1
|
Ren C, Bailey AO, VanderPorten E, Oh A, Phung W, Mulvihill MM, Harris SF, Liu Y, Han G, Sandoval W. Quantitative Determination of Protein–Ligand Affinity by Size Exclusion Chromatography Directly Coupled to High-Resolution Native Mass Spectrometry. Anal Chem 2018; 91:903-911. [DOI: 10.1021/acs.analchem.8b03829] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | - Aaron O. Bailey
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | | | | | | | | | | | | | | | | |
Collapse
|
2
|
Yefremova Y, Melder FTI, Danquah BD, Opuni KFM, Koy C, Ehrens A, Frommholz D, Illges H, Koelbel K, Sobott F, Glocker MO. Apparent activation energies of protein-protein complex dissociation in the gas-phase determined by electrospray mass spectrometry. Anal Bioanal Chem 2017; 409:6549-6558. [PMID: 28900708 DOI: 10.1007/s00216-017-0603-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/09/2017] [Accepted: 08/23/2017] [Indexed: 11/30/2022]
Abstract
We have developed a method to determine apparent activation energies of dissociation for ionized protein-protein complexes in the gas phase using electrospray ionization mass spectrometry following the Rice-Ramsperger-Kassel-Marcus quasi-equilibrium theory. Protein-protein complexes were formed in solution, transferred into the gas phase, and separated from excess free protein by ion mobility filtering. Afterwards, complex disassembly was initiated by collision-induced dissociation with step-wise increasing energies. Relative intensities of ion signals were used to calculate apparent activation energies of dissociation in the gas phase by applying linear free energy relations. The method was developed using streptavidin tetramers. Experimentally determined apparent gas-phase activation energies for dissociation ([Formula: see text]) of complexes consisting of Fc parts from immunoglobulins (IgG-Fc) and three closely related protein G' variants (IgG-Fc•protein G'e, IgG-Fc•protein G'f, and IgG-Fc•protein G'g) show the same order of stabilities as can be inferred from their in-solution binding constants. Differences in stabilities between the protein-protein complexes correspond to single amino acid residue exchanges in the IgG-binding regions of the protein G' variants. Graphical abstract Electrospray mass spectrometry and collision-induced dissociation delivers apparent activation energies and supramolecular bond force constants of protein-protein complexes in the gas phase.
Collapse
Affiliation(s)
- Yelena Yefremova
- Proteome Center Rostock, University Rostock Medical Center, Schillingallee 69, 18059, Rostock, Germany
| | - F Teresa I Melder
- Proteome Center Rostock, University Rostock Medical Center, Schillingallee 69, 18059, Rostock, Germany
| | - Bright D Danquah
- Proteome Center Rostock, University Rostock Medical Center, Schillingallee 69, 18059, Rostock, Germany
| | - Kwabena F M Opuni
- Proteome Center Rostock, University Rostock Medical Center, Schillingallee 69, 18059, Rostock, Germany.,School of Pharmacy, University of Ghana, P.O. Box LG43, Legon Accra, Ghana
| | - Cornelia Koy
- Proteome Center Rostock, University Rostock Medical Center, Schillingallee 69, 18059, Rostock, Germany
| | - Alexandra Ehrens
- University of Applied Sciences Bonn-Rhein-Sieg, von-Liebig-Str. 20, 53359, Rheinbach, Germany.,University Hospital of Bonn, Sigmung-Freud-Str. 25, 53105, Bonn, Germany
| | - David Frommholz
- University of Applied Sciences Bonn-Rhein-Sieg, von-Liebig-Str. 20, 53359, Rheinbach, Germany
| | - Harald Illges
- University of Applied Sciences Bonn-Rhein-Sieg, von-Liebig-Str. 20, 53359, Rheinbach, Germany
| | - Knut Koelbel
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Frank Sobott
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Michael O Glocker
- Proteome Center Rostock, University Rostock Medical Center, Schillingallee 69, 18059, Rostock, Germany.
| |
Collapse
|
3
|
Cubrilovic D, Biela A, Sielaff F, Steinmetzer T, Klebe G, Zenobi R. Quantifying protein-ligand binding constants using electrospray ionization mass spectrometry: a systematic binding affinity study of a series of hydrophobically modified trypsin inhibitors. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1768-77. [PMID: 22869298 DOI: 10.1007/s13361-012-0451-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 07/12/2012] [Accepted: 07/17/2012] [Indexed: 05/22/2023]
Abstract
NanoESI-MS is used for determining binding strengths of trypsin in complex with two different series of five congeneric inhibitors, whose binding affinity in solution depends on the size of the P3 substituent. The ligands of the first series contain a 4-amidinobenzylamide as P1 residue, and form a tight complex with trypsin. The inhibitors of the second series have a 2-aminomethyl-5-chloro-benzylamide as P1 group, and represent a model system for weak binders. The five different inhibitors of each group are based on the same scaffold and differ only in the length of the hydrophobic side chain of their P3 residue, which modulates the interactions in the S3/4 binding pocket of trypsin. The dissociation constants (K(D)) for high affinity ligands investigated by nanoESI-MS ranges from 15 nM to 450 nM and decreases with larger hydrophobic P3 side chains. Collision-induced dissociation (CID) experiments of five trypsin and benzamidine-based complexes show a correlation between trends in K(D) and gas-phase stability. For the second inhibitor series we could show that the effect of imidazole, a small stabilizing additive, can avoid the dissociation of the complex ions and as a result increases the relative abundance of weakly bound complexes. Here the K(D) values ranging from 2.9 to 17.6 μM, some 1-2 orders of magnitude lower than the first series. For both ligand series, the dissociation constants (K(D)) measured via nanoESI-MS were compared with kinetic inhibition constants (K(i)) in solution.
