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Yanaka S, Uchiyama S. Current status and issues of protein solution biophysics-Session 1SDP. Biophys Rev 2020; 12:263-264. [PMID: 32248431 DOI: 10.1007/s12551-020-00671-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 02/26/2020] [Indexed: 02/07/2023] Open
Affiliation(s)
- Saeko Yanaka
- Institute for Molecular Science, National Institutes of Natural Sciences, Tokyo, Japan. .,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Tokyo, Japan.
| | - Susumu Uchiyama
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Tokyo, Japan.,Graduate School of Engineering, Osaka University, Osaka, Japan
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2
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Akashi S, Downard KM. Effect of charge on the conformation of highly basic peptides including the tail regions of histone proteins by ion mobility mass spectrometry. Anal Bioanal Chem 2016; 408:6637-48. [DOI: 10.1007/s00216-016-9777-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 06/28/2016] [Accepted: 07/06/2016] [Indexed: 10/21/2022]
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3
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Amirbekyan K, Duchemin N, Benedetti E, Joseph R, Colon A, Markarian SA, Bethge L, Vonhoff S, Klussmann S, Cossy J, Vasseur JJ, Arseniyadis S, Smietana M. Design, Synthesis, and Binding Affinity Evaluation of Hoechst 33258 Derivatives for the Development of Sequence-Specific DNA-Based Asymmetric Catalysts. ACS Catal 2016. [DOI: 10.1021/acscatal.6b00495] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Karen Amirbekyan
- Institut
des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM Place Eugène Bataillon, 34095 Montpellier, France
- Department
of Physical Chemistry, Yerevan State University, 1 Alex Manoogian, Yerevan 0025, Armenia
| | - Nicolas Duchemin
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Erica Benedetti
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Rinah Joseph
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Aude Colon
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Shiraz A. Markarian
- Department
of Physical Chemistry, Yerevan State University, 1 Alex Manoogian, Yerevan 0025, Armenia
| | - Lucas Bethge
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Stephan Vonhoff
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Sven Klussmann
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Janine Cossy
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Jean-Jacques Vasseur
- Institut
des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM Place Eugène Bataillon, 34095 Montpellier, France
| | - Stellios Arseniyadis
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
- School
of Biological and Chemical Sciences, Queen Mary University of London, Joseph Priestley Building, Mile End Road, London E1 4NS, United Kingdom
| | - Michael Smietana
- Institut
des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM Place Eugène Bataillon, 34095 Montpellier, France
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4
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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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5
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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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6
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Determination of Peptide and Protein Disulfide Linkages by MALDI Mass Spectrometry. Top Curr Chem (Cham) 2012; 331:79-116. [DOI: 10.1007/128_2012_384] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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7
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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.
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8
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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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9
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Zencheck WD, Xiao H, Nolen BJ, Angeletti RH, Pollard TD, Almo SC. Nucleotide- and activator-dependent structural and dynamic changes of arp2/3 complex monitored by hydrogen/deuterium exchange and mass spectrometry. J Mol Biol 2009; 390:414-27. [PMID: 19298826 DOI: 10.1016/j.jmb.2009.03.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Accepted: 03/03/2009] [Indexed: 11/16/2022]
Abstract
Arp2/3 complex plays a central role in the de novo nucleation of filamentous actin as branches on existing filaments. The complex must bind ATP, protein activators [e.g., Wiskott-Aldrich syndrome protein (WASp)], and the side of an actin filament to form a new actin filament. Amide hydrogen/deuterium exchange coupled with mass spectrometry was used to examine the structural and dynamic properties of the mammalian Arp2/3 complex in the presence of both ATP and the activating peptide segment from WASp. Changes in the rate of hydrogen exchange indicate that ATP binding causes conformational rearrangements of Arp2 and Arp3 that are transmitted allosterically to the Arp complex (ARPC)1, ARPC2, ARPC4, and ARPC5 subunits. These data are consistent with the closure of nucleotide-binding cleft of Arp3 upon ATP binding, resulting in structural rearrangements that propagate throughout the complex. Binding of the VCA domain of WASp to ATP-Arp2/3 further modulates the rates of hydrogen exchange in these subunits, indicating that a global conformational reorganization is occurring. These effects may include the direct binding of activators to Arp3, Arp2, and ARPC1; alterations in the relative orientations of Arp2 and Arp3; and the long-range transmission of activator-dependent signals to segments proposed to be involved in binding the F-actin mother filament.
