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Wang L, Zhang W, Shao Y, Zhang D, Guo G, Wang X. Analytical methods for obtaining binding parameters of drug–protein interactions: A review. Anal Chim Acta 2022; 1219:340012. [DOI: 10.1016/j.aca.2022.340012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 11/30/2022]
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2
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Soloviev Z, Bullock JMA, James JMB, Sauerwein AC, Nettleship JE, Owens RJ, Hansen DF, Topf M, Thalassinos K. Structural mass spectrometry decodes domain interaction and dynamics of the full-length Human Histone Deacetylase 2. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140759. [PMID: 35051665 PMCID: PMC8825994 DOI: 10.1016/j.bbapap.2022.140759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 01/11/2022] [Indexed: 11/30/2022]
Abstract
Human Histone Deacetylase 2 (HDAC2) belongs to a conserved enzyme superfamily that regulates deacetylation inside cells. HDAC2 is a drug target as it is known to be upregulated in cancers and neurodegenerative disorders. It consists of globular deacetylase and C-terminus intrinsically-disordered domains [1-3]. To date, there is no full-length structure of HDAC2 available due to the high intrinsic flexibility of its C-terminal domain. The intrinsically-disordered domain, however, is known to be important for the enzymatic function of HDAC2 [1, 4]. Here we combine several structural Mass Spectrometry (MS) methodologies such as denaturing, native, ion mobility and chemical crosslinking, alongside biochemical assays and molecular modelling to study the structure and dynamics of the full-length HDAC2 for the first time. We show that MS can easily dissect heterogeneity inherent within the protein sample and at the same time probe the structural arrangement of the different conformers present. Activity assays combined with data from MS and molecular modelling suggest how the structural dynamics of the C-terminal domain, and its interactions with the catalytic domain, regulate the activity of this enzyme.
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Affiliation(s)
- Zoja Soloviev
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6AR, UK.
| | - Joshua M A Bullock
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
| | - Juliette M B James
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6AR, UK
| | - Andrea C Sauerwein
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
| | - Joanne E Nettleship
- PPUK, Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford OX11 0FA, UK; Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - Raymond J Owens
- PPUK, Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford OX11 0FA, UK; Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - D Flemming Hansen
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6AR, UK
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK; Centre for Structural Systems Biology, Heinrich-Pette-Institut, Leibniz-Institut für Experimentelle Virologie, Hamburg, Germany
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6AR, UK.
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3
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Elhabashy H, Merino F, Alva V, Kohlbacher O, Lupas AN. Exploring protein-protein interactions at the proteome level. Structure 2022; 30:462-475. [DOI: 10.1016/j.str.2022.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/26/2021] [Accepted: 02/02/2022] [Indexed: 02/08/2023]
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4
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Chi Q, Liu YZ, Wang X. Study on the Structural Effect of Maltoligosaccharides on Cytochrome c Complexes Stabilities by Native Mass Spectrometry. NATURAL PRODUCTS AND BIOPROSPECTING 2018; 8:57-61. [PMID: 29380206 PMCID: PMC5803145 DOI: 10.1007/s13659-017-0150-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 12/13/2017] [Indexed: 05/05/2023]
Abstract
Noncovalent interactions between ligands and targeting proteins are essential for understanding molecular mechanisms of proteins. In this work, we investigated the interaction of Cytochrome c (Cyt c) with maltoligosaccharides, namely maltose (Mal II), maltotriose (Mal III), maltotetraose (Mal IV), maltopentaose (Mal V), maltohexaose (Mal VI) and maltoheptaose (Mal VII). Using electrospray ionization mass spetrometry (ESI-MS) assay, the 1:1 and 1:2 complexes formed by Cyt c with maltoligosaccharide ligand were observed. The corresponding association constants were calculated according to the deconvoluted spectra. The order of the relative binding affinities of the selected oligosaccharides with Cyt c were as Mal III > Mal IV > Mal II > Mal V > Mal VI > Mal VII. The results indicated that the stability of noncovalent protein complexes was intimately correlated to the molecular structure of bound ligand. The relevant functional groups that could form H-bonds, electrostatic or hydrophobic forces with protein's amino residues played an important role for the stability of protein complexes. In addition, the steric structure of ligand was also critical for an appropriate interaction with the binding pocket of proteins.