Collapse
Affiliation(s)
- Dragana Cubrilovic
- Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland
| | | | | | | | | | | |
Collapse
|
4
|
Liu Y, Su B, Wang X. Study on the noncovalent interactions of saikosaponins and cytochrome c by electrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:719-27. [PMID: 22368050 DOI: 10.1002/rcm.6151] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
RATIONALE The study of interactions between protein and pharmaceutical molecules including natural extracts has become of increasing interest in biological and biomedical research. An investigation of the interaction between saikosaponins and cytochrome c (Cyt c) by electrospray ionization mass spectrometry (ESI-MS) is described in this study. Saikosaponins are found in Bupleurum falcatum (a flowering plant), and they are glycosides that consist of saccharides and the sapogenins of triterpenoids. METHODS Seven model molecules of saccharides and triterpenes, namely maltose (Mal II), maltotriose (Mal III), raffinose (Raf), and stachyose (Sta), glycyrrhetinic acid (Gly), ursolic acid (Urs) and oleanic acid (Ole), were chosen to perform a series of ESI-MS control experiments for the exploration of the interaction groups in saikosaponins with Cyt c. The dissociation constants of detected noncovalent complexes were determined by using a direct ESI-MS assay. RESULTS We have observed in the ESI mass spectra the formation of Cyt c complexes with saikosaponins a and c, and these saccharides, with 1:1 and 1:2 stoichiometry. Our results showed that no complex ions of triterpenes and Cyt c were detected in the ESI-MS and similar Kd values were obtained for the Cyt c complexes of saikosaponins and saccharides. This demonstrates that the glycosyl moiety in the saikosaponins is the effective interaction group with Cyt c. We propose that saikosaponins and saccharides interact with Cyt c by hydrogen bonds. The binding affinity of these six ligands with Cyt c is shown to be in the order Ssa > Ssc > Raf, Mal III > Sta ≥ Mal II. CONCLUSIONS The ESI-MS methodology presented in this study enables us to investigate the interactions of saikosaponins with Cyt c, and allows the direct determination of binding constants. These results could guide further research for providing insights into the structure-binding relationship of ligands with Cyt c.
Collapse
Affiliation(s)
- Yingzhi Liu
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei, 430074, PR China
| | | | | |
Collapse
|
5
|
Darii E, Saravanamuthu G, Afonso C, Alves S, Gut I, Tabet JC. Possible conformational change within the desolvated and cationized sBBI/trypsin non-covalent complex during the collision-induced dissociation process. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:1725-1734. [PMID: 21598332 DOI: 10.1002/rcm.5039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) has become an analytical technique widely used for the investigation of non-covalent protein-protein and protein-ligand complexes due to the soft desolvation conditions that preserve the stoichiometry of the interacting partners. Dissociation studies of solvated or desolvated complexes (in the source and in the collision cell, respectively) allow access to information on protein conformation and localization of the metal ions involved in protein structure stabilization and biological activity. The complex of bovine trypsin and small soybean Bowman-Birk inhibitor (sBBI) was studied by ESI-MS to determine changes occurring within the complex during its transfer from droplets to the gas phase independently of the ion polarity. Under collision-induced dissociation (CID) conditions, unexpected binding of the Ca(2+) ion (cofactor of native trypsin) to the inhibitor molecule was observed within the desolvated sBBI/trypsin/Ca(2+) complex (with a 1:1:1 stoichiometry). This formal gas-phase migration of the calcium ion from trypsin to the inhibitor may be related to conformational rearrangements in the solvent-free and likely collapsed complex. However, under conditions leading to the increase in complex charge state, the appearance of the cationized trypsin molecule was detected during complex dissociation, thus reflecting different pathways of the evolution of complex conformation.
