Vibrational Circular Dichroism Spectra of Proteins in the Amide III Region: Measurement and Correlation of Bandshape to Secondary Structure

Enhanced Prediction Accuracy of Protein Secondary Structure Using Hydrogen Exchange Fourier Transform Infrared Spectroscopy

“…For each protein, a set of six unbuffered aqueous solutions was prepared with a concentration of about 100 mg/mL with varying ratios of H 2 O:D 2 O (0, 20, 40, 60, 80, and 100%, v/v D 2 O). This provides a solvent environment for the protein samples that is consistent with our previous FTIR-and VCD-based structural analyses on these same reference proteins (24,26) except for the effects of deuteration. Aliquots of about ϳ15 L were placed in a commercial refillable cell (Graseby-Specac PN 1012) consisting of CaF 2 windows separated by a 6-m mylar spacer.…”

“…We, here, combine H-D exchange (in an equilibrium sense) with FTIR spectra of a training set of proteins to improve both the accuracy and extent of prediction of fractional secondary structure in these proteins. Using a consistent bandshape analysis scheme based on PC/FA and our previously detailed (23,24,26) restricted multiple regression (RMR) method of correlation with secondary structure, we compare this H-D exchange enhanced FTIR approach with results from ordinary FTIR in H 2 O and D 2 O as well as with ECDbased analyses for the same set of proteins.…”

“…The principal component method of factor analysis (PC/FA) (23,24,26) provides a means of determining the most common response and the major variance of a system to a perturbation. By a study of the spectral response to systematic H-D exchange, we have the potential of selectively removing the more tertiary structure-sensitive components of the spectra (major variance with deuteration) from the common response.…”

Simulations of oligopeptide vibrational CD: Effects of isotopic labeling

“…Examples are known where a common secondary structure type, such as an α‐helix, gives rise to a conserved VCD bandshape but one shifted to different frequencies in different peptides 12, 20–22. In analogy to band shape based ir studies23–26 and to well‐established electronic CD studies,5, 6, 27–30 we have in the past developed empirical correlations of amide I and II31–33 and even amide III34 VCD band shapes with secondary structure.…”

Optical spectroscopic differentiation of various equilibrium denatured states of horse cytochrome c

“…The native state VCD does have an anomalous band at ϳ 1600 cm Ϫ1 that is difficult to assign at this time. It might be noted that cyt c also had anomalous VCD in the amide III region, 56 which may be influenced by mixing with d-d transitions of the Fe-heme chromophore. 57 The VCD spectra of the native state cyt c thermal denaturation (Figure 6a) confirms the change observed in FTIR.…”