The Chemical Shift Baseline for High‐Pressure NMR Spectra of Proteins

Abstract

High-pressure (HP) NMR spectroscopy is an important method for detecting rare functional states of proteins by analyzing the pressure response of chemical shifts. However, for the analysis of the shifts it is mandatory to understand the origin of the observed pressure dependence. Here we present experimental HP NMR data on the (15) N-enriched peptide bond model, N-methylacetamide (NMA), in water, combined with quantum-chemical computations of the magnetic parameters using a pressure-sensitive solvation model. Theoretical analysis of NMA and the experimentally used internal reference standard 4,4-dimethyl-4-silapentane-1-sulfonic (DSS) reveal that a substantial part of observed shifts can be attributed to purely solvent-induced electronic polarization of the backbone. DSS is only marginally responsive to pressure changes and is therefore a reliable sensor for variations in the local magnetic field caused by pressure-induced changes of the magnetic susceptibility of the solvent.

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

“…Largely linear chemical shift perturbations of resonances were observed throughout the spectrum (Figure 2). Such changes correspond to local bonding effects [28–30] and minor changes in the protein structure [16] and changes the effect of solvent on protein backbone chemical shifts [31]. Some portion of the chemical shift changes could also arise from the small pressure sensitivity of the pH of the Tris buffer employed [32].…”

“…Some portion of the chemical shift changes could also arise from the small pressure sensitivity of the pH of the Tris buffer employed [32]. Due to the difficulty in interpretation of chemical shift perturbations of proteins under high-hydrostatic pressure [31], these were not analyzed further in quantitative detail.…”

Pressure dependence of side chain 1H and 15N-chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH2

“…These conformational contributions have to be separated from other chemical shift contributions as they are observed even in non-folded model compounds as a consequence of compression and rearrangement of the water shell. A non-linear pressure response of chemical shifts can even be determined experimentally in the peptide bond model N-methyl acetamide and is supported by quantum chemical calculations (Frach et al 2016). However, random-coil peptides are better suited models for protein work.…”

The SAMPL6 challenge on predicting octanol–water partition coefficients from EC-RISM theory

“…The (decadic) partition coefficient of a molecule is related to the Gibbs energy of transfer, Δ trans G 0 , and therefore, via a thermodynamic cycle where the gas phase contributions cancel out, to the individual (standard) Gibbs energies, G 0 , of the compound in the respective solvent ("wat" for water and "oct" for octanol) by where R is the molar gas constant and T is the temperature (298.15 K in this work). While the conceptual and theoretical basis for calculating these individual Gibbs energies is the same as in our previous works [3,6,14,17], only neutral tautomers ("microstates", subscript "t") need to be considered whose Gibbs energies can be calculated via the discrete partition function approximation over conformations ("c") by Note that we here drop the superscript "0" indicating the standard state for simplicity, assuming infinite dilution conditions at an arbitrary formal concentration. The total Gibbs energy is then given by a similar partition function over the individual microstates as Within the EC-RISM formalism the Gibbs energy per conformation and per microstate is defined as where E sol tc represents the electronic energy of a conformation in solution and ex,corr tc is the corrected excess chemical potential, ignoring entropic contributions from rotational and vibrational degrees of freedom.…”

“…These are applied in the QC calculations from which, after convergence of an iterative cycle, the wave function of the solute in solution as well as the excess chemical potential at infinite dilution and other properties of the fully polarized solute can be determined [12,13]. As usual, we took the sum of the polarized electronic energy and the excess chemical potential as an estimate of the Gibbs energy of the molecule in solution to calculate derived properties such as solvation Gibbs energies (by referencing to a gas phase calculation), acidity constants, partition and distribution coefficients, or tautomer and conformational populations of molecules under ambient and extreme conditions in a variety of solvents [14][15][16][17][18][19][20][21].…”