151
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Thomas RM, Feeney J, Nicholson RB, Pain RH, Roberts GC. Identification by n.m.r. spectroscopy of a stable intermediate structure in the unfolding of staphylococcal beta-lactamase. Biochem J 1983; 215:525-9. [PMID: 6607049 PMCID: PMC1152432 DOI: 10.1042/bj2150525] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The unfolding of beta-lactamase (penicillinase) from Staphylococcus aureus by guanidinium chloride was followed by using n.m.r. spectroscopy. On the basis of the observation of resonances corresponding to histidine, tyrosine and other amino acid side chains, the existence of a stable partially folded species was demonstrated. These experiments provide detailed characterization of the intermediate that confirms and extends previous characterization by absorption and c.d. spectroscopy and by flow properties. In addition, they show that residues in the N-terminal third of the molecule are affected by the native-to-intermediate transition. Persistent non-equivalence of the two imidazole C2 proton resonances at high guanidinium chloride concentrations is discussed in terms of local sequence effects on the chemical shift.
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152
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Smith GA, Hesketh RT, Metcalfe JC, Feeney J, Morris PG. Intracellular calcium measurements by 19F NMR of fluorine-labeled chelators. Proc Natl Acad Sci U S A 1983; 80:7178-82. [PMID: 6417665 PMCID: PMC390017 DOI: 10.1073/pnas.80.23.7178] [Citation(s) in RCA: 159] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Symmetrically substituted difluoro derivatives of 1,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid (nFBAPTA) show large 19F NMR chemical shifts on chelating divalent cations. The complexes of Ca2+ with 4FBAPTA and 5FBAPTA show fast and slow exchange behavior, respectively, and the chemical shift or the areas of the resonances from the free and complexed forms can be used to determine the free Ca2+ concentration. The measurement of the free Ca2+ concentration by either ligand is unaffected by free Mg2+ concentrations less than 10 mM, by pH 6-8, or by contaminating divalent ions of high affinity (Zn2+, Fe2+, Mn2+). The tetraacetoxymethyl ester derivative of 5FBAPTA was used to load mouse thymocytes with 5FBAPTA to intracellular concentrations of 1 mM, and the 19F spectrum indicated a free intracellular Ca2+ concentration [( Ca]i) of 250 nM. The [Ca]i was increased to 350 nM by addition of succinylated concanavalin A at mitogenic concentrations, and the addition of A23187 saturated the intracellular chelator with Ca2+ from the external medium. The method provides a measurement of [Ca]i and other divalent cation concentrations with direct identification of the ionic species chelated.
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153
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Birdsall B, Roberts GC, Feeney J, Dann JG, Burgen AS. Trimethoprim binding to bacterial and mammalian dihydrofolate reductase: a comparison by proton and carbon-13 nuclear magnetic resonance. Biochemistry 1983; 22:5597-604. [PMID: 6418202 DOI: 10.1021/bi00293a022] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The binding of trimethoprim to dihydrofolate reductase from L1210 mouse lymphoma cells has been studied by measuring the changes in chemical shift of nuclei of the ligand that accompanying binding. The 6- and 2',6'-proton chemical shifts of bound trimethoprim have been determined by transfer of saturation experiments, and the 2-carbon chemical shift has been determined by using [2-13C]trimethoprim. The changes in proton chemical shift are substantially smaller than those accompanying binding to bacterial dihydrofolate reductase [Cayley, P. J., Albrand, J. P., Feeney, J., Robert, G. C. K., Piper, E. A., & Burgen, A. S. V. (1979) Biochemistry 18, 3886]. It is shown that this difference arises largely from the fact that trimethoprim adopts different conformations when bound to mammalian and to bacterial dihydrofolate reductase. The proton chemical shifts are interpreted in terms of ring-current contributions from the two aromatic rings of trimethoprim itself and the nearby aromatic amino acid residues of the enzyme. The latter have been located by using the refined crystallographic coordinates of the Lactobacillus casei and Escherichia coli reductases in their complexes with methotrexate [Bolin, J. T., Filman, D. J., Matthews, D. A. & Kraut, J. (1982) J. Biol. Chem. 257, 13650], under the assumption that, as indicated by the 13C chemical shifts, the diaminopyrimidine ring of trimethoprim binds in the same way as does the corresponding part of methotrexate. With use of these assumptions, the conformation of trimethoprim bound to the dihydrofolate reductases from L. casei, E. coli, and L1210 cells has been calculated.(ABSTRACT TRUNCATED AT 250 WORDS)
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154
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Cox DW, Morris PG, Feeney J, Bachelard HS. 31P-n.m.r. studies on cerebral energy metabolism under conditions of hypoglycaemia and hypoxia in vitro. Biochem J 1983; 212:365-70. [PMID: 6882378 PMCID: PMC1152055 DOI: 10.1042/bj2120365] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A system has been developed for performing 31P-n.m.r. studies on cerebral tissues superfused in vitro, and gives results comparable with those reported from studies in vivo. Under optimal superfusion conditions [10 mM-glucose and O2/CO2 (19:1)] the tissue concentrations of phosphocreatine and ATP were calculated to be approx. 3.1 and 1.3 mumol/g respectively. When the glucose of the superfusing medium was lowered to 0.5 mM, slightly decreased sugar phosphate peaks were observed, but there was no detectable change in [ATP] or [phosphocreatine]. At 0.2 mM-glucose, significantly decreased concentrations of phosphocreatine and ATP were observed. Substitution of pyruvate plus malate for glucose did not decrease levels of phosphocreatine and ATP. When the superfusing medium was gassed with air/CO2 (19:1; 'mild hypoxia'), there was an appreciable fall in sugar phosphates and phosphocreatine with no detectable effect on ATP. In the presence of N2/CO2 (19:1; 'severe hypoxia', since O2 was not completely excluded), concentrations of phosphocreatine fell considerably, but with little effect on ATP. The results demonstrate the feasibility of studying cerebral energy metabolism in vitro using the non-invasive 31P-n.m.r. technique and are discussed in relation to the sensitivity of cerebral tissues to metabolic insults in vitro and in vivo.