Collapse
Affiliation(s)
- Ekaterina Darii
- Equipe de Spectrométrie de masse, Institut Parisien de Chimie Moléculaire, UMR 7201, Université Pierre et Marie Curie-Paris 6, 4 place Jussieu, 75252 Paris Cedex 05, France
| | | | | | | | | | | |
Collapse
|
6
|
Wang X, Zhao W, Lin X, Su B, Liu J. Observation of symmetric denaturation of hemoglobin subunits by electrospray ionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:1306-1311. [PMID: 20963788 DOI: 10.1002/jms.1843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 09/01/2010] [Indexed: 05/30/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) has been used to characterize the denaturation of porcine hemoglobin (Hb) induced by solvent changes. This work provides evidence for the symmetric nature of Hb denaturation and demonstrates that heme losses from α- and β-monomers occur in parallel, in response to the addition of acid and organic co-solvents in solution. When subject to one of the following solution conditions (pH 3.2-4.0 or 15-30% acetonitrile-water or 30-45% methanol-water solution), α- and β-globins undergo symmetric dissociation to release the heme groups, which is detected by ESI-MS. Circular dichroism (CD) and fluorescence spectroscopy (FS) data show that the acid-induced and organic solvent-induced heme release, as observed in the mass spectra, can probably be ascribed to different aspects of the conformational changes taking place in the protein. The acidity of the solvent has a significant effect on the secondary structure, whereas organic content level in solution (15-30% acetonitrile or 30-45% methanol) tends to destroy the tertiary structure of Hb globins, both leading to release of the heme from each subunit.
Collapse
Affiliation(s)
- Xian Wang
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei 430074, People's Republic of China.
| | | | | | | | | |
Collapse
|
7
|
Lin X, Zhao W, Wang X. Characterization of conformational changes and noncovalent complexes of myoglobin by electrospray ionization mass spectrometry, circular dichroism and fluorescence spectroscopy. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:618-626. [PMID: 20527030 DOI: 10.1002/jms.1747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) was employed to monitor the heme release and the conformational changes of myoglobin (Mb) under different solvent conditions, and to observe ligand bindings of Mb. ESI-MS, complemented by circular dichroism and fluorescence spectroscopy, was used to study the mechanism of acid- and organic solvent-induced denaturation by probing the changes in the secondary and the tertiary structure of Mb. The results obtained show that complete disruption of the heme-protein interactions occurs when Mb is subjected to one of the following solution conditions: pH 3.2-3.6, or solution containing 20-30% acetonitrile or 40-50% methanol. Outside these ranges, Mb is present entirely in its native state (binding with a heme group) or as apomyoglobin (i.e. without the heme). Spectroscopic data demonstrate that the denaturation mechanism of Mb induced by acid may be significantly different from that by the organic solvent. Low pH reduces helices in Mb, whereas certain organic content level in solution results in the loss of the tertiary structure. ESI-MS conditions were established to observe the H(2)O- and CO-bound Mb complexes, respectively. H(2)O binding to metmyoglobin (17,585 Da), where the heme iron is in the ferric oxidation state, is observed in ESI-MS. CO binding to Mb (17,595 Da), on the other hand, can be only observed after the heme iron is reduced to the ferrous form. Therefore, ESI-MS combined with spectroscopic techniques provides a useful means for probing the formation of ligand-binding complexes and characterizing protein conformational changes.
Collapse
Affiliation(s)
- Xin Lin
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei 430074, China
| | | | | |
Collapse
|
8
|
Łegowska A, Lesner A, Bulak E, Jaśkiewicz A, Sieradzan A, Cydzik M, Stefanowicz P, Szewczuk Z, Rolka K. Inhibitory activity of double-sequence analogues of trypsin inhibitor SFTI-1 from sunflower seeds: an example of peptide splicing. FEBS J 2010; 277:2351-9. [PMID: 20412298 DOI: 10.1111/j.1742-4658.2010.07650.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Four 28-amino acid peptides were synthesized whose sequences comprised two molecules of trypsin inhibitor sunflower trypsin inhibitor 1 (SFTI-1) bound through a peptide bond. The peptides in their reactive positions (5 and 19 of the peptide chain) contain two Lys ([KK]BiSFTI-1) and two Phe ([FF]BiSFTI-1) residues, along with a combination of the amino acid residues named thereafter [KF]BiSFTI-1 and [FK]BiSFTI-1. Association constants of the analogues determined with trypsin and chymotrypsin, respectively, indicated that they were potent inhibitors of cognate proteinases. An MS study of the associates revealed that incubation of the compounds with the proteinases resulted in cutting out a fragment of the peptide chain to restore the native monocyclic molecule of SFTI-1 or its analogue [Phe(5)]SFTI-1. This process, analogous to that of the DNA and protein splicing, can be referred to as 'peptide splicing'.
