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Ren J, Sherry AD, Malloy CR. Band inversion amplifies 31 P- 31 P nuclear overhauser effects: Relaxation mechanism and dynamic behavior of ATP in the human brain by 31 P MRS at 7 T. Magn Reson Med 2016; 77:1409-1418. [PMID: 27060982 DOI: 10.1002/mrm.26236] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/22/2016] [Accepted: 03/14/2016] [Indexed: 01/07/2023]
Abstract
PURPOSE To develop an improved method to measure the 31 P nuclear Overhauser effect (NOE) for evaluation of adenosine triphosphate (ATP) dynamics in terms of correlation time (τc ), and contribution of dipole-dipole (DD) and chemical shift anisotropy (CSA) mechanisms to T1 relaxation of ATP in human brain. METHODS The NOE of ATP in human brain was evaluated by monitoring changes in magnetization in the β-ATP signal following a band inversion of all downfield 31 P resonances. The magnetization changes observed were analyzed using the Bloch-McConnell-Solomon formulation to evaluate the relaxation and motion dynamic parameters that describe interactions of ATP with cellular solids in human brain tissue. RESULTS The maximal transient NOE, observed as a reduction in the β-ATP signal, was 24 ± 2% upon band inversion of γ- and α-ATP, which is 2-3-fold higher than achievable by frequency-selective inversion of either γ- or α-ATP. The rate of 31 P-31 P cross relaxation (0.21 ± 0.02 s-1 ) led to a τc value of (9.1 ± 0.8) × 10-8 s for ATP in human brain. The T1 relaxation of β-ATP is dominated by CSA over the DD mechanism (60%: 40%). CONCLUSIONS The band inversion method proved effective in amplifying 31 P NOE, and thus facilitating ATP τc and relaxation measurements. This technique renders ATP a potentially useful reporter molecule for cellular environments. Magn Reson Med 77:1409-1418, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
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Affiliation(s)
- Jimin Ren
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390.,Department of Radiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - A Dean Sherry
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390.,Department of Radiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390.,Department of Chemistry, University of Texas at Dallas, Richardson, TX, 75080
| | - Craig R Malloy
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390.,Department of Radiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390.,VA North Texas Health Care System, Dallas, TX, 75216
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2
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Groves P, Strzelecka-Kiliszek A, Sekrecka-Belniak A, Canales A, Jiménez-Barbero J, Bandorowicz-Pikula J, Pikula S, Cañada FJ. Exploring NMR methods as a tool to select suitable fluorescent nucleotide analogues. Org Biomol Chem 2014; 11:5332-8. [PMID: 23842795 DOI: 10.1039/c3ob40159f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Fluorescent analogues provide important tools for biochemical/biophysical research. However, the analogues contain chemical modifications much larger than those known to affect ligand-binding, such as the inversion of a carbon centre or substitution of an atom. We lack experimental tools and protocols to select the most appropriate fluorescent analogue. Herein, we use several NMR spectroscopy methods, including Saturation Transfer Difference (STD), STD competition and transferred nuclear Overhauser effect spectroscopy (Tr-NOESY), as tools to select appropriate fluorescent probes. Annexin A6 (AnxA6) is a ubiquitous protein that forms in vitro GTP-induced ion channels. We used this protein as a model and screened guanosine triphosphate (GTP) and four fluorescent analogues against AnxA6. STD reported that the GTP moiety of all ligands made similar contacts with the protein, despite additional interactions between the fluorescent tags and AnxA6. Competition STD experiments verified that the analogues and GTP bind to the same site. Tr-NOESY indicated that the bound conformation of the base relative to ribose is altered for some analogues compared to GTP. MANT-GTP or the BODIPY thioester of guanosine 5'-O-(3-thiotriphosphate) are the most suitable fluorescent analogues for AnxA6, according to NMR. These results reveal NMR as a useful technique to select and design proper fluorescent tags for biochemical/biophysical assays.
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Affiliation(s)
- Patrick Groves
- Chemical Biology Division, Instituto de Tecnologia Química e Biológica (ITQB-UNL), Oeiras, Portugal.
