The Thermodynamics of Nucleotide Binding to Protein

Beaudette, Norman V.; Langerman, Neal; Biltonen, Rodney L.

doi:10.3109/10409238009105433

Cited by 22 publications

(15 citation statements)

References 49 publications

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“…Our thermodynamic analyses indicate that the initial association of RNA with the NS3 protein is driven by a favorable enthalpy change. Favorable negative enthalpy changes are generally associated with contributions from hydrogen bonds, van der Waal's interactions, or ionic interactions [43]. The importance of electrostatic interactions for the binding of RNA to the NS3 protein was further noted in our fluorescence spectroscopy.…”

Section: Discussionmentioning

confidence: 54%

Energetics of RNA binding by the West Nile virus RNA triphosphatase

et al. 2006

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The West Nile virus (WNV) RNA genome harbors the characteristic methylated cap structure present at the 5 0 end of eukaryotic mRNAs. In the present study, we report a detailed study of the binding energetics and thermodynamic parameters involved in the interaction between RNA and the WNV RNA triphosphatase, an enzyme involved in the synthesis of the RNA cap structure. Fluorescence spectroscopy assays revealed that the initial interaction between RNA and the enzyme is characterized by a high enthalpy of association and that the minimal RNA binding site of NS3 is 13 nucleotides. In order to provide insight into the relationship between the enzyme structure and RNA binding, we also correlated the effect of RNA binding on protein structure using both circular dichroism and denaturation studies as structural indicators. Our data indicate that the protein undergoes structural modifications upon RNA binding, although the interaction does not significantly modify the stability of the protein.

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Section: Discussionmentioning

confidence: 54%

Energetics of RNA binding by the West Nile virus RNA triphosphatase

et al. 2006

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“…3. Interaction parameters calculated in this fashion for a number of glutamate dehydrogenase ternary complexes are listed in Table I. Eftink and Biltonen (6) and Hinz (14) have recently reviewed the thermodynamics of protein-ligand interactions; Beaudette and Langerman have reviewed the more limited field of the thermodynamics of nucleotide binding to proteins (15); while Subramanian has reviewed the specific area that is of primary interest here, the thermodynamics of pyridine nucleotide dehydrogenases and their reactions (16).…”

Section: Thermodynamic Parameters Of the Formation Of T-glutamatementioning

confidence: 99%

A Unifying Model of the Thermodynamics of Formation of Dehydrogenase‐Ligand Complexes

Fisher

1988

Advances in Enzymology - And Related Areas of Molecular Biology

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“…In general, a large favorable entropy change may be due to the release of either ions or water molecules upon complex formation (29). To address the former possibility, the ionic strength dependence of TRAP binding trp leader RNA was investigated.…”

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confidence: 99%

Kinetic and Thermodynamic Analysis of the Interaction between TRAP (trp RNA-binding Attenuation Protein) of Bacillus subtilis and trp Leader RNA

Baumann

Otridge²,

Gollnick

1996

Journal of Biological Chemistry

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In Bacillus subtilis, expression of the tryptophan biosynthetic genes is regulated in response to tryptophan by an RNA-binding protein called TRAP (trp RNA-binding attenuation protein). TRAP has been shown to contain 11 identical subunits arranged in a symmetrical ring. Kinetic and thermodynamic parameters of the interaction between tryptophan-activated TRAP and trp leader RNA were studied. Results from glycerol gradients and mobility shift gels indicate that two TRAP 11-mers bind to each trp leader RNA. A filter binding assay was used to determine an apparent binding constant of 8.0 ؎ 1.3 ؋ 10 9 M ؊1 (K d ‫؍‬ 0.12 ؎ 0.02 nM) for TRAP and an RNA containing residues ؉36 to ؉92 of the trp leader RNA in 1 mM L-tryptophan at 37°C. The temperature dependence of K app was somewhat unexpected demonstrating that the ⌬H of the interaction is highly unfavorable at ؉15.9 kcal mol ؊1. Therefore, the interaction is completely driven by a ⌬S of ؉97 cal mol ؊1 K ؊1 . The interaction between tryptophan-activated TRAP and trp leader RNA displayed broad salt and pH activity profiles. Finally, the rate of RNA dissociation from the RNA⅐TRAP⅐tryptophan ternary complex was found to be very slow in high concentrations of tryptophan (>40 M) but increased in lower tryptophan concentrations. This suggests that dissociation of tryptophan from the ternary complex is the rate-limiting step in RNA dissociation.In Bacillus subtilis, the genes for tryptophan biosynthesis are regulated in response to tryptophan by an RNA-binding protein called TRAP (trp RNA-binding attenuation protein; Refs. 1-3). TRAP regulates expression of the trp genes in three ways, all of which involve TRAP binding RNA in a tryptophandependent manner (3). The trp operon (trpEDCFBA), which contains 6 of the 7 genes required for L-tryptophan biosynthesis, is regulated by transcription attenuation within a 204-nucleotide leader region preceding the first structural gene, trpE (1-2). In the presence of L-tryptophan, TRAP binds the nascent trp leader transcript (4) at a series of 11 G/UAG repeats between residues ϩ36 and ϩ91 ( Fig. 1; Refs. 5-7). This binding prevents formation of an anti-terminator secondary structure which allows a transcription terminator to form and transcription halts in the leader region (1, 8). When L-tryptophan is limiting, TRAP does not bind, the anti-terminator forms, and the operon is expressed.TRAP also regulates translation of two trp genes, trpE (2, 9) and trpG (10), apparently by two different mechanisms. Control of trpE translation is believed to be mediated by TRAP binding to the same series of G/UAG repeats in the leader segment of trp mRNAs that have escaped termination at the attenuator. This binding is thought to alter the RNA secondary structure so as to sequester the trpE ribosome binding site in a stem-loop structure, thus reducing translation initiation (2).trpG is the only tryptophan biosynthetic gene not located within the trp operon and is located within a folic acid biosynthetic operon (11). Regulation of trpG translation occurs wh...

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The Thermodynamics of Nucleotide Binding to Protein

Cited by 22 publications

References 49 publications

Energetics of RNA binding by the West Nile virus RNA triphosphatase

Energetics of RNA binding by the West Nile virus RNA triphosphatase

A Unifying Model of the Thermodynamics of Formation of Dehydrogenase‐Ligand Complexes

Kinetic and Thermodynamic Analysis of the Interaction between TRAP (trp RNA-binding Attenuation Protein) of Bacillus subtilis and trp Leader RNA

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