251
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Melnyk RA, Hewitt KM, Lacy DB, Lin HC, Gessner CR, Li S, Woods VL, Collier RJ. Structural determinants for the binding of anthrax lethal factor to oligomeric protective antigen. J Biol Chem 2005; 281:1630-5. [PMID: 16293620 DOI: 10.1074/jbc.m511164200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Anthrax lethal toxin assembles at the surface of mammalian cells when the lethal factor (LF) binds via its amino-terminal domain, LF(N), to oligomeric forms of activated protective antigen (PA). LF x PA complexes are then trafficked to acidified endosomes, where PA forms heptameric pores in the bounding membrane and LF translocates through these pores to the cytosol. We used enhanced peptide amide hydrogen/deuterium exchange mass spectrometry and directed mutagenesis to define the surface on LF(N) that interacts with PA. A continuous surface encompassing one face of LF(N) became protected from deuterium exchange when LF(N) was bound to a PA dimer. Directed mutational analysis demonstrated that residues within this surface on LF(N) interact with Lys-197 on two PA subunits simultaneously, thereby showing that LF(N) spans the PA subunit:subunit interface and explaining why heptameric PA binds a maximum of three LF(N) molecules. Our results elucidate the structural basis for anthrax lethal toxin assembly and may be useful in developing drugs to block toxin action.
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Affiliation(s)
- Roman A Melnyk
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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252
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Guan JQ, Chance MR. Structural proteomics of macromolecular assemblies using oxidative footprinting and mass spectrometry. Trends Biochem Sci 2005; 30:583-92. [PMID: 16126388 DOI: 10.1016/j.tibs.2005.08.007] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2005] [Revised: 07/14/2005] [Accepted: 08/16/2005] [Indexed: 11/20/2022]
Abstract
Understanding the composition, structure and dynamics of macromolecules and their assemblies is at the forefront of biological science today. Hydroxyl-radical-mediated protein footprinting using mass spectrometry can define macromolecular structure, macromolecular assembly and conformational changes of macromolecules in solution based on measurements of reactivity of amino acid side-chain groups with covalent-modification reagents. Subsequent to oxidation by reactive oxygen species, proteins are digested by specific proteases to generate peptides for analysis by mass spectrometry. Accurate measurements of side-chain reactivity are achieved using quantitative liquid-chromatography-coupled mass spectrometry, whereas the side-chain sites within the macromolecular probes are identified using tandem mass spectrometry. In addition, the use of footprinting data in conjunction with computational modeling approaches is a powerful new method for testing and refining structural models of macromolecules and their complexes.
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Affiliation(s)
- Jing-Qu Guan
- Case Center for Proteomics and Mass Spectrometry, 930 BRB, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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253
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Lanman J, Prevelige PE. Kinetic and mass spectrometry-based investigation of human immunodeficiency virus type 1 assembly and maturation. Adv Virus Res 2005; 64:285-309. [PMID: 16139598 DOI: 10.1016/s0065-3527(05)64009-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jason Lanman
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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254
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Lu J, Witcher DR, White MA, Wang X, Huang L, Rathnachalam R, Beals JM, Kuhstoss S. IL-1beta epitope mapping using site-directed mutagenesis and hydrogen-deuterium exchange mass spectrometry analysis. Biochemistry 2005; 44:11106-14. [PMID: 16101294 DOI: 10.1021/bi0505464] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hu007, a humanized IgG1 monoclonal antibody, binds and neutralizes human, cynomolgus, and rabbit IL-1beta but only weakly binds to mouse and rat IL-1beta. Biacore experiments demonstrated that Hu007 and the type-I IL-1 receptor competed for binding to IL-1beta. Increasing salt concentrations decrease the association rate with only moderate effects on the dissociation rate, suggesting that long-range electrostatics are critical for formation of the initial complex. To understand the ligand-binding specificity of Hu007, we have mapped the critical residues involved in the recognition of IL-1beta. Selected residues in cynomolgus IL-1beta were mutated to the corresponding residues in mouse IL-1beta, and the effects of the changes on binding were evaluated by surface plasmon resonance measurements using Biacore. Specifically, substitution of F150S decreased binding affinity by 100-fold, suggesting the importance of hydrophobic interactions in stabilizing the antibody/antigen complex. Substitution of three amino acids near the N- and C-terminal regions of cIL-1beta with those found in mouse IL-1beta (V3I/S5Q/F150S) decreased the binding affinity of Hu007 to IL-1beta by about 1000-fold. Conversely, mutating the corresponding residues in mouse IL-1beta to the human sequence resulted in an increase in binding affinity of about 1000-fold. Hydrogen-deuterium exchange/mass spectrometry analysis confirmed that these regions of IL-1beta were protected from exchange because of antibody binding. The results from this study demonstrate that Hu007 binds to a region located in the open end of the beta-barrel structure of IL-1beta and blocks binding of IL-1beta to its receptor.
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Affiliation(s)
- Jirong Lu
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, USA.
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255
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Del Mar C, Greenbaum EA, Mayne L, Englander SW, Woods VL. Structure and properties of alpha-synuclein and other amyloids determined at the amino acid level. Proc Natl Acad Sci U S A 2005; 102:15477-82. [PMID: 16223878 PMCID: PMC1266128 DOI: 10.1073/pnas.0507405102] [Citation(s) in RCA: 166] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The structure of alpha-synuclein (alpha-syn) amyloid was studied by hydrogen-deuterium exchange by using a fragment separation-MS analysis. The conditions used made it possible to distinguish the exchange of unprotected and protected amide hydrogens and to define the order/disorder boundaries at close to amino acid resolution. The soluble alpha-syn monomer exchanges its amide hydrogens with water hydrogens at random coil rates, consistent with its natively unstructured condition. In assembled amyloid, long N-terminal and C-terminal segments remain unprotected (residues 1- approximately 38 and 102-140), although the N-terminal segment shows some heterogeneity. A continuous middle segment (residues approximately 39-101) is strongly protected by systematically H-bonded cross-beta structure. This segment is much too long to fit the amyloid ribbon width, but non-H-bonded amides expected for direction-changing loops are not apparent. These results and other known constraints specify that alpha-syn amyloid adopts a chain fold like that suggested before for amyloid-beta [Petkova et al. (2002) Proc. Natl. Acad Sci. USA 99, 16742-16747] but with a short, H-bonded interlamina turn. More generally, we suggest that the prevalence of accidental amyloid formation derives mainly from the exceptional ability of the main chain in a structurally relaxed beta-conformation to adapt to and energy-minimize side-chain mismatching. Seeding specificity, strain variability, and species barriers then arise because newly added parallel in-register chains must faithfully reproduce the same set of adaptations.