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Affiliation(s)
- Quan Chi
- 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
| | - Ying-Zhi 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, People's Republic of China
| | - 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.
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Abstract
The present review covers recent advances and important applications of affinity capillary electrophoresis (ACE). It provides an overview about various ACE types, including ACE-MS, the multiple injection mode, the use of microchips and field-amplified sample injection-ACE. The most common scenarios of the studied affinity interactions are protein-drug, protein-metal ion, protein-protein, protein-DNA, protein-carbohydrate, carbohydrate-drug, peptide-peptide, DNA-drug and antigen-antibody. Approaches for the improvements of ACE in term of precision, rinsing protocols and sensitivity are discussed. The combined use of computer simulation programs to support data evaluation is presented. In conclusion, the performance of ACE is compared with other techniques such as equilibrium dialysis, parallel artificial membrane permeability assay, high-performance affinity chromatography as well as surface plasmon resonance, ultraviolet, circular dichroism, nuclear magnetic resonance, Fourier transform infrared, fluorescence, MS and isothermal titration calorimetry.
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6
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Determinants of protein–ligand complex formation in the thyroid hormone receptor α: A molecular dynamics simulation study. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.03.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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7
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Seo Y, Andaya A, Bleiholder C, Leary JA. Differentiation of CC vs CXC Chemokine Dimers with GAG Octasaccharide Binding Partners: An Ion Mobility Mass Spectrometry Approach. J Am Chem Soc 2013; 135:4325-32. [DOI: 10.1021/ja310915m] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Youjin Seo
- Departments of Chemistry and
Molecular and Cellular Biology, University of California, Davis, California 95616, United States
| | - Armann Andaya
- Departments of Chemistry and
Molecular and Cellular Biology, University of California, Davis, California 95616, United States
| | - Christian Bleiholder
- Department of Chemistry and
Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Julie A. Leary
- Departments of Chemistry and
Molecular and Cellular Biology, University of California, Davis, California 95616, United States
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8
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Abstract
Native state mass spectrometry (MS) has been recognised as a rapid, sensitive, and high throughput method to directly investigate protein-ligand interactions for some time, however there are few examples reporting this approach as a screening method to identify relevant protein–fragment interactions in fragment-based drug discovery (FBDD). In this paper an overview of native state MS will be presented, highlighting the attractive properties of this method within the context of fragment screening applications. A summary of published examples using MS for fragment screening will be described and reflection on the outlook for the future adoption and implementation of native state MS as a complementary fragment screening method will be presented.