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3
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Bouguet-Bonnet S, Yemloul M, Canet D. New Application of Proton Nuclear Spin Relaxation Unraveling the Intermolecular Structural Features of Low-Molecular-Weight Organogel Fibers. J Am Chem Soc 2012; 134:10621-7. [DOI: 10.1021/ja303679z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Sabine Bouguet-Bonnet
- Méthodologie RMN (CRM2, UMR 7036,
UL-CNRS), Université de Lorraine, Campus Aiguillettes, B.P. 70239, 54506 Vandœuvre-lès-Nancy
(cedex), France
| | - Mehdi Yemloul
- Méthodologie RMN (CRM2, UMR 7036,
UL-CNRS), Université de Lorraine, Campus Aiguillettes, B.P. 70239, 54506 Vandœuvre-lès-Nancy
(cedex), France
| | - Daniel Canet
- Méthodologie RMN (CRM2, UMR 7036,
UL-CNRS), Université de Lorraine, Campus Aiguillettes, B.P. 70239, 54506 Vandœuvre-lès-Nancy
(cedex), France
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4
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Takemoto C, Spremulli LL, Benkowski LA, Ueda T, Yokogawa T, Watanabe K. Unconventional decoding of the AUA codon as methionine by mitochondrial tRNAMet with the anticodon f5CAU as revealed with a mitochondrial in vitro translation system. Nucleic Acids Res 2009; 37:1616-27. [PMID: 19151083 PMCID: PMC2655697 DOI: 10.1093/nar/gkp001] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Mitochondrial (mt) tRNAMet has the unusual modified nucleotide 5-formylcytidine (f5C) in the first position of the anticodon. This tRNA must translate both AUG and AUA as methionine. By constructing an in vitro translation system from bovine liver mitochondria, we examined the decoding properties of the native mt tRNAMet carrying f5C in the anticodon compared to a transcript that lacks the modification. The native mt Met-tRNA could recognize both AUA and AUG codons as Met, but the corresponding synthetic tRNAMet lacking f5C (anticodon CAU), recognized only the AUG codon in both the codon-dependent ribosomal binding and in vitro translation assays. Furthermore, the Escherichia coli elongator tRNAMetm with the anticodon ac4CAU (ac4C = 4-acetylcytidine) and the bovine cytoplasmic initiator tRNAMet (anticodon CAU) translated only the AUG codon for Met on mt ribosome. The codon recognition patterns of these tRNAs were the same on E. coli ribosomes. These results demonstrate that the f5C modification in mt tRNAMet plays a crucial role in decoding the nonuniversal AUA codon as Met, and that the genetic code variation is compensated by a change in the tRNA anticodon, not by a change in the ribosome. Base pairing models of f5C-G and f5C-A based on the chemical properties of f5C are presented.
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Affiliation(s)
- Chie Takemoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.
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5
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Maity H, Lin Y, Jarori GK. Structure of triphosphoryl nucleotide bound at the active site of yeast hexokinase: 1H-nuclear magnetic resonance study. JOURNAL OF PROTEIN CHEMISTRY 2002; 21:265-77. [PMID: 12168697 DOI: 10.1023/a:1019745303509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Conformation of a nonhydrolyzable adenosine triphosphate (ATP) analogue, adenylyl-(beta,gamma-methylene)-diphosphonate (AMPPCP) bound at the active site of yeast hexokinase-PII was determined by proton two-dimensional transferred nuclear Overhauser effect spectroscopy (TRNOESY) and molecular dynamics simulations. The effect of the glucose-induced domain closure on the conformation of the nucleotide was evaluated by making measurements on two different complexes: PII AMPPCPMg(II) and PII-Glc.AMPPCPMg(Il). TRNOE measurements were made at 500 MHz, 10 degress C, as a function of several mixing times varying in the range of 40 to 200 ms. Interproton distances derived from the analysis of NOE buildup curves were used as restraints in molecular dynamics simulations to determine the conformation of the enzyme bound nucleotide. The adenosine moiety was found to bind in high anti conformation with a glycosidic torsion angle chi = 48 +/- 5 degrees in both complexes. However, significant differences in the conformations of the ribose and triphosphoryl chain of the nucleotide are observed between the two complexes. The phase angles of pseudorotation P in PII.AMPPCPMg(II) and PII.Glc.AMPPCPMg(II) are 87 degrees and 77 degrees, describing a OE and OT4 sugar pucker and the amplitudes of the sugar pucker (tau) are 37 degrees and 61 degrees, respectively.
