1
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Prasannan CB, Villar MT, Artigues A, Fenton AW. Identification of regions of rabbit muscle pyruvate kinase important for allosteric regulation by phenylalanine, detected by H/D exchange mass spectrometry. Biochemistry 2013; 52:1998-2006. [PMID: 23418858 DOI: 10.1021/bi400117q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mass spectrometry has been used to determine the number of exchangeable backbone amide protons and the associated rate constants that are altered when rabbit muscle pyruvate kinase (rM1-PYK) binds either the allosteric inhibitor (phenylalanine) or a nonallosteric analogue of the inhibitor. Alanine is used as the nonallosteric analogue because it binds competitively with phenylalanine but elicits a negligible allosteric inhibition, i.e., a negligible reduction in the affinity of rM1-PYK for the substrate, phosphoenolpyruvate. This experimental design is expected to distinguish changes in the protein caused by effector binding (i.e., those changes common upon the addition of alanine vs phenylalanine) from changes associated with allosteric regulation (i.e., those elicited by the addition of phenylalanine binding, but not alanine binding). High-quality peptic fragments covering 98% of the protein were identified. Changes in both the number of exchangeable protons per peptide and in the rate constant associated with exchange highlight regions of the protein with allosteric roles. The set of allosterically relevant peptides identified by this technique includes residues previously identified by mutagenesis to have roles in allosteric regulation by phenylalanine.
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Affiliation(s)
- Charulata B Prasannan
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, MS 3030, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, United States
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2
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Brock A. Fragmentation hydrogen exchange mass spectrometry: A review of methodology and applications. Protein Expr Purif 2012; 84:19-37. [DOI: 10.1016/j.pep.2012.04.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 04/13/2012] [Indexed: 01/19/2023]
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3
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Siu KKW, Asmus K, Zhang AN, Horvatin C, Li S, Liu T, Moffatt B, Woods VL, Howell PL. Mechanism of substrate specificity in 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidases. J Struct Biol 2010; 173:86-98. [PMID: 20554051 DOI: 10.1016/j.jsb.2010.06.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 06/02/2010] [Accepted: 06/02/2010] [Indexed: 10/19/2022]
Abstract
5'-Methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN) plays a key role in the methionine-recycling pathway of bacteria and plants. Despite extensive structural and biochemical studies, the molecular mechanism of substrate specificity for MTAN remains an outstanding question. Bacterial MTANs show comparable efficiency in hydrolyzing MTA and SAH, while the plant enzymes select preferentially for MTA, with either no or significantly reduced activity towards SAH. Bacterial and plant MTANs show significant conservation in the overall structure, and the adenine- and ribose-binding sites. The observation of a more constricted 5'-alkylthio binding site in Arabidopsis thalianaAtMTAN1 and AtMTAN2, two plant MTAN homologues, led to the hypothesis that steric hindrance may play a role in substrate selection in plant MTANs. We show using isothermal titration calorimetry that SAH binds to both Escherichia coli MTAN (EcMTAN) and AtMTAN1 with comparable micromolar affinity. To understand why AtMTAN1 can bind but not hydrolyze SAH, we determined the structure of the protein-SAH complex at 2.2Å resolution. The lack of catalytic activity appears to be related to the enzyme's inability to bind the substrate in a catalytically competent manner. The role of dynamics in substrate selection was also examined by probing the amide proton exchange rates of EcMTAN and AtMTAN1 via deuterium-hydrogen exchange coupled mass spectrometry. These results correlate with the B factors of available structures and the thermodynamic parameters associated with substrate binding, and suggest a higher level of conformational flexibility in the active site of EcMTAN. Our results implicate dynamics as an important factor in substrate selection in MTAN.
