Chemical cross-linking and mass spectrometry for mapping three-dimensional structures of proteins and protein complexes.

Chemical cross-linking of proteins, an established method in protein chemistry, has gained renewed interest in combination with mass spectrometric analysis of the reaction products for elucidating low-resolution three-dimensional protein structures and interacting sequences in protein complexes. The identification of the large number of cross-linking sites from the complex mixtures generated by chemical cross-linking, however, remains a challenging task. This review describes the most popular cross-linking reagents for protein structure analysis and gives an overview of the strategies employing intra- or intermolecular chemical cross-linking and mass spectrometry. The various approaches described in the literature to facilitate detection of cross-linking products and also computer software for data analysis are reviewed. Cross-linking techniques combined with mass spectrometry and bioinformatic methods have the potential to provide the basis for an efficient structural characterization of proteins and protein complexes.

[1]  A. Sinz,et al.  Mapping low-resolution three-dimensional protein structures using chemical cross-linking and Fourier transform ion-cyclotron resonance mass spectrometry. , 2003, Rapid communications in mass spectrometry : RCM.

[2]  Chris G de Koster,et al.  Chemical cross-linking and mass spectrometry for protein structural modeling. , 2003, Journal of molecular biology.

[3]  Birgit Schilling,et al.  MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides , 2003, Journal of the American Society for Mass Spectrometry.

[4]  D. Gershon.  Mass spectrometry goes mainstream , 2003, Nature.

[5]  W. Davidson,et al.  The Spatial Organization of Apolipoprotein A-I on the Edge of Discoidal High Density Lipoprotein Particles , 2003, Journal of Biological Chemistry.

[6]  C. Ihling,et al.  Nano-high-performance liquid chromatography in combination with nano-electrospray ionization Fourier transform ion-cyclotron resonance mass spectrometry for proteome analysis. , 2003, Rapid communications in mass spectrometry : RCM.

[7]  A. Scaloni,et al.  Probing the dimeric structure of porcine aminoacylase 1 by mass spectrometric and modeling procedures. , 2003, Biochemistry.

[8]  R Zenobi,et al.  MALDI ionization: the role of in-plume processes. , 2003, Chemical reviews.

[9]  Malin M. Young,et al.  A top down approach to protein structural studies using chemical cross-linking and Fourier transform mass spectrometry. , 2003, Rapid communications in mass spectrometry : RCM.

[10]  P. Prevelige,et al.  Identification of novel interactions in HIV-1 capsid protein assembly by high-resolution mass spectrometry. , 2003, Journal of molecular biology.

[11]  Klaus Dreisewerd,et al.  The desorption process in MALDI. , 2003, Chemical reviews.

[12]  Michael Karas,et al.  Ion formation in MALDI: the cluster ionization mechanism. , 2003, Chemical reviews.

[13]  Lei Zhang,et al.  PAX3-FKHR Transformation Increases 26 S Proteasome-dependent Degradation of p27Kip1, a Potential Role for Elevated Skp2 Expression* , 2003, The Journal of Biological Chemistry.

[14]  David Fenyö,et al.  A modular cross-linking approach for exploring protein interactions. , 2002, Journal of the American Chemical Society.

[15]  Nathan E Hall,et al.  Characterization of an Antagonist Interleukin-6 Dimer by Stable Isotope Labeling, Cross-linking, and Mass Spectrometry* , 2002, The Journal of Biological Chemistry.

[16]  L. Grivell,et al.  A structure for the yeast prohibitin complex: Structure prediction and evidence from chemical crosslinking and mass spectrometry , 2002, Protein science : a publication of the Protein Society.

[17]  T. Sixma,et al.  Identification of cross-linked peptides for protein interaction studies using mass spectrometry and 18O labeling. , 2002, Analytical chemistry.

[18]  A. Marshall,et al.  Resolution of 11,000 compositionally distinct components in a single electrospray ionization Fourier transform ion cyclotron resonance mass spectrum of crude oil. , 2002, Analytical chemistry.

[19]  K. Tomer,et al.  Identification of components of protein complexes using a fluorescent photo-cross-linker and mass spectrometry. , 2002, Analytical chemistry.

[20]  Gordon A Anderson,et al.  Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/FTICR , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[21]  L. Pannell,et al.  Intramolecular cross-linking experiments on cytochrome c and ribonuclease A using an isotope multiplet method. , 2002, Rapid communications in mass spectrometry : RCM.

[22]  H. Steen,et al.  GPMAW--a software tool for analyzing proteins and peptides. , 2001, Trends in biochemical sciences.

[23]  A. Sinz,et al.  Mapping protein interfaces with a fluorogenic cross-linker and mass spectrometry: application to nebulin-calmodulin complexes. , 2001, Biochemistry.