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Affiliation(s)
- Haripada Maity
- Department of Biological Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
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6
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Eyschen J, Vitoux B, Marraud M, Cung MT, Branlant G. Engineered glycolytic glyceraldehyde-3-phosphate dehydrogenase binds the anti conformation of NAD+ nicotinamide but does not experience A-specific hydride transfer. Arch Biochem Biophys 1999; 364:219-27. [PMID: 10190977 DOI: 10.1006/abbi.1999.1116] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Glycolytic glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a NAD-dependent oxidoreductase which catalyzes the oxidative phosphorylation of d-glyceraldehyde-3-phosphate (G3P) to form 1, 3-diphosphoglycerate. The currently accepted mechanism involves an oxidoreduction step followed by a phosphorylation. GAPDH is classified as a B-specific oxidoreductase. The inspection of several crystal structures of GAPDHs indicates that the efficient hydride transfer from the hemithioacetal intermediate to the C4 position of the pyridinium si face requires optimal nicotinamidium-protein contacts for a suitable pyridinium-ring orientation. In previous studies carried out on Escherichia coli GAPDH (C. Corbier, A. Mougin, Y. Mely, H. W. Adolph, M. Zeppezauer, D. Gerard, A. Wonacott, and G. Branlant, Biochimie 72, 545-554, 1990; J. Eyschen, C. Corbier, B. Vitoux, G. Branlant, and M. T. Cung, Protein Pept. Lett. 1, 19-24, 1994), the role of the invariant Asn 313 residue, as an anchor which favors the syn orientation of the nicotinamide ring, was examined. Here, we report further investigations on the molecular factors responsible for the cofactor stereospecificity. Two single [Gly317] and [Ala317] GAPDH mutants and one double [Thr313-Gly317] GAPDH mutant were constructed on the basis of a molecular modelling study from the crystal structure of holo GAPDH from E. coli (E. Duée, L. Olivier-Deyris, E. Fanchon, C. Corbier, G. Branlant, and O. Dideberg, J. Mol. Biol. 257, 814-838, 1996). The Kd constants of [Ala317], [Gly317], and [Thr313-Gly317] GAPDH mutants for NAD are 5, 13, and 300 times higher than that of wild-type GAPDH. Transferred nuclear Overhauser effect spectroscopy demonstrates that the wild-type syn orientation of bound nicotinamide remains unchanged in the [Gly317] and [Ala317] mutants, whereas a conformational equilibrium between the syn and anti forms occurs in the [Thr313-Gly317] double mutant with a preference for the anti conformer. Although the double mutant preferably binds the nicotinamide ring in an anti conformation, it still exhibits B hydride transfer stereospecificity. Yet, the catalytic efficiency is much less than that of the wild type. This indicates that the holo GAPDH mutant fraction with an anti orientation of bound NAD is not capable of forming the ternary complex with G3P which would be required for an efficient A-specific catalytic process. The reasons of this catalytic inefficiency are discussed in relation with the historical and functional models which were advanced to explain the stereospecificity of NAD(P)-dependent dehydrogenases.
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Affiliation(s)
- J Eyschen
- UMR 7567 CNRS-UHP, Maturation des ARN et Enzymologie Moléculaire, B. P. 239, Vandoeuvre-lès-Nancy, 54506, France
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7
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Vincent SJ, Zwahlen C, Post CB, Burgner JW, Bodenhausen G. The conformation of NAD+ bound to lactate dehydrogenase determined by nuclear magnetic resonance with suppression of spin diffusion. Proc Natl Acad Sci U S A 1997; 94:4383-8. [PMID: 9113998 PMCID: PMC20731 DOI: 10.1073/pnas.94.9.4383] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/1996] [Accepted: 02/03/1997] [Indexed: 02/04/2023] Open
Abstract
We have reinvestigated the conformation of NAD+ bound to dogfish lactate dehydrogenase (LDH) by using an NMR experiment that allows one to exploit nuclear Overhauser effects to determine internuclear distances between pairs of protons, without perturbation of spin-diffusion effects from other protons belonging either to the cofactor or to the binding pocket of the enzyme. The analysis indicates that the structure of bound NAD+ is in accord with the conformation determined in the solid state by x-ray diffraction for the adenosine moiety, but deviates significantly from that of the nicotinamide. The NMR data indicate conformational averaging about the glycosidic bond of the nicotinamide nucleotide. In view of the strict stereospecificity of catalysis by LDH and the conformational averaging of bound NAD+ that we infer from solution-state NMR, we suggest that LDH binds the cofactor in both syn and anti conformations, but that binding interactions in the syn conformation are not catalytically productive.