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Affiliation(s)
- Wendy D Zencheck
- Department of Biochemistry, Yeshiva University, Bronx, NY 10461, USA
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10
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Grandori R, Santambrogio C, Brocca S, Invernizzi G, Lotti M. Electrospray-ionization mass spectrometry as a tool for fast screening of protein structural properties. Biotechnol J 2009; 4:73-87. [DOI: 10.1002/biot.200800250] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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11
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Sutherland BW, Toews J, Kast J. Utility of formaldehyde cross-linking and mass spectrometry in the study of protein-protein interactions. JOURNAL OF MASS SPECTROMETRY : JMS 2008; 43:699-715. [PMID: 18438963 DOI: 10.1002/jms.1415] [Citation(s) in RCA: 181] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
For decades, formaldehyde has been routinely used to cross-link proteins in cells, tissue, and in some instances, even entire organisms. Due to its small size, formaldehyde can readily permeate cell walls and membranes, resulting in efficient cross-linking, i.e. the formation of covalent bonds between proteins, DNA, and other reactive molecules. Indeed, formaldehyde cross-linking is an instrumental component of many mainstream analytical/cell biology techniques including chromatin immunoprecipitation (ChIP) of protein-DNA complexes found in nuclei; immunohistological analysis of protein expression and localization within cells, tissues, and organs; and mass spectrometry (MS)-compatible silver-staining methodologies used to visualize low abundance proteins in polyacrylamide gels. However, despite its exquisite suitability for use in the analysis of protein environments within cells, formaldehyde has yet to be commonly employed in the directed analysis of protein-protein interactions and cellular networks. The general purpose of this article is to discuss recent advancements in the use of formaldehyde cross-linking in combination with MS-based methodologies. Key advantages and limitations to the use of formaldehyde over other cross-linkers and technologies currently used to study protein-protein interactions are highlighted, and formaldehyde-based experimental approaches that are proving very promising in their ability to accurately and efficiently identify novel protein-protein and multiprotein interaction complexes are presented.
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Affiliation(s)
- Brent W Sutherland
- Biomedical Research Centre, University of British Columbia, Vancouver, BC V6T-1Z3, Canada
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12
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Sensitive light-scattering detection–magnetophoretic acceleration mass analysis of single microparticles in an atmosphere. Anal Bioanal Chem 2008; 391:701-7. [DOI: 10.1007/s00216-008-2035-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2007] [Revised: 01/30/2008] [Accepted: 02/28/2008] [Indexed: 10/22/2022]
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13
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Abstract
The rate of drug discovery is greatly dependent on the development and improvement of rapid and reliable analytical methods that allow screening for protein-ligand interactions. The solution-based methods for investigating protein-ligand interactions by mass spectrometry (MS), which are discussed in this paper, are hydrogen/deuterium exchange of protein backbone amide hydrogens, and photoaffinity labeling. Moreover, MS analysis of intact noncovalent protein-ligand complexes is described. Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) with its ultra-high resolution and excellent mass accuracy is also considered herein as it is gaining increasing popularity for a mass spectrometric investigation of protein-ligand interactions.
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Affiliation(s)
- Andrea Sinz
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle, Germany.