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Affiliation(s)
- Karen K W Siu
- Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada
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4
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Chan SL, Low LY, Hsu S, Li S, Liu T, Santelli E, Le Negrate G, Reed JC, Woods VL, Pascual J. Molecular mimicry in innate immunity: crystal structure of a bacterial TIR domain. J Biol Chem 2009; 284:21386-92. [PMID: 19535337 DOI: 10.1074/jbc.c109.007591] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Macrophages detect pathogen infection via the activation of their plasma membrane-bound Toll-like receptor proteins (TLRs). The heterotypic interaction between the Toll/interleukin-1 receptor (TIR) domains of TLRs and adaptor proteins, like Myeloid differentiation primary response gene 88 (MyD88), is the first intracellular step in the signaling pathway of the mammalian innate immune response. The hetero-oligomerization of the TIRs of the receptor and adaptor brings about the activation of the transcription factor NF-kappaB, which regulates the synthesis of pro-inflammatory cytokines. Here, we report the first crystal structure of a bacterial TIR domain solved at 2.5 A resolution. The three-dimensional fold of Paracoccus denitrificans TIR is identical to that observed for the TIR of human TLRs and MyD88 proteins. The structure shows a unique dimerization interface involving the DD-loop and EE-loop residues, whereas leaving the BB-loop highly exposed. Peptide amide hydrogen-deuterium exchange mass spectrometry also reveals that the same region is used for dimerization in solution and in the context of the full-length protein. These results, together with a functional interaction between P. denitrificans TIR and MyD88 visualized in a co-immunoprecipitation assay, further substantiate the model that bacterial TIR proteins adopt structural mimicry of the host active receptor TIR domains to interfere with the signaling of TLRs and their adaptors to decrease the inflammatory response.
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Affiliation(s)
- Siew Leong Chan
- Inflammation and Infectious Diseases Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, California 92037, USA
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5
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Scholten A, Aye TT, Heck AJR. A multi-angular mass spectrometric view at cyclic nucleotide dependent protein kinases: in vivo characterization and structure/function relationships. MASS SPECTROMETRY REVIEWS 2008; 27:331-353. [PMID: 18381623 DOI: 10.1002/mas.20166] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Mass spectrometry has evolved in recent years to a well-accepted and increasingly important complementary technique in molecular and structural biology. Here we review the many contributions mass spectrometry based studies have made in recent years in our understanding of the important cyclic nucleotide activated protein kinase A (PKA) and protein kinase G (PKG). We both describe the characterization of kinase isozymes, substrate phosphorylation, binding partners and post-translational modifications by proteomics based methodologies as well as their structural and functional properties as revealed by native mass spectrometry, H/D exchange MS and ion mobility. Combining all these mass spectrometry based data with other biophysical and biochemical data has been of great help to unravel the intricate regulation of kinase function in the cell in all its magnificent complexity.
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Affiliation(s)
- Arjen Scholten
- Biomolecular Mass Spectrometry & Proteomics Group, Utrecht Institute of Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Sorbonnelaan 16, 3584CA, Utrecht, The Netherlands
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6
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Kornev AP, Taylor SS, Ten Eyck LF. A generalized allosteric mechanism for cis-regulated cyclic nucleotide binding domains. PLoS Comput Biol 2008; 4:e1000056. [PMID: 18404204 PMCID: PMC2275311 DOI: 10.1371/journal.pcbi.1000056] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Accepted: 03/11/2008] [Indexed: 11/19/2022] Open
Abstract
Cyclic nucleotides (cAMP and cGMP) regulate multiple intracellular processes and are thus of a great general interest for molecular and structural biologists. To study the allosteric mechanism of different cyclic nucleotide binding (CNB) domains, we compared cAMP-bound and cAMP-free structures (PKA, Epac, and two ionic channels) using a new bioinformatics method: local spatial pattern alignment. Our analysis highlights four major conserved structural motifs: 1) the phosphate binding cassette (PBC), which binds the cAMP ribose-phosphate, 2) the "hinge," a flexible helix, which contacts the PBC, 3) the beta(2,3) loop, which provides precise positioning of an invariant arginine from the PBC, and 4) a conserved structural element consisting of an N-terminal helix, an eight residue loop and the A-helix (N3A-motif). The PBC and the hinge were included in the previously reported allosteric model, whereas the definition of the beta(2,3) loop and the N3A-motif as conserved elements is novel. The N3A-motif is found in all cis-regulated CNB domains, and we present a model for an allosteric mechanism in these domains. Catabolite gene activator protein (CAP) represents a trans-regulated CNB domain family: it does not contain the N3A-motif, and its long range allosteric interactions are substantially different from the cis-regulated CNB domains.