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9
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Photoactivable Amino Acid Bioisosteres and Mass Spectrometry: Snapshots of in Vivo 3D Protein Structures. Chembiochem 2012; 14:181-3. [DOI: 10.1002/cbic.201200742] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Indexed: 01/18/2023]
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10
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Hopper JTS, Rawlings A, Afonso JP, Channing D, Layfield R, Oldham NJ. Evidence for the preservation of native inter- and intra-molecular hydrogen bonds in the desolvated FK-binding protein·FK506 complex produced by electrospray ionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1757-1767. [PMID: 22797884 DOI: 10.1007/s13361-012-0430-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 06/06/2012] [Accepted: 06/06/2012] [Indexed: 06/01/2023]
Abstract
It is now well established that electrospray ionization (ESI) is capable of introducing noncovalent protein assemblies into a desolvated environment, thereby allowing their analysis by mass spectrometry. The degree to which native interactions from the solution phase are preserved in this environment is less clear. Site-directed mutagenesis of FK506-binding protein (FKBP) has been employed to probe specific intra- and inter-molecular interactions within the complex between FKBP and its ligand FK506. Collisional activation of wild-type and mutant-FKBP•FK506 ions, generated by ESI, demonstrated that removal of native protein-ligand interactions formed between residues Asp37, Tyr82, and FK506 significantly destabilized the complex. Mutation of Arg42 to Ala42, or Tyr26 to Phe26 also resulted in lower energy dissociation of the FKBP·FK506 complex. Although these residues do not form direct H-bonds to FK506, they interact with Asp37, ensuring its correct orientation to associate with the ligand. Comparison with solution-based affinity measurements of these mutants has been discussed, including the stabilization afforded by ordered water molecules. Ion mobility spectrometry (IMS) has been employed to provide gas-phase structural information on the unfolding of the complexes. The [M + 6H](6+) complexes of the wild-type and mutants have been shown to resist unfolding and retain compact conformations. However, removal of the basic Arg42 residue was found to induce significant structural weakening of the [M + 7H](7+) complex when raised to dissociation-level energies. Overall, destabilization of the FKBP·FK506 complex, resulting from targeted removal of specific H-bonds, provides evidence for the preservation of these interactions in the desolvated wild-type complex.
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11
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Torres DA, Azagarsamy MA, Thayumanavan S. Supramolecular displacement-mediated activation of a silent fluorescence probe for label-free ligand screening. J Am Chem Soc 2012; 134:7235-7. [PMID: 22500607 DOI: 10.1021/ja301204z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We report a new approach for the rapid screening of analyte binding affinities for a target protein. We demonstrate that a molecular probe, with a pro-fluorophore substrate and ligand moieties, can be hindered from enzymatic access when bound to the target protein. When analytes displace the probe from the protein's binding pocket, a fluorescence profile is generated. This profile is used to discriminate analytes based on their relative binding affinities.
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Affiliation(s)
- Diego Amado Torres
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, USA
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12
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Pacholarz KJ, Garlish RA, Taylor RJ, Barran PE. Mass spectrometry based tools to investigate protein–ligand interactions for drug discovery. Chem Soc Rev 2012; 41:4335-55. [DOI: 10.1039/c2cs35035a] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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13
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Kang Y, Terrier P, Ding C, Douglas DJ. Solution and gas-phase H/D exchange of protein-small-molecule complexes: Cex and its inhibitors. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:57-67. [PMID: 22006406 DOI: 10.1007/s13361-011-0263-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2011] [Revised: 09/20/2011] [Accepted: 09/23/2011] [Indexed: 05/31/2023]
Abstract
The properties of noncovalent complexes of the enzyme exo-1,4-β-D-glycanase ("Cex") with three aza-sugar inhibitors, deoxynojirimycin (X(2)DNJ), isofagomine lactam (X(2)IL), and isofagomine (X(2)IF), have been studied with solution and gas-phase hydrogen deuterium exchange (H/Dx) and measurements of collision cross sections of gas-phase ions. In solution, complexes have lower H/Dx levels than free Cex because binding the inhibitors blocks some sites from H/Dx and reduces fluctuations of the protein. In mass spectra of complexes, abundant Cex ions are seen, which mostly are formed by dissociation of complexes in the ion sampling interface. Both complex ions and Cex ions formed from a solution containing complexes have lower cross sections than Cex ions from a solution of Cex alone. This suggests the Cex ions formed by dissociation "remember" their solution conformations. For a given charge, ions of the complexes have greater gas-phase H/Dx levels than ions of Cex. Unlike cross sections, H/Dx levels of the complexes do not correlate with the relative gas-phase binding strengths measured by MS/MS. Cex ions from solutions with or without inhibitors, which have different cross sections, show the same H/Dx level after 15 s, indicating the ions may fold or unfold on the seconds time scale of the H/Dx experiment. Thus, cross sections show that complexes have more compact conformations than free protein ions on the time scale of ca. 1 ms. The gas-phase H/Dx measurements show that at least some complexes retain different conformations from the Cex ions on a time scale of seconds.
