Amide V band

Fig. 8. Theoretical simulation of VCD (top) and IR absorption (bottom) spectra of alanine dodecapeptides for the amide V bands for a fully a-helical conformation (left) and a fully left-handed 3i-helical conformation (right). The simulations are for the same three isotopically labeled (13C on the amide C=0 for four Ala residues selected in sequence) peptides as in Figure 7 N-terminal tetrad (4AL1), middle (4AL2), and C-terminal (4AL4). The 13C feature is the same for all sequences, confirming the experimentally found unfolding of the C-terminus. The agreement with the shapes in Figure 7 is near quantitative. Reprinted from Silva, R. A. G. D., Kubelka, J., Decatur, S. M., Bour, R, and Keiderling, T. A. (2000a). Proc. Natl. Acad. Sci. USA 97, 8318-8323. 2000 National Academy of Science, U.S.A.

The amide VI band is associated with C=0 out-of-plane bending, and the amide V band corresponds to the N-H out-of-plane bending. Both modes are associated with the changes in crystal modification as we (11) and others (21) noted by x-ray diffraction in polyamides. For nylon 66 the spectra of the untreated and iodine-potassium iodide desorbed samples are identical although that of the complexed polyamide (12) differs significantly. Evidence from polarized low frequency, particularly of the 140 and 100 cm"1 bands of the ion is also definitive on this point and has... 

The amide V band of secondary amides appears near 700 cm and is characteristic of N—H out-of-plane deformation (Miyazawa et al., 1956, 1958 Kessler and... 

The amide V band occurs for hydrogen-bonded secondary amides near 720 cm . The band usually is broad and of medium intensity. 

Fig. 1. Comparison of amide V VCD for an identical sample of poly-L-lysine in D20 as measured on the UIC dispersive instrument (top) and on the ChirallRFT-VCD instrument (at Vanderbilt University, kindly made available by Prof. Prasad Polavarapu). Sample spectra were run at the same resolution for the same total time ( 1 h) in each case. The FTIR absorbance spectrum of the sample is shown below. VCD spectra are offset for sake of comparison. Each ideal baseline is indicated by a thin line, the scale providing a measure of amplitude. Noise can be estimated as the fluctuation in the baseline before and after the amide V, which indicates the S/N advantage of the single band dispersive measurement.

Fig. 10. Comparison of VCD spectra of four proteins in H2O (left, amide I + II) and D2O (right, amide V + IF) with dominant secondary structure contributions from G -helix (myoglobin, MYO, top), /3-sheet (immunoglobin, IMUN), both helix and sheet (lactoferrin, LCF) and no structure (o -casein, CAS, bottom). The comparisons emphasize the distinct band shapes developed in the amide I and V for each structural type. Note the reduced S/N in the F O-based spectra and the shape changes upon H/D exchange for helix and sheet (and mixed) structures, but relatively little for the unstructured CAS.

A major problem in unfolding studies of large proteins is irreversibility. In a study of elastase temperature-induced denaturation, second-derivative FTIR show a distinct loss of several sharp amide V features (dominant /3-sheet components and growth in broadened bands at 1645 and 1668 cm-1 (Byler et al., 2000). These features persisted on cooling, indicating lack of reversibility, a feature common to longer multidomain proteins. A graphic example of this is seen in the triosephosphate... 

Fig. 9.28 Analysis of the CH-stretching region (3000-2800 cm ) and the amide I band around 1650 cm V (a) ER-FTIR spectrum of poly(2-ethyl-2-oxazoline) (PEOx) as grown on the triflate functionalized HUT SAM. (b) ER-FTIR spectrum of HUT SAM. (c) Subtraction result of (a)-(b). (d) Bulk spectrum of PEOx. In the spectrum to the left, a significant shift...

Other mixed vibration bands known as the amide III, IV and V bands have been identified in various regions of the spectrum but they are of limited diagnostic value. 

Protein Amide I/amide II band (cm-1) CD peaks (nm) Specific activity Km y v max... 

