Thermodynamic and Activation Parameters for Binding of a Pyrene-Labeled Substrate by the Tetrahymena Ribozyme: Docking Is Not Diffusion-Controlled and Is Driven by a Favorable Entropy Change

Yi Li, Philip C. Bevilacqua, David Mathews, Douglas H. Turner

Research output: Contribution to journalArticle

51 Citations (Scopus)

Abstract

Association and dissociation rates for the pyrene-(pyr)-labeled oligoribonucleotide substrate pyrCUCU binding to the L-21 Seal group I ribozyme are reported as a function of temperature. Combined with thermodynamic parameters for binding of pyrCUCU to rGGAGAA, the results allow calculation of the activation and thermodynamic parameters for docking of pyrCUCU into the catalytic core of the ribozyme. The activation enthalpy for docking is 22 keal/mol, much larger than the ~4 keal/mol expected for a diffusion-controlled process. Thus, docking is not diffusion-controlled. The activation and equilibrium entropies for docking are favorable at 21 and 37 eu, respectively. The results suggest the rate-limiting step and the driving force for docking may involve desolvation of RNA functional groups or of Mg2+ ions.

Original languageEnglish (US)
Pages (from-to)14394-14399
Number of pages6
JournalBiochemistry
Volume34
Issue number44
DOIs
StatePublished - Jan 1 1995

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Tetrahymena
Catalytic RNA
Entropy
Thermodynamics
Chemical activation
Oligoribonucleotides
Substrates
Catalytic Domain
RNA
Ions
Temperature
Functional groups
Seals
Enthalpy
pyrene
GIR1 ribozyme

All Science Journal Classification (ASJC) codes

  • Biochemistry

Cite this

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title = "Thermodynamic and Activation Parameters for Binding of a Pyrene-Labeled Substrate by the Tetrahymena Ribozyme: Docking Is Not Diffusion-Controlled and Is Driven by a Favorable Entropy Change",
abstract = "Association and dissociation rates for the pyrene-(pyr)-labeled oligoribonucleotide substrate pyrCUCU binding to the L-21 Seal group I ribozyme are reported as a function of temperature. Combined with thermodynamic parameters for binding of pyrCUCU to rGGAGAA, the results allow calculation of the activation and thermodynamic parameters for docking of pyrCUCU into the catalytic core of the ribozyme. The activation enthalpy for docking is 22 keal/mol, much larger than the ~4 keal/mol expected for a diffusion-controlled process. Thus, docking is not diffusion-controlled. The activation and equilibrium entropies for docking are favorable at 21 and 37 eu, respectively. The results suggest the rate-limiting step and the driving force for docking may involve desolvation of RNA functional groups or of Mg2+ ions.",
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T1 - Thermodynamic and Activation Parameters for Binding of a Pyrene-Labeled Substrate by the Tetrahymena Ribozyme

T2 - Docking Is Not Diffusion-Controlled and Is Driven by a Favorable Entropy Change

AU - Li, Yi

AU - Bevilacqua, Philip C.

AU - Mathews, David

AU - Turner, Douglas H.

PY - 1995/1/1

Y1 - 1995/1/1

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AB - Association and dissociation rates for the pyrene-(pyr)-labeled oligoribonucleotide substrate pyrCUCU binding to the L-21 Seal group I ribozyme are reported as a function of temperature. Combined with thermodynamic parameters for binding of pyrCUCU to rGGAGAA, the results allow calculation of the activation and thermodynamic parameters for docking of pyrCUCU into the catalytic core of the ribozyme. The activation enthalpy for docking is 22 keal/mol, much larger than the ~4 keal/mol expected for a diffusion-controlled process. Thus, docking is not diffusion-controlled. The activation and equilibrium entropies for docking are favorable at 21 and 37 eu, respectively. The results suggest the rate-limiting step and the driving force for docking may involve desolvation of RNA functional groups or of Mg2+ ions.

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