[24]  K N Houk,et al.  Quantitative evaluation of the lengths of homobifunctional protein cross‐linking reagents used as molecular rulers , 2001, Protein science : a publication of the Protein Society.

[25]  M E Belov,et al.  High-throughput proteomics using high-efficiency multiple-capillary liquid chromatography with on-line high-performance ESI FTICR mass spectrometry. , 2001, Analytical chemistry.

[26]  H. Khorana,et al.  Mapping of contact sites in complex formation between transducin and light-activated rhodopsin by covalent crosslinking: Use of a photoactivatable reagent , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[27]  H. Khorana,et al.  Mapping of contact sites in complex formation between light-activated rhodopsin and transducin by covalent crosslinking: Use of a chemically preactivated reagent , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[28]  Ting Chen,et al.  Algorithms for identifying protein cross-links via tandem mass spectrometry , 2001, J. Comput. Biol..

[29]  M. Steinmetz,et al.  Isotope-tagged cross-linking reagents. A new tool in mass spectrometric protein interaction analysis. , 2001, Analytical chemistry.

[30]  T. Veenstra,et al.  Packed capillary reversed-phase liquid chromatography with high-performance electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for proteomics. , 2001, Analytical chemistry.

[31]  L. Jong,et al.  A new crosslinker for mass spectrometric analysis of the quaternary structure of protein complexes , 2001, Journal of the American Society for Mass Spectrometry.

[32]  S. Benkovic,et al.  Mapping protein - Protein interactions in the bacteriophage T4 DNA polymerase holoenzyme using a novel trifunctional photo-cross-linking and affinity reagent [11] , 2000 .

[33]  Malin M. Young,et al.  High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry , 2000, Proc. Natl. Acad. Sci. USA.

[34]  M. Mann,et al.  A generic strategy to analyze the spatial organization of multi-protein complexes by cross-linking and mass spectrometry. , 2000, Analytical chemistry.

[35]  David L. Smith,et al.  Investigating the Higher Order Structure of Proteins , 2000 .

[36]  Martin Kussmann,et al.  Chemical cross‐linking with thiol‐cleavable reagents combined with differential mass spectrometric peptide mapping—A novel approach to assess intermolecular protein contacts , 2000, Protein science : a publication of the Protein Society.

[37]  V. Anderson,et al.  Protein cross-links: universal isolation and characterization by isotopic derivatization and electrospray ionization mass spectrometry. , 1999, Analytical biochemistry.

[38]  F W McLafferty,et al.  Biomolecule Mass Spectrometry , 1999, Science.

[39]  M. Smith,et al.  Universal isolation of cross-linked peptides: application to neurofibrillary tangles. , 1999, Bioconjugate chemistry.

[40]  F. McLafferty,et al.  Electron Capture Dissociation of Multiply Charged Protein Cations. A Nonergodic Process , 1998 .

[41]  A. Marshall,et al.  Fourier transform ion cyclotron resonance mass spectrometry: a primer. , 1998, Mass spectrometry reviews.

[42]  B. Spengler.  Post-source decay analysis in matrix-assisted laser desorption/ionization mass spectrometry of biomolecules† , 1997 .

[43]  R. Anderegg,et al.  Comprehensive on-line LC/LC/MS of proteins. , 1997, Analytical chemistry.

[44]  J. Yates,et al.  The quadrupole ion trap mass spectrometer--a small solution to a big challenge. , 1997, Analytical biochemistry.

[45]  J. Loo,et al.  Studying noncovalent protein complexes by electrospray ionization mass spectrometry. , 1997, Mass spectrometry reviews.

[46]  J. Jorgenson,et al.  Separation of nanoliter samples of biological amines by a comprehensive two-dimensional microcolumn liquid chromatography system. , 1995, Analytical chemistry.

[47]  E. Kosower,et al.  Bromobimane probes for thiols. , 1995, Methods in enzymology.

[48]  F W McLafferty,et al.  Infrared multiphoton dissociation of large multiply charged ions for biomolecule sequencing. , 1994, Analytical chemistry.

[49]  B. Chait,et al.  High-accuracy mass measurement as a tool for studying proteins. , 1994, Current Opinion in Biotechnology.

[50]  D. Wilbur,et al.  Radiohalogenation of proteins: an overview of radionuclides, labeling methods, and reagents for conjugate labeling. , 1992, Bioconjugate chemistry.

[51]  L. Hood,et al.  Structural analysis of proteins by capillary HPLC electrospray tandem mass spectrometry , 1991 .

