Relationship between Nonlinear Pressure-Induced Chemical Shift Changes and Thermodynamic Parameters

Previous investigations of the sensitivity of the lac repressor to high-hydrostatic pressure have led to varying conclusions. Here high-pressure solution NMR spectroscopy is used to provide an atomic level view of the pressure induced structural transition of the lactose repressor regulatory domain (LacI* RD) bound to the ligand IPTG. As the pressure is raised from ambient to 3 kbar the native state of the protein is converted to a partially unfolded form. Estimates of rotational correlation times using transverse optimized relaxation indicates that a monomeric state is never reached and that the predominate form of the LacI* RD is dimeric throughout this pressure change. Spectral analysis suggests that the pressure-induced transition is localized and is associated with a volume change of approximately −115 ml/mol and an average pressure dependent change in compressibility of approximately 30 ml mol−1 kbar−1. In addition, a subset of resonances emerge at high-pressures indicating the presence of a non-native but folded alternate state.

show abstract

“…The volume normalized compressibility (ΔV°/Δβ′) of 0.3 is comparable to that found previously for other proteins (e.g. HPr [29]).…”

Section: Resultssupporting

confidence: 86%

Solution NMR investigation of the response of the lactose repressor core domain dimer to hydrostatic pressure

Fuglestad

Stetz

Belnavis

et al. 2017

Biophysical Chemistry

View full text Add to dashboard Cite

show abstract

“…Intuitively, this is because residues near cavities have more space to sample multiple conformations upon compression, resulting in structural fluctuations of the protein between sub-states in the fast regime on the NMR timescale18,26 . Since both nonlinear chemical shift changes and compressibility probe for the volume-dependent local environment a residue resides in, measuring the nonlinear coefficient of chemical shift changes and compressibility can go handin-hand for more accurate characterization of cavities in proteins (as has been linked mathematically in the past68 ). Remarkably, the cavities in the WT ARNT PAS-B were not initially observed in the solution structure31 , showing the potential of pressure-NMR as the means of rapidly identifying smaller cavities from moderate resolution structures where cavities and/or ligand binding pockets are not obvious31 .…”

mentioning

confidence: 99%

High-Pressure NMR Reveals Volume and Compressibility Differences Between Two Stably Folded Protein Conformations

Gagné

Aramini

et al. 2020

Preprint

View full text Add to dashboard Cite

Proteins often interconvert between different conformations in ways critical to their function. However, manipulating the equilibrium positions and kinetics of such conformational transitions has been traditionally challenging. Pressure is an effective thermodynamic variable for favoring the population of high energy protein conformational states with smaller volumes, as elegantly demonstrated in its use for biophysical studies of unfolding transitions. Here, we investigate the pressure-dependent effects of the interconversion of two stably-folded conformations of the Y456T variant of the aryl hydrocarbon receptor nuclear translocator (ARNT) Period/ARNT/Single-minded PAS-B domain. We previously discovered that ARNT PAS-B Y456T spontaneously interconverts between two structures primarily differing by a three-residue β-strand slip, inverting its topology in the process. This change collapses the internal cavities of the WT-like (WT) conformation of this protein as it adopts the slipped conformation (SLIP). Using pressure-NMR to conduct thermodynamic and kinetic analyses of the interconversion of ARNT PAS-B, we provide data that support two key predictions of this process: the SLIP conformation is both smaller and less compressible than the WT conformation, and the interconversion proceeds through a chiefly-unfolded intermediate state. We also find that the pressure-dependent NMR chemical shift changes and the residue-specific compressibility both predict which amino acid residues are near protein cavities. We demonstrate that pressure-NMR is a powerful approach for characterizing protein conformational switching and can provide unique information that is not easily accessible through other techniques.

show abstract

“…Note that the definition of B * 2 given by Beck Erlach et al (2014) differs to that given in Eq. 9.5 by a factor of 2 taken into account in Eq.…”

Section: Description Of Pressure Effects In Multistate Systemsmentioning

confidence: 99%

High Pressure NMR Methods for Characterizing Functional Substates of Proteins

Kalbitzer

2015

Subcellular Biochemistry

Self Cite

View full text Add to dashboard Cite

Proteins usually exist in multiple conformational states in solution. High pressure NMR spectroscopy is a well-suited method to identify these states. In addition, these states can be characterized by their thermodynamic parameters, the free enthalpies at ambient pressure, the partial molar volumes, and the partial molar compressibility that can be obtained from the analysis of the high pressure NMR data. Two main types of states of proteins exist, functional states and folding states. There is a strong link between these two types, the functional states represent essential folding states (intermediates), other folding states may have no functional meaning (optional folding states). In this chapter, this concept is tested on the Ras protein, an important proto-oncogen in humans where all substates required by theory can be identified experimentally by high pressure NMR spectroscopy. Finally, we show how these data can be used to develop allosteric inhibitors of proteins.

show abstract

Relationship between Nonlinear Pressure-Induced Chemical Shift Changes and Thermodynamic Parameters

Cited by 23 publications

References 36 publications

Solution NMR investigation of the response of the lactose repressor core domain dimer to hydrostatic pressure

Solution NMR investigation of the response of the lactose repressor core domain dimer to hydrostatic pressure

High-Pressure NMR Reveals Volume and Compressibility Differences Between Two Stably Folded Protein Conformations

High Pressure NMR Methods for Characterizing Functional Substates of Proteins

Contact Info

Product

Resources

About