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Affiliation(s)
- S J Vincent
- Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA
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8
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Xiang B, Markham GD. The conformation of inosine 5'-monophosphate (IMP) bound to IMP dehydrogenase determined by transferred nuclear overhauser effect spectroscopy. J Biol Chem 1996; 271:27531-5. [PMID: 8910338 DOI: 10.1074/jbc.271.44.27531] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
IMP dehydrogenase (IMPDH) catalyzes the NAD-dependent synthesis of xanthosine 5'-monophosphate which is the rate-limiting step in guanine nucleotide biosynthesis. Although IMPDH is the target of numerous chemotherapeutic agents, nothing has been known about the conformation of the enzyme-bound substrates. The conformation of IMP bound to human type II IMP dehydrogenase has been determined by two-dimensional transferred nuclear Overhauser effect NMR spectroscopy at 600 MHz. NOE buildup rates were determined by recording NOESY spectra at numerous mixing times. The cross-relaxation rates determined from the initial NOE build-up rates were used to calculate inter-proton distances of bound IMP. The conformation of the enzyme-bound IMP was obtained by molecular modeling with energy minimization using the experimentally determined inter-proton distance constraints. The glycosidic torsion angle of the bound nucleotide is anti and the sugar is in the C2-endo-conformation. This conformation places H2 of IMP, which is transferred to NAD in the reaction, in a position clear of the rest of the molecule in order to facilitate the reaction.
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Affiliation(s)
- B Xiang
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
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9
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Tipton PA, Quinn TP, Peisach J, Cook PF. Role of the divalent metal ion in the NAD:malic enzyme reaction: an ESEEM determination of the ground state conformation of malate in the E:Mn:malate complex. Protein Sci 1996; 5:1648-54. [PMID: 8844853 PMCID: PMC2143473 DOI: 10.1002/pro.5560050818] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The conformation of L-malate bound at the active site of Ascaris suum malic enzyme has been investigated by electron spin echo envelope modulation spectroscopy. Dipolar interactions between Mn2+ bound to the enzyme active site and deuterium specifically placed at the 2-position, the 3R-position, and the 3S-position of L-malate were observed. The intensities of these interactions are related to the distance between each deuterium and Mn2+. Several models of possible Mn-malate complexes were constructed using molecular graphics techniques, and conformational searches were conducted to identify conformers of malate that meet the distance criteria defined by the spectroscopic measurements. These searches suggest that L-malate binds to the enzyme active site in the trans conformation, which would be expected to be the most stable conformer in solution, not in the gauche conformer, which would be more similar to the conformation required for oxidative decarboxylation of oxalacetate formed from L-malate at the active site of the enzyme.
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Affiliation(s)
- P A Tipton
- Department of Biochemistry, University of Missouri-Columbia 65211, USA.
