Infrared Spectrum of Phosphoenol Pyruvate: Computational and Experimental Studies

Abstract

The infrared spectrum of phosphoenol pyruvate (PEP) in aqueous solution was studied experimentally and theoretically in its fully ionized, singly protonated and doubly protonated form. The density functional theory with the B3LYP functional and with the 6-31G(d,p), 6-31++G(d,p), and 6-311++G(d,p) basis sets were used in the theoretical study. The calculations with the two latter basis sets and the CPCM continuum model for water showed good agreement with the experiments except for vibrations assigned to hydroxyl groups. These needed to be modeled with explicit water molecules. The effects of deuteration and of (13)C(2,3) labeling of PEP were reproduced by the calculations.

Two sides of the same coin: How enzymes distort substrates and vice versa. An infrared spectroscopic view on pyruvate kinase and Ca2+-ATPase

“…3. The observed shifts are in line with those expected from spectra in aqueous solution and can be assigned to specific vibrations from tabulated assignments [25] and density functional theory (DFT) calculations [59]. This has identified the absorption of four substrate vibrations in the binding-induced difference spectrum: the antisymmetric and symmetric COO − stretching vibrations (1590 and 1415 cm −1 , respectively), the C-O(-P) stretching vibration (1214 cm −1 ) and the symmetric PO 3 2− stretching vibration (968 cm −1 ).…”

“…These differences were interpreted according to DFT calculations [59] in terms of a rotation of the carboxylate group around the adjacent C-C bond by a few degrees [43]. They are observed although the monovalent ion does not directly coordinate to the carboxylate group.…”

Molecular Characterization of DNA Double Strand Breaks with Tip‐Enhanced Raman Scattering

“…Zuschriften 1190 cm À1 [24,25] confirming that the phosphodiester fragment is hydrogen-terminated at the lesion site. The appearance of these bands indicates 3'-bond cleavage occurred in one strand and 5'-bond cleavage on the second strand (blue arrows).…”

Following Enzyme Activity with Infrared Spectroscopy

“…The series of solid line spectra in Figure 1A represent the catalytic reaction during 30 minutes and the dotted line is the last spectrum of the control experiments. The positive band at 1174 cm −1 is due to the formation of pyruvate [26], and the negative bands at 974 cm −1 and 1103 cm −1 are caused by PEP consumption [27]. Similarly, absorption at 1240, and 918 cm −1 is assigned to ATP production while the negative band at 941 cm −1 is due to ADP consumption [28,29].…”

“…Similarly, absorption at 1240, and 918 cm −1 is assigned to ATP production while the negative band at 941 cm −1 is due to ADP consumption [28,29]. These bands are assigned as follows: the band at 1174 cm −1 is due to the C-CH 3 stretching vibration of pyruvate [30], and the bands at 1103 and 974 cm −1 are due to -PO 3 2− stretching vibrations of PEP [27]. The bands arising at 1240 cm −1 and 918 cm −1 are from the β-PO 2 − and the P-O-P groups of ATP, respectively, while the β-PO 3 2− and P-O-P groups of ADP are observed at 941 cm −1 [28,29,31].…”