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155
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Feeney J, Birdsall B, Roberts GC, Burgen AS. Use of transferred nuclear Overhauser effect measurements to compare binding of coenzyme analogues to dihydrofolate reductase. Biochemistry 1983; 22:628-33. [PMID: 6220734 DOI: 10.1021/bi00272a016] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Transferred nuclear Overhauser effect measurements have been made on complexes of NADP+ and thioNADP+ with Lactobacillus casei dihydrofolate reductase to provide information about the glycosidic bond conformations in these complexes. Both NADP+ and thioNADP+ are shown to have very similar anti conformations about their adenine glycosidic bonds when bound to the enzyme. However, their nicotinamide glycosidic bond conformations are very different: while NADP+ binds in an exclusively anti conformation, thioNADP+ binds with a distribution of syn/anti conformations very similar to that observed in nicotinamide mononucleotides in free solution (approximately 50:50). Thus for thioNADP+, binding to the enzyme does not significantly perturb the potential function for rotation about the nicotinamide glycosidic bond. Earlier NMR studies [Hyde, E. I., Birdsall, B., Roberts, G. C. K., Feeney, J., & Burgen, A. S. V. (1980) Biochemistry 19, 3738] had indicated that large downfield 1H shifts of the nicotinamide ring protons (0.61-1.36 ppm) are detected on binding NADP+ while only very small shifts (less than 0.1 ppm) are observed in complexes with thioNADP+. The chemical shift and conformational findings are best explained if the thionicotinamide ring extends into solution making essentially no contacts with the enzyme.
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156
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Mansour TE, Morris PG, Feeney J, Roberts GC. A 31P-nmr study of the intact liver fluke Fasciola hepatica. BIOCHIMICA ET BIOPHYSICA ACTA 1982; 721:336-40. [PMID: 7159598 DOI: 10.1016/0167-4889(82)90087-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
31P-NMR techniques offer a useful method of studying changes in the metabolism of intact parasitic worms. The liver flukes, Fasciola hepatica, provide good quality 31P high resolution NMR spectra for at least 6 h under anaerobic conditions. The levels of ATP remain constant throughout this period. There is no signal for phosphocreatine or phosphoarginine. In contrast to the findings in mammalian tissues, there is a distinct peak for the terminal phosphate of ADP. A number of signals are observed in the phosphodiester region of the spectrum the largest of which is identified as L-alpha-glycerophosphoryl choline. Serotonin (5-hydroxytryptamine) causes an appreciable increase in the levels of sugar phosphates when the flukes are incubated in the absence of glucose. The addition of glucose also causes a marked increase in the signals for the hexose phosphate.