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Affiliation(s)
- Yang Kang
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
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14
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Stengel F, Aebersold R, Robinson CV. Joining forces: integrating proteomics and cross-linking with the mass spectrometry of intact complexes. Mol Cell Proteomics 2011; 11:R111.014027. [PMID: 22180098 PMCID: PMC3316738 DOI: 10.1074/mcp.r111.014027] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein assemblies are critical for cellular function and understanding their physical organization is the key aim of structural biology. However, applying conventional structural biology approaches is challenging for transient, dynamic, or polydisperse assemblies. There is therefore a growing demand for hybrid technologies that are able to complement classical structural biology methods and thereby broaden our arsenal for the study of these important complexes. Exciting new developments in the field of mass spectrometry and proteomics have added a new dimension to the study of protein-protein interactions and protein complex architecture. In this review, we focus on how complementary mass spectrometry-based techniques can greatly facilitate structural understanding of protein assemblies.
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Affiliation(s)
- Florian Stengel
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA United Kingdom
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15
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Yan F, Che FY, Nieves E, Weiss LM, Angeletti RH, Fiser A. Photo-assisted peptide enrichment in protein complex cross-linking analysis of a model homodimeric protein using mass spectrometry. Proteomics 2011; 11:4109-15. [PMID: 21834138 PMCID: PMC3465073 DOI: 10.1002/pmic.201100015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 07/16/2011] [Accepted: 07/29/2011] [Indexed: 11/11/2022]
Abstract
MS analysis of cross-linked peptides can be used to probe protein contact sites in macromolecular complexes. We have developed a photo-cleavable cross-linker that enhances peptide enrichment, improving the signal-to-noise ratio of the cross-linked peptides in mass spectrometry analysis. This cross-linker utilizes nitro-benzyl alcohol group that can be cleaved by UV irradiation and is stable during the multiple washing steps used for peptide enrichment. The enrichment method utilizes a cross-linker that aids in eliminating contamination resulting from protein-based retrieval systems, and thus, facilitates the identification of cross-linked peptides. Homodimeric pilM protein from Pseudomonas aeruginosa 2192 (pilM) was investigated to test the specificity and experimental conditions. As predicted, the known pair of lysine side chains within 14 Å was cross-linked. An unexpected cross-link involving the protein's amino terminus was also detected. This is consistent with the predicted mobility of the amino terminus that may bring the amino groups within 19 Å of one another in solution. These technical improvements allow this method to be used for investigating protein-protein interactions in complex biological samples.
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Affiliation(s)
- Funing Yan
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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16
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Uetrecht C, Heck AJR. Modern biomolecular mass spectrometry and its role in studying virus structure, dynamics, and assembly. Angew Chem Int Ed Engl 2011; 50:8248-62. [PMID: 21793131 PMCID: PMC7159578 DOI: 10.1002/anie.201008120] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Indexed: 01/04/2023]
Abstract
Over a century since its development, the analytical technique of mass spectrometry is blooming more than ever, and applied in nearly all aspects of the natural and life sciences. In the last two decades mass spectrometry has also become amenable to the analysis of proteins and even intact protein complexes, and thus begun to make a significant impact in the field of structural biology. In this Review, we describe the emerging role of mass spectrometry, with its different technical facets, in structural biology, focusing especially on structural virology. We describe how mass spectrometry has evolved into a tool that can provide unique structural and functional information about viral-protein and protein-complex structure, conformation, assembly, and topology, extending to the direct analysis of intact virus capsids of several million Dalton in mass. Mass spectrometry is now used to address important questions in virology ranging from how viruses assemble to how they interact with their host.