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Affiliation(s)
- Charyl Del Mar
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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256
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Borch J, Jørgensen TJD, Roepstorff P. Mass spectrometric analysis of protein interactions. Curr Opin Chem Biol 2005; 9:509-16. [PMID: 16125435 DOI: 10.1016/j.cbpa.2005.08.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2005] [Accepted: 08/11/2005] [Indexed: 11/20/2022]
Abstract
Mass spectrometry is a powerful tool for identification of interaction partners and structural characterization of protein interactions because of its high sensitivity, mass accuracy and tolerance towards sample heterogeneity. Several tools that allow studies of protein interaction are now available and recent developments that increase the confidence of studies of protein interaction by mass spectrometry include quantification of affinity-purified proteins by stable isotope labeling and reagents for surface topology studies that can be identified by mass-contributing reporters (e.g. isotope labels, cleavable cross-linkers or fragment ions. The use of mass spectrometers to study protein interactions using deuterium exchange and for analysis of intact protein complexes recently has progressed considerably.
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Affiliation(s)
- Jonas Borch
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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257
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Carter JM, Gurevich VV, Prossnitz ER, Engen JR. Conformational differences between arrestin2 and pre-activated mutants as revealed by hydrogen exchange mass spectrometry. J Mol Biol 2005; 351:865-78. [PMID: 16045931 DOI: 10.1016/j.jmb.2005.06.048] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2005] [Revised: 06/16/2005] [Accepted: 06/19/2005] [Indexed: 11/21/2022]
Abstract
Arrestins are regulatory proteins that bind specifically to ligand-activated phosphorylated G protein-coupled receptors to terminate G protein-mediated signaling, cause the internalization of the receptor-arrestin complex, and initiate additional intracellular signaling cascades. Multiple lines of evidence suggest that arrestin normally exists in an inactive basal state and undergoes conformational activation in the process of receptor binding. "Pre-activated" phosphorylation-independent arrestin mutants display increased binding to ligand-activated but unphosphorylated receptors. The mutations are believed to expose key receptor-binding regions, allowing the mutants to mimic, to some extent, the transition of arrestin to its active state. In the present study, amide hydrogen exchange (HX) and mass spectrometry (MS) were used to examine the inactive conformation of wild-type arrestin2 and compare its solution conformation with two pre-activated mutants (R169E and 3A (I385A, V386A, F387A)). The results suggest an unexpected level of structural organization within arrestin elements containing clathrin and adaptin2-binding sites that were previously believed to be completely disordered. Increased deuterium incorporation was observed in both mutant forms compared with wild-type, indicating a change in the conformation of the mutants. Three regions demonstrated significant differences in deuterium incorporation: the first 33 residues of the N terminus and residues 243-255 (both previously implicated in receptor interaction), and residues 271-299. The results suggest that subtle differences in conformation are responsible for the significant difference in biological activity displayed by pre-activated arrestin mutants and that similar changes occur in the process of arrestin binding to the receptor.
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Affiliation(s)
- Jennifer M Carter
- Department of Chemistry, University of New Mexico, Albuquerque, NM 87131, USA
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258
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Iyer GH, Garrod S, Woods VL, Taylor SS. Catalytic independent functions of a protein kinase as revealed by a kinase-dead mutant: study of the Lys72His mutant of cAMP-dependent kinase. J Mol Biol 2005; 351:1110-22. [PMID: 16054648 DOI: 10.1016/j.jmb.2005.06.011] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2005] [Revised: 06/02/2005] [Accepted: 06/06/2005] [Indexed: 11/29/2022]
Abstract
A highly conserved lysine in subdomain II is required for high catalytic activity among the protein kinases. This lysine interacts directly with ATP and mutation of this residue leads to a classical "kinase-dead" mutant. This study describes the biophysical and functional properties of a kinase-dead mutant of cAMP-dependent kinase where Lys72 was replaced with His. Although the mutant protein is less stable than the wild-type catalytic subunit, it is fully capable of binding ATP. The results highlight the effect of the mutation on stability and overall organization of the protein, especially the small lobe. Phosphorylation of the activation loop by a heterologous kinase, 3-phosphoinositide-dependent protein kinase-1 (PDK-1) also contributes dramatically to the global organization of the entire active site region. Deuterium-exchange mass spectrometry (DXMS) indicates a concerted stabilization of the entire active site following the addition of this single phosphate to the activation loop. Furthermore the mutant C-subunit is capable of binding both the type I and II regulatory subunits, but only after phosphorylation of the activation loop. This highlights the role of the large lobe as a scaffold for the regulatory subunits independent of catalytic competency and suggests that kinase dead members of the protein kinase superfamily may still have other important biological roles although they lack catalytic activity.
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Affiliation(s)
- Ganesh H Iyer
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive 0654, La Jolla, CA 92093-0654, USA
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259
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Lee T, Hoofnagle AN, Resing KA, Ahn NG. Hydrogen exchange solvent protection by an ATP analogue reveals conformational changes in ERK2 upon activation. J Mol Biol 2005; 353:600-12. [PMID: 16185715 DOI: 10.1016/j.jmb.2005.08.029] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Revised: 08/15/2005] [Accepted: 08/16/2005] [Indexed: 11/17/2022]
Abstract
Structural and kinetic studies have provided extensive information about the molecular mechanisms of kinase activation by phosphorylation. However, it is still unclear how changes in protein dynamics and flexibility contribute to catalytic function. Mass spectrometry was used to probe changes in hydrogen/deuterium exchange in the MAP kinase, ERK2, in the presence and absence of the ATP analogue, AMP-PNP. In both active and inactive forms of ERK2, protection from hydrogen exchange by AMP-PNP binding was observed within conserved ATP binding motifs in the N-terminal lobe, which are known to directly interact with nucleotide in various protein kinases. In contrast, higher protection from exchange by AMP-PNP was observed in active ERK2 compared to inactive ERK2, in a region corresponding to the conserved DFG motif, which is located in the C-terminal lobe and coordinates Mg2+ at the catalytic site. Thus, AMP-PNP binding simultaneously protects residues within the N and C terminus in the active form of ERK2, but not the inactive form. This demonstrates that ERK2 binds nucleotide in two modes, in which active ERK2 adopts a closed conformation following nucleotide binding in solution, while inactive ERK2 adopts an open conformation. The finding provides novel evidence that phosphorylation of ERK2 facilitates interdomain closure, allowing proper orientation between ATP and substrate to facilitate phosphoryl transfer.