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157
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Birdsall B, Gronenborn A, Hyde EI, Clore GM, Roberts GC, Feeney J, Burgen AS. Hydrogen-1, carbon-13, and phosphorus-31 nuclear magnetic resonance studies of the dihydrofolate reductase-nicotinamide adenine dinucleotide phosphate-folate complex: characterization of three coexisting conformational states. Biochemistry 1982; 21:5831-8. [PMID: 6817782 DOI: 10.1021/bi00266a017] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The Lactobacillus casei dihydrofolate reductase-folate-NADP+ complex is shown by 1H and 13C NMR to exist in three interconverting conformational states, I, IIa, and IIb. The proportions of the three states, as estimated from the intensities of the three separate 13C resonances observed in the complex containing [3-carboxamido-13C]NADP+, are pH dependent. State I predominates at low pH and states IIa and IIb predominate at high pH; the ratio IIa:IIb is pH independent. The pH dependence of the interconversion of states I and IIa + IIb can be explained by a model in which a group on the enzyme has a pK of less than 5 in state IIa + IIb and greater than 7 in state I. 1H, 13C, and 31P NMR has been used to characterize the structural differences between the three states of the complex. As judged by the 1H and 13C chemical shifts of the bound coenzyme, states I and IIa are similar to one another but quite different from state IIb. This difference appears to be a localized one, since only the nicotinamide 2 and 4 protons, nicotinamide 3-carboxamide 13C, and pteridine 7 proton show differences in chemical shift between these states. These differences are, however, large--up to 1.4 ppm for 1H and 2 ppm for 13C. The remaining coenzyme protons, as well as the three 31P nuclei, are unaffected. Studies of the C2 proton resonances of the seven histidine residues show that the ionizable group responsible for the interconversion of states I and IIa + IIb is not a histidine (although two histidines show slight differences in environment between states IIa and IIb); the possible identity of this ionizable group and the nature of the conformational differences between the states are discussed.
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158
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Weinstein HJ, Griffin TW, Feeney J, Cohen HJ, Propper RD, Sallan SE. Pharmacokinetics of continuous intravenous and subcutaneous infusions of cytosine arabinoside. Blood 1982; 59:1351-3. [PMID: 7082832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The pharmacokinetics of continuous subcutaneous cytosine arabinoside (ara-C) infusions were compared with continuous intravenous infusions. Steady-state serum ara-C levels and myelosuppression were similar with both routes of administration. CSF/serum ara-C ratios ranged from 0.14 to 0.91 (mean, 0.58). Continuous subcutaneous ara-C infusions were a convenient and reliable alternative to intravenous infusions.
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159
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Birdsall B, Burgen AS, Hyde EI, Roberts GC, Feeney J. Negative cooperativity between folinic acid and coenzyme in their binding to Lactobacillus casei dihydrofolate reductase. Biochemistry 1981; 20:7186-95. [PMID: 6797469 DOI: 10.1021/bi00528a021] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The binding of folinic acid (5-formyl-5,6,7,8-tetrahydrofolate) to Lactobacillus casei dihydrofolate reductase has been measured. The natural 6S, alpha S diastereoisomer has a binding constant of 1.3 (+/- 0.6) X 10(8) M-1 at pH 6.0, 25 degrees C; the 6R, alpha S diastereoisomer binds approximately 10(4)-fold more weakly. The natural diastereoisomer of folinic acid binds negatively cooperatively with the coenzymes NADP+ and NADPH, binding 3 times more weakly in the presence of NADP+ and 600 times more weakly in the presence of NADPH than to the enzyme alone. Negative cooperativity has been unequivocally distinguished from competition by measurements of coenzyme binding as a function of folinic acid concentration, of the effects of folinic acid on the 1H and 31P chemical shifts of the bound coenzyme, and of the effects of folinic acid on the coenzyme dissociation rate constant. The latter experiments also give evidence for the coexistence of two slowly interconverting conformational forms of the ternary enzyme-coenzyme-folinic acid complex. Small changes in structure of the oxidized coenzymes have substantial effects on the cooperativity with folinic acid, with the thionicotinamide analogue showing positive rather than negative cooperativity. The changes in environment of the bound coenzyme produced by folinic acid, as revealed by 1H and 31P NMR, demonstrate clearly that the negative cooperativity shown by NADP+ and NADPH, respectively, arises by two structurally distinct mechanisms.
