15N NMR relaxation studies of free and inhibitor-bound 4- oxalocrotonate tautomerase: Backbone dynamics and entropy changes of an enzyme upon inhibitor binding

James Stivers, C. Abeygunawardana, A. S. Mildvan, C. P. Whitman

Research output: Contribution to journalArticle

Abstract

The solution secondary structure of 4-oxalocrotonate tautomerase (4- OT), a 41 kDa homohexamer with 62 residues per subunit, consist of an α- helix, two β-strands, a β-hairpin, two loops, two turns, and a C-terminal coil [Stivers et al. (1996) Protein Sci. 5, 729-741]. The general base, proline-I, as well as the two loops and the β-hairpin have been shown to compromise the active site [Stivers et al. (1996) Biochemistry 35, 814- 823]. The backbone dynamics of both the free enzyme and its complex with a substrate analog have been studied by 1H-detected 15N relaxation rates and NOE determination, at 500 and 600 MHz. Analysis of the data using the model-free formalism showed that the nanosecond to picosecond motion of 53 of the 60 backbone 15N-H vectors was highly restricted with a mean order parameter 2> = 0.87 ± 0.03. The lowest backbone mobility (S2 > 0.90) is found in the β1-strand, loop 2, and turn 2. Greater backbone mobility is found in the active site (0.5 ≤ S2 ≤ 0.83) and at C terminal residues 58- 62 (0.03 ≤ S2 ≤ 0.70). A τ(m) value for the free hexamer of 13.7 ns at 42 °C was determined, consistent with a compact globular molecule of 41 kDa. Saturation of 4-OT with the analog of the dienolic intermediate and linear competitive inhibitor cis,cis-muconate (4) (K(D) = 0.59 mM) increased the backbone S2 of seven residues and decreased the backbone S2 of another eight residues, both at the active site and at the antiparallel β1-β1 interface. The S2 values of the other 44 detectable NH vectors were not altered by the binding of 4. The increases in S2, resulting from the 'freezing' of the backbone NH vectors of seven residues upon the binding of 4, correspond to an unfavorable entropic contribution to ΔG(bmdmg) of 3.2 ± 1.1 kcal/mol. This freezing is partially compensated for by the mobilization of the other eight residues, since the decreases in S2 for these residues correspond to an entropic contribution to binding of -1.9 ± 0.1 kcal/mol. These entropy changes, resulting solely from alterations in high-frequency motion, are significant compared to the overall ΔG(binding) = -4.6 kcal/mol for 4. Other effects of the binding of 4 include (1) changes in 15N and NH chemical shifts localized to the active site and (2) increases in the exchange contributions (R(ex) to I/T2 of backbone 15N resonances at the active site and a the subunit interface, reflecting microsecond to millisecond motions which may play a role in substrate binding (k(on) ≤ 4 x 106 M-1 s-1) and/or catalysis (k(cat) = 103 s- 1).

Original languageEnglish (US)
Pages (from-to)16036-16047
Number of pages12
JournalBiochemistry®
Volume35
Issue number50
DOIs
StatePublished - 1996

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Entropy
Enzyme Inhibitors
Catalytic Domain
Nuclear magnetic resonance
Freezing
Enzymes
Biochemistry
Chemical shift
Substrates
Proline
Catalysis
Molecules
4-oxalocrotonate tautomerase
Proteins

ASJC Scopus subject areas

  • Biochemistry

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15N NMR relaxation studies of free and inhibitor-bound 4- oxalocrotonate tautomerase : Backbone dynamics and entropy changes of an enzyme upon inhibitor binding. / Stivers, James; Abeygunawardana, C.; Mildvan, A. S.; Whitman, C. P.

In: Biochemistry®, Vol. 35, No. 50, 1996, p. 16036-16047.