Collapse
Affiliation(s)
- Anna Łegowska
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.
| | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Native MS: an ’ESI‚ way to support structure- and fragment-based drug discovery. Future Med Chem 2010; 2:35-50. [DOI: 10.4155/fmc.09.141] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The success of early drug-discovery programs depends on the adequate combination of complementary and orthogonal technologies allowing hit/lead compounds to be optimized and improve therapeutic activity. Among the available biophysical methods, native MS recently emerged as an efficient method for compound-binding screening. Native MS is a highly sensitive and accurate screening technique. This review provides a description of the general approach and an overview of the possible characterization of ligand-binding properties. How native MS supports structure- and fragment-based drug research will also be discussed, with examples from the literature and internal developments. Native MS shows strong potential for in-depth characterization of ligand-binding properties. It is also a reliable screening technique in drug-discovery processes.
Collapse
|
10
|
Bovet C, Ruff M, Eiler S, Granger F, Wenzel R, Nazabal A, Moras D, Zenobi R. Monitoring ligand modulation of protein-protein interactions by mass spectrometry: estrogen receptor alpha-SRC1. Anal Chem 2008; 80:7833-9. [PMID: 18778086 DOI: 10.1021/ac8007169] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many drugs and chemicals exert their biological effect by modulating protein-protein interactions. In vitro approaches to characterize these mechanisms are often based on indirect measurements (e.g., fluorescence). Here, we used mass spectrometry (MS) to directly monitor the effect of small-molecule ligands on the binding of a coactivator peptide (SRC1) by the human estrogen receptor alpha ligand binding domain (hERalpha LBD). Nanoelectrospray mass spectrometry (nanoESI-MS) and high-mass matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) combined with chemical cross-linking were employed to follow these processes. The chemical cross-linking protocol used prior to high-mass MALDI analysis allows detection of intact noncovalent complexes. The binding of intact hERalpha LBD homodimer with two coactivator peptides was detected with nanoESI-MS and high-mass MALDI-MS only in the presence of an agonist ligand. Furthermore, high-mass MALDI-MS revealed an increase of the homodimer abundance after incubating the receptor with a ligand, independent of the ligand character (i.e., agonist, antagonist). The binding characteristics of the compounds tested by MS correlate very well with their biological activity reported by cell-based assays. High-mass MALDI appears to be an efficient and simple tool for directly monitoring ligand regulation mechanisms involved in protein-protein interactions. Furthermore, the combination of both MS methods allows identifying and characterizing endocrine-disrupting compounds or new drug compounds in an efficient way.
Collapse
Affiliation(s)
- Cédric Bovet
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Bovet C, Wortmann A, Eiler S, Granger F, Ruff M, Gerrits B, Moras D, Zenobi R. Estrogen receptor-ligand complexes measured by chip-based nanoelectrospray mass spectrometry: an approach for the screening of endocrine disruptors. Protein Sci 2007; 16:938-46. [PMID: 17400923 PMCID: PMC2206638 DOI: 10.1110/ps.062664107] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In the present report, a method based on chip-based nanoelectrospray mass spectrometry (nanoESI-MS) is described to detect noncovalent ligand binding to the human estrogen receptor alpha ligand-binding domain (hERalpha LBD). This system represents an important environmental interest, because a wide variety of molecules, known as endocrine disruptors, can bind to the estrogen receptor (ER) and induce adverse health effects in wildlife and humans. Using proper experimental conditions, the nanoESI-MS approach allowed for the detection of specific ligand interactions with hERalpha LBD. The relative gas-phase stability of selected hERalpha LBD-ligand complexes did not mirror the binding affinity in solution, a result that demonstrates the prominent role of hydrophobic contacts for stabilizing ER-ligand complexes in solution. The best approach to evaluate relative solution-binding affinity by nanoESI-MS was to perform competitive binding experiments with 17beta-estradiol (E2) used as a reference ligand. Among the ligands tested, the relative binding affinity for hERalpha LBD measured by nanoESI-MS was 4-hydroxtamoxifen approximately diethylstilbestrol > E2 >> genistein >> bisphenol A, consistent with the order of the binding affinities in solution. The limited reproducibility of the bound to free protein ratio measured by nanoESI-MS for this system only allowed the binding constants (K(d)) to be estimated (low nanomolar range for E2). The specificity of nanoESI-MS combined with its speed (1 min/ligand), low sample consumption (90 pmol protein/ligand), and its sensitivity for ligand (30 ng/mL) demonstrates that this technique is a promising method for screening suspected endocrine disrupting compounds and to qualitatively evaluate their binding affinity.