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160
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Feeney J, Bordsall B, Albrnad J, Roberts GC, Burgen A, Charlton P, Young D. Corrections - Hydrogen-1 Nuclear Resonance Study of the Complexes of Two Diastereoisomers of Folinic Acid with Dihydrofolate Reductase. Biochemistry 1981. [DOI: 10.1021/bi00528a601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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161
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Feeney J. A promising start. Trends Analyt Chem 1981. [DOI: 10.1016/0165-9936(91)80014-j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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162
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Birdsall B, Gronenborn A, Clore GM, Roberts GC, Feeney J, Burgen AS. 13C NMR evidence for three slowly interconverting conformations of the dihydrofolate reductase-NADP+-folate complex. Biochem Biophys Res Commun 1981; 101:1139-44. [PMID: 6796080 DOI: 10.1016/0006-291x(81)91566-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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163
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Roberts GC, Feeney J, Burgen AS, Daluge S. The charge state of trimethoprim bound to Lactobacillus casei dihydrofolate reductase. FEBS Lett 1981; 131:85-8. [PMID: 6793401 DOI: 10.1016/0014-5793(81)80893-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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164
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Gronenborn A, Birdsall B, Hyde E, Roberts G, Feeney J, Burgen A. 1H and 31P NMR characterization of two conformations of the trimethoprim-NADP+-dihydrofolate reductase complex. Mol Pharmacol 1981; 20:145-53. [PMID: 6793843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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165
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Feeney J, Birdsall B, Albrand JP, Roberts GC, Burgen AS, Charlton PA, Young DW. Hydrogen-1 nuclear magnetic resonance study of the complexes of two diastereoisomers of folinic acid with dihydrofolate reductase. Biochemistry 1981; 20:1837-42. [PMID: 6784760 DOI: 10.1021/bi00510a019] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The 1H chemical shifts for the formyl and benzoyl protons of the individual diastereoisomeres of folinic acid bound to dihydrofolate reductase have been measured. For the tightly bound biologically active 6S, alpha S isomer, the "bound" signals were assigned by using transfer of saturation methods. In this case, only one of the two rotameric states of the formyl group in folinic acid (form I) is bound to the enzyme. The H3' and H5' benzoyl protons have identical shifts in the bound state (as do the H2' and H6' protons). This equivalence is attributed to flipping of the benzoyl ring about the N10-C4' and C1'-CO bonds in the bound state. In the case of the biologically inactive 6R, alpha S isomer, both rotameric forms (I and II) bind to the enzyme. The "bound" shifts for the formyl and aromatic protons are different in the complexes with the 6S, alpha S and 6R, alpha S isomers, indicating that the pteridine ring and benzoyl moiety are binding in different environments in their enzyme complexes. The glutamic acid moiety is probably binding at the same site in the two complexes.
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166
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Gronenborn A, Birdsall B, Hyde EI, Roberts GC, Feeney J, Burgen AS. Effects of coenzyme binding on histidine residues of Lactobacillus casei dihydrofolate reductase. Biochemistry 1981; 20:1717-22. [PMID: 6784757 DOI: 10.1021/bi00510a003] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The effects of coenzyme binding on the seven histidine C2 proton resonances of Lactobacillus casei dihydrofolate reductase have been determined. Binary complexes containing NADP+, NADPH, and their hypoxanthine, thionicotinamide, and acetylpyridine analogues, together with ternary complexes containing the inhibitors trimethoprim or methotrexate, have been examined. Four of the histidine residues are affected by coenzyme binding. The largest effect-a marked upfield shift (0.85 ppm) of the C2 proton resonance-is seen for His-64. The hypoxanthine analogue of the coenzyme was found to produce a smaller upfield shift and, in addition, a decrease in the pK of His-64. The effects on this reductase are discussed in the light of the crystal structure [Matthews, D. A., Alden, R. A., Bolin, J. T., Filman, D. J., Freer, S. T., Hamlin, R., Hol, W. G. J., Kisliuk, R. L., Pastore, E. J., Plante, L. T., Xuong, N., & Kraut, J. (1978) J. Biol. Chem. 253, 6946], and it is concluded that His-64 is close to a carboxyl group in the free enzyme and that the hypoxanthine ring binds in a somewhat different orientation to the adenine ring. The effects on histidine resonances A, E, and G are significantly different for oxidized and reduced coenzymes. The changes in pK of the histidines giving rise to resonances A and E (probably His-22 and His-18) are discussed in terms of ligand-induced conformational changes, which differ for NADP+ and NADPH.
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167
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Gronenborn A, Birdsall B, Hyde EI, Roberts GCK, Feeney J, Burgen ASV. Direct observation by NMR of two coexisting conformations of an enzyme–ligand complex in solution. Nature 1981. [DOI: 10.1038/290273a0] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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168
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Roth K, Kimber B, Feeney J. Data shift accumulation and alternate delay accumulation techniques for overcoming the dynamic range problem. ACTA ACUST UNITED AC 1980. [DOI: 10.1016/0022-2364(80)90077-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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169
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Birdsall B, Feeney J, Roberts GC, Burgen AS. The use of saturation transfer NMR experiments to monitor the conformational selection accompanying ligand-protein interactions. FEBS Lett 1980; 120:107-9. [PMID: 6777193 DOI: 10.1016/0014-5793(80)81057-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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170
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Birdsall B, Gronenborn A, Hyde EI, Roberts GC, Feeney J, Burgen AS. Demonstration and characterization of two co-existing conformations of an enzyme complex by n.m.r. Biochem Soc Trans 1980; 8:637. [PMID: 7450269 DOI: 10.1042/bst0080637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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171
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Hyde EI, Birdsall B, Roberts GC, Feeney J, Burgen AS. Proton nuclear magnetic resonance saturation transfer studies of coenzyme binding to Lactobacillus casei dihydrofolate reductase. Biochemistry 1980; 19:3738-46. [PMID: 6773550 DOI: 10.1021/bi00557a015] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The chemical shifts of all the aromatic proton and anomeric proton resonances of NADP+, NADPH, and several structural analogues have been determined in their complexes with Lactobacillus casei dihydrofolate reductase by double-resonance (saturation transfer) experiments. The binding of NADP+ to the enzyme leads to large (0.9-1.6 ppm) downfield shifts of all the nicotinamide proton resonances and somewhat smaller upfield shifts of the adenine proton resonance. The latter signals show very similar chemical shifts in the binary and ternary complexes of NADP+ and the binary complexes of several other coenzymes, suggesting that the environment of the adenine ring is similar in all cases. In contrast, the nicotinamide proton resonances show much greater variability in position from one complex to another. The data show that the environments of the nicotinamide rings of NADP+, NADPH, and the thionicotinamide and acetylpyridine analogues of NADP+ in their binary complexes with the enzyme are quite markedly different from one another. Addition of folate or methotrexate to the binary complex has only modest effects on the nicotinamide ring of NADP+, but trimethoprim produces a substantial change in its environment. The dissociation rate constant of NADP+ from a number of complexes was also determined by saturation transfer.