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Affiliation(s)
- Charlotte Uetrecht
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht (The Netherlands)
- Netherlands Proteomics Centre (The Netherlands)
- Present address: Molecular Biophysics, Uppsala University, Uppsala (Sweden)
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht (The Netherlands)
- Netherlands Proteomics Centre (The Netherlands)
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17
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Uetrecht C, Heck AJR. Moderne biomolekulare Massenspektrometrie und ihre Bedeutung für die Erforschung der Struktur, der Dynamik und des Aufbaus von Viren. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201008120] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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18
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Dubinsky L, Krom BP, Meijler MM. Diazirine based photoaffinity labeling. Bioorg Med Chem 2011; 20:554-70. [PMID: 21778062 DOI: 10.1016/j.bmc.2011.06.066] [Citation(s) in RCA: 283] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Revised: 06/19/2011] [Accepted: 06/24/2011] [Indexed: 10/17/2022]
Abstract
Diazirines are among the smallest photoreactive groups that form a reactive carbene upon light irradiation. This feature has been widely utilized in photoaffinity labeling to study ligand-receptor, ligand-enzyme and protein-protein interactions, and in the isolation and identification of unknown proteins. This review summarizes recent advances in the use of diazirines in photoaffinity labeling.
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Affiliation(s)
- Luba Dubinsky
- Department of Chemistry and National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
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19
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Ramisetty SR, Washburn MP. Unraveling the dynamics of protein interactions with quantitative mass spectrometry. Crit Rev Biochem Mol Biol 2011; 46:216-28. [PMID: 21438726 DOI: 10.3109/10409238.2011.567244] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Knowledge of structure and dynamics of proteins and protein complexes is important to unveil the molecular basis and mechanisms involved in most biological processes. Protein complex dynamics can be defined as the changes in the composition of a protein complex during a cellular process. Protein dynamics can be defined as conformational changes in a protein during enzyme activation, for example, when a protein binds to a ligand or when a protein binds to another protein. Mass spectrometry (MS) combined with affinity purification has become the analytical tool of choice for mapping protein-protein interaction networks and the recent developments in the quantitative proteomics field has made it possible to identify dynamically interacting proteins. Furthermore, hydrogen/deuterium exchange MS is emerging as a powerful technique to study structure and conformational dynamics of proteins or protein assemblies in solution. Methods have been developed and applied for the identification of transient and/or weak dynamic interaction partners and for the analysis of conformational dynamics of proteins or protein complexes. This review is an overview of existing and recent developments in studying the overall dynamics of in vivo protein interaction networks and protein complexes using MS-based methods.
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20
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Rappsilber J. The beginning of a beautiful friendship: cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes. J Struct Biol 2010; 173:530-40. [PMID: 21029779 PMCID: PMC3043253 DOI: 10.1016/j.jsb.2010.10.014] [Citation(s) in RCA: 319] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 10/21/2010] [Accepted: 10/21/2010] [Indexed: 11/17/2022]
Abstract
After more than a decade of method development, cross-linking in combination with mass spectrometry and bioinformatics is finally coming of age. This technology now provides improved opportunities for modelling by mapping structural details of functional complexes in solution. The structure of proteins or protein complexes is ascertained by identifying amino acid pairs that are positioned in close proximity to each other. The validity of this technique has recently been benchmarked for large multi-protein complexes, by comparing cross-link data with that from a crystal structure of RNA polymerase II. Here, the specific nature of this cross-linking data will be discussed to assess the technical challenges and opportunities for model building. We believe that once remaining technological challenges of cross-linking/mass spectrometry have been addressed and cross-linking/mass spectrometry data has been incorporated into modelling algorithms it will quickly become an indispensable companion of protein and protein complex modelling and a corner-stone of integrated structural biology.
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Affiliation(s)
- Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Mayfield Road, Edinburgh, EH9 3JR Scotland, UK.