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10
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Seio K, Wada T, Sakamoto K, Yokoyama S, Sekine M. Chemical Synthesis and Conformational Properties of a New Cyclouridylic Acid Having an Ethylene Bridge between the Uracil 5-Position and 5‘-Phosphate Group. J Org Chem 1996. [DOI: 10.1021/jo951756x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kohji Seio
- Department of Life Science, Tokyo Institute of Technology, Nagatsuta, Midoriku, Yokohama 226, Japan, and Department of Biophysics and Biochemistry, The University of Tokyo, Hongo, Bunkyoku, Tokyo 113, Japan
| | - Takeshi Wada
- Department of Life Science, Tokyo Institute of Technology, Nagatsuta, Midoriku, Yokohama 226, Japan, and Department of Biophysics and Biochemistry, The University of Tokyo, Hongo, Bunkyoku, Tokyo 113, Japan
| | - Kensaku Sakamoto
- Department of Life Science, Tokyo Institute of Technology, Nagatsuta, Midoriku, Yokohama 226, Japan, and Department of Biophysics and Biochemistry, The University of Tokyo, Hongo, Bunkyoku, Tokyo 113, Japan
| | - Shigeyuki Yokoyama
- Department of Life Science, Tokyo Institute of Technology, Nagatsuta, Midoriku, Yokohama 226, Japan, and Department of Biophysics and Biochemistry, The University of Tokyo, Hongo, Bunkyoku, Tokyo 113, Japan
| | - Mitsuo Sekine
- Department of Life Science, Tokyo Institute of Technology, Nagatsuta, Midoriku, Yokohama 226, Japan, and Department of Biophysics and Biochemistry, The University of Tokyo, Hongo, Bunkyoku, Tokyo 113, Japan
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11
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Zheng J, Post CB. Variation in Protein Indirect Relaxation Effects in One- and Two-Dimensional Exchange-Transferred Overhauser Experiments. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp952960r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Jie Zheng
- Department of Medicinal Chemistry and Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1333
| | - Carol Beth Post
- Department of Medicinal Chemistry and Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1333
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12
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Affiliation(s)
- G P Mullen
- Department of Biochemistry, University of Connecticut Health Center, Farmington 06032, USA
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13
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Song S, Vander Velde D, Gunn CW, Himes RH. Conformation of ATP and ADP bound to N10-formyltetrahydrofolate synthetase determined by TRNOE NMR spectroscopy. Biochemistry 1994; 33:693-8. [PMID: 8292596 DOI: 10.1021/bi00169a010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
ATP and ADP bind to N10-CHO-H4folate synthetase from Clostridium cylindrosporum at four identical sites. Although both ADP and ATP bind to the enzyme with essentially the same Ka values as the Mg2+.nucleotide complexes, only the Mg2+.nucleotides are kinetically active. Using transferred nuclear Overhauser effect (TRNOE) NMR spectroscopy, we have measured the time-dependent NOE buildup rates of selected protons in ADP and ATP bound to N10-CHO-H4folate synthetase after preirradiating protons H1', H2', H3', and H4'. The results were used to calculate interproton distances. In order to define the conformations of ADP and ATP bound to the enzyme, we used the TRNOE distance constraints in a distance geometry algorithm. The results of the distance geometry calculations suggest that, within experimental error, the conformations of both ADP and ATP (with or without Mg2+) have an average glycosidic torsion angle X (O4'-C1'-N9-C8) of 100 degrees +/- 20 degrees and a sugar pucker angle psi' (C5'-C4'-C3'-O3') of 85 degrees +/- 5 degrees. These values are consistent with a nucleotide structure generated by computer modeling after energy minimization, which has X = 90 degrees +/- 6 degrees and psi' = 81 degrees, indicating a high-anti and C3'-endo conformation.
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Affiliation(s)
- S Song
- Department of Biochemistry, University of Kansas, Lawrence 66045
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14
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Martínez A, Abeygunawardana C, Haavik J, Flatmark T, Mildvan AS. Conformation and interaction of phenylalanine with the divalent cation at the active site of human recombinant tyrosine hydroxylase as determined by proton NMR. Biochemistry 1993; 32:6381-90. [PMID: 8100148 DOI: 10.1021/bi00076a011] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Recombinant human tyrosine hydroxylase has been purified as a metal-free apoenzyme (apo-hTH1) which tightly binds one Fe2+, Co2+, or Zn2+ per subunit with activation only by Fe2+ and competitive inhibition by the other cations. L-tyrosine and L-phenylalanine are alternative substrates for this enzyme, giving similar Vmax values, although the KM value for phenylalanine is about 8-fold greater than for tyrosine. Apo-hTH1 enhances the paramagnetic effects of Co2+ on 1/T1 and 1/T2 values of the protons of enzyme-bound phenylalanine both in the presence and in the absence of the oxidized form of the cofactor L-erythro-7,8-dihydrobiopterin (BH2), which was used as an inactive analog of the natural cofactor (6R)-1-erythro-tetrahydrobiopterin (BH4). No effects of hTH1-Zn2+ on 1/T1 or 1/T2 are found. From paramagnetic effects of hTH1-Co2+ on 1/T1 of phenylalanine protons at 250 and 600 MHz, in the presence of BH2, a correlation time (tau c) of 1.8 +/- 0.1 ps was found. Using this tau c value, and assuming that only one proton of the pairs H3,H5, and H2,H6 is experiencing the total paramagnetic effect (asymmetric limiting case), distances from enzyme-bound Co2+ to phenylalanine (+/- 1.2 A) of 6.1 A (H3 or H5), 6.3 A (H2 or H6), 7.0 A (H4), 7.3 A (H alpha), > or = 7.4 