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Hyde EI, Birdsall B, Roberts GC, Feeney J, Burgen AS. Phosphorus-31 nuclear magnetic resonance studies of the binding of oxidized coenzymes to Lactobacillus casei dihydrofolate reductase. Biochemistry 1980; 19:3746-54. [PMID: 6773551 DOI: 10.1021/bi00557a016] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The 31P NMR spectra of NADP+ and a number of its structural analogues have been obtained from their binary and ternary complexes with Lactobacillus casei dihydrofolate reductase. The 2'-phosphate resonance is shifted downfield 2.7-2.9 ppm in all cases. Line-shape analysis of this resonance as a function of coenzyme concentration gave values for the dissociation rate constant of the coenzyme from many of the complexes. The values obtained are discussed in terms of the kinetic mechanism of coenzyme binding. The chemical shifts of the pyrophosphate resonances vary from one complex to another over a range of 3.8 ppm. The assignment of these signals to the individuals pyrophosphate 31P nuclei and the structural origins of the chemical shift changes are discussed. From these data, and the 1H NMR experiments describedin the preceding paper [Hyde, E. I., Birdsall, B., Roberts, G. C. K., Feeney, J., & Burgen, A. S. V. (1980) Biochemistry (third paper of four in this issue)], it is concluded that the "nicotinamide" end of the thionicotinamide and acetylpyridine coenzyme analogue binds to the enzyme quite differently from that of the natural coenzyme NADP+.
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173
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Cayley P, Feeney J, Kimber B. 31P n.m.r. studies of complexes of NADPH and NADP+ with Escherichia coli dihydrofolate reductase. Int J Biol Macromol 1980. [DOI: 10.1016/0141-8130(80)90084-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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174
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Roberts GC, Feeney J, Birdsall B, Charlton P, Young D. Methotrexate binding to dihydrofolate reductase. Nature 1980; 286:309. [PMID: 7402318 DOI: 10.1038/286309a0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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175
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Wyeth P, Gronenborn A, Birdsall B, Roberts GC, Feeney J, Burgen AS. Histidine residues of Lactobacillus casei dihydrofolate reductase: paramagnetic relaxation and deuterium-exchange studies and partial assignments. Biochemistry 1980; 19:2608-15. [PMID: 6772202 DOI: 10.1021/bi00553a012] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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176
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Feeney J, Roberts GC, Kaptein R, Birdsall B, Gronenborn A, Burgen AS. Photo-CIDNP studies of the influence of ligand binding on the surface accessibility of aromatic residues in dihydrofolate reductase. Biochemistry 1980; 19:2466-72. [PMID: 6770894 DOI: 10.1021/bi00552a026] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The surface accessibility of the histidine, tyrosine, and tryptophan residues of Lactobacillus casei dihydrofolate reductase has been determined from 360-MHz 1H photochemically induced dynamic nuclear polarization (photo-CIDNP) NMR experiments. In the absence of ligands, four (or perhaps five) of the seven histidine residues and at least one of the four tryptophan residues are accessible to a flavin dye molecule. One of the five tyrosine residues is also slightly accessible. Of the accessible histidine residues, one becomes inaccessible on the binding of NADP+ and one on the binding of p-aminobenzoyl glutamate. These have been assigned to residues which interact directly with these two ligands. One histidine residue (probably His-22) shows an increase in accessibility on addition of folate or methotrexate to the enzyme . NADP+ complex. In addition, the binding of several ligands, notably trimethoprim, leads to an increase in the accessibility of a tryptophan residue. This is clear evidence for ligand-induced conformational changes in dihydrofolate reductase and allows us to identify some of the residues involved.