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Affiliation(s)
- Thomas Lee
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
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260
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Neuwald AF. Evolutionary clues to eukaryotic DNA clamp-loading mechanisms: analysis of the functional constraints imposed on replication factor C AAA+ ATPases. Nucleic Acids Res 2005; 33:3614-28. [PMID: 16082778 PMCID: PMC1160110 DOI: 10.1093/nar/gki674] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ring-shaped sliding clamps encircle DNA and bind to DNA polymerase, thereby preventing it from falling off during DNA replication. In eukaryotes, sliding clamps are loaded onto DNA by the replication factor C (RFC) complex, which consists of five distinct subunits (A–E), each of which contains an AAA+ module composed of a RecA-like α/β ATPase domain followed by a helical domain. AAA+ ATPases mediate chaperone-like protein remodeling. Despite remarkable progress in our understanding of clamp loaders, it is still unclear how recognition of primed DNA by RFC triggers ATP hydrolysis and how hydrolysis leads to conformational changes that can load the clamp onto DNA. While these questions can, of course, only be resolved experimentally, the design of such experiments is itself non-trivial and requires that one first formulate the right hypotheses based on preliminary observations. The functional constraints imposed on protein sequences during evolution are potential sources of information in this regard, inasmuch as these presumably are due to and thus reflect underlying mechanisms. Here, rigorous statistical procedures are used to measure and compare the constraints imposed on various RFC clamp-loader subunits, each of which performs a related but somewhat different, specialized function. Visualization of these constraints, within the context of the RFC structure, provides clues regarding clamp-loader mechanisms—suggesting, for example, that RFC-A possesses a triggering component for DNA-dependent ATP hydrolysis. It also suggests that, starting with RFC-A, four RFC subunits (A–D) are sequentially activated through a propagated switching mechanism in which a conserved arginine swings away from a position that disrupts the catalytic Walker B region and into contact with DNA thread through the center of the RFC/clamp complex. Strong constraints near regions of interaction between subunits and with the clamp likewise provide clues regarding possible coupling of hydrolysis-driven conformational changes to the clamp's release and loading onto DNA.
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Affiliation(s)
- Andrew F Neuwald
- Cold Spring Harbor Laboratory, 1 Bungtown Road, PO Box 100, Cold Spring Harbor, NY 11724, USA.
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261
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Xiao H, Hoerner JK, Eyles SJ, Dobo A, Voigtman E, Mel'cuk AI, Kaltashov IA. Mapping protein energy landscapes with amide hydrogen exchange and mass spectrometry: I. A generalized model for a two-state protein and comparison with experiment. Protein Sci 2005; 14:543-57. [PMID: 15659380 PMCID: PMC2253406 DOI: 10.1110/ps.041001705] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Protein amide hydrogen exchange (HDX) is a convoluted process, whose kinetics is determined by both dynamics of the protein and the intrinsic exchange rate of labile hydrogen atoms fully exposed to solvent. Both processes are influenced by a variety of intrinsic and extrinsic factors. A mathematical formalism initially developed to rationalize exchange kinetics of individual amide hydrogen atoms is now often used to interpret global exchange kinetics (e.g., as measured in HDX MS experiments). One particularly important advantage of HDX MS is direct visualization of various protein states by observing distinct protein ion populations with different levels of isotope labeling under conditions favoring correlated exchange (the so-called EX1 exchange mechanism). However, mildly denaturing conditions often lead to a situation where the overall HDX kinetics cannot be clearly classified as either EX1 or EX2. The goal of this work is to develop a framework for a generalized exchange model that takes into account multiple processes leading to amide hydrogen exchange, and does not require that the exchange proceed strictly via EX1 or EX2 kinetics. To achieve this goal, we use a probabilistic approach that assigns a transition probability and a residual protection to each equilibrium state of the protein. When applied to a small protein chymotrypsin inhibitor 2, the algorithm allows complex HDX patterns observed experimentally to be modeled with remarkably good fidelity. On the basis of the model we are now in a position to begin to extract quantitative dynamic information from convoluted exchange kinetics.
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Affiliation(s)
- Hui Xiao
- Department of Chemistry, University of Massachusetts at Amherst, 710 North Pleasant Street, LGRT#701 Amherst, MA 01003, USA
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262
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Catalina MI, Fischer MJE, Dekker FJ, Liskamp RMJ, Heck AJR. Binding of a diphosphorylated-ITAM peptide to spleen tyrosine kinase (Syk) induces distal conformational changes: a hydrogen exchange mass spectrometry study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:1039-51. [PMID: 15914019 DOI: 10.1016/j.jasms.2005.02.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2004] [Revised: 02/09/2005] [Accepted: 02/09/2005] [Indexed: 05/02/2023]
Abstract
Structural flexibility plays a crucial role in protein function. To assess whether specific structural changes are associated with the binding of an immunoreceptor tyrosine-based activation motif (ITAM) to the tandem Src homology-2 domains (tSH2) of the spleen tyrosine kinase [EC 2.7.7.112] (Syk), we used an approach based on protein hydrogen/deuterium exchange in the presence and absence of the diphosphorylated ITAM peptide. The protein deuterium uptake by the intact Syk protein was monitored in time by electrospray mass spectrometry, which revealed a dramatic relative decrease in deuterium uptake when the protein was bound to the ITAM peptide, suggesting an overall change in protein dynamics. Subsequently, the deuterium incorporation of individual segments of the protein was investigated using proteolysis and matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) peptide mass-analysis, which revealed that several regions of Syk tSH2 are significantly more protected from exchange in the presence of the ITAM peptide. Four protected regions encompass the phosphotyrosine and hydrophobic binding sites on the SH2 domains, whereas two other protected regions are located in the inter-SH2 linker motif and do not make any direct contacts with the peptide. Interestingly, our data suggest that binding of the ITAM peptide to Syk tSH2 induces distal structural effects on the protein that stabilize the inter-SH2 linker region, possibly by raising the degree of helical structure upon binding.
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Affiliation(s)
- M Isabel Catalina
- Department of Biomolecular Mass Spectrometry, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
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263
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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.