Collapse
Affiliation(s)
- Cédric Bovet
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Ye H. Simultaneous determination of protein aggregation, degradation, and absolute molecular weight by size exclusion chromatography–multiangle laser light scattering. Anal Biochem 2006; 356:76-85. [PMID: 16839514 DOI: 10.1016/j.ab.2006.05.025] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2006] [Revised: 05/12/2006] [Accepted: 05/17/2006] [Indexed: 10/24/2022]
Abstract
The feasibility of size exclusion chromotography (SEC)-multiangle laser-light scattering as a technique to investigate aggregation and degradation of glycosylated and nonglycosylated proteins, and antibodies under various conditions such as addition of detergent, changes in pH, and variation of protein concentration and heat stress temperature was examined. Separation of proteins and their aggregates was performed using SEC-high-performance liquid chromatography. Detection of analytes was carried out with on-line UV, refractive index, and multiangle laser light-scattering detectors. Quantification and molecular weight determination were performed using commercial software. Aggregation and degradation were examined under various conditions and quantitative results are presented for bovine serum albumin, choriogonadotropin, glyceraldehyde-3-phosphate dehydrogenase, Herceptin, and ReoPro. This method can simultaneously determine both the quantities and the molecular weights of macromolecules from a single injection. The determination of molecular weight is absolute which avoids misleading results caused by molecular shape or interactions with the column matrix. This technique is valuable not only for assessing the extent of aggregation but also for effectively monitoring molecule degradation as evidenced by molecular weight reduction and change in monomer amount.
Collapse
Affiliation(s)
- Hongping Ye
- Division of Pharmaceutical Analysis, Food and Drug Administration, 1114 Market Street, Room 1002, St. Louis, MO 63101, USA.
| |
Collapse
|
13
|
Hofstadler SA, Sannes-Lowery KA. Applications of ESI-MS in drug discovery: interrogation of noncovalent complexes. Nat Rev Drug Discov 2006; 5:585-95. [PMID: 16816839 DOI: 10.1038/nrd2083] [Citation(s) in RCA: 171] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
For many years, analytical mass spectrometry has had numerous supporting roles in the drug development process, including the assessment of compound purity; quantitation of absorption, distribution, metabolism and excretion; and compound-specific pharmacokinetic analyses. More recently, mass spectrometry has emerged as an effective technique for identifying lead compounds on the basis of the characterization of noncovalent ligand-macromolecular target interactions. This approach offers several attractive properties for screening applications in drug discovery compared with other strategies, including the small quantities of target and ligands required, and the capacity to study ligands or targets without having to label them. Here, we review the application of electrospray ionization mass spectrometry to the interrogation of noncovalent complexes, highlighting examples from drug discovery efforts aimed at a range of target classes.
Collapse
Affiliation(s)
- Steven A Hofstadler
- Ibis Therapeutics, A Division of ISIS Pharmaceuticals, 1891 Rutherford Road, Carlsbad, California 92008, USA.
| | | |
Collapse
|
14
|
Di Tullio A, Reale S, De Angelis F. Molecular recognition by mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2005; 40:845-65. [PMID: 16034845 DOI: 10.1002/jms.896] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
A recent major advance in the field of mass spectrometry in the biomolecular sciences is represented by the study of the supramolecular interactions among two or more partners in the gas phase. A great deal of chemistry and most of biochemistry concerns molecular interactions taking place in solution. The electrospray technique, which allows direct sampling from solution, and soft ionization of the solute without deposition into the analyte of large amounts of energy, guarantees in many cases the survival of noncovalent bondings and, hence, the direct analysis of the supramolecular complexes present in the condensed phase. The proper preparation of the solution to be studied and also the expert and accurate setting and use of the instrumental parameters are the prerequisites for gaining results as to the specific interactions between, for instance, a protein conformationally modified by its specific metal ion, eventually, and a ligand molecule. The analysis of the charge state of the protein itself and of the modifications of the complex integrity by activating collisions are also methods for studying the biomolecule-molecule interactions. Accordingly, this new mass spectrometric approach to the supramolecular chemistry, which could be also defined as 'supramolecular mass spectrometry', allows the study of ion-protein, protein-protein, protein-ligand and DNA-drug interactions. Chiral recognition can also be performed in the gas phase, studying by electrospray mass spectrometry the fragmentation of diastereomeric complex ions. Not the least, a deep insight can also be obtained into the formation and nature of inclusion complexes like those formed with crown ethers, cyclodextrins and calixarenes as host molecules. All these topics are treated to a certain extent in this special feature article.
Collapse
Affiliation(s)
- Alessandra Di Tullio
- Department of Chemistry, Chemical Engineering and Material, University of L'Aquila, Via Vetoio Coppito II, I-67010 Coppito L'Aquila Italy
| | | | | |
Collapse
|
15
|
Heck AJR, Van Den Heuvel RHH. Investigation of intact protein complexes by mass spectrometry. MASS SPECTROMETRY REVIEWS 2004; 23:368-89. [PMID: 15264235 DOI: 10.1002/mas.10081] [Citation(s) in RCA: 359] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Mass spectrometry has grown in recent years to a well-accepted and increasingly important complementary technique in structural biology. Especially electrospray ionization mass spectrometry is well suited for the detection of non-covalent protein complexes and their interactions with DNA, RNA, ligands, and cofactors. Over the last decade, significant advances have been made in the ionization and mass analysis techniques, which makes the investigation of even larger and more heterogeneous intact assemblies feasible. These technological developments have paved the way to study intact non-covalent protein-protein interactions, assembly and disassembly in real time, subunit exchange, cooperativity effects, and effects of cofactors, allowing us a better understanding of proteins in cellular processes. In this review, we describe some of the latest developments and several highlights.