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177
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Feeney J, Roberts GC, Thomson JW, King RW, Griffiths DV, Burgen AS. Proton nuclear magnetic resonance studies of the effects of ligand binding on tryptophan residues of selectively deuterated dihydrofolate reductase from Lactobacillus casei. Biochemistry 1980; 19:2316-21. [PMID: 6770892 DOI: 10.1021/bi00552a006] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We have prepared a selectively deuterated dihydrofolate reductase in which all the aromatic protons except the C(2) protons of tryptophan have been replaced by deuterium and have examined the 1H NMR spectra of its complexes with folate, trimethoprim, methotrexate, NADP+, and NADPH. One of the four Trp C(2)-proton resonance signals (signal P at 3.66 ppm from dioxane) has been assigned to Trp-21 by examining the NMR spectrum of a selectively deuterated N-bromosuccinimide-modified dihydrofolate reductase. This signal is not perturbed by NADPH, indicating that the coenzyme is not binding close to the 2 position of Trp-21. This contrasts markedly with the 19F shift (2.7 ppm) observed for the 19F signal of Trp-21 in the NADPH complex with the 6-fluorotryptophan-labeled enzyme. In fact the crystal structure of the enzyme . methotrexate . NADPH shows that the carboxamide group of the reduced nicotinamide ring is near to the 6 position of Trp-21 but remote from its 2 position. The nonadditivity of the 1H chemical-shift contributions for signals tentatively assigned to Trp-5 and -133 indicates that these residues are influenced by ligand-induced conformational changes.
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178
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Cayley PJ, Albrand JP, Feeney J, Roberts GC, Piper EA, Burgen AS. Nuclear magnetic resonance studies of the binding of trimethoprim to dihydrofolate reductase. Biochemistry 1979; 18:3886-95. [PMID: 114205 DOI: 10.1021/bi00585a008] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The resonances of the aromatic protons of trimethoprim [2,4-diamino-5-(3',4',5'-trimethoxybenzyl)pyrimidine] in its complexes with dihydrofolate reductases from Lactobacillus casei and Escherichia coli cannot be directly observed. Their chemical shifts have been determined by transfer of saturation experiments and by difference spectroscopy using [2',6'-2H2]trimethoprim. The complex of 2,4-diamino-5-(3',4'-dimethoxy-5'-bromobenzyl)pyrimidine with the L. casei enzyme has also been examined. At room temperature, the 2',6'-proton resonance of bound trimethoprim is very broad (line width great than 30 Hz); with the E. coli enzyme, the resonance sharpens with increasing temperature so as to be clearly visible by difference spectroscopy at 45 degrees C. This line broadening is attributed to an exchange contribution, arising from the slow rate of "flipping" about the C7-C1' bond of bound trimethoprim. The transfer of saturation measurements were also used to determine the dissociation rate constants of the complexes. In the course of these experiments, a decrease in intensity of the resonance of the 2',6'-proton resonance of free trimethoprim on irradiation at the resonance of the 6 proton of free trimethoprim was observed, which only occurred in the presence of the enzyme. This is interpreted as a nuclear Overhauser effect between two protons of the bound ligand transferred to those of the free ligand by the exchange of the ligand between the two states. The chemical shift changes observed on the binding of trimethoprim to dihydrofolate reductase are interpreted in terms of the ring-current shift contributions from the two aromatic rings of trimethoprim and from that of phenylalanine-30. On the basis of this analysis of the chemical shifts, a model for the structure of the enzyme-trimethoprim complex is proposed. This model is consistent with the (indirect) observation of a nuclear Overhauser effect between the 2',6' and 6 protons of bound trimethoprim.
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179
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Albrand J, Birdsall B, Feeney J, Roberts G, Burgen A. The use of transferred nuclear Overhauser effects in the study of the conformations of small molecules bound to proteins. Int J Biol Macromol 1979. [DOI: 10.1016/0141-8130(79)90008-4] [Citation(s) in RCA: 90] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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180
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Degelaen J, Feeney J, Roberts GC, Burgen AS, Frère JM, Ghuysen JM. NMR evidence for the structure of the complex between penicillin and the DD-carboxypeptidase of Streptomyces R61. FEBS Lett 1979; 98:53-6. [PMID: 428542 DOI: 10.1016/0014-5793(79)80150-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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181
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Kimber BJ, Feeney J, Roberts GC, Birdsall B, Griffiths DV, Burgen AS, Sykes BD. Proximity of two tryptophan residues in dihydrofolate reductase determined by 19f NMR. Nature 1978; 271:184-5. [PMID: 622158 DOI: 10.1038/271184a0] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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182
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Birdsall B, Roberts GC, Feeney J, Burgen AS. 31P NMR studies of the binding of adenosine-2'-phosphate to Lactobacillus casei dihydrofolate reductase. FEBS Lett 1977; 80:313-6. [PMID: 19299 DOI: 10.1016/0014-5793(77)80465-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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183
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Kimber BJ, Griffiths DV, Birdsall B, King RW, Scudder P, Feeney J, Roberts GC, Burgen AS. 19 Fnuclear magnetic resonance studies of ligand binding to 3-fluorotyrosine-and 6-fluorotryptophan-containing dihydrofolate reductase from Lactobacillus casei. Biochemistry 1977; 16:3492-500. [PMID: 19051 DOI: 10.1021/bi00634a032] [Citation(s) in RCA: 67] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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184
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Birdsall B, Griffiths DV, Roberts GC, Feeney J, Burgen A. 1H nuclear magnetic resonance studies of Lactobacillus casei dihydrofolate reductase: effects of substrate and inhibitor binding on the histidine residues. PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON. SERIES B, BIOLOGICAL SCIENCES 1977; 196:251-65. [PMID: 16268 DOI: 10.1098/rspb.1977.0040] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The effects of the binding of substrates and inhibitors (folate, dihydrofolate, folinic acid, trimethoprim, methotrexate and aminopterin) to
Lactobacillus casei
dihydrofolate reductase on the histidine residues of the enzyme have been studied by
1
H n. m. r. spectroscopy. The more weakly binding (rapidly exchanging) inhibitors 2, 4-diaminopyrimidine and
p
-aminobenzoyl-l-glutamate, which can be regarded as ‘fragments’ of methotrexate, have also been studied as an aid in interpreting the effects of the strongly-binding ligands.