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21
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Baslé E, Joubert N, Pucheault M. Protein chemical modification on endogenous amino acids. ACTA ACUST UNITED AC 2010; 17:213-27. [PMID: 20338513 DOI: 10.1016/j.chembiol.2010.02.008] [Citation(s) in RCA: 301] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Revised: 01/29/2010] [Accepted: 02/11/2010] [Indexed: 12/15/2022]
Abstract
Chemical modification of protein is an arduous but fruitful task. Many chemical methods have been developed for such purpose by carefully balancing reactivity and selectivity. Now both chemists and biologists have in hand an arsenal of tools from which they can select a relevant reaction to tackle their problems. This review focuses on the various chemical transformations available for selective modification of proteins. It also provides a brief overview of some of their main applications, including detection of protein interactions, preparation of bioconjugates, and protein microarrays.
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Affiliation(s)
- Emmanuel Baslé
- Molecular Chemistry and Photonic, UMR 6510 CPM, Centre National de la Recherche Scientifique, Université de Rennes1, 263 Avenue du Général Leclerc, 35042 Rennes cedex, France
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22
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Uetrecht C, Rose RJ, van Duijn E, Lorenzen K, Heck AJR. Ion mobility mass spectrometry of proteins and proteinassemblies. Chem Soc Rev 2010; 39:1633-55. [DOI: 10.1039/b914002f] [Citation(s) in RCA: 381] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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23
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Cheng KW, Wong CC, Wang M, He QY, Chen F. Identification and characterization of molecular targets of natural products by mass spectrometry. MASS SPECTROMETRY REVIEWS 2010; 29:126-155. [PMID: 19319922 DOI: 10.1002/mas.20235] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Natural products, and their derivatives and mimics, have contributed to the development of important therapeutics to combat diseases such as infections and cancers over the past decades. The value of natural products to modern drug discovery is still considerable. However, its development is hampered by a lack of a mechanistic understanding of their molecular action, as opposed to the emerging molecule-targeted therapeutics that are tailored to a specific protein target(s). Recent advances in the mass spectrometry-based proteomic approaches have the potential to offer unprecedented insights into the molecular action of natural products. Chemical proteomics is established as an invaluable tool for the identification of protein targets of natural products. Small-molecule affinity selection combined with mass spectrometry is a successful strategy to "fish" cellular targets from the entire proteome. Mass spectrometry-based profiling of protein expression is also routinely employed to elucidate molecular pathways involved in the therapeutic and possible toxicological responses upon treatment with natural products. In addition, mass spectrometry is increasingly utilized to probe structural aspects of natural products-protein interactions. Limited proteolysis, photoaffinity labeling, and hydrogen/deuterium exchange in conjunction with mass spectrometry are sensitive and high-throughput strategies that provide low-resolution structural information of non-covalent natural product-protein complexes. In this review, we provide an overview on the applications of mass spectrometry-based techniques in the identification and characterization of natural product-protein interactions, and we describe how these applications might revolutionize natural product-based drug discovery.
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Affiliation(s)
- Ka-Wing Cheng
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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Hopper JTS, Oldham NJ. Collision induced unfolding of protein ions in the gas phase studied by ion mobility-mass spectrometry: the effect of ligand binding on conformational stability. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:1851-8. [PMID: 19643633 DOI: 10.1016/j.jasms.2009.06.010] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2009] [Revised: 06/11/2009] [Accepted: 06/13/2009] [Indexed: 05/19/2023]
Abstract
Ion mobility spectrometry, with subsequent mass spectrometric detection, has been employed to study the stability of compact protein conformations of FK-binding protein, hen egg-white lysozyme, and horse heart myoglobin in the presence and absence of bound ligands. Protein ions, generated by electrospray ionization from ammonium acetate buffer, were activated by collision with argon gas to induce unfolding of their compact structures. The collisional cross sections (Omega) of folded and unfolded conformations were measured in the T-Wave mobility cell of a Waters Synapt HDMS (Waters, Altrincham, UK) employing a calibration against literature values for a range of protein standards. In the absence of activation, collisional cross section measurements were found to be consistent with those predicted for folded protein structures. Under conditions of defined collisional activation energies partially unfolded conformations were produced. The degree of unfolding and dissociation induced by these defined collision energies are related to the stability of noncovalent intra- and intermolecular interactions within protein complexes. These findings highlight the additional conformational stability of protein ions in the gas phase resulting from ligand binding.
