5 research outputs found
Substrate Distortion Contributes to the Catalysis of Orotidine 5′-Monophosphate Decarboxylase
Orotidine 5′-monophosphate
decarboxylase (ODCase) accelerates
the decarboxylation of orotidine 5′-monophosphate (OMP) to
uridine 5′-monophosphate (UMP) by 17 orders of magnitude. Eight
new crystal structures with ligand analogues combined with computational
analyses of the enzyme’s short-lived intermediates and the
intrinsic electronic energies to distort the substrate and other ligands
improve our understanding of the still controversially discussed reaction
mechanism. In their respective complexes, 6-methyl-UMP displays significant
distortion of its methyl substituent bond, 6-amino-UMP shows the competition
between the K72 and C6 substituents for a position close to D70, and
the methyl and ethyl esters of OMP both induce rotation of the carboxylate
group substituent out of the plane of the pyrimidine ring. Molecular
dynamics and quantum mechanics/molecular mechanics computations of
the enzyme–substrate complex also show the bond between the
carboxylate group and the pyrimidine ring to be distorted, with the
distortion contributing a 10–15% decrease of the ΔΔ<i>G</i><sup>⧧</sup> value. These results are consistent
with ODCase using both substrate distortion and transition-state stabilization,
primarily exerted by K72, in its catalysis of the OMP decarboxylation
reaction
Additional file 4: Figure S4. of Low-intensity pulsed ultrasound rescues insufficient salivary secretion in autoimmune sialadenitis
Bands of Western blot analysis for the cropped images in Fig. 3a (A), 3b (B) and 3c (C) are provided in this file. (TIFF 5449 kb
Additional file 2: Figure S2. of Low-intensity pulsed ultrasound rescues insufficient salivary secretion in autoimmune sialadenitis
Quantification of the fluorescence intensity in Fig. 1C. **p < 0.01 (n = 4). (TIFF 897 kb
Additional file 3: Figure S3. of Low-intensity pulsed ultrasound rescues insufficient salivary secretion in autoimmune sialadenitis
Bands of Western blot analysis for the cropped images in Fig. 2c are provided in this file. (TIFF 1856 kb
Additional file 1: Figure S1. of Low-intensity pulsed ultrasound rescues insufficient salivary secretion in autoimmune sialadenitis
Schematic representation of the in vitro LIPUS system used. A cell culture plate with medium was placed in the ultrasound field at a distance of about 1 mm from the transducer to optimize beam uniformity across the target region. (TIFF 1093 kb