Collapse
Affiliation(s)
- Albert J R Heck
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands.
| | | |
Collapse
|
16
|
Hoard-Fruchey HM, Goetzman E, Benson L, Naylor S, Vockley J. Mammalian Electron Transferring Flavoprotein·Flavoprotein Dehydrogenase Complexes Observed by Microelectrospray Ionization-Mass Spectrometry and Surface Plasmon Resonance. J Biol Chem 2004; 279:13786-91. [PMID: 14744856 DOI: 10.1074/jbc.m313914200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microelectrospray ionization-mass spectrometry was used to directly observe electron transferring flavoprotein.flavoprotein dehydrogenase interactions. When electron transferring flavoprotein and porcine dimethylglycine dehydrogenase or sarcosine dehydrogenase were incubated together in the absence of substrate, a relative molecular mass corresponding to the flavoprotein.electron transferring flavoprotein complex was observed, providing the first direct observation of these mammalian complexes. When an acyl-CoA dehydrogenase family member, human short chain acyl-CoA dehydrogenase, was incubated with dimethylglycine dehydrogenase and electron transferring flavoprotein, the microelectrospray ionization-mass spectrometry signal for the dimethylglycine dehydrogenase.electron transferring flavoprotein complex decreased, indicating that the acyl-CoA dehydrogenases have the ability to compete with the dimethylglycine dehydrogenase/sarcosine dehydrogenase family for access to electron transferring flavoprotein. Surface plasmon resonance solution competition experiments revealed affinity constants of 2.0 and 5.0 microm for the dimethylglycine dehydrogenase-electron transferring flavoprotein and short chain acyl-CoA dehydrogenase-electron transferring flavoprotein interactions, respectively, suggesting the same or closely overlapping binding motif(s) on electron transferring flavoprotein for dehydrogenase interaction.
Collapse
Affiliation(s)
- Heidi M Hoard-Fruchey
- Departments of Biochemistry and Molecular Biology and Medical Genetics, Mayo Clinic and Foundation, Rochester, Minnesota 55905, USA
| | | | | | | | | |
Collapse
|
17
|
van den Burg HA, Spronk CAEM, Boeren S, Kennedy MA, Vissers JPC, Vuister GW, de Wit PJGM, Vervoort J. Binding of the AVR4 elicitor of Cladosporium fulvum to chitotriose units is facilitated by positive allosteric protein-protein interactions: the chitin-binding site of AVR4 represents a novel binding site on the folding scaffold shared between the invertebrate and the plant chitin-binding domain. J Biol Chem 2004; 279:16786-96. [PMID: 14769793 DOI: 10.1074/jbc.m312594200] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The attack of fungal cell walls by plant chitinases is an important plant defense response to fungal infection. Anti-fungal activity of plant chitinases is largely restricted to chitinases that contain a noncatalytic, plant-specific chitin-binding domain (ChBD) (also called Hevein domain). Current data confirm that the race-specific elicitor AVR4 of the tomato pathogen Cladosporium fulvum can protect fungi against plant chitinases, which is based on the presence of a novel type of ChBD in AVR4 that was first identified in invertebrates. Although these two classes of ChBDs (Hevein and invertebrate) are sequentially unrelated, they share structural homology. Here, we show that the chitin-binding sites of these two classes of ChBDs have different topologies and characteristics. The K(D), DeltaH, and DeltaS values obtained for the interaction between AVR4 and chito-oligomers are comparable with those obtained for Hevein. However, the binding site of AVR4 is larger than that of Hevein, i.e. AVR4 interacts strictly with chitotriose, whereas Hevein can also interact with the monomer N-acetylglucosamine. Moreover, binding of additional AVR4 molecules to chitin occurs through positive cooperative protein-protein interactions. By this mechanism AVR4 is likely to effectively shield chitin on the fungal cell wall, preventing the cell wall from being degraded by plant chitinases.
Collapse
Affiliation(s)
- Harrold A van den Burg
- Laboratorie of Biochemistry, Wageningen University, NL-6703 HA Wageningen, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Yan X, Watson J, Ho PS, Deinzer ML. Mass Spectrometric Approaches Using Electrospray Ionization Charge States and Hydrogen-Deuterium Exchange for Determining Protein Structures and Their Conformational Changes. Mol Cell Proteomics 2004; 3:10-23. [PMID: 14623985 DOI: 10.1074/mcp.r300010-mcp200] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Electrospray ionization (ESI) mass spectrometry (MS) is a powerful analytical tool for elucidating structural details of proteins in solution especially when coupled with amide hydrogen/deuterium (H/D) exchange analysis. ESI charge-state distributions and the envelopes of charges they form from proteins can provide an abundance of information on solution conformations that is not readily available through other biophysical techniques such as near ultraviolet circular dichroism (CD) and tryptophan fluorescence. The most compelling reason for the use of ESI-MS over nuclear magnetic resonance (NMR) for measuring H/D after exchange is that larger proteins and lesser amounts of samples can be studied. In addition, MS can provide structural details on transient or folding intermediates that may not be accessible by CD, fluorescence, and NMR because these techniques measure the average properties of large populations of proteins in solution. Correlations between measured H/D and calculated parameters that are often available from crystallographic data can be used to extend the range of structural details obtained on proteins. Molecular dynamics and energy minimization by simulation techniques such as assisted model building with energy refinement (AMBER) force field can be very useful in providing structural models of proteins that rationalize the experimental H/D exchange results. Charge-state envelopes and H/D exchange information from ESI-MS data used complementarily with NMR and CD data provides the most powerful approach available to understanding the structures and dynamics of proteins in solution.