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Affiliation(s)
- Alexandr P. Kornev
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California, United States of America
| | - Susan S. Taylor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
| | - Lynn F. Ten Eyck
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California, United States of America
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
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7
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Brock M, Fan F, Mei FC, Li S, Gessner C, Woods VL, Cheng X. Conformational analysis of Epac activation using amide hydrogen/deuterium exchange mass spectrometry. J Biol Chem 2007; 282:32256-63. [PMID: 17785454 DOI: 10.1074/jbc.m706231200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Exchange proteins directly activated by cAMP (Epac) play important roles in mediating the effects of cAMP through the activation of downstream small GTPases, Rap. To delineate the mechanism of Epac activation, we probed the conformation and structural dynamics of Epac using amide hydrogen/deuterium exchange and structural modeling. Our studies show that cAMP induces significant conformational changes that lead to a spatial rearrangement of the regulatory components of Epac and allows the exposure of the catalytic core for effector binding without imposing significant conformational change on the catalytic core. Homology modeling and comparative structural analyses of the cAMP binding domains of Epac and cAMP-dependent protein kinase (PKA) lead to a model of Epac activation, in which Epac and PKA activation by cAMP employs the same underlying principle, although the detailed structural and conformational changes associated with Epac and PKA activation are significantly different.
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Affiliation(s)
- Melissa Brock
- Department of Pharmacology and Toxicology and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1031, USA
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8
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Golynskiy M, Li S, Woods VL, Cohen SM. Conformational studies of the manganese transport regulator (MntR) from Bacillus subtilis using deuterium exchange mass spectrometry. J Biol Inorg Chem 2007; 12:699-709. [PMID: 17342524 DOI: 10.1007/s00775-007-0216-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2006] [Accepted: 01/31/2007] [Indexed: 10/23/2022]
Abstract
The manganese transport regulator (MntR) of Bacillus subtilis is a metalloregulatory protein responsible for regulation of genes involved in manganese uptake by this organism. MntR belongs to the iron-responsive DtxR family, but is allosterically regulated by manganese and cadmium ions. Having previously characterized the metal binding affinities of this protein as well as the DNA-binding activation profiles for the relevant metal ions, we have focused the current study on investigating the structural changes of MntR in solution upon binding divalent transition metal ions. Deuterium exchange mass spectrometry was utilized to investigate the deuterium exchange dynamics between apo-MntR, Co(2+)-MntR, Cd(2+)-MntR, and Mn(2+)-MntR. Comparing the rates of deuteration of each metal-bound form of MntR reveals that the N-terminal DNA-binding motif is more mobile in solution than the C-terminal dimerization domain. Furthermore, significant protection from deuterium exchange is observed in the helices that contribute metal-chelating amino acids to form the metal binding site of MntR. In contrast, the bulk of the DNA-binding winged helix-turn-helix motif shows no difference in deuterium exchange upon metal binding. Mapping of the deuteration patterns onto the crystal structures of MntR yields insight into how metal binding affects the protein structure and complements earlier studies on the mechanism of MntR. Metal binding acts to rigidify MntR, thereby limiting the mobility of the protein and reducing the entropic cost of DNA binding.
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Affiliation(s)
- Misha Golynskiy
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0358, USA
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9
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Brudler R, Gessner CR, Li S, Tyndall S, Getzoff ED, Woods VL. PAS domain allostery and light-induced conformational changes in photoactive yellow protein upon I2 intermediate formation, probed with enhanced hydrogen/deuterium exchange mass spectrometry. J Mol Biol 2006; 363:148-60. [PMID: 16952373 PMCID: PMC2575420 DOI: 10.1016/j.jmb.2006.07.078] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 07/24/2006] [Accepted: 07/28/2006] [Indexed: 11/21/2022]
Abstract
Photoactive yellow protein (PYP) is a small bacterial photoreceptor that undergoes a light-activated reaction cycle. PYP is also the prototypical Per-Arnt-Sim (PAS) domain. PAS domains, found in diverse multi-domain proteins from bacteria to humans, mediate protein-protein interactions and function as sensors and signal transducers. Here, we investigate conformational and dynamic changes in solution in wild-type PYP upon formation of the long-lived putative signaling intermediate I2 with enhanced hydrogen/deuterium exchange mass spectrometry (DXMS). The DXMS results showed that the central beta-sheet remains stable but specific external protein segments become strongly deprotected. Light-induced disruption of the dark-state hydrogen bonding network in I2 produces increased flexibility and opening of PAS core helices alpha3 and alpha4, releases the beta4-beta5 hairpin, and propagates conformational changes to the central beta-sheet. Surprisingly, the first approximately 10 N-terminal residues, which are essential for fast dark-state recovery from I2, become more protected. By combining the DXMS results with our crystallographic structures, which reveal detailed changes near the chromophore but limited protein conformational change, we propose a mechanism for I2 state formation. This mechanism integrates the results from diverse biophysical studies of PYP, and links an allosteric T to R-state conformational transition to three pathways for signal propagation within the PYP fold. On the basis of the observed changes in PYP plus commonalities shared among PAS domain proteins, we further propose that PAS domains share this conformational mechanism, which explains the versatile signal transduction properties of the structurally conserved PYP/PAS module by framework-encoded allostery.