Research output: Contribution to journalArticle

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abstract = "The solution secondary structure of 4-oxalocrotonate tautomerase (4- OT), a 41 kDa homohexamer with 62 residues per subunit, consist of an α- helix, two β-strands, a β-hairpin, two loops, two turns, and a C-terminal coil [Stivers et al. (1996) Protein Sci. 5, 729-741]. The general base, proline-I, as well as the two loops and the β-hairpin have been shown to compromise the active site [Stivers et al. (1996) Biochemistry 35, 814- 823]. The backbone dynamics of both the free enzyme and its complex with a substrate analog have been studied by 1H-detected 15N relaxation rates and NOE determination, at 500 and 600 MHz. Analysis of the data using the model-free formalism showed that the nanosecond to picosecond motion of 53 of the 60 backbone 15N-H vectors was highly restricted with a mean order parameter 2> = 0.87 ± 0.03. The lowest backbone mobility (S2 > 0.90) is found in the β1-strand, loop 2, and turn 2. Greater backbone mobility is found in the active site (0.5 ≤ S2 ≤ 0.83) and at C terminal residues 58- 62 (0.03 ≤ S2 ≤ 0.70). A τ(m) value for the free hexamer of 13.7 ns at 42 °C was determined, consistent with a compact globular molecule of 41 kDa. Saturation of 4-OT with the analog of the dienolic intermediate and linear competitive inhibitor cis,cis-muconate (4) (K(D) = 0.59 mM) increased the backbone S2 of seven residues and decreased the backbone S2 of another eight residues, both at the active site and at the antiparallel β1-β1 interface. The S2 values of the other 44 detectable NH vectors were not altered by the binding of 4. The increases in S2, resulting from the 'freezing' of the backbone NH vectors of seven residues upon the binding of 4, correspond to an unfavorable entropic contribution to ΔG(bmdmg) of 3.2 ± 1.1 kcal/mol. This freezing is partially compensated for by the mobilization of the other eight residues, since the decreases in S2 for these residues correspond to an entropic contribution to binding of -1.9 ± 0.1 kcal/mol. These entropy changes, resulting solely from alterations in high-frequency motion, are significant compared to the overall ΔG(binding) = -4.6 kcal/mol for 4. Other effects of the binding of 4 include (1) changes in 15N and NH chemical shifts localized to the active site and (2) increases in the exchange contributions (R(ex) to I/T2 of backbone 15N resonances at the active site and a the subunit interface, reflecting microsecond to millisecond motions which may play a role in substrate binding (k(on) ≤ 4 x 106 M-1 s-1) and/or catalysis (k(cat) = 103 s- 1).",
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T1 - 15N NMR relaxation studies of free and inhibitor-bound 4- oxalocrotonate tautomerase

T2 - Backbone dynamics and entropy changes of an enzyme upon inhibitor binding

AU - Stivers, James

AU - Abeygunawardana, C.

AU - Mildvan, A. S.

AU - Whitman, C. P.

