A Large Solvent Isotope Effect on Protein Association Thermodynamics

Eginton, Christopher; Beckett, Dorothy

doi:10.1021/bi400952m

Cited by 12 publications

(12 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…First, measurements of wtBirA dimerization performed in H 2 O and D 2 O over a range of temperatures indicate that solvent release is the major thermodynamic driving force for dimer formation. 32 The large unfavorable dimerization enthalpy reflects the penalty associated with the removal of solvent from the protein surface, and the correspondingly large favorable entropy, −TΔS°, arises from the release of this solvent to the bulk. Second, consistent with solvent release also serving as the major driving force for BirA variant dimerization, the solvent isotope effect measured at 20 °C is identical for wtBirA and variants regardless of the location of the alanine substitution.…”

Section: ■ Discussionmentioning

confidence: 99%

Heat Capacity Changes and Disorder-to-Order Transitions in Allosteric Activation

Cressman

Beckett

2015

Biochemistry

Self Cite

View full text Add to dashboard Cite

Allosteric coupling in proteins is ubiquitous but incompletely understood, particularly in systems characterized by coupling over large distances. Binding of the allosteric effector, bio-5'-AMP, to the Escherichia coli biotin protein ligase, BirA, enhances the protein's dimerization free energy by -4 kcal/mol. Previous studies revealed that disorder-to-order transitions at the effector binding and dimerization sites, which are separated by 33 Å, are integral to functional coupling. Perturbations to the transition at the ligand binding site alter both ligand binding and coupled dimerization. Alanine substitutions in four loops on the dimerization surface yield a range of energetic effects on dimerization. A glycine to alanine substitution at position 142 in one of these loops results in a complete loss of allosteric coupling, disruption of the disorder-to-order transitions at both functional sites, and a decreased affinity for the effector. In this work, allosteric communication between the effector binding and dimerization surfaces in BirA was further investigated by performing isothermal titration calorimetry measurements on nine proteins with alanine substitutions in three dimerization surface loops. In contrast to BirAG142A, at 20 °C all variants bind to bio-5'-AMP with free energies indistinguishable from that measured for wild-type BirA. However, the majority of the variants exhibit altered heat capacity changes for effector binding. Moreover, the ΔCp values correlate with the dimerization free energies of the effector-bound proteins. These thermodynamic results, combined with structural information, indicate that allosteric activation of the BirA monomer involves formation of a network of intramolecular interactions on the dimerization surface in response to bio-5'-AMP binding at the distant effector binding site.

show abstract

Section: ■ Discussionmentioning

confidence: 99%

Heat Capacity Changes and Disorder-to-Order Transitions in Allosteric Activation

Cressman

Beckett

2015

Biochemistry

Self Cite

View full text Add to dashboard Cite

show abstract

“…A more recent study of D 2 O effects in the biotin repressor found water reorganization was important in protein dimerization [42]. In studying binding of DNA to the cAMP repressor protein·cAMP complex, Shi et al found a more positive enthalpy in D 2 O than H 2 O [43].…”

Section: 1 Thermodynamic Solvent Isotope Effectsmentioning

confidence: 99%

Thermodynamics and solvent linkage of macromolecule–ligand interactions

Duff

Howell

2015

Methods

View full text Add to dashboard Cite

Binding involves two steps, desolvation and association. While water is ubiquitous and occurs at high concentration, it is typically ignored. In vitro experiments typically use infinite dilution conditions, while in vivo, the concentration of water is decreased due to the presence of high concentrations of molecules in the cellular milieu. This review discusses isothermal titration calorimetry approaches that address the role of water in binding. For example, use of D2O allows the contribution of solvent reorganization to the enthalpy component to be assessed. Further, the addition of osmolytes will decrease the water activity of a solution and allow effects on Ka to be determined. In most cases, binding becomes tighter in the presence of osmolytes as the desolvation penalty associated with binding is minimized. In other cases, the osmolytes prefer to interact with the ligand or protein, and if their removal is more difficult than shedding water, then binding can be weakened. These complicating layers can be discerned by different slopes in ln(Ka) vs osmolality plots and by differential scanning calorimetry in the presence of the osmolyte.

show abstract

“…Thus, the effect of the H 2 O/D 2 O exchange on the B-A transition is relatively small. Large effects resulting from an H 2 O/D 2 O exchange have been reported in the literature for protein stability, dynamics and association (Cioni and Strambini 2002 ; Sasisanker et al 2004 ; Eginton and Beckett 2013 ). Recent simulations on a RNA hairpin (Pathak and Bandyopadhyay 2017 ) indicate a large effect induced by an H 2 O/D 2 O exchange on its thermal stability.…”

Section: Discussionmentioning

confidence: 87%

Kinetics of the B-A transition of DNA: analysis of potential contributions to a reaction barrier

Pörschke

2018

Eur Biophys J

View full text Add to dashboard Cite

Because of open problems in the relation between results obtained by relaxation experiments and molecular dynamics simulations on the B-A transition of DNA, relaxation measurements of the B-A dynamics have been extended to a wider range of conditions. Field-induced reaction effects are measured selectively by the magic angle technique using a novel cell construction preventing perturbations from cell window anisotropy. The kinetics was recorded for the case of poly[d(AT)] up to the salt concentration limit of 4.4 mM, where aggregation does not yet interfere. Now experimental data on the B-A dynamics are available for poly[d(AT)] at salt concentrations of 0.18, 0.73, 2.44 and 4.4 mM. In all cases, a spectrum of time constants is found, ranging from ~ 10 μs up to components approaching ~ 1 ms. The relatively small dependence of these data on the salt concentration indicates that electrostatic effects on the kinetics are not as strong as may be expected. The ethanol content at the transition center is a linear function of the logarithm of the salt concentration, and the slope is close to that expected from polyelectrolyte theory. The B-A transition dynamics was also measured in D2O at a salt concentration of 2.4 mM: the center of the transition is found at 20.0 mol/l H2O and at 20.1 mol/l D2O with an estimated accuracy of ± 0.1 mol/l; the spectrum of time constants at the respective transition centers is very similar. The experimental results are discussed regarding the data obtained by molecular dynamics simulations.

show abstract

A Large Solvent Isotope Effect on Protein Association Thermodynamics

Cited by 12 publications

References 43 publications

Heat Capacity Changes and Disorder-to-Order Transitions in Allosteric Activation

Heat Capacity Changes and Disorder-to-Order Transitions in Allosteric Activation

Thermodynamics and solvent linkage of macromolecule–ligand interactions

Kinetics of the B-A transition of DNA: analysis of potential contributions to a reaction barrier

Contact Info

Product

Resources

About