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Affiliation(s)
- Ronald Brudler
- Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chris R. Gessner
- Department of Medicine and Biomedical Sciences Graduate Program, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA
| | - Sheng Li
- Department of Medicine and Biomedical Sciences Graduate Program, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA
| | - Sammy Tyndall
- Department of Medicine and Biomedical Sciences Graduate Program, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA
| | - Elizabeth D. Getzoff
- Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Virgil L. Woods
- Department of Medicine and Biomedical Sciences Graduate Program, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA
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10
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Hagman C, Tsybin YO, Håkansson P. Solution-phase deuterium/hydrogen exchange at a specific residue using nozzle-skimmer and electron capture dissociation mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2006; 20:661-5. [PMID: 16447307 DOI: 10.1002/rcm.2339] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Information about protein conformation can be obtained with hydrogen/deuterium exchange (HDX) mass spectrometry. The isotopic solution-phase exchange of specific amide hydrogen atoms can be followed using low-vacuum nozzle-skimmer collision-induced dissociation (CID). In this study, the nozzle-skimmer technique was complemented by electron capture dissociation (ECD) Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). The solution-phase exchange at a specific residue is monitored by comparing isotopic distributions of two consecutive b- or c-type ions. While nozzle-skimmer fragmentation takes place in the low-vacuum region of the mass spectrometer, ECD occurs at ultra-high vacuum within the mass analyzer cell of the FTICR mass spectrometer. The dissociations take place at 10(-4) and 10(-9) mbar, respectively. Low-vacuum nozzle-skimmer fragmentation can result in intramolecular exchange between product ions and solvent molecules in the gas phase. Consequently, the solution-phase information about protein or peptide conformation is lost. It was not possible to monitor isotopic solution-phase exchange at the eighth residue in substance P, (Phe)8, with nozzle-skimmer CID. By using the in-cell ECD fragmentation method, the solution-phase exchange at the (Phe)8 residue was preserved during mass spectrometric analysis. This result shows the complementary aspects of applying fragmentation at low and at high vacuum, when studying isotopic exchange in solution at specific residues using FTICRMS.
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Affiliation(s)
- Charlotte Hagman
- Department of Engineering Sciences, Division of Ion Physics, Uppsala University, Uppsala, Box 534 S-751 21, Sweden.
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11
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Derunes C, Burgess R, Iraheta E, Kellerer R, Becherer K, Gessner CR, Li S, Hewitt K, Vuori K, Pasquale EB, Woods VL, Ely KR. Molecular determinants for interaction of SHEP1 with Cas localize to a highly solvent-protected region in the complex. FEBS Lett 2005; 580:175-8. [PMID: 16364304 DOI: 10.1016/j.febslet.2005.11.070] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2005] [Revised: 11/08/2005] [Accepted: 11/28/2005] [Indexed: 10/25/2022]
Abstract
Protein-protein interactions between SHEP and Cas proteins influence cellular signaling through tyrosine kinases, as well as integrin-mediated signaling, and may be linked to antiestrogen resistance. Data from past studies suggests that association between SHEP and Cas proteins is critical for these cellular effects. In this study, the interacting domains of each protein were co-expressed in bacteria and a soluble stable complex was purified. Deuterium exchange mass spectrometry was used to define regions that are buried when SHEP1 is in complex with Cas. The results reveal four segments in SHEP1 that are highly protected, including a region (residues 619-640) that contains a key residue, tyrosine 635, required for association with Cas. This region is predominately hydrophilic, yet remains protected from solvent in the complex.