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14
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Mazon H, Gábor K, Leys D, Heck AJR, van der Oost J, van den Heuvel RHH. Transcriptional activation by CprK1 is regulated by protein structural changes induced by effector binding and redox state. J Biol Chem 2007; 282:11281-90. [PMID: 17303561 DOI: 10.1074/jbc.m611177200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The transcriptional activator CprK1 from Desulfitobacterium-hafniense, a member of the ubiquitous cAMP receptor protein/fumarate nitrate reduction regulatory protein family, activates transcription of genes encoding proteins involved in reductive dehalogenation of chlorinated aromatic compounds. 3-chloro-4-hydroxyphenylacetate is a known effector for CprK1, which interacts tightly with the protein, and induces binding to a specific DNA sequence ("dehalobox," TTAAT--ATTAA) located in the promoter region of chlorophenol reductive dehalogenase genes. Despite the availability of recent x-ray structures of two CprK proteins in distinct states, the mechanism by which CprK1 activates transcription is poorly understood. In the present study, we have investigated the mechanism of CprK1 activation and its effector specificity. By using macromolecular native mass spectrometry and DNA binding assays, analogues of 3-chloro-4-hydroxyphenylacetate that have a halogenated group at the ortho position and a chloride or acetic acid group at the para position were found to be potent effectors for CprK1. By using limited proteolysis it was demonstrated that CprK1 requires a cascade of structural events to interact with dehalobox dsDNA. Upon reduction of the intermolecular disulfide bridge in oxidized CprK1, the protein becomes more dynamic, but this alone is not sufficient for DNA binding. Activation of CprK1 is a typical example of allosteric regulation; the binding of a potent effector molecule to reduced CprK1 induces local changes in the N-terminal effector binding domain, which subsequently may lead to changes in the hinge region and as such to structural changes in the DNA binding domain that are required for specific DNA binding.
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Affiliation(s)
- Hortense Mazon
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
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15
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:127-38. [PMID: 17199253 PMCID: PMC7166443 DOI: 10.1002/jms.1070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In order to keep subscribers up‐to‐date with the latest developments in their field, John Wiley & Sons are providing a current awareness service in each issue of the journal. The bibliography contains newly published material in the field of mass spectrometry. Each bibliography is divided into 11 sections: 1 Books, Reviews & Symposia; 2 Instrumental Techniques & Methods; 3 Gas Phase Ion Chemistry; 4 Biology/Biochemistry: Amino Acids, Peptides & Proteins; Carbohydrates; Lipids; Nucleic Acids; 5 Pharmacology/Toxicology; 6 Natural Products; 7 Analysis of Organic Compounds; 8 Analysis of Inorganics/Organometallics; 9 Surface Analysis; 10 Environmental Analysis; 11 Elemental Analysis. Within each section, articles are listed in alphabetical order with respect to author (6 Weeks journals ‐ Search completed at 4th. Oct. 2006)
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Shi X, Takamizawa A, Nishimura Y, Hiraoka K, Akashi S. Stability analysis for double-stranded DNA oligomers and their noncovalent complexes with drugs by laser spray. JOURNAL OF MASS SPECTROMETRY : JMS 2006; 41:1086-95. [PMID: 16830356 DOI: 10.1002/jms.1069] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Laser spray, which is a newly developed ionization technique, can characterize the stability of noncovalent complexes in the solution phase. By using this advantage, laser spray has been applied to probe the intrinsic stability of double-stranded DNA (dsDNA) sequences and their binding affinities with various drugs in the solution phase. Systematic experiments were carried out using six 16-mer and three 22-mer dsDNA oligomers, together with the complexes of the 16-mer dsDNA with minor groove binders: berenil, Hoechst 33342, DAPI, and netropsin. Dissociation curves for each dsDNA or each complex were plotted as a function of laser power. The laser power (E50%), where 50% of each dsDNA or each complex was dissociated, was compared with its melting temperature (Tm) determined by UV spectroscopy. Linear correlations between E50% and Tm were obtained not only for the dsDNA oligomers (correlation factor r = 0.9835) but also for the 16-mer dsDNA complexes with minor groove binders (r = 0.9966). In addition, laser spray has successfully clarified the binding affinities of a 16-mer dsDNA with two intercalators: daunomycin and nogalamycin. In the case of the dsDNA-daunomycin complex, by changing the molar ratio of dsDNA : drug from 1 : 1 to 1 : 5, the concentration-dependent stability of the complex was confirmed by laser spray. The present results demonstrate that laser spray mass spectrometry can be a powerful and convenient method to investigate the relative binding affinities of dsDNA-ligand complexes in the solution phase, which could be applied to the early stage of high-throughput screening of drugs targeting for dsDNA.
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Affiliation(s)
- Xiangguo Shi
- International Graduate School of Arts and Sciences, Yokohama City University, Tsurumi-ku, Yokohama Kanagawa 230-0045, Japan
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