Báo cáo khoa học: Insight into the phosphodiesterase mechanism from combined QM ⁄ MM free energy simulations pot

... Journal 278 (2011) 2579–2595 ª 2011 The Authors Journal compilation ª 2011 FEBS 2595 Insight into the phosphodiesterase mechanism from combined QM ⁄ MM free energy simulations Kin-Yiu Wong* and Jiali ... without the formation of the intermediate. The estimated reaction energy from the reactant to product in Fig. 3 is )17.4 kcalÆmol )1 , whereas the...

Ngày tải lên: 14/03/2014, 23:20

... 0.34, the intrinsic A 0 value measured for the immobile probe in vitrified medium [27]. Taking into account the additive rule of the anisotropies, we calculated the initial anisotropy value for the ... as these probes are either immobilized for the former (Fig. 8) or only slowly mobile for the latter (Fig. 9C). This suggests that the acrylodan emission transition moment is...

Ngày tải lên: 07/03/2014, 15:20

... 20–564), and the model is composed of residues 25–540. The overall structure of the model of IPU and the mutated residues in this study are shown in Fig. 3. To elucidate the mechanism of the substrate ... carried out using panose as the substrate. The anomeric forms of t he hydrolysate are equilibrated immediately by the addition of ammonium hydroxide, and the change in...

Ngày tải lên: 19/02/2014, 16:20

... illustrates the quality of the experimental data (Fig. 2B). Reconstruction of the overall shape of the PLDa2 from the X-ray scattering data was achieved by the ab initio modeling program dammin [24]. The ... calculated from the SAXS pattern. The balls represent the dummy atoms used in the simulated annealing procedure of program DAMMIN [24] to restore the models....

Ngày tải lên: 19/02/2014, 02:20

... analysis, the purified enzyme was activated by incubation with 2 mm MnCl 2 in 10 mm Tris ⁄ HCl pH 8.0 for 30 min at 37 °C, and then the free metal ion was removed by dialysis against 10 mm Tris ⁄ HCl ... measuring the formation of urea from l-arginine or agmatine in 50 mm glycine ⁄ NaOH pH 9.0. In studying the effect of pH on enzyme activities, buffers used were...

Ngày tải lên: 20/02/2014, 02:21

... is the surface pressure. These data were then recorded as the variation of DG Mix with monolayer surface pressure (Table 3). Numer- ical data were calculated from compression isotherms using the ... 2006 The Authors Journal compilation ª 2006 FEBS 3793 was the minimum bulk concentration required to sat- urate the air ⁄ water interface with the peptide under these experimen...

Ngày tải lên: 07/03/2014, 12:20

... both the K m and the V max of the reaction. The K m for d-serine synthesis increased from 1.9 mm in the absence of GRIP fragment (filled circles) to 3.4 in its presence (empty circles), whereas the ... we immunoprecipitated the transfected SR from the COS7 cells and investigated whether the PDZ6 domain of GRIP effectively associated with the carboxy-terminal end of SR...

Ngày tải lên: 30/03/2014, 03:20

... the changes introduced in the redox cofactor environment upon complex formation. They are therefore related to the specificity and the strength of the protein–protein interaction. Therefore, the ... FNR using the same binding site also supports the idea of the similarity in the recognition mechanisms for ET proteins [5]. Additional examples can also be found in the superf...

Ngày tải lên: 31/03/2014, 07:20

... indicating that the environ- ment of tryptophan residues is essentially conserved in the mutant enzyme. On the other hand, the absence of major differences in the CD spectra of the wild-type and ... of the manganese ions. This, together with the fact that the positions of other Fig. 4. A superimposition of the structures of B. caldovelox arginase (red), rat liver arginase...

Ngày tải lên: 21/02/2014, 01:21

... starting from Leu1. Therefore, the requirement of Val at the N-terminus might be depen- dent on the conformation of each protease. It would be interesting to test whether or not the substitution of the ... N-termini of the processed forms were not the 69th substituted amino acids, but entirely Ile70. These results show that thermolysin attacks the Xaa69-Ile70 bond of the m...

Ngày tải lên: 16/03/2014, 06:20