed study of the interactions of a hexameric duplex d(5'GCATGC) with three types of ligated first-row transition metal dications M(2+): metallated bleomycins, singly, doubly, and triply ligated metallophenanthrolines and [M(triethylenetetramine)](2+). The singly, doubly, and triply metallated species were found to dissociate by noncovalent separation into two strands with metal ions attached either to one or to both. Relative gas-phase stabilities of the double-stranded oligodeoxynucleotide (ODN)-M(2+) complexes were found to follow the order Mn(II) > Fe(II) > Co(II) > Ni(II) > Zn(II) > Cu(II). Overall, the presence of metal dications is found to increase the gas-phase stability of the duplex against noncovalent dissociation with the exception of one and three copper dications. An analysis of the dissociation pathways and relative gas-phase stabilities of the species that were investigated provided a basis for the assessment of the possible binding modes between duplex oligonucleotides and metallocomplexes.
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Affiliation(s)
- Janna Anichina
- Department of Chemistry, York University, Toronto, Ontario, Canada M3J 1P3
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Feil SW, Koyanagi GK, Anichina J, Bohme DK. Chemical stability and reactivity of deprotonated oligonucleotides (DNA) in the gas phase: protonation and solvation with hydrogen bromide. J Phys Chem B 2008; 112:10375-81. [PMID: 18651764 DOI: 10.1021/jp804193u] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Selected deprotonated oligodeoxynucleotides generated by electrospray ionization were exposed to a variety of neutral molecules in the gas phase at room temperature in flowing helium gas at 0.35 Torr. Single-stranded [AGTCTG-nH]n- and single- and double-stranded [GCATGC-nH]n- anions were found to be remarkably unreactive with strong oxidants (O3, O2, N2O) and potential intercalators (benzene, pyridine, toluene, and quinoxaline). Hydration also was observed to be inefficient. However, [AGTCTG-nH]n- anions with n=2, 3, 4, and 5 were seen to be sequentially protonated and/or hydrobrominated with HBr (but not damaged) and displayed an interesting "end effect" against protonation. Measurements are provided for the rate coefficients of reaction and the efficiencies of protonation. These experimental results point toward the exciting prospect of measuring the intrinsic chemistry of other bare DNA-like anions, including double-stranded oligonucleotide anions in the gas phase at room temperature.
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Affiliation(s)
- Stefan W Feil
- Department of Chemistry, Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada
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Shi X, Takamizawa A, Nishimura Y, Hiraoka K, Akashi S. Thermal unfolding of proteins probed by laser spray mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:1430-1436. [PMID: 18393330 DOI: 10.1002/rcm.3517] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The stability and conformational changes of cytochrome c (cyt c) at different temperatures and pH have been well examined so far by using various analytical methods. We have found that laser spray mass spectrometry enables much faster and more convenient monitoring of those changes of cyt c compared with other methods. The results correlated well with circular dichroism (CD) experiments under relatively acidic conditions, which destabilize the protein. Laser spray mass spectra of cyt c at various pH were obtained at different levels of laser power. Bimodal charge-state distributions of the protein were observed in laser spray mass spectra, indicating the two-state model of structural change; the lower charges correspond to the folded state, the higher charges to the unfolded state. Based on this result, the presumed denaturation curve of the protein was plotted as a function of laser power, and laser power by which 50% of the protein was assumed to be denatured, E50%, as obtained at each pH. We also examined the melting temperatures, Tm, of cyt c at various values of pH by using CD spectroscopy. The correlation coefficient between E50% and Tm for cyt c was 0.999, demonstrating an excellent correlation. Furthermore, laser spray analysis of ubiquitin, which is found to be more thermally stable than cyt c, gave a higher E50% than cyt c. These results indicate that laser spray mass spectrometry can be an extremely convenient method for probing thermal stabilities and dynamic conformational changes of proteins with subtle structural differences caused by slight changes in pH.