[52]  T. R. Trautman,et al.  Sustained off-resonance irradiation for collision-activated dissociation involving Fourier transform mass spectrometry. Collision-activated dissociation technique that emulates infrared multiphoton dissociation , 1991 .

[53]  R. Cooks,et al.  Ion isolation and sequential stages of mass spectrometry in a quadrupole ion trap mass spectrometer , 1990 .

[54]  S. Ghosh,et al.  Use of maleimide-thiol coupling chemistry for efficient syntheses of oligonucleotide-enzyme conjugate hybridization probes. , 1990, Bioconjugate chemistry.

[55]  R. Yost,et al.  Tandem mass spectrometry: quadrupole and hybrid instruments. , 1990, Methods in enzymology.

[56]  M. Mann,et al.  Electrospray ionization for mass spectrometry of large biomolecules. , 1989, Science.

[57]  J. V. Staros.  Membrane-impermeant crosslinking reagents: probes of the structure and dynamics of membrane proteins , 1988 .

[58]  M. Karas,et al.  Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. , 1988, Analytical chemistry.

[59]  L. Orgel,et al.  Synthesis of an amplifiable reporter RNA for bioassays. , 1986, Nucleic acids research.

[60]  R. W. Wright,et al.  Enhancement by N-hydroxysulfosuccinimide of water-soluble carbodiimide-mediated coupling reactions. , 1986, Analytical biochemistry.

[61]  M. Morales,et al.  Stabilization of a primary loop in myosin subfragment 1 with a fluorescent crosslinker. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[62]  G. Roberts,et al.  Cross-linking of protein by ω-maleimido alkanoylN-hydroxysuccinimido esters , 1983 .

[63]  G. Newton,et al.  Bimane fluorescent labels: labeling of normal human red cells under physiological conditions. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[64]  P. K. Smith,et al.  A new cleavable reagent for cross-linking and reversible immobilization of proteins. , 1979, Biochemical and biophysical research communications.

[65]  T. Ji,et al.  Photochemical cross-linking of cell membranes. A test for natural and random collisional cross-links by millisecond cross-linking. , 1977, The Journal of biological chemistry.

[66]  S. Liu,et al.  Spontaneous, reversible protein cross-linking in the human erythrocyte membrane. Temperature and pH dependence. , 1977, Biochemistry.

[67]  A J Lomant,et al.  Chemical probes of extended biological structures: synthesis and properties of the cleavable protein cross-linking reagent [35S]dithiobis(succinimidyl propionate). , 1976, Journal of molecular biology.

[68]  S. Kent,et al.  Formation of non-amidine products in the reaction of primary amines with imido esters. , 1975, Biochemical and biophysical research communications.

[69]  C. Hou,et al.  Subunit composition, function, and spatial arrangement in the Ca2+-and Mg2+-activated adenosine triphosphatases of Escherichia coli and Salmonella typhimurium. , 1975, Archives of biochemistry and biophysics.

[70]  A. Marshall,et al.  Fourier Transform Ion Cyclotron Resonance Spectroscopy , 1974 .

[71]  P. Cuatrecasas,et al.  Adsorbents for affinity chromatography. Use of N-hydroxysuccinimide esters of agarose. , 1972, Biochemistry.

[72]  H. Dürr.  Carbenes, Nitrenes and Arynes. Von T. L. Gilchrist u. C. W. Rees. Th. Nelson and Sons Ltd., London 1969. 1. Aufl., 131 S., geb. $ 21.— , 1971 .

[73]  S. Avrameas,et al.  Coupling of enzymes to proteins with glutaraldehyde. Use of the conjugates for the detection of antigens and antibodies. , 1969, Immunochemistry.

[74]  B. Anderson,et al.  Inactivation of yeast alcohol dehydrogenase by N-alkylmaleimides. , 1968, Archives of biochemistry and biophysics.

[75]  C. F. Brewer,et al.  Evidence for possible nonspecific reactions between N-ethylmaleimide and proteins☆ , 1967 .

[76]  P. A. Martic,et al.  Kinetics of the reaction of N-ethylmaleimide with cysteine and some congeners. , 1966, Archives of biochemistry and biophysics.

[77]  F. C. Hartman,et al.  Bifunctional Reagents. Cross-Linking of Pancreatic Ribonuclease with a Diimido Ester1 , 1966 .

[78]  D. Koshland,et al.  A Procedure for the Selective Modification of Carboxyl Groups in Proteins , 1966 .

[79]  O. Blumenfeld,et al.  Reactions of N-ethylmaleimide with peptides and amino acids. , 1964, The Biochemical journal.

[80]  M. Ludwig,et al.  The Reaction of Imidoesters with Proteins and Related Small Molecules , 1962 .