A (H beta-pro-S), and > or = 7.6 A (H beta-pro-R) were calculated. The distances to H3 or H5 and to H2 or H6 are slightly increased to 6.8 and 7.0 A, respectively, if each proton of both degenerate pairs equally experiences the paramagnetic effect of Co2+ (symmetric limiting case). These distances place the aromatic ring of phenylalanine in the second coordination sphere of the metal, which would permit an Fe-bound oxy or peroxy species to approach molecular contact with C3/C4, suggesting a direct role of Fe2+ in the hydroxylation reaction. The same correlation time and similar distances were found in the absence of BH2 with H4 of phenylalanine slightly closer to the metal. In the ternary hTH1-Zn(2+).BH2.phenylalanine complex, eight interproton distances in the enzyme-bound phenylalanine were determined by NOESY spectra at 600 MHz at 35-, 50-, and 75-ms mixing times. The conformation of enzyme-bound phenylalanine, consistent with the six Co(2+)-proton distances and the eight interproton distances, is partially extended with torsional angles chi 1 = 97 degrees +/- 3 degrees and chi 2 = -78 degrees +/- 2 degrees.
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Affiliation(s)
- A Martínez
- Department of Biochemistry, University of Bergen, Norway
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15
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Improved methods for solvent suppression and baseline correction in two-dimensional transferred NOE experiments. ACTA ACUST UNITED AC 1992. [DOI: 10.1016/0022-2364(92)90192-a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Koide S, Yokoyama S, Matsuzawa H, Miyazawa T, Ohta T. Conformational equilibrium of an enzyme catalytic site in the allosteric transition. Biochemistry 1992; 31:5362-8. [PMID: 1606160 DOI: 10.1021/bi00138a017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The dynamic equilibrium of a catalytic site between active and inactive conformations, the missing link between the structure and function of allosteric enzymes, was identified using protein engineering and NMR techniques. Kinetic analyses of the wild-type and three mutants of Thermus L-lactate dehydrogenase established that the allosteric property of the enzyme is associated with a concerted transition between the high-affinity (R) and low-affinity (T) states. By introducing mutations, we prepared an enzyme in which the R and T states were balanced. The conformation of the enzyme-bound coenzyme, NAD+, which interacts directly with the substrate, was analyzed using NMR spectroscopy. NAD+ bound to the mutant enzyme was in a conformational mixture of the active and inactive forms, while NAD+ took on predominantly one of the two forms when it was bound to the other enzymes we had analyzed. We interpret this to mean that the catalytic site is in equilibrium between the two conformations. The ratio of the conformers of each enzyme agreed with the [T]/[R] ratio as determined by kinetic analyses. Therefore, it is the identified conformational equilibrium of the catalytic site that governs the allosteric regulation of the enzyme activity.
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Affiliation(s)
- S Koide
- Department of Agricultural Chemistry, University of Tokyo, Japan
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17
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Landy SB, Ray BD, Plateau P, Lipkowitz KB, Rao BD. Conformation of MgATP bound to nucleotidyl and phosphoryl transfer enzymes 1H-transferred NOE measurements on complexes of methionyl tRNA synthetase and pyruvate kinase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 205:59-69. [PMID: 1555604 DOI: 10.1111/j.1432-1033.1992.tb16751.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The conformations of MgATP bound to a nucleotidyl transfer enzyme, methionyl tRNA synthetase and a phosphoryl transfer enzyme, pyruvate kinase, were studied by transferred NOE (TRNOE) measurements in 1H NMR. The experiments were performed on D2O solutions at 276 MHz and 300 MHz, and 10 degrees C in the presence of approximately a tenfold excess of substrate over the enzyme (sites). Selective inversion of chosen resonances was accomplished with an appropriately tailored DANTE sequence consisting of 100 phase-alternating hard 1.8 degree pulses. NOE measurements were made in terms of difference spectra (with and without inversion) at 6-8 delay times ranging from 10-500 ms following the DANTE sequence. A full complement of ten NOE build-up curves obtained for each enzyme complex was analyzed by using the complete relaxation-matrix method (which includes all the non-exchangeable protons in MgATP) suitably modified to include exchange between bound and free substrate. Molecular mechanics computations were used to examine the energetic implications of the NOE-determined structure. The final structures obtained for MgATP bound to the two enzymes were very similar to each other, with a 3'-endo sugar pucker and an anti conformation with a glycosidic torsional angle (O'4-C'1-N9-C8) of 39 degrees +/- 4 degrees. Both enzymes contain multiple binding sites for MgATP and hence the structure obtained in each case represents an average due to chemical exchange. However, TRNOE experiments performed on a tryptic fragment of methionyl tRNA synthetase which has a single MgATP binding site, show that the same structure fits these measurements as well. This evidence, coupled with the striking similarity of the structures deduced, for the two enzyme complexes, and the reciprocal sixth-power dependence of NOE on interproton distance, strongly suggests that the conformations at the individual binding sites of both the enzymes are virtually identical. This conclusion is in contrast with multiple conformations of MgATP bound to pyruvate kinase, proposed by Rosevear, P.R., Fox, T.L. & Mildvan, A.S. (1987) Biochemistry 26, 3487-3493.