p
-Aminobenzoyl-l-glutamate binds to two sites on the enzyme; binding to the stronger site is competitive with methotrexate, and affects three histidine residues, denoted H
A
, H
E
and H
F
. The second site is 30-fold weaker, is not competitive with methotrexate, and affects a single histidine residue (either H
B
or H
C
). The binding to the first site is 25-fold stronger in the presence of 2, 4-diaminopyrimidine, while binding to the second site is unaffected. Folate, dihydrofolate and folinic acid have identical effects on the histidine residues; the p
K
of H
E
is increased from 6.54 to 6.75, and that of H
F
from 6.54 to
ca
. 7.2, while the C2-H resonance of H
A
is shifted downfield. Methotrexate and aminopterin affect the same three histidine residues as does folate; for H
A
and H
F
the effects are the same as those produced by folate, while the p
K
of H
E
is decreased from 6.54 to 6.2. Trimethoprim and 2,4-diaminopyrimidine have effects very similar to those of methotrexate, with the exception that histidine H
F
is not affected by these compounds (which lack the
p
-amino-benzoyl-l-glutamate moiety).
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185
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Feeney J, Roberts GC, Birdsall B, Griffiths DV, King RW, Scudder P, Burgen A. 1H nuclear magnetic resonance studies of the tyrosine residues of selectively deuterated Lactobacillus casei dihydrofolate reductase. PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON. SERIES B, BIOLOGICAL SCIENCES 1977; 196:267-90. [PMID: 16269 DOI: 10.1098/rspb.1977.0041] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A selectively deuterated dihydrofolate reductase, in which all the aromatic protons except the 2, 6-protons of the tyrosine residues have been replaced by deuterium, has been prepared from
Lactobacillus casei
grown on a mixture of normal and deuterated amino acids. The aromatic region of the
1
H n. m. r. spectrum of this enzyme contains only resonances from the five tyrosine residues. For each tyrosine, the 2- and 6-protons have the same chemical shift, indicating rapid interconversion of the two conformers related by 180° rotation about the C
β
-C
γ
bond. The effects of substrate, inhibitor and coenzyme binding on the tyrosine residues have been investigated; four of the five residues are affected by ligand binding. Using the weakly binding ligands 2, 4-diaminopyrimidine and
p
-nitrobenzoyl-l-glutamate to connect the spectra of the free enzyme with those of the complexes, it is possible to give a detailed description of the effects of ligand binding on individual residues. In the binary complexes, methotrexate affects three tyrosine residues, only one of which is affected by folate, indicating a significant difference in the mode of binding of substrates and inhibitors. The co-enzymes NADP
+
and NADPH lead to broadly similar changes in the spectrum, except for one resonance which is shifted in opposite directions by the two co-enzymes. The oxidized and reduced coenzymes also differ in their effects on the changes produced by inhibitor binding; the spectrum of the enzyme-NADPH-methotrexate complex is similar to that of the enzyme-methotrexate complex, while that of the enzyme-NADP
+
-methotrexate complex is not. In contrast to the behaviour seen in the binary complexes, the spectrum of the enzyme-NADP
+
-folate complex is very similar to that of enzyme-NADP
+
-methotrexate. Evidence is presented that some, at least, of the changes in chemical shift of the tyrosine residues are due to ligand-induced conformational changes. The binding of
p
-nitrobenzoyl-l-glutamate to the enzyme-2, 4-diamino-pyrimidine complex is found to be tighter than that to the enzyme alone.
