Pressure response of amide one-bond J-couplings in model peptides and proteins

Koehler, Joerg; Erlach, Markus Beck; Crusca, Edson; Kremer, Werner; Munte, Cláudia Elisabeth; Meier, Alexander; Kalbitzer, Hans Robert

doi:10.1007/s10858-014-9850-2

Cited by 5 publications

(3 citation statements)

References 28 publications

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“…Since its first publication, the PURGE pulse sequence has been used on a regular basis by the team that created it, − along with several other groups, − and even suggested in a Nature protocol . Despite this visibility, the PURGE pulse sequence has not become routine in metabolomics.…”

Section: Alternate Water Suppression Techniques and Avoiding Some Of ...mentioning

confidence: 99%

Alternatives to Nuclear Overhauser Enhancement Spectroscopy Presat and Carr–Purcell–Meiboom–Gill Presat for NMR-Based Metabolomics

2017

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NMR metabolomics are primarily conducted with 1D nuclear Overhauser enhancement spectroscopy (NOESY) presat for water suppression and Carr–Purcell–Meiboom–Gill (CPMG) presat as a T2 filter to remove macromolecule signals. Others pulse sequences exist for these two objectives but are not often used in metabolomics studies, because they are less robust or unknown to the NMR metabolomics community. However, recent improvements on alternative pulse sequences provide attractive alternatives to 1D NOESY presat and CPMG presat. We focus this perspective on PURGE, a water suppression technique, and PROJECT presat, a T2 filter. These two pulse sequences, when optimized, performed at least on par with 1D NOESY presat and CPMG presat, if not better. These pulse sequences were tested on common samples for metabolomics, human plasma, and urine.

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Section: Alternate Water Suppression Techniques and Avoiding Some Of ...mentioning

confidence: 99%

Alternatives to Nuclear Overhauser Enhancement Spectroscopy Presat and Carr–Purcell–Meiboom–Gill Presat for NMR-Based Metabolomics

2017

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“…Blue circles represent positive correlation coefficients (r > 0), whereas red circles represent negative correlation coefficients (r < 0). The lower left half shows the actual values of the correlation coefficient rounded to 1 digit after the decimal point coil peptides indicating a possible conformational response for the amide 1 J NH-N -couplings Koehler et al (2014). In the IDPs α-synuclein the 3 J HN-Hα -coupling constants are pressure dependent and also indicate a shift of the conformational equilibrium with pressure (Roche et al 2013).…”

Section: Origin Of the Pressure Dependent Chemical Shift Changesmentioning

confidence: 99%

Pressure dependence of side chain 13C chemical shifts in model peptides Ac-Gly-Gly-Xxx-Ala-NH2

et al. 2017

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For evaluating the pressure responses of folded as well as intrinsically unfolded proteins detectable by NMR spectroscopy the availability of data from well-defined model systems is indispensable. In this work we report the pressure dependence of C chemical shifts of the side chain atoms in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH (Xxx, one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of a number of nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The size of the polynomial pressure coefficients B and B is dependent on the type of atom and amino acid studied. For H, N and C the first order pressure coefficient B is also correlated to the chemical shift at atmospheric pressure. The first and second order pressure coefficients of a given type of carbon atom show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure also are weakly correlated. The downfield shifts of the methyl resonances suggest that gauche conformers of the side chains are not preferred with pressure. The valine and leucine methyl groups in the model peptides were assigned using stereospecificallyC enriched amino acids with the pro-R carbons downfield shifted relative to the pro-S carbons.

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“…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].…”

Section: Resultsmentioning

confidence: 99%

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

Fuglestad

Stetz

Belnavis

et al. 2017

Biophysical Chemistry

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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.

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Pressure response of amide one-bond J-couplings in model peptides and proteins

Cited by 5 publications

References 28 publications

Alternatives to Nuclear Overhauser Enhancement Spectroscopy Presat and Carr–Purcell–Meiboom–Gill Presat for NMR-Based Metabolomics

Alternatives to Nuclear Overhauser Enhancement Spectroscopy Presat and Carr–Purcell–Meiboom–Gill Presat for NMR-Based Metabolomics

Pressure dependence of side chain 13C chemical shifts in model peptides Ac-Gly-Gly-Xxx-Ala-NH2

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

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