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Affiliation(s)
- Jonathan T S Hopper
- School of Chemistry, University of Nottingham, University Park, Nottingham, United Kingdom
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Jiang J, Zeng D, Li S. Photogenerated Quinone Methides as Protein Affinity Labeling Reagents. Chembiochem 2009; 10:635-8. [DOI: 10.1002/cbic.200800700] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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KONG XL. Nanodiamonds Used as a Platform for Studying Noncovalent Interaction by MALDI-MS. CHINESE J CHEM 2008. [DOI: 10.1002/cjoc.200890326] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Ho JTC, White JF, Grisshammer R, Hess S. Analysis of a G protein-coupled receptor for neurotensin by liquid chromatography-electrospray ionization-mass spectrometry. Anal Biochem 2007; 376:13-24. [PMID: 18294946 DOI: 10.1016/j.ab.2007.12.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 11/29/2007] [Accepted: 12/21/2007] [Indexed: 11/17/2022]
Abstract
The type 1 neurotensin receptor (NTS1) belongs to the G protein-coupled receptor (GPCR) family. GPCRs are involved in important physiological processes, but for many GPCRs ligand binding sites and other structural features have yet to be elucidated. Comprehensive analyses by mass spectrometry (MS) could address such issues, but they are complicated by the hydrophobic nature of the receptors. Recombinant NTS1 must be purified in the presence of detergents to maintain solubility and functionality of the receptor, to allow testing of ligand, or to allow G protein interaction. However, detergents are detrimental to MS analyses. Hence, steps need to be taken to substitute the detergents with MS-compatible polar/organic solvents. Here we report the characterization of NTS1 by electrospray ionization (ESI)-MS with emphasis on methods to transfer intact NTS1 or its proteolytic peptides into compatible solvents by protein precipitation and liquid chromatography (LC) prior to ESI-MS analyses. Molecular mass measurement of intact recombinant NTS1 was performed using a mixture of chloroform/methanol/aqueous trifluoroacetic acid as the mobile phase for size exclusion chromatography-ESI-MS analysis. In a separate experiment, NTS1 was digested with a combination of cyanogen bromide and trypsin and/or chymotrypsin. Subsequent reversed phase LC-ESI-tandem MS analysis resulted in greater than 80% sequence coverage of the NTS1 protein, including all seven transmembrane domains. This work represents the first comprehensive analysis of recombinant NTS1 using MS.
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MESH Headings
- Chromatography, Gel
- Chromatography, Liquid/methods
- Chymotrypsin/metabolism
- Cyanogen Bromide/chemistry
- Receptors, G-Protein-Coupled/analysis
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/metabolism
- Receptors, Neurotensin/analysis
- Receptors, Neurotensin/chemistry
- Receptors, Neurotensin/metabolism
- Spectrometry, Mass, Electrospray Ionization/methods
- Trypsin/metabolism
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Affiliation(s)
- Jenny T C Ho
- Proteome Exploration Laboratory, Beckman Institute, MC 139-74, California Institute of Technology, Pasadena, CA 91125, USA
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Affinity selection-mass spectrometry screening techniques for small molecule drug discovery. Curr Opin Chem Biol 2007; 11:518-26. [PMID: 17931956 DOI: 10.1016/j.cbpa.2007.07.011] [Citation(s) in RCA: 151] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Revised: 07/21/2007] [Accepted: 07/27/2007] [Indexed: 11/24/2022]
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