Change in Volume Upon Inhibitor Binding to Carbonic Anhydrases by Fluorescent Pressure Shift Assay

Skvarnavičius, Gediminas; Matulis, Daumantas; Petrauskas, Vytautas

doi:10.1007/978-3-030-12780-0_7

Cited by 2 publications

(3 citation statements)

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“…The change in volume in textbooks of Thermodynamics is defined as the partial derivative of the Gibbs energy with respect to pressure; thus, the change in volume upon protein–ligand binding at a constant temperature, T , is where p denotes the pressure, and Δ G b is the change in the standard Gibbs energy of binding (the standard state is defined as 1 mol/L concentrations of the participating substances at 1 bar pressure and the activity coefficients are equal to 1). 32 This equation shows that to obtain Δ V b , we first need to determine Δ G b at various pressures. In experiments, usually the dissociation equilibrium constant, K d , is determined, while the change in the Gibbs energy is calculated using the equation Δ G b = RT ln K d .…”

Section: Resultsmentioning

confidence: 99%

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Protein–Ligand Binding Volume Determined from a Single 2D NMR Spectrum with Increasing Pressure

et al. 2021

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Proteins undergo changes in their partial volumes in numerous biological processes such as enzymatic catalysis, unfolding–refolding, and ligand binding. The change in the protein volume upon ligand binding—a parameter termed the protein–ligand binding volume—can be extensively studied by high-pressure NMR spectroscopy. In this study, we developed a method to determine the protein–ligand binding volume from a single two-dimensional (2D) 1 H– 15 N heteronuclear single quantum coherence (HSQC) spectrum at different pressures, if the exchange between ligand-free and ligand-bound states of a protein is slow in the NMR time-scale. This approach required a significantly lower amount of protein and NMR time to determine the protein–ligand binding volume of two carbonic anhydrase isozymes upon binding their ligands. The proposed method can be used in other protein–ligand systems and expand the knowledge about protein volume changes upon small-molecule binding.

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Section: Resultsmentioning

confidence: 99%

“…Illustration of the protein–ligand binding volume Δ V b . , W denotes water molecules that the protein (P) and ligand (L) release into bulk water after their partial dehydration upon binding.…”

Section: Introductionmentioning

confidence: 99%

Protein–Ligand Binding Volume Determined from a Single 2D NMR Spectrum with Increasing Pressure

et al. 2021

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“…However, the Gibbs energy of protein–ligand binding (and subsequently affinity) is also a function of pressure-related volumetric parameters: the changes in the protein volume and compressibility upon binding a ligand. 4 The protein–ligand binding volume, Δ V b , quantifies the difference between the molar volumes of ligand-bound and ligand-free protein states. 5,6 Studies of proteins exposed to high hydrostatic pressures are also necessary since they can reveal less populated protein states that are unobservable at ambient pressure.…”

Section: Introductionmentioning

confidence: 99%