Collapse
Affiliation(s)
- Xuguang Yan
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA
| | | | | | | |
Collapse
|
19
|
Abstract
Tandem mass spectrometry is becoming an increasingly important analytical technology in the clinical laboratory environment. Applications in toxicology and therapeutic drug monitoring have opened the door for tandem mass spectrometry and now we are seeing a vast array of new applications being developed. It has been the combination of tandem mass spectrometry with sample introduction techniques employing atmospheric pressure ionization that has enabled this technology to be readily implemented in the clinical laboratory. Although its major research applications started with pharmacology and proteomics, tandem mass spectrometry is being used for a great variety of analyses from steroids to catecholamines to peptides. As with chromatographic methods, tandem mass spectrometry is most cost effective when groups of compounds need to be measured simultaneously. However as the price/performance of this technology continues to improve, it will become even more widely utilized for clinical laboratory applications.
Collapse
Affiliation(s)
- Kent C Dooley
- Department of Pathology and Laboratory Medicine, IWK Health Centre and Department of Pathology, Dalhousie University Medical School, Halifax, Nova Scotia, Canada.
| |
Collapse
|
20
|
Gabelica V, Karas M, De Pauw E. Calibration of Ion Effective Temperatures Achieved by Resonant Activation in a Quadrupole Ion Trap. Anal Chem 2003; 75:5152-9. [PMID: 14708790 DOI: 10.1021/ac034473a] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The present paper describes a calibration of the ion effective temperatures as a function of the resonant activation amplitude in a quadrupole ion trap mass spectrometer. MS/MS experiments are performed on leucine enkephalin (M + H)+, bradykinin (M + H)+, (M + 2H)2+, and (M + 3H)3+, and ubiquitin (M + 11H)11+. For each amplitude, the effective temperature is calculated as the temperature that would give the same dissociation rate constant as the one observed and is calculated using published Arrhenius parameters. The effective temperature is found to be linearly dependent on the activation amplitude on the range investigated. The dependence of the slope and of the intercept of the T(eff) = f (amplitude) functions on the parent ion m/z is examined and an equation is derived to calibrate the ion effective temperature between 365 and 600 K. Below 365 K, a deviation from linearity is expected. Above 600 K, the validity of the equation will depend on whether the rapid energy exchange limit is still reached. Calculating backward, the Arrhenius parameters from the measured dissociation rates using this calibration show excellent agreement with the published values. The calibration can therefore be used to determine Arrhenius activation parameters from dissociation kinetics under resonant activation in quadrupole ion trap mass spectrometers.
Collapse
Affiliation(s)
- Valérie Gabelica
- Institüt für Pharmazeutische Chemie, Johann-Wolfgang Goethe Universität Frankfurt, Marie-Curie Strasse 9-11, D-60439 Frankfurt am Main, Germany.
| | | | | |
Collapse
|
21
|
Daniel JM, McCombie G, Wendt S, Zenobi R. Mass spectrometric determination of association constants of adenylate kinase with two noncovalent inhibitors. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2003; 14:442-8. [PMID: 12745213 DOI: 10.1016/s1044-0305(03)00132-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Noncovalent complexes between chicken muscle adenylate kinase and two inhibitors, P(1),P(4)-di(adenosine-5')tetraphosphate (Ap4A) and P(1),P(5)-di(adenosine-5') pentaphosphate (Ap5A), were investigated with electrospray ionization mass spectrometry under non-denaturing conditions. The nonconvalent nature and the specificity of the complexes are demonstrated with a number of control experiments. Titration experiments allowed the association constants for inhibitor binding to be determined. Problems with concentration dependent ion yields are circumvented by a data evaluation method that is insensitive to the overall ionization efficiency. The K(a) values found were 9.0 x 10(4) M(-1) (Ap4A) and 4.0 x 10(7) M(-1) (Ap5A), respectively, in very good agreement with available literature data.