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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
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264
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Xiao H, Kaltashov IA. Transient structural disorder as a facilitator of protein-ligand binding: native H/D exchange-mass spectrometry study of cellular retinoic acid binding protein I. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:869-79. [PMID: 15907702 DOI: 10.1016/j.jasms.2005.02.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2004] [Revised: 02/14/2005] [Accepted: 02/17/2005] [Indexed: 05/02/2023]
Abstract
Binding of all-trans Retinoic Acid (RA) to Cellular Retinoic Acid Binding Protein I (CRABP I) does not result in significant changes of the protein tertiary structure, even though the binding site is inaccessible in a static apo-protein conformation. One of the proposed scenarios for the protein-ligand binding process invokes the notion of a flexible portal region adjacent to the binding site, while another model suggests that the requisite dynamic events are induced by dimerization of the apo-protein in solution. In this work, RA binding to CRABP I is studied in dilute solutions (low micro-molar range), where no dimer and/or oligomer formation occurs. Modulation of backbone dynamics within various segments of the protein by its ligand is assessed using a combination of hydrogen exchange, electrospray ionization mass spectrometry, and collision-induced dissociation of protein ions in the gas phase. Consistent with the portal model of ligand entry, several protein segments (most of them containing residues making hydrophobic contacts to RA in the holo-form of the protein) are flexible in the absence of the ligand. At the same time, the two segments containing arginine residues forming a salt bridge with RA form the least flexible region in the apo-form of the protein. Although the presence of RA in solution reduces flexibility of all protein segments, the largest effect is observed within four strands that form one of the two beta-sheets enveloping a cavity which houses the ligand-binding site. These results are consistent with a model in which ligand binding occurs through a partially unstructured state of the protein with unobstructed access to the ligand-binding site. This intermediate (whose core is formed by the two stable arginine-containing strands) corresponds to a relatively low-energy local minimum on the apo-protein energy surface and is frequently sampled under native conditions.
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Affiliation(s)
- Hui Xiao
- Department of Chemistry, University of Massachusetts at Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA
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265
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Lísal J, Lam TT, Kainov DE, Emmett MR, Marshall AG, Tuma R. Functional visualization of viral molecular motor by hydrogen-deuterium exchange reveals transient states. Nat Struct Mol Biol 2005; 12:460-6. [PMID: 15834422 DOI: 10.1038/nsmb927] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2004] [Accepted: 03/22/2005] [Indexed: 11/09/2022]
Abstract
Molecular motors undergo cyclical conformational changes and convert chemical energy into mechanical work. The conformational dynamics of a viral packaging motor, the hexameric helicase P4 of dsRNA bacteriophage phi8, was visualized by hydrogen-deuterium exchange and high-resolution mass spectrometry. Concerted changes of exchange kinetics revealed a cooperative unit that dynamically links ATP-binding sites and the central RNA-binding channel. The cooperative unit is compatible with a structure-based model in which translocation is mediated by a swiveling helix. Deuterium labeling also revealed the transition state associated with RNA loading, which proceeds via opening of the hexameric ring. The loading mechanism is similar to that of other hexameric helicases. Hydrogen-deuterium exchange provides an important link between time-resolved spectroscopic observations and high-resolution structural snapshots of molecular machines.
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Affiliation(s)
- Jirí Lísal
- Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
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266
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Burns-Hamuro LL, Barraclough DM, Taylor SS. Identification and functional analysis of dual-specific A kinase-anchoring protein-2. Methods Enzymol 2005; 390:354-74. [PMID: 15488188 DOI: 10.1016/s0076-6879(04)90022-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Since the cloning of dual-specificity A kinase-anchoring protein 2 (D-AKAP2), there has been considerable progress in understanding the structural features of this AKAP and its interaction with protein kinase A (PKA). The domain organization of D-AKAP2 is quite unique, containing two tandem, putative RGS domains, a PKA-binding motif, and a PDZ (PSD95/Dlg/ZO1)-binding motif. Although the function of D-AKAP2 has remained elusive, several reports suggest that D-AKAP2 is targeted to cotransporters in the kidney and that it may play a role in regulating transporter activity. In addition, the finding that a single nucleotide polymorphism in the PKA-binding region of D-AKAP2 may contribute to increased morbidity and mortality emphasizes the potential importance of this protein in pathogenesis. The first part of this article focuses on initial efforts to identify and clone D-AKAP2, followed by tissue localization and expression profiles. The latter half of the article focuses on the domain organization of D-AKAP2 and its interaction with PKA. Finally, a comprehensive analysis of the PKA binding motif is described, which has led to the development of novel peptides derived from D-AKAP2 that can be useful tools in probing the function of this AKAP in cellular and animal models.
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267
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Jørgensen TJD, Gårdsvoll H, Ploug M, Roepstorff P. Intramolecular Migration of Amide Hydrogens in Protonated Peptides upon Collisional Activation. J Am Chem Soc 2005; 127:2785-93. [PMID: 15725037 DOI: 10.1021/ja043789c] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Presently different opinions exist as to the degree of scrambling of amide hydrogens in gaseous protonated peptides and proteins upon collisional activation in tandem mass spectrometry experiments. This unsettled controversy is not trivial, since only a very low degree of scrambling is tolerable if collision-induced dissociation (CID) should provide reliable site-specific information from (1)H/(2)H exchange experiments. We have explored a series of unique, regioselectively deuterium-labeled peptides as model systems to probe for intramolecular amide hydrogen migration under low-energy collisional activation in an orthogonal quadrupole time-of-flight electrospray ionization (Q-TOF ESI) mass spectrometer. These peptides contain a C-terminal receptor-binding sequence and an N-terminal nonbinding region. When the peptides form a receptor complex, the amide hydrogens of the interacting sequences are protected against exchange with the solvent, while the amide hydrogens of the nonbinding sequences exchange rapidly with the solvent. We have utilized such long-lived complexes to generate peptides labeled with deuterium in either the binding or nonbinding region, and the expected regioselectivity of this labeling was confirmed after pepsin proteolysis. CID of such deuterated peptides, [M + 2H](2+), yielded fragment ions (b- and y-ions) having a deuterium content that resemble the theoretical values calculated for 100% scrambling. Thus, complete randomization of all hydrogen atoms attached to nitrogen and oxygen occurs in the gaseous peptide ion prior to its dissociation.
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Affiliation(s)
- Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark.
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268
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Rist W, Rodriguez F, Jørgensen TJD, Mayer MP. Analysis of subsecond protein dynamics by amide hydrogen exchange and mass spectrometry using a quenched-flow setup. Protein Sci 2005; 14:626-32. [PMID: 15689511 PMCID: PMC2279298 DOI: 10.1110/ps.041098305] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Amide hydrogen exchange (HX) in combination with mass spectrometry (MS) is a powerful tool to analyze the folding and dynamics of proteins. In the traditional methodology the exchange time is controlled by manual pipetting, thereby limiting the time resolution to several seconds. Some conformational changes in proteins, however, occur in the subsecond time scale, making it desirable to perform HX at shorter time intervals down to the limit set by the intrinsic chemical exchange rate. We now report the development of the first completely on-line quenched-flow setup that allows the performance of HX experiments in the 100-sec to 30-sec time scale, on-line proteolytic digestion using immobilized proteases, rapid desalting, and MS analysis. We show that conformational fluctuations in the range of seconds can be detected and protection factors as small as 10 reproducibly determined. Using this setup we investigated the conformational properties of Escherichia coli heat-shock transcription factor sigma32 free in solution. Our results indicate that the C-terminal sigma4 domain of sigma32, which is responsible for the recognition of the -35 region of heat shock promoters, contains more extensive secondary structure than expected when compared with the structure of the homologous sigma-factor sigmaA in complex with the RNA-polymerase. This setup should be very useful for a more accurate analysis of structural motions in proteins in the subsecond to second time scale relevant to allostery and enzyme function.
