Evaluation of NMR diffusion measurements for the conformational analysis of flexible peptides.
ABSTRACT The use of diffusion coefficients measured with pulsed-field gradient NMR spectroscopy for the determination of the relative population of conformers in solutions of the human Growth Hormone peptide fragment, hGH(9-19), has been studied in aqueous and in trifluoroethanol (TFE)/ water solutions. The peptide is a good model compound for this study because it adopts a predominantly random coil conformation in aqueous solution and is helical in TFE. The results of the diffusion measurements suggest that the peptide exhibits predominantly random coil structures in aqueous solution and adopts a more helical conformation in solutions containing increasing mole fractions of TFE, consistent with the qualitative findings of the standard CD and NMR experiments to probe peptide conformation. These results indicate that diffusion coefficients measured with NMR can provide additional information about temperature- and solvent-induced changes in the extent of the helical conformer for hGH(9-19) in aqueous solution and in solutions containing various mole fraction of TFE, respectively.
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ABSTRACT: NMR spectroscopy and molecular dynamics (MD) simulation analyses of the chiral molecular micelles poly-(sodium undecyl-(L,L)-leucine-valine) (poly-SULV) and poly-(sodium undecyl-(L,L)- valine-leucine) (poly-(SUVL)) are reported. Both molecular micelles are used as chiral selectors in electrokinetic chromatography and each consists of covalently linked surfactant chains with chiral dipeptide headgroups. To provide experimental support for the structures from MD simulations, NOESY spectra were used to identify protons in close spatial proximity. Results from the NOESY analyses were then compared to radial distribution functions from MD simulations. In addition, the hydrodynamic radii of both molecular micelles were calculated from NMR-derived diffusion coefficients. Corresponding radii from the MD simulations were found to be in agreement with these experimental results. NMR diffusion experiments were also used to measure association constants for polar and non-polar binaphthyl analytes binding to both molecular micelles. Poly(SUVL) was found to bind the non-polar analyte enantiomers more strongly, while the more polar analyte enantiomers interacted more strongly with poly(SULV). MD simulations in tum showed that poly(SUL V) had a more open structure that gave greater access for water molecules to the dipeptide headgroup region.Open Journal of Physical Chemistry 11/2012; 2(4):240-251.
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ABSTRACT: Conformations of the designed peptide Betanova in 42% trifluoroethanol/water (v/v) were explored. Circular dichroism (CD) observations provided no evidence for the presence of significant amounts of beta-structures in water, in TFE/water, or in ethanol/water. Nuclear magnetic resonance (NMR) diffusion experiments showed no significant difference in the hydrodynamic radius of the peptide in water and in 42% TFE/water. However, calculations indicated that the hydrodynamic radii of the triple-stranded beta-sheet, originally proposed for Betanova by Kortemme et al. (Science 1998, 281, 253-256), and a variety of partially folded forms of Betanova would be similar and likely could not be convincingly distinguished by diffusion experiments. Temperature coefficients (Deltadelta/DeltaT) of the peptide N--H chemical shifts are similar in water and 42% TFE/water, implying that most of these protons are highly solvent exposed in both solvents and likely do not participate in intramolecular hydrogen bonding interactions. Possible exceptions to this conclusion are the Lys9 and Lys15 residues, where a more positive coefficient may indicate that these residues are involved to some extent in local turn structures. Peptide proton-solvent fluorine intermolecular nuclear Overhauser effect (NOE)s at 25 degrees C were consistent with the presence of a mixture of conformations, which could include the triple-stranded beta-sheet structure as a minor component. At 0 degrees C, peptide-TFE NOEs indicated that TFE interacts strongly enough with many protons of Betanova that alcohol-peptide interactions persist for times of the order of nanoseconds, appreciably longer than the encounter time characteristic of mutual diffusion of TFE and the solute.Biopolymers 10/2010; 93(10):893-903. · 2.88 Impact Factor