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Affiliation(s)
- S B Landy
- Department of Physics, Indiana University-Purdue University, (IUPUI), Indianapolis 46205-2810
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Coats EA, Wiese M, Chi HL, Cordes HP, Seydel JK. Computer Modeling and NMR Studies of Interactions Between Phospholipids and Benzylamines. ACTA ACUST UNITED AC 1992. [DOI: 10.1002/qsar.2660110308] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Weber DJ, Mullen GP, Mildvan AS. Conformation of an enzyme-bound substrate of staphylococcal nuclease as determined by NMR. Biochemistry 1991; 30:7425-37. [PMID: 1854746 DOI: 10.1021/bi00244a009] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The dinucleoside phosphodiester dTdA is a slow substrate of staphylococcal nuclease (kcat = 3.8 X 10(-3) s-1) that forms binary E-S and ternary E-M-S complexes with Ca2+, Mn2+, Co2+, and La3+. The enzyme enhances the paramagnetic effects of Co2+ on 1/T1 and 1/T2 of the phosphorus and on 1/T1 of six proton resonances of dTdA, and these effects are abolished by binding of the competitive inhibitor 3',5'-pdTp. From paramagnetic effects of Co2+ on 1/T2 of phosphorus, koff of dTdA from the ternary E-Co(2+)-dTdA complex is greater than or equal to 4.8 X 10(4) s-1 and kon greater than or equal to 1.4 X 10(6) M-1 s-1, indicating the 1/T1 values to be in fast exchange. From paramagnetic effects of enzyme-bound Co2+ on 1/T1 of phosphorus and protons, with use of a correlation time of 1.6 ps on the basis of 1/T1 values at 250 and 600 MHz, 7 metal-nucleus distances and 9 lower-limit metal-nucleus distances are calculated. The long Co2+ to 31P distance of 4.1 +/- 0.9 A, which is intermediate between that expected for direct phosphoryl coordination (3.31 +/- 0.02 A) and a second sphere complex with an intervening water ligand (4.75 +/- 0.02 A), suggests either a distorted inner sphere complex or the rapid averaging of 18% inner sphere and 82% second sphere complexes and may explain the reduced catalytic activity with small dinucleotide substrates. Seventeen interproton distances and 108 lower limit interproton distances in dTdA in the ternary E-La(3+)-dTdA complex were determined by NOESY spectra at 50-, 100-, and 200-ms mixing times. While metal-substrate and interproton distances alone did not yield a unique structure, the combination of both sets of distances yielded a very narrow range of conformations for enzyme-bound dTdA, which was highly extended, with no base stacking, with high-anti glycosidic torsional angles for dT (64 degrees less than or equal to chi less than or equal to 73 degrees) and dA (66 degrees less than or equal to chi less than or equal to 68 degrees) and predominantly C-2'-endo sugar puckers for both nucleosides. Although the individual nucleosides are like those of B-DNA, their unstacked conformation, which is inappropriate for base pairing, as well as the conformational angles alpha and gamma of dA and zeta of dT, rule out B-DNA.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- D J Weber
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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Williams JS, Rosevear PR. Nuclear overhauser effect studies of the conformations of Mg(alpha, beta-methylene)ATP bound to E. coli isoleucyl-tRNA synthetase. Biochem Biophys Res Commun 1991; 176:682-9. [PMID: 2025282 DOI: 10.1016/s0006-291x(05)80238-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Internuclear distances obtained from transferred nuclear Overhauser effects were used in combination with distance geometry calculations to define the E. coli isoleucyl-tRNA synthetase bound conformation of Mg(alpha, beta-methylene)ATP both in the absence and in the presence of the cognate and noncognate amino acids L-isoleucine and L-valine, respectively. A single nucleotide structure having an anti adenine-ribose glycosidic torsional angle of -114 degrees was found to satisfy the experimental distance constraints. The nearly identical anti glycosidic torsional