Evidence of a Structural Defect in Ice VII and the Side-Chain-Dependent Response of Small Model Peptides to Increased Pressure

Abstract

The effect of high pressure on the OH stretch of dilute HOD in D2O was examined using high pressure FTIR. It was found that at pressures directly above the ice VI to ice VII transition, ice VII displays a splitting in the OH absorption indicative of differing hydrogen bonding environments. This result is contrary to published structures of ice VII in which each OH oscillator should experience an identical electronic environment. The anomalous band was found to decrease in absorbance and finally disappear at ~43.0 kbar. In addition, the pressure response of the amide I′ and II′ bands of three small model peptides was examined. Analysis of these bands’ response to increased pressure indicates significant side chain dependence of their structural rearrangement, which may play a role in the composition of full length proteins of barophilic organisms.

Efficient Computation of Difference Vibrational Spectra in Isothermal–Isobaric Ensemble

“…The IR difference spectra in Figure 3b show the analogous transition, consistent with experimental IR measurements. 38,67 Comparing the line shapes of velocity correlation in (a) to those of the IR spectra in (b), we find that the amplitudes in the low-frequency region below 3400 cm −1 are generally more emphasized in the latter. This feature is understood from the fact that the transition moment of OH stretch is augmented by strong hydrogen bonds in the low-frequency region, 9,14,73 the trend of which has been commonly observed for various hydrogen-bonded systems.…”

“…In addition, a Monte Carlo simulation has failed to confirm this picture. Therefore, we apply our analytical method of difference vibrational spectra for liquid water to resolve this issue in comparison with experimental IR ,,,, and Raman ,,, spectroscopies.…”

Amino acid side chain contribution to protein FTIR spectra: impact on secondary structure evaluation

“…Besides physical parameters such as temperature (Anderson et al 2014) or pressure (Scott and Vanderkooi 2011), most variability comes from the environment of the side chain including H-bonds, local pH, local polarity of the medium, coupling with other vibrations (Bagchi et al 2009), etc. which cannot be accessed nor taken properly into account.…”

“…The key issue for the purpose of this work is that the actual amino acid side chain contributions in the amide I–amide II spectral region depends on many parameters. Besides physical parameters such as temperature (Anderson et al 2014 ) or pressure (Scott and Vanderkooi 2011 ), most variability comes from the environment of the side chain including H-bonds, local pH, local polarity of the medium, coupling with other vibrations (Bagchi et al 2009 ), etc. which cannot be accessed nor taken properly into account.…”