Collapse
Affiliation(s)
- Jürg M Daniel
- Department of Chemistry, Swiss Federal Institute of Technology, ETH, CH-8093, Zürich, Switzerland
| | | | | | | |
Collapse
|
22
|
David WM, Brodbelt JS. Threshold dissociation energies of protonated amine/polyether complexes in a quadrupole ion trap. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2003; 14:383-392. [PMID: 12686485 DOI: 10.1016/s1044-0305(03)00070-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) is increasingly used to probe the nature of noncovalent complexes; however, assessing the relevance of gas-phase results to structures of complexes in solution requires knowledge of the types of interactions that are maintained in a solventless environment and how these might compare to key interactions in solution. This study addresses the factors impacting the strength of hydrogen bonding noncovalent interactions in the gas phase. Hydrogen bonded complexes consisting of ammonium ions bound to polydentate ethers are transported to the gas phase with ESI, and energy-variable collisional activated dissociation (CAD) is used to map the relative dissociation energies. The measured relative dissociation energies are correlated with the gas-phase basicities and steric factors of the amine and polyether constituents. To develop correlations between hydrogen bonding strength and structural features of the donor and acceptor molecules, a variety of amines with different gas-phase basicities and structures were selected, including primary, secondary, and tertiary amines, as well as those that are bidentate to promote intramolecular hydrogen bonding. The acceptor molecules are polydentate ethers, such as 18-crown-6. Four primary factors influence the observed dissociation energies of the polyether/ammonium ion complexes: the gas-phase basicities of the polyether and amine, steric effects of the amines, conformational flexibility of the polyethers, and the inhibition of intramolecular hydrogen bonds of the guest ammonium ions in the resulting ammonium/polyether noncovalent complexes.
Collapse
Affiliation(s)
- Wendi M David
- Department of Chemistry and Biochemistry, University of Texas, Austin 78712, USA
| | | |
Collapse
|
23
|
Schlosser G, Pocsfalvi G, Malorni A, Puerta A, de Frutos M, Vékey K. Detection of immune complexes by matrix-assisted laser desorption/ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2003; 17:2741-2747. [PMID: 14673821 DOI: 10.1002/rcm.1239] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) was used to detect an immune complex formed between beta-lactoglobulin and polyclonal anti-beta-lactoglobulin antibody in the gas phase. The most important experimental parameters to detect such a specific antibody-antigen complex by MALDI were the use of solutions at near-neutral pH and of sinapinic acid matrix prepared by the dried-droplet method. Under such conditions, predominantly one but also two molecules of antigen protein were complexed by the antibody. Specific formation of the antibody-antigen complex was confirmed by performing competitive reactions. Addition of antibody to a 1:1 mixture of beta-lactoglobulin and one control protein resulted not only in the appearance of the expected antibody-antigen complex, but also in a strong decrease in the free beta-lactoglobulin signal, while the abundance of the control protein was not influenced.
Collapse
Affiliation(s)
- Gitta Schlosser
- Chemical Research Center, Hungarian Academy of Sciences, Budapest, Hungary
| | | | | | | | | | | |
Collapse
|
24
|
Breuker K, Oh H, Horn DM, Cerda BA, McLafferty FW. Detailed unfolding and folding of gaseous ubiquitin ions characterized by electron capture dissociation. J Am Chem Soc 2002; 124:6407-20. [PMID: 12033872 DOI: 10.1021/ja012267j] [Citation(s) in RCA: 272] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The unfolding enthalpy of the native state of ubiquitin in solution is 5 to 8 times that of its gaseous ions, as determined by electron capture dissociation (ECD) mass spectrometry. Although two-state folding occurs in solution, the three-state gaseous process proposed for this by Clemmer and co-workers based on ion mobility data is supported in general by ECD mass spectra, including relative product yields, distinct Delta H(unfolding) values between states, site-specific melting temperatures, and folding kinetics indicating a cooperative process. ECD also confirms that the 13+ ions represent separate conformers, possibly with side-chain solvated alpha-helical structures. However, the ECD data on the noncovalent bonding in the 5+ to 13+ ions, determined overall in 69 of the 75 interresidue sites, shows that thermal unfolding proceeds via a diversity of intermediates whose conformational characteristics also depend on charge site locations. As occurs with increased acidity in solution, adding 6 protons to the 5+ ions completely destroys their tertiary noncovalent bonding. However, solvation of the newly protonated sites to the backbone instead increases the stability of the secondary structure (possibly an alpha-helix) of these gaseous ions, while in solution these new sites aid denaturation by solvation in the aqueous medium. Extensive ion equilibration can lead to even more compact and diverse conformers. The three-state unfolding of gaseous ubiquitin appears to involve ensembles of individual chain conformations in a "folding funnel" of parallel reaction paths. This also provides a further caution for characterizing solution conformers from their gas-phase behavior.
Collapse
Affiliation(s)
- Kathrin Breuker
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853-1301, USA
| | | | | | | | | |
Collapse
|
25
|
|
26
|
Bibliography. Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2001; 36:1164-1171. [PMID: 11747111 DOI: 10.1002/jms.97] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
|