The filtered preparation of gum arabic contained 13 pg/mg protein (dry wt). When a 0.01% (w v) aqueous solution, at pH 6.5, was exposed to a Ge IRE, no polysaccharide was observed to adsorb from a flowing solution at the aqueous/solid interface, as the characteristic C-0 stretching bands of gum arabic were not visible in the water-subtracted spectra. The protein (1.3%) associated with gum arabic demonstrated a high affinity for the Ge surface, adsorbing from a flowing solution at a concentration of 1.3 ppm, while polysaccharide, present at a concentration of 100 ppm, did not adsorb on the IRE. Distinct Amide I and Amide II bands of this adsorbed protein are visible in the water subtracted spectra. At the end of 4 hr, the 1549 cm 1 band intensity was 0.9 mAU. Rinsing with Milli-Q water (pH 6.5) did not affect the Amide II band intensity, indicating that the protein was firmly adsorbed to the Ge surface. 

At a gum arabic concentration of 0.1% (w v), protein and a small amount of polysaccharide were detected at the Ge surface as shown in Figure 5. The Amide II band intensity increased slowly and steadily throughout the initial 4-hr period, as shown in Figure 6. The Amide II band intensity peaked at approximately 11 mAU however, protein adsorption did not stop before the water rinse was initiated. Polysaccharide adsorbed rapidly onto the IRE... 

At a gum arabic concentration of 1.0% (w v), polysaccharide was detected at the Ge surface within the first minute of exposure to the flowing solution as shown in the first spectrum (T 0 min) in Figure 7. The intensities of both the protein and polysaccharide bands then rose rapidly in a 15-min period of time as shown in Figure 6. The 1070 cm 1 polysaccharide band plateaued at 14.7 mAU after 30 min whereas the Amide II band stabilized at 12.5 mAU after approximately 2 hr. The intensity of the 1070 cm 1 polysaccharide band dropped rapidly when Milli-Q water was pumped through the flow cell. A 90% decrease in the 1070 cm 1 band intensity occurred over the 4-hr rinse period. The final intensity of this band was not significantly different from the intensity observed when gum arabic was adsorbed onto germanium at a concentration that was 10 times less. The protein was more firmly bound to the IRE surface as indicated by the Amide II band intensity which dropped less than 10% during the rinse period. Only 15% less protein remained firmly attached to the Ge IRE when it was adsorbed from a gum arabic solution concentration of 0.1% as compared to 1%. Experiments to study adsorption of proteins and polysaccharides on copper and nickel are not yet complete, but appear to show similar trends. 

At the low protein concentration (0.01% w v) used in our studies, the signal from protein can be assumed to be entirely due to adsorbed material. Very little or no change in the Amide II band intensities occurred when protein in the bulk phase was replaced by saline or water during the rinse period. Protein remaining after the saline rinse can be considered as firmly adsorbed material. 

Fig. 2 DRIFT spectra of PVFA-co-PVAm modified ZnO particles where the degree of the PVFA-co-PVAm hydrolysis was varied a degree of hydrolysis = 0% b degree of hydrolysis = 10% c degree of hydrolysis = 30% d degree of hydrolysis = 50% and e degree of hydrolysis > 90%, desalted. The molar mass of the non-hydrolysed PVFA polymer was 340 000 g mol-1, during the adsorption the pH was pH = 8. The spectra show the overtone amide-II band at v = 3053 cm-1 (A), the amide-I band at v = 1675 cm-1 (71), the NH deformation vibration at v = 1590 cm-1 (C), the amide-H band at v = 1540 cm-1 (/.)). (v = wave number, a.u. = arbitrary units according to Kubelka and Munk)...

Aspidofiline (CXXXVI), one of the simplest members of the group, was the first alkaloid to be isolated from A. pyrifolium (79). It was readily separated from the accompanying pyrifoline by virtue of its alkali solubility. The phenolic hydroxyl group so indicated is confirmed by the bathochromic shift of the UV-spectrum observed on addition of alkali. The spectrum is characteristic of a 17-hydroxy-V-acyldihydroindole and the IR-spectrum shows a hydrogen-bonded amide carbonyl band at... 

The studies by Miyazawa, Shimanouchi, and Mizushima (1422, 1424) have already been mentioned in the discussion of vt, the in-plane N—H bending mode. The amide I band, a carbonyl stretching mode, shifts downward with Av/v = - -0.028, whereas the amide II band, a mixture of i j(CN) and r6(NH), shifts upward with Av/v = —0.045. Although this upward shift is in the direction expected for Vb, Mizushima et al. feel that the shift should be attributed in part to double bond character induced in the C—bond when the H bond is formed. ... 

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