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Affiliation(s)
- Xiangguo Shi
- International Graduate School of Arts and Sciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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Nardo L, Bondani M, Andreoni A. DNA-ligand binding mode discrimination by characterizing fluorescence resonance energy transfer through lifetime measurements with picosecond resolution. Photochem Photobiol 2008; 84:101-10. [PMID: 18173709 DOI: 10.1111/j.1751-1097.2007.00204.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a method for distinguishing between minor groove binders and base intercalators that is based on measurements of the fluorescence lifetime of a donor (D) in the presence of an acceptor (A). The D-A pair is separated by a short double helix DNA with which the ligands interact. By plotting the D fluorescence lifetime as a function of the ligand-to-base pair concentration ratio we find a clear signature that distinguishes between the two binding mechanisms: minor groove binding induces an asymptotic decrease of the D fluorescence lifetime, while intercalation gives a monotonically increasing lifetime and the appearance of an additional short lifetime. We assayed Quinacrine, Hoechst and 4'-6'diamidine-2-phenyl indole, which in control experiments performed on oligodeoxyribonucleotides (oligos) lacking the A are demonstrated not to interfere with the D fluorescence. The changes in fluorescence lifetimes measured in the case of dual-labeled oligos are thus caused by structural changes in the DNA that modify the D-A distance. The appearance of the short-lived transient in the fluorescence decay of Ds attached to dual-labeled oligos upon binding of an intercalator can be interpreted as denaturation.
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Affiliation(s)
- Luca Nardo
- Dipartimento di Fisica e Matematica, Universita' degli Studi dell'Insubria, Como, Italy.
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Wang Z, Guo X, Liu Z, Cui M, Song F, Liu S. Studies on alkaloids binding to GC-rich human survivin promoter DNA using positive and negative ion electrospray ionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2008; 43:327-335. [PMID: 17968851 DOI: 10.1002/jms.1320] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) was used to investigate the binding of 13 alkaloids to two GC-rich DNA duplexes which are critical sequences in human survivin promoter. Negative ion ESI-MS was first applied to screen the binding of the alkaloids to the duplexes. Six alkaloids (including berberine, jatrorrhizine, palmatine, reserpine, berbamine, and tetrandrine) show complexation with the target DNA sequences. Relative binding affinities were estimated from the negative ion ESI data, and the alkaloids show a binding preference to the duplex with higher GC content. Positive ion ESI mass spectra of the complexes were also recorded and compared with those obtained in negative ion mode. Only the 1 : 1 complex with berbamine was observed with lower abundance in the positive ion mass spectrum while complexes with the other alkaloids were absolutely absent. Collision-induced dissociation (CID) experiments indicate that the complexes with the protoberberine alkaloids (berberine, jatrorrhizine, and palmatine) dissociate via base loss and covalent cleavage. In contrast, product ion spectra of the complexes with the alkaloids reserpine, berbamine, and tetrandrine show the predominant loss of a neutral alkaloid molecule, accompanied by base loss and covalent cleavage to a lesser extent. A comparison of the gas-phase behaviors of complexes with the alkaloids to those with the traditional DNA binders has suggested an intercalative binding mode of these alkaloids to the target DNA duplexes.
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Affiliation(s)
- Zhaofu Wang
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun Center of Mass Spectrometry, Changchun, 130022, P R China
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Smith SI, Guziec LJ, Guziec FS, Hasinoff BB, Brodbelt JS. Evaluation of relative DNA binding affinities of anthrapyrazoles by electrospray ionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:681-8. [PMID: 17405184 DOI: 10.1002/jms.1205] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Binding interactions of a new series of anthrapyrazoles (APs) with DNA were evaluated by electrospray ionization mass spectrometry (ESI-MS). Relative binding affinities were estimated from the ESI-MS data based on the fraction of bound DNA for DNA/anthrapyrazole mixtures, and they show a correlation to the shift in melting point of the DNA measured from a previous study. Minimal sequence specificity was observed for the series of anthrapyrazoles. Upon collisionally activated dissociation of the duplex/anthrapyrazole complexes, typically ejection of the ligand was the dominant pathway for most of the complexes. However, for complexes containing AP2 or mitoxantrone, strand separation with the ligand remaining on one of the single strands was observed, indicative of a different binding mode or stronger binding.
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Affiliation(s)
- Suncerae I Smith
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
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Akashi S. Structural and Functional Characterization of Biological Macromolecules by Mass Spectrometry. YAKUGAKU ZASSHI 2006; 126:915-29. [PMID: 17016021 DOI: 10.1248/yakushi.126.915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Mass spectrometry has widely been used as a tool for identification of proteins in the research fields of biochemistry and clinical chemistry because it can provide accurate information on molecular masses of biological molecules with a small amount of sample in a short time. If mass spectrometry is properly used, it can also give information on the tertiary structure or on the molecular interactions of biological macromolecules. The present paper focuses on the role of mass spectrometry as a tool for the investigation on the tertiary structure of proteins and on the biological molecular interactions that play essential roles in various biological events.
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Affiliation(s)
- Satoko Akashi
- International Graduate School of Arts and Sciences, Yokohama City University, Japan.
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