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Affiliation(s)
- Wolfgang Rist
- Zentrum für Molekulare Biologie Heidelberg, Universität Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
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269
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Busenlehner LS, Armstrong RN. Insights into enzyme structure and dynamics elucidated by amide H/D exchange mass spectrometry. Arch Biochem Biophys 2005; 433:34-46. [PMID: 15581564 DOI: 10.1016/j.abb.2004.09.002] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2004] [Revised: 09/02/2004] [Indexed: 11/25/2022]
Abstract
Conformational changes and protein dynamics play an important role in the catalytic efficiency of enzymes. Amide H/D exchange mass spectrometry (H/D exchange MS) is emerging as an efficient technique to study the local and global changes in protein structure and dynamics due to ligand binding, protein activation-inactivation by modification, and protein-protein interactions. By monitoring the selective exchange of hydrogen for deuterium along a peptide backbone, this sensitive technique probes protein motions and structural elements that may be relevant to allostery and function. In this report, several applications of H/D exchange MS are presented which demonstrate the unique capability of amide hydrogen/deuterium exchange mass spectrometry for examining dynamic and structural changes associated with enzyme catalysis.
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Affiliation(s)
- Laura S Busenlehner
- Department of Biochemistry, Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, TN 37232-0416, USA.
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270
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Yao ZP, Tito P, Robinson CV. Site‐Specific Hydrogen Exchange of Proteins: Insights into the Structures of Amyloidogenic Intermediates. Methods Enzymol 2005; 402:389-402. [PMID: 16401516 DOI: 10.1016/s0076-6879(05)02012-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
We describe the use of nano-electrospray ionization (nano-ESI) mass spectrometry (MS) for monitoring hydrogen exchange. Using this approach, we have compared the fluctuations in structure of the wild-type human lysozyme with those of the Asp67His and Ile56Thr variants, the two amyloidogenic forms of the protein. The results revealed that a significant region of the structure was transiently unfolded in both variants compared with the wild-type protein. Using peptic digestion, we located the region of the protein involved in the unfolding reaction to the beta-domain and adjacent C-helix. This unfolding reaction is proposed to facilitate the initial stages of the fibril formation process. Also by this approach, we discovered that binding of an antibody fragment to the proteins prevents the unfolding events. These observations, therefore, not only highlight the use of MS to monitor and locate regions of enhanced hydrogen exchange kinetics, even in proteins that are prone to aggregation, but also demonstrate the use of such an approach to discover potential therapies.
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271
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Yang J, Garrod SM, Deal MS, Anand GS, Woods VL, Taylor S. Allosteric network of cAMP-dependent protein kinase revealed by mutation of Tyr204 in the P+1 loop. J Mol Biol 2004; 346:191-201. [PMID: 15663937 DOI: 10.1016/j.jmb.2004.11.030] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2004] [Revised: 11/11/2004] [Accepted: 11/12/2004] [Indexed: 11/24/2022]
Abstract
Previous studies on the catalytic subunit of cAMP-dependent protein kinase (PKA) identified a conserved interaction pair comprised of Tyr204 from the P+1 loop and Glu230 at the end of the alphaF-helix. Single-point mutations of Tyr204 to Ala (Y204A) and Glu230 to Gln (E230Q) both resulted in alterations in enzymatic kinetics. To understand further the molecular basis for the altered kinetics and the structural role of each residue, we analyzed the Y204A and the E230Q mutants using hydrogen/deuterium (H/D) exchange coupled with mass spectrometry and other biophysical techniques. The fact that the mutants exhibit distinct molecular properties, supports previous hypotheses that these two residues, although in the same interaction node, contribute to the same enzymatic functions through different molecular pathways. The Tyr204 mutation appears to affect the dynamic properties, while the Glu230 mutation affects the surface electrostatic profile of the enzyme. Furthermore, H/D exchange analysis defines the dynamic allosteric range of Tyr204 to include the catalytic loop and three additional distant surface regions, which exhibit increased deuterium exchange in the Y204A but not the E230Q mutant. Interestingly, these are the exact regions that previously showed decreased deuterium exchange upon binding of the RIalpha regulatory subunit of PKA. We propose that these sites, coupled with the P+1 loop through Tyr204, represent one of the major allosteric networks in the kinase. This coupling provides a coordinated response for substrate binding and enzyme catalysis. H/D exchange analysis also further defines the stable core of the catalytic subunit to include the alphaE, alphaF and alphaH-helix. All these observations lead to an interesting new way to view the structural architecture and allosteric conformational regulation of the protein kinase molecule.
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Affiliation(s)
- Jie Yang
- Howard Hughes Medical Institute, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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272
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Jablonowska A, Bakun M, Kupniewska-Kozak A, Dadlez M. Alzheimer's Disease Aβ Peptide Fragment 10–30 Forms a Spectrum of Metastable Oligomers with Marked Preference for N to N and C to C Monomer Termini Proximity. J Mol Biol 2004; 344:1037-49. [PMID: 15544811 DOI: 10.1016/j.jmb.2004.09.083] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2004] [Revised: 08/18/2004] [Accepted: 09/22/2004] [Indexed: 12/11/2022]
Abstract
Oligomers of Abeta peptide have been indicated recently as a possible main causative agent of Alzheimer's disease. However, information concerning their structural properties is very limited. Here Abeta oligomers are studied by non-covalent complexes mass spectrometry and disulfide rearrangement. As a model molecule, an Abeta fragment spanning residues 10-30 (Abeta10-30) has been used. This model peptide is known to contain the core region responsible for Abeta aggregation to fibrils. Non-covalent complexes mass spectrometry indicates that, at neutral pH, monomers are accompanied by oligomers up to hexamers of gradually decreasing population. H-2H exchange studies and direct monomer exchange rate measurements with the use of 15N labeled peptides and mass spectrometry show a fast exchange of monomeric units between oligomers. Disulfide exchange studies of cysteine tagged Abeta10-30 and its mutant show proximity of N-N and C-C termini of monomers in oligomers. The presented data underscore a dynamic character for pre-nucleation forms of Abeta, however, with a marked tendency for parallel strand orientation in oligomers.