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Affiliation(s)
- Céline Derunes
- Cancer Center, The Burnham Institute for Medical Research, La Jolla, CA 92037, USA
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12
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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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13
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Derunes C, Briknarová K, Geng L, Li S, Gessner CR, Hewitt K, Wu S, Huang S, Woods VI, Ely KR. Characterization of the PR domain of RIZ1 histone methyltransferase. Biochem Biophys Res Commun 2005; 333:925-34. [PMID: 15964548 DOI: 10.1016/j.bbrc.2005.05.190] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Accepted: 05/25/2005] [Indexed: 10/25/2022]
Abstract
RIZ1 (PRDM2) and PRDI-BF1 (PRDM1) are involved in B cell differentiation and the development of B cell lymphomas. These proteins are expressed in two forms that differ by the presence or absence of a PR domain. The protein product that retains the PR domain is anti-tumorigenic while the product that lacks the PR domain is oncogenic and over-expressed in tumor cells. The conserved PR domain is homologous to the SET domain from a family of histone methyltransferases. RIZ1 is also a histone methyltransferase and methylates lysine 9 in histone H3. This activity has been mapped to the PR domain. In the present study, deuterium exchange mass spectrometry was used to define the structural boundaries of the RIZ1 PR domain and to map sites of missense mutations that occur in human cancers and reduce methyltransferase activity. Flexible segments were selectively deleted to produce protein products that crystallize for structural studies. Segments at the carboxyl terminus of the PR domain that are involved in methylation of H3 were shown to be flexible, similar to SET domains, suggesting that the PR and SET methyltransferases may belong to an emerging class of proteins that contain mobile functional regions.
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Affiliation(s)
- Céline Derunes
- Cancer Center, The Burnham Institute, La Jolla, CA 92037, USA
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14
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Pantano S, Zaccolo M, Carloni P. Molecular basis of the allosteric mechanism of cAMP in the regulatory PKA subunit. FEBS Lett 2005; 579:2679-85. [PMID: 15862309 DOI: 10.1016/j.febslet.2005.02.084] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Revised: 02/22/2005] [Accepted: 02/23/2005] [Indexed: 11/20/2022]
Abstract
The second messenger cyclic Adenosine MonoPosphate (cAMP) mediates many biological process by interacting with structurally conserved nucleotide binding domains (cNBD's). Here, we use molecular dynamics simulations on RIIbeta-PKA, one of the best characterized members of the cNBD family, in presence and absence of cAMP. The results of our calculations are fully consistent with the available experimental data and suggest that the key factor of the cAMP allosteric mechanism in cNBDS's is the increased flexibility of the protein upon ligand release along with a mechanical coupling between helical segments. In addition, our calculations provide a rationale for the experimentally observed cAMP selective binding to PKA.
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Affiliation(s)
- Sergio Pantano
- International School for Advanced Studies (ISAS) and INFM - DEMOCRITOS Modeling Center for Research in Atomistic Simulation, Trieste, Italy.
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15
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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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16
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Vigil D, Blumenthal DK, Heller WT, Brown S, Canaves JM, Taylor SS, Trewhella J. Conformational differences among solution structures of the type Ialpha, IIalpha and IIbeta protein kinase A regulatory subunit homodimers: role of the linker regions. J Mol Biol 2004; 337:1183-94. [PMID: 15046986 DOI: 10.1016/j.jmb.2004.02.028] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2003] [Revised: 02/05/2004] [Accepted: 02/09/2004] [Indexed: 11/23/2022]
Abstract
The regulatory (R) subunits of the cAMP-dependent protein kinase (protein kinase A or PKA) are multi-domain proteins responsible for conferring cAMP-dependence and localizing PKA to specific subcellular locations. There are four isoforms of the R subunit in mammals that are similar in molecular mass and domain organization, but clearly serve different biological functions. Although high-resolution structures are available for the cAMP-binding domains and dimerization/docking domains of two isoforms, there are no high-resolution structures of any of the intact R subunit homodimer isoforms. The results of small-angle X-ray scattering studies presented here indicate that the RIalpha, RIIalpha, and RIIbeta homodimers differ markedly in overall shape, despite extensive sequence homology and similar molecular masses. The RIIalpha and RIIbeta homodimers have very extended, rod-like shapes, whereas the RIalpha homodimer likely has a compact Y-shape. Based on a comparison of the R subunit sequences, we predict that the linker regions are the likely cause of these large differences in shape among the isoforms. In addition, we show that cAMP binding does not cause large conformational changes in type Ialpha or IIalpha R subunit homodimers, suggesting that the activation of PKA by cAMP involves only local conformational changes in the R subunits.