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186
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Birdsall B, Burgen AS, Feeney J, Rodriguez de Miranda JF, Roberts GC. Co-operativity in ligand binding to dihydrofolate reductase [proceedings]. Br J Pharmacol 1977; 59:521P. [PMID: 843754 PMCID: PMC1667929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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187
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Birdsall B, Burgen AS, Feeney J, Roberts GC. 31P and 1H n.m.r. studies of coenzyme binding to dihydrofolate reductase [proceedings]. Br J Pharmacol 1977; 59:520P. [PMID: 843753 PMCID: PMC1667930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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188
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Murray CP, Feeney J. A comparison of hexamine hippurate and sulphamethizolein patients with indwelling catheters following pelvic-floor surgery. IRISH MEDICAL JOURNAL 1977; 69:97-8. [PMID: 852964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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189
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Griffiths DV, Feeney J, Roberts GC, Burgen AS. Preparation of selectively deuterated aromatic amino acids for use in 1H NMR studies of proteins. BIOCHIMICA ET BIOPHYSICA ACTA 1976; 446:479-85. [PMID: 990287 DOI: 10.1016/0005-2795(76)90014-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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190
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191
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Feeney J. Nuclear magnetic resonance. Nature 1976. [DOI: 10.1038/261727c0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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192
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Feeney J. Improved component vicinal coupling constants for calculating side-chain conformations in amino acids. ACTA ACUST UNITED AC 1976. [DOI: 10.1016/0022-2364(76)90052-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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193
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Feeney J, Birdsall B, Roberts GC, Burgen AS. 31P NMR studies of NADPH and NADP+ binding to L. casei dihydrofolate reductase. Nature 1975; 257:564-6. [PMID: 241022 DOI: 10.1038/257564a0] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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194
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Batchelor J, Feeney J, Roberts G. Carbon-13 NMR protonation shifts of amines, carboxylic acids and amino acids. ACTA ACUST UNITED AC 1975. [DOI: 10.1016/0022-2364(75)90146-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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195
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Way JL, Birdsall B, Feeney J, Roberts GC, Burgen AS. A nuclear magnetic resonance study of nicotinamide adenine dinucleotide phosphate binding to Lactobacillus casei dihydrofolate reductase. Biochemistry 1975; 14:3470-5. [PMID: 238594 DOI: 10.1021/bi00686a028] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The binding of NADP+ to dihydrofolate reductase (EC 1.5.1.3) in the presence and absence of substrate analogs has been studied using 1H and 13C nuclear magnetic resonance (NMR). NADP+ binds strongly to the enzyme alone and in the presence of folate, aminopterin, and methotrexate with a stoichiometry of 1 mol of NADP+/mol of enzyme. In the 13C spectra of the binary and ternary complexes, separate signals were observed for the carboxamide carbon of free and bound [13CO]NADP+ (enriched 90% in 13C). The 13C signal of the NADP+-reductase complex is much broader than that in the ternary complex with methotrexate because of exchange line broadening on the binary complex signal. From the difference in line widths (17.5 +/- 3.0 Hz) an estimate of the dissociation rate constant of the binary complex has been obtained (55 +/- 10 sec-1). The dissociation rate of the NADP+-reductase complex is not the rate-limiting step in the overall reaction. In the various complexes studied large 13C chemical shifts were measured for bound [13CO]NADP+ relative to free NADP+ (upfield shifts of 1.6-4.3 ppm). The most likely origin of the bound shifts lies in the effects on the shieldings of electric fields from nearby charged groups. For the NADP+-reductase-folate system two 13C signals from bound NADP+ are observed indicating the presence of more than one form of the ternary complex. The IH spectra of the binary and ternary complexes confirm both the stoichiometry and the value of the dissociation rate constant obtained from the 13C experiments. Substantial changes in the IH spectrum of the protein were observed in the different complexes and these are distinct from those seen in the presence of NADPH.
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196
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Birdsall B, Birdsall NJ, Feeney J, Thornton J. A nuclear magnetic resonance investigation of the conformation of nicotinamide mononucleotide in aqueous solution. J Am Chem Soc 1975; 97:2845-50. [PMID: 1133337 DOI: 10.1021/ja00843a039] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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197
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198
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Dell A, Williams DH, Morris HR, Smith GA, Feeney J, Roberts GC. Structure revision of the antibiotic echinomycin. J Am Chem Soc 1975; 97:2497-502. [PMID: 1133418 DOI: 10.1021/ja00842a029] [Citation(s) in RCA: 223] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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199
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Brown JP, Feeney J, Burgen AS. A nuclear magnetic resonance study of the interaction between vanomycin and acetyl-D-alanyl-D-alanine in aqueous solution. Mol Pharmacol 1975; 11:119-25. [PMID: 235732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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200
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Brown JP, Terenius L, Feeney J, Burgen AS. A structure-activity study by nuclear magnetic resonance of peptide interactions with vancomycin. Mol Pharmacol 1975; 11:126-32. [PMID: 1124076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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