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Affiliation(s)
- Agnieszka Jablonowska
- Department of Biophysics, Institute of Biochemistry and Biophysics, PAS, ul. Pawińskiego 5A, 02-106 Warsaw, Poland
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273
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Liang ZX, Tsigos I, Lee T, Bouriotis V, Resing KA, Ahn NG, Klinman JP. Evidence for Increased Local Flexibility in Psychrophilic Alcohol Dehydrogenase Relative to Its Thermophilic Homologue. Biochemistry 2004; 43:14676-83. [PMID: 15544338 DOI: 10.1021/bi049004x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The psychrophilic alcohol dehydrogenase (psADH) cloned from Antarctic Moraxella sp. TAE123 exhibits distinctive catalytic parameters in relation to the homologous thermophilic alcohol dehydrogenase (htADH) from Bacillus stearothermophilus LLD-R. Amide hydrogen-deuterium (H/D) exchange studies using Fourier-transformed infrared (FTIR) spectroscopy and mass spectrometry (MS) were conducted to investigate whether the differences are caused by variation in either global or regional protein flexibility. The FTIR H/D exchange study suggested that psADH does not share similar global flexibility with htADH at their physiologically relevant temperatures as has been predicted by the "corresponding state" hypothesis. However, the MS H/D exchange study revealed a more complicated picture concerning the flexibility of the two homologous enzymes. Analysis of the deuteration and exchange rates of protein-derived peptides suggested that only some functionally important regions in psADH that are involved in substrate and cofactor binding exhibit greater flexibility compared to htADH at low temperature (10 degrees C). These observations strongly suggest that variable conformational flexibility between the two protein forms is a local phenomenon, and that global H/D exchange measurement by FTIR can be misleading and should be used with discretion. These results are supportive of the idea that functionally important local flexibility can be uncoupled from global thermal stability. The structural factors underlying the differences in local protein flexibility and catalysis between htADH and psADH are discussed in conjunction with results from crystallographic and fluorescence spectroscopy studies.
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Affiliation(s)
- Zhao-Xun Liang
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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274
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Hoerner JK, Xiao H, Dobo A, Kaltashov IA. Is there hydrogen scrambling in the gas phase? Energetic and structural determinants of proton mobility within protein ions. J Am Chem Soc 2004; 126:7709-17. [PMID: 15198619 DOI: 10.1021/ja049513m] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The extent of internal hydrogen exchange (scrambling) within multiply charged solvent-free protein ions was investigated using a small model protein. The site-specific backbone amide protection data were obtained using protein ion fragmentation in the gas phase and compared with the available NMR data. Only minimal scrambling was detected when relatively high-energy collisional activation was used to fragment intact protein ions, while low-energy fragmentation resulted in more significant but not random internal exchange. Increased conformational flexibility of protein ions in the gas phase did not have any effect on the extent of hydrogen scrambling under the conditions of higher-energy collisional activation but resulted in totally random redistribution of labile hydrogen atoms when the protein ion fragmentation was induced by multiple low-energy collisions.
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Affiliation(s)
- Joshua K Hoerner
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, USA
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275
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Santrůcek J, Strohalm M, Kadlcík V, Hynek R, Kodícek M. Tyrosine residues modification studied by MALDI-TOF mass spectrometry. Biochem Biophys Res Commun 2004; 323:1151-6. [PMID: 15451417 DOI: 10.1016/j.bbrc.2004.08.214] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2004] [Indexed: 11/17/2022]
Abstract
Amino acid residue-specific reactivity in proteins is of great current interest in structural biology as it provides information about solvent accessibility and reactivity of the residue and, consequently, about protein structure and possible interactions. In the work presented tyrosine residues of three model proteins with known spatial structure are modified with two tyrosine-specific reagents: tetranitromethane and iodine. Modified proteins were specifically digested by proteases and the mass of resulting peptide fragments was determined using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Our results show that there are only small differences in the extent of tyrosine residues modification by tetranitromethane and iodine. However, data dealing with accessibility of reactive residues obtained by chemical modifications are not completely identical with those obtained by nuclear magnetic resonance and X-ray crystallography. These interesting discrepancies can be caused by local molecular dynamics and/or by specific chemical structure of the residues surrounding.
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Affiliation(s)
- Jirí Santrůcek
- Department of Biochemistry and Microbiology, Institute of Chemical Technology, Technická 5, 16628 Prague 6, Czech Republic.
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276
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Busenlehner LS, Codreanu SG, Holm PJ, Bhakat P, Hebert H, Morgenstern R, Armstrong RN. Stress Sensor Triggers Conformational Response of the Integral Membrane Protein Microsomal Glutathione Transferase 1†. Biochemistry 2004; 43:11145-52. [PMID: 15366924 DOI: 10.1021/bi048716k] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Microsomal glutathione (GSH) transferase 1 (MGST1) is a trimeric, integral membrane protein involved in cellular response to chemical or oxidative stress. The cytosolic domain of MGST1 harbors the GSH binding site and a cysteine residue (C49) that acts as a sensor of oxidative and chemical stress. Spatially resolved changes in the kinetics of backbone amide H/D exchange reveal that the binding of a single molecule of GSH/trimer induces a cooperative conformational transition involving movements of the transmembrane helices and a reordering of the cytosolic domain. Alkylation of the stress sensor preorganizes the helices and facilitates the cooperative transition resulting in catalytic activation.
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Affiliation(s)
- Laura S Busenlehner
- Department of Biochemistry, Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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277
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Hoofnagle AN, Stoner JW, Lee T, Eaton SS, Ahn NG. Phosphorylation-dependent changes in structure and dynamics in ERK2 detected by SDSL and EPR. Biophys J 2004; 86:395-403. [PMID: 14695281 PMCID: PMC1303804 DOI: 10.1016/s0006-3495(04)74115-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Mitogen-activated protein kinases are regulated by occupancy at two phosphorylation sites near the active site cleft. Previous studies using hydrogen exchange to investigate the canonical mitogen-activated protein kinase, extracellular signal-regulated protein kinase-2, have shown that phosphorylation alters backbone conformational mobility >10 A distal to the site of phosphorylation, including decreased mobility within amino acids 102-105 and increased mobility within 108-109. To further describe changes after enzyme activation, site-directed spin labeling at amino acids 101, 105-109, 111, 112 and electron paramagnetic resonance spectroscopy were used to investigate this region. The anisotropic hyperfine splitting of the spin labels in glassy samples was unchanged by phosphorylation, consistent with previous crystallographic studies that indicate no structural change in this region. At positions 101, 111, and 112, the mobility of the spin label was unchanged by diphosphorylation, consistent with little or no conformational change. However, diphosphorylation caused small but significant changes in rotational diffusion rates at positions 105-108 and altered proportions of probe in a motionally constrained state at positions 105, 107, and 109. Thus, electron paramagnetic resonance indicates reproducible changes in nanosecond side-chain mobilities at specific residues within the interdomain region, far from the site of phosphorylation and conformational change.