angles observed in all three complexes demonstrate that the conformation of the adenosine moiety of the enzyme-bound nucleotide is not sensitive to the presence or to the nature of the amino acid bound at the aminoacyladenylate site. In addition, the acceptable range of Mg(alpha, beta-methylene)ATP conformations bound to the E. coli isoleucyl-tRNA synthetase was found to be nearly identical to that previously determined for the E. coli methionyl-tRNA synthetase (Williams and Rosevear (1991) J. Biol. Chem. 266, 2089-2098). Thus, the predicted structural homology between the isoleucyl- and methionyl-tRNA synthetases, both members of the same class of synthetases on the basis of common consensus sequences, is further supported by consensus enzyme-bound nucleotide conformations.
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Affiliation(s)
- J S Williams
- Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston 77225
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Nuclear Overhauser effect studies on the conformations of Mg(alpha, beta-methylene)ATP bound to Escherichia coli methionyl-tRNA synthetase. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)52213-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Mullen GP, Vaughn JB, Shenbagamurthi P, Mildvan AS. NMR studies of the active site of DNA polymerase I and of a 50-residue peptide fragment of the enzyme. Biochem Pharmacol 1990; 40:69-81. [PMID: 2196883 DOI: 10.1016/0006-2952(90)90181-j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Transferred nuclear Overhauser effects (NOEs) and selective T1 measurements were used to determine interproton distances in the substrates Mg2+dATP and Mg2+TTP bound to the large fragment of DNA polymerase I (Pol I). The distances are consistent with high anti, O1' endo conformations for the enzyme-bound substrates, similar to nucleotides of B-DNA. These substrate conformations show little or no change when the complementary RNA templates (rU)57 or (rA)50 are bound. In contrast, multiple conformations, including syn and anti species, are required to fit the interproton distances measured on the enzyme-bound guanine nucleotide substrates Mg2+dGTP and Mg2+ddGTP. These multiple substrate conformations simplify to a single high anti, O1' endo conformation when the complementary template (rC)37 is bound, possibly due to base-pairing with the template, as in the active complex. In the presence of both template and primer, enzyme-bound Mg2+ddGTP reverts to multiple conformations. This ability of Pol I to decrease the fraction of bound substrate which is appropriate for primer elongation may be an error-preventing mechanism. In all cases, the conformations of the average nucleotide of the enzyme-bound RNA templates are also B-like. Transferred NOEs from protons of the enzyme to those of bound dNTP substrates suggest hydrophobic (Ile, Leu) and an aromatic amino acid (Tyr) at the substrate binding site. Peptide I, a synthetic 50-residue peptide based on residues 728 to 777 of the Pol I sequence, containing the conserved sequence L-I-Y-G, retains significant secondary and tertiary structure in solution as found by circular dichroism (CD) and 2D NMR. While the X-ray structure shows 48% helix in this region, the sequence specific NOESY analysis suggests 18% helix, and the preservation of two of the three beta turns. Peptide I shows tight binding of dNTP substrates, the substrate analog 2',3'-trinitrophenyl-ATP, and duplex DNA, providing direct evidence that the active site for polymerization lies in this region of the enzyme, with the substrate binding along the O-helix near Leu-764, Ile-765, and Tyr-766. Another synthetic peptide, peptide II, based on residues 840 to 888 of the Pol I sequence also retains much secondary structure as detected by CD but does not bind the substrate analog TNP-ATP.
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Affiliation(s)
- G P Mullen
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205
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