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N2 - The solution secondary structure of 4-oxalocrotonate tautomerase (4- OT), a 41 kDa homohexamer with 62 residues per subunit, consist of an α- helix, two β-strands, a β-hairpin, two loops, two turns, and a C-terminal coil [Stivers et al. (1996) Protein Sci. 5, 729-741]. The general base, proline-I, as well as the two loops and the β-hairpin have been shown to compromise the active site [Stivers et al. (1996) Biochemistry 35, 814- 823]. The backbone dynamics of both the free enzyme and its complex with a substrate analog have been studied by 1H-detected 15N relaxation rates and NOE determination, at 500 and 600 MHz. Analysis of the data using the model-free formalism showed that the nanosecond to picosecond motion of 53 of the 60 backbone 15N-H vectors was highly restricted with a mean order parameter 2> = 0.87 ± 0.03. The lowest backbone mobility (S2 > 0.90) is found in the β1-strand, loop 2, and turn 2. Greater backbone mobility is found in the active site (0.5 ≤ S2 ≤ 0.83) and at C terminal residues 58- 62 (0.03 ≤ S2 ≤ 0.70). A τ(m) value for the free hexamer of 13.7 ns at 42 °C was determined, consistent with a compact globular molecule of 41 kDa. Saturation of 4-OT with the analog of the dienolic intermediate and linear competitive inhibitor cis,cis-muconate (4) (K(D) = 0.59 mM) increased the backbone S2 of seven residues and decreased the backbone S2 of another eight residues, both at the active site and at the antiparallel β1-β1 interface. The S2 values of the other 44 detectable NH vectors were not altered by the binding of 4. The increases in S2, resulting from the 'freezing' of the backbone NH vectors of seven residues upon the binding of 4, correspond to an unfavorable entropic contribution to ΔG(bmdmg) of 3.2 ± 1.1 kcal/mol. This freezing is partially compensated for by the mobilization of the other eight residues, since the decreases in S2 for these residues correspond to an entropic contribution to binding of -1.9 ± 0.1 kcal/mol. These entropy changes, resulting solely from alterations in high-frequency motion, are significant compared to the overall ΔG(binding) = -4.6 kcal/mol for 4. Other effects of the binding of 4 include (1) changes in 15N and NH chemical shifts localized to the active site and (2) increases in the exchange contributions (R(ex) to I/T2 of backbone 15N resonances at the active site and a the subunit interface, reflecting microsecond to millisecond motions which may play a role in substrate binding (k(on) ≤ 4 x 106 M-1 s-1) and/or catalysis (k(cat) = 103 s- 1).

AB - The solution secondary structure of 4-oxalocrotonate tautomerase (4- OT), a 41 kDa homohexamer with 62 residues per subunit, consist of an α- helix, two β-strands, a β-hairpin, two loops, two turns, and a C-terminal coil [Stivers et al. (1996) Protein Sci. 5, 729-741]. The general base, proline-I, as well as the two loops and the β-hairpin have been shown to compromise the active site [Stivers et al. (1996) Biochemistry 35, 814- 823]. The backbone dynamics of both the free enzyme and its complex with a substrate analog have been studied by 1H-detected 15N relaxation rates and NOE determination, at 500 and 600 MHz. Analysis of the data using the model-free formalism showed that the nanosecond to picosecond motion of 53 of the 60 backbone 15N-H vectors was highly restricted with a mean order parameter 2> = 0.87 ± 0.03. The lowest backbone mobility (S2 > 0.90) is found in the β1-strand, loop 2, and turn 2. Greater backbone mobility is found in the active site (0.5 ≤ S2 ≤ 0.83) and at C terminal residues 58- 62 (0.03 ≤ S2 ≤ 0.70). A τ(m) value for the free hexamer of 13.7 ns at 42 °C was determined, consistent with a compact globular molecule of 41 kDa. Saturation of 4-OT with the analog of the dienolic intermediate and linear competitive inhibitor cis,cis-muconate (4) (K(D) = 0.59 mM) increased the backbone S2 of seven residues and decreased the backbone S2 of another eight residues, both at the active site and at the antiparallel β1-β1 interface. The S2 values of the other 44 detectable NH vectors were not altered by the binding of 4. The increases in S2, resulting from the 'freezing' of the backbone NH vectors of seven residues upon the binding of 4, correspond to an unfavorable entropic contribution to ΔG(bmdmg) of 3.2 ± 1.1 kcal/mol. This freezing is partially compensated for by the mobilization of the other eight residues, since the decreases in S2 for these residues correspond to an entropic contribution to binding of -1.9 ± 0.1 kcal/mol. These entropy changes, resulting solely from alterations in high-frequency motion, are significant compared to the overall ΔG(binding) = -4.6 kcal/mol for 4. Other effects of the binding of 4 include (1) changes in 15N and NH chemical shifts localized to the active site and (2) increases in the exchange contributions (R(ex) to I/T2 of backbone 15N resonances at the active site and a the subunit interface, reflecting microsecond to millisecond motions which may play a role in substrate binding (k(on) ≤ 4 x 106 M-1 s-1) and/or catalysis (k(cat) = 103 s- 1).

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