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Affiliation(s)
- Andrew N Hoofnagle
- School of Medicine, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA
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278
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Hamuro Y, Anand GS, Kim JS, Juliano C, Stranz DD, Taylor SS, Woods VL. Mapping intersubunit interactions of the regulatory subunit (RIalpha) in the type I holoenzyme of protein kinase A by amide hydrogen/deuterium exchange mass spectrometry (DXMS). J Mol Biol 2004; 340:1185-96. [PMID: 15236976 DOI: 10.1016/j.jmb.2004.05.042] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Accepted: 05/13/2004] [Indexed: 11/24/2022]
Abstract
Protein kinase A (PKA), a central locus for cAMP signaling in the cell, is composed of regulatory (R) and catalytic (C) subunits. The C-subunits are maintained in an inactive state by binding to the R-subunit dimer in a tetrameric holoenzyme complex (R(2)C(2)). PKA is activated by cAMP binding to the R-subunits which induces a conformational change leading to release of the active C-subunit. Enzymatic activity of the C-subunit is thus regulated by cAMP via the R-subunit, which toggles between cAMP and C-subunit bound states. The R-subunit is composed of a dimerization/docking (D/D) domain connected to two cAMP-binding domains (cAMP:A and cAMP:B). While crystal structures of the free C-subunit and cAMP-bound states of a deletion mutant of the R-subunit are known, there is no structure of the holoenzyme complex or of the cAMP-free state of the R-subunit. An important step in understanding the cAMP-dependent activation of PKA is to map the R-C interface and characterize the mutually exclusive interactions of the R-subunit with cAMP and C-subunit. Amide hydrogen/deuterium exchange mass spectrometry is a suitable method that has provided insights into the different states of the R-subunit in solution, thereby allowing mapping of the effects of cAMP and C-subunit on different regions of the R-subunit. Our study has localized interactions with the C-subunit to a small contiguous surface on the cAMP:A domain and the linker region. In addition, C-subunit binding causes increased amide hydrogen exchange within both cAMP-domains, suggesting that these regions become more flexible in the holoenzyme and are primed to bind cAMP. Furthermore, the difference in the protection patterns between RIalpha and the previously studied RIIbeta upon cAMP-binding suggests isoform-specific differences in cAMP-dependent regulation of PKA activity.
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Affiliation(s)
- Yoshimoto Hamuro
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0656, USA
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279
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Black BE, Foltz DR, Chakravarthy S, Luger K, Woods VL, Cleveland DW. Structural determinants for generating centromeric chromatin. Nature 2004; 430:578-82. [PMID: 15282608 DOI: 10.1038/nature02766] [Citation(s) in RCA: 318] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2004] [Accepted: 06/15/2004] [Indexed: 01/30/2023]
Abstract
Mammalian centromeres are not defined by a consensus DNA sequence. In all eukaryotes a hallmark of functional centromeres--both normal ones and those formed aberrantly at atypical loci--is the accumulation of centromere protein A (CENP-A), a histone variant that replaces H3 in centromeric nucleosomes. Here we show using deuterium exchange/mass spectrometry coupled with hydrodynamic measures that CENP-A and histone H4 form sub-nucleosomal tetramers that are more compact and conformationally more rigid than the corresponding tetramers of histones H3 and H4. Substitution into histone H3 of the domain of CENP-A responsible for compaction is sufficient to direct it to centromeres. Thus, the centromere-targeting domain of CENP-A confers a unique structural rigidity to the nucleosomes into which it assembles, and is likely to have a role in maintaining centromere identity.
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Affiliation(s)
- Ben E Black
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, California 92093, USA
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280
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Liang ZX, Lee T, Resing KA, Ahn NG, Klinman JP. Thermal-activated protein mobility and its correlation with catalysis in thermophilic alcohol dehydrogenase. Proc Natl Acad Sci U S A 2004; 101:9556-61. [PMID: 15210941 PMCID: PMC470713 DOI: 10.1073/pnas.0403337101] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Temperature-dependent hydrogen-deuterium (H/D) exchange of the thermophilic alcohol dehydrogenase (htADH) has been studied by using liquid chromatography-coupled mass spectrometry. Analysis of the changes in H/D exchange patterns for the protein-derived peptides suggests that some regions of htADH are in a rigid conformational substate at reduced temperatures with limited cooperative protein motion. The enzyme undergoes two discrete transitions at approximately 30 and 45 degrees C to attain a more dynamic conformational substate. Four of the five peptides exhibiting the transition above 40 degrees C are in direct contact with the cofactor, and the NAD(+)-binding affinity is also altered in this temperature range, implicating a change in the mobility of the cofactor-binding domain >45 degrees C. By contrast, the five peptides exhibiting the transition at 30 degrees C reside in the substrate-binding domain. This transition coincides with a change in the activation energy of k(cat) for hydride transfer, leading to a linear correlation between k(cat) and the weighted average exchange rate constant k(HX(WA)) for the five peptides. These observations indicate a direct coupling between hydride transfer and protein mobility in htADH, and that an increased mobility is at least partially responsible for the reduced E(act) at high temperature. The data provide support for the hypothesis that protein dynamics play a key role in controlling hydrogen tunneling at enzyme active sites.
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Affiliation(s)
- Zhao-Xun Liang
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
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281
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Lee T, Hoofnagle AN, Kabuyama Y, Stroud J, Min X, Goldsmith EJ, Chen L, Resing KA, Ahn NG. Docking motif interactions in MAP kinases revealed by hydrogen exchange mass spectrometry. Mol Cell 2004; 14:43-55. [PMID: 15068802 DOI: 10.1016/s1097-2765(04)00161-3] [Citation(s) in RCA: 232] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2003] [Revised: 02/17/2004] [Accepted: 02/23/2004] [Indexed: 10/26/2022]
Abstract
Protein interactions between MAP kinases and substrates, activators, and scaffolding proteins are regulated by docking site motifs, one containing basic residues proximal to Leu-X-Leu (DEJL) and a second containing Phe-X-Phe (DEF). Hydrogen exchange mass spectrometry was used to identify regions in MAP kinases protected from solvent by docking motif interactions. Protection by DEJL peptide binding was observed in loops spanning beta7-beta8 and alphaD-alphaE in p38alpha and ERK2. In contrast, protection by DEF binding to ERK2 revealed a distinct hydrophobic pocket for Phe-X-Phe binding formed between the P+1 site, alphaF helix, and the MAP kinase insert. In inactive ERK2, this pocket is occluded by intramolecular interactions with residues in the activation lip. In vitro assays confirm the dependence of Elk1 and nucleoporin binding on ERK2 phosphorylation, and provide a structural basis for preferential involvement of active ERK in substrate binding and nuclear pore protein interactions.