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Affiliation(s)
- Dominico Vigil
- Department of Chemistry and Biochemistry and Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92037, USA
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17
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Garcia RA, Pantazatos D, Villarreal FJ. Hydrogen/Deuterium Exchange Mass Spectrometry for Investigating Protein-Ligand Interactions. Assay Drug Dev Technol 2004; 2:81-91. [PMID: 15090213 DOI: 10.1089/154065804322966342] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Amide hydrogen/deuterium exchange mass spectrometry is rapidly becoming a powerful method for high-resolution analyses of protein dynamics, structure, and function. Hydrogen/deuterium exchange approaches can provide information that greatly augments and refines information derived from high-resolution structural studies, and can provide detailed information on native protein structure when structural information is unavailable. Application of this method for rapid analyses of protein-ligand complexes could prove useful for studies of important disease-related protein complexes. The following review covers fundamentals of hydrogen/deuterium exchange and its applications to the study of protein-ligand complexes. In addition, hydrogen/deuterium exchange mass spectrometry studies on a protein-inhibitor complex are presented.
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Affiliation(s)
- Ricardo A Garcia
- Department of Medicine, University of California, San Diego, CA 92093-0613, USA.
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Pantazatos D, Kim JS, Klock HE, Stevens RC, Wilson IA, Lesley SA, Woods VL. Rapid refinement of crystallographic protein construct definition employing enhanced hydrogen/deuterium exchange MS. Proc Natl Acad Sci U S A 2004; 101:751-6. [PMID: 14715906 PMCID: PMC321753 DOI: 10.1073/pnas.0307204101] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Crystallographic efforts often fail to produce suitably diffracting protein crystals. Unstructured regions of proteins play an important role in this problem and considerable advantage can be gained in removing them. We have developed a number of enhancements to amide hydrogen/high-throughput and high-resolution deuterium exchange MS (DXMS) technology that allow rapid identification of unstructured regions in proteins. To demonstrate the utility of this approach for improving crystallization success, DXMS analysis was attempted on 24 Thermotoga maritima proteins with varying crystallization and diffraction characteristics. Data acquisition and analysis for 21 of these proteins was completed in 2 weeks and resulted in the localization and prediction of several unstructured regions within the proteins. When compared with those targets of known structure, the DXMS method correctly localized even small regions of disorder. DXMS analysis was then correlated with the propensity of such targets to crystallize and was further used to define truncations that improved crystallization. Truncations that were defined solely on DXMS analysis demonstrated greatly improved crystallization and have been used for structure determination. This approach represents a rapid and generalized method that can be applied to structural genomics or other targets in a high-throughput manner.
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Affiliation(s)
- Dennis Pantazatos
- Department of Medicine, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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Zawadzki KM, Taylor SS. cAMP-dependent protein kinase regulatory subunit type IIbeta: active site mutations define an isoform-specific network for allosteric signaling by cAMP. J Biol Chem 2003; 279:7029-36. [PMID: 14625280 DOI: 10.1074/jbc.m310804200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
cAMP-dependent protein kinase (cAPK) contains a regulatory (R) subunit dimer bound to two catalytic (C) subunits. Each R monomer contains two cAMP-binding domains, designated A and B. The sequential binding of two cAMPs releases active C. We describe here the properties of RIIbeta and two mutant RIIbeta subunits, engineered by converting a conserved Arg to Lys in each cAMP-binding domain thereby yielding a protein that contains one intact, high affinity cAMP-binding site and one defective site. Structure and function were characterized by circular dichroism, steady-state fluorescence, surface plasmon resonance and holoenzyme activation assays. The Ka for RIIbeta is 610 nM, which is 10-fold greater than its Kd(cAMP) and significantly higher than for RIalpha and RIIalpha. The Arg mutant proteins demonstrate that the conserved Arg is important for both cAMP binding and organization of each domain and that binding to domain A is required for activation. The Ka of the A domain mutant protein is 21-fold greater than that of wild-type and the Kd(cAMP) is increased 7-fold, confirming that cAMP must bind to the mutated site to initiate activation. The domain B mutant Ka is 2-fold less than its Kd(cAMP), demonstrating that, unlike RIalpha, cAMP can access the A site even when the B site is empty. Removal of the B domain yields a Ka identical to the Kd(cAMP) of full-length RIIbeta, indicating that the B domain inhibits holoenzyme activation for RIIbeta. In RIalpha, removal of the B domain generates a protein that is more difficult to activate than the wild-type protein.
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Affiliation(s)
- Kerri M Zawadzki
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093-0654, USA
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