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Affiliation(s)
- Thomas Lee
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA
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282
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Beckett D. Linked equilibria in biotin repressor function: thermodynamic, structural, and kinetic analysis. Methods Enzymol 2004; 379:209-34. [PMID: 15051360 DOI: 10.1016/s0076-6879(04)79012-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Affiliation(s)
- Dorothy Beckett
- Department of Chemistry and Biochemistry, University of Maryland, College Park 20742, USA
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283
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Lanman J, Prevelige PE. High-sensitivity mass spectrometry for imaging subunit interactions: hydrogen/deuterium exchange. Curr Opin Struct Biol 2004; 14:181-8. [PMID: 15093832 DOI: 10.1016/j.sbi.2004.03.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, advances in mass spectrometry have provided unprecedented knowledge of protein expression within cells. It has become apparent that many proteins function as macromolecular complexes. Structural genomics programs are determining the fold of these proteins at an increasing rate and electron microscopic tomography potentially provides a means to determine the location of these complexes within the cell. A complete understanding of the molecular mechanism of these proteins requires detailed information on the interactions and dynamics within the complex. Recent advances in mass spectrometry now make it possible to use hydrogen/deuterium exchange to detect intersubunit interfaces and dynamics within supramolecular complexes.
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Affiliation(s)
- Jason Lanman
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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284
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Turunen O, Jänis J, Fenel F, Leisola M. Engineering the Thermotolerance and pH Optimum of Family 11 Xylanases by Site-Directed Mutagenesis. Methods Enzymol 2004; 388:156-67. [PMID: 15289069 DOI: 10.1016/s0076-6879(04)88014-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Affiliation(s)
- Ossi Turunen
- Laboratory of Bioprocess Engineering, Helsinki University of Technology, Finland
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285
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Xu G, Takamoto K, Chance MR. Radiolytic Modification of Basic Amino Acid Residues in Peptides: Probes for Examining Protein−Protein Interactions. Anal Chem 2003; 75:6995-7007. [PMID: 14670063 DOI: 10.1021/ac035104h] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein footprinting utilizing hydroxyl radicals coupled with mass spectrometry has become a powerful technique for mapping the solvent accessible surface of proteins and examining protein-protein interactions in solution. Hydroxyl radicals generated by radiolysis or chemical methods efficiently react with many amino acid residue side chains, including the aromatic and sulfur-containing residues along with proline and leucine, generating stable oxidation products that are valuable probes for examining protein structure. In this study, we examine the radiolytic oxidation chemistry of histidine, lysine, and arginine for comparison with their metal-catalyzed oxidation products. Model peptides containing arginine, histidine, and lysine were irradiated using white light from a synchrotron X-ray source or a cesium-137 gamma-ray source. The rates of oxidation and the radiolysis products were primarily characterized by electrospray mass spectrometry including tandem mass spectrometry. Arginine is very sensitive to radiolytic oxidation, giving rise to a characteristic product with a 43 Da mass reduction as a result of the loss of guanidino group and conversion to gamma-glutamyl semialdehyde, consistent with previous metal-catalyzed oxidation studies. Histidine was oxidized to generate a mixture of products with characteristic mass changes primarily involving rupture of and addition to the imidazole ring. Lysine was converted to hydroxylysine or carbonylysine by radiolysis. The development of methods to probe these residues due to their high frequency of occurrence, their typical presence on the protein surface, and their frequent participation in protein-protein interactions considerably extends the utility of protein footprinting.
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Affiliation(s)
- Guozhong Xu
- Department of Physiology & Biophysics, Department of Biochemistry, and Center for Synchrotron Biosciences, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461-1602, USA
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Kiselar JG, Janmey PA, Almo SC, Chance MR. Structural analysis of gelsolin using synchrotron protein footprinting. Mol Cell Proteomics 2003; 2:1120-32. [PMID: 12966145 DOI: 10.1074/mcp.m300068-mcp200] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein footprinting provides detailed structural information on protein structure in solution by directly identifying accessible and hydroxyl radical-reactive side chain residues. Radiolytic generation of hydroxyl radicals using millisecond pulses of a synchrotron "white" beam results in the formation of stable side chain oxidation products, which can be digested with proteases for mass spectrometry (MS) analysis. Liquid chromatography-coupled MS and tandem MS methods allow for the quantitation of the ratio of modified and unmodified peptides and identify the specific side chain probes that are oxidized, respectively. The ability to monitor the changes in accessibility of multiple side chain probes by monitoring increases or decreases in their oxidation rates as a function of ligand binding provides an efficient and powerful tool for analyzing protein structure and dynamics. In this study, we probe the detailed structural features of gelsolin in its "inactive" and Ca2+-activated state. Oxidation rate data for 81 peptides derived from the trypsin digestion of gelsolin are presented; 60 of these peptides were observed not to be oxidized, and 21 had detectable oxidation rates. We also report the Ca2+-dependent changes in oxidation for all 81 peptides. Fifty-nine remained unoxidized, five increased their oxidation rate, and two experienced protections. Tandem mass spectrometry was used to identify the specific side chain probes responsible for the Ca2+-insensitive and Ca2+-dependent responses. These data are consistent with crystallographic data for the inactive form of gelsolin in terms of the surface accessibility of reactive residues within the protein. The results demonstrate that radiolytic protein footprinting can provide detailed structural information on the conformational dynamics of ligand-induced structural changes, and the data provide a detailed model for gelsolin activation.
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Affiliation(s)
- Janna G Kiselar
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York, 10461-1602, USA
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287
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Back JW, de Jong L, Muijsers AO, de Koster CG. Chemical cross-linking and mass spectrometry for protein structural modeling. J Mol Biol 2003; 331:303-13. [PMID: 12888339 DOI: 10.1016/s0022-2836(03)00721-6] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The growth of gene and protein sequence information is currently so rapid that three-dimensional structural information is lacking for the overwhelming majority of known proteins. In this review, efforts towards rapid and sensitive methods for protein structural characterization are described, complementing existing technologies. Based on chemical cross-linking and offering the analytical speed and sensitivity of mass spectrometry these methodologies are thought to contribute valuable tools towards future high throughput protein structure elucidation.
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Affiliation(s)
- Jaap Willem Back
- Swammerdam Institute for Life Sciences (SILS), Mass Spectrometry group, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV, Amsterdam, The Netherlands.
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