Ne will be the cyclization from the sugar in to the furanose kind. It occurs accompanied on the BMS-309403 web proton transfer from O4XGAL to O4FADH. We located that this step supports the highest barrier of your whole mechanism: 23.4 + 0.4 kcal/mol. This agrees with the measurements of Sobrado et. al. who determined that this formation on the furanose ring is sensible slower than the opening course of action TcUGM. The absolutely free energy change of 
the step is two.9 + 0.2 kcal/mol. In Fig. S5 panel a) we show the evolution from the distances involved within the definition in the 
reaction coordinate z 4 d8 {d9 {d10, while panel displays the dihedral angles that determine the orientation of the hydroxyl groups at positions 4 and 5. It is observed that, at the beginning of the process, the two hydroxyl groups change their orientation in a concerted way, while O4XGAL and C1XGAL approximate to each other. These movements destroy the H-bond interaction between O5XGAL and O4FADH and, initially, also drive the H atom to be transferred away from O4FADH. However, once the O4XGAL-C1XGAL distance gets short enough, a fine tuning in the orientation of the hydroxyl group at position 4 is observed. This reorientation takes its H atom closer to O4FADH. Initially, while all these rearrangements take place, the H-O4XGAL bond hardly stretches. Only when the O4XGAL-C1XGAL distance gets N-Desmethylclozapine site smaller than 2.3 A, the H-O4XGAL bond starts to weaken. At the transition Galactopyranose/Galactofuranose Tautomerization in Trypanosoma cruzi C-N single bond. Our results thus indicate that the adduct between Galf and FADH becomes rather weak when N5FADH adopts the sp3 hybridization. The enlargement of the C1XGALN5FADH distance was also described by Huang et. al. However, it that case, the final value was somewhat smaller than in our calculations. In order to check the final distance between C1XGAL and N5FADH we re-simulated the transference using longer simulation times for each window, as well as employing larger QM subsystems. However, we consistently obtained the same result. Moreover, the H transference was simulated applying a restriction on the C1XGAL-N5FADH distance, so that it was forced to get values smaller than 1.65 A. These calculations { 0 provided higher DGr and DGr than PubMed ID:http://jpet.aspetjournals.org/content/124/1/16 those obtained without the restriction. Besides, when an unrestricted MD was performed on the products of the restricted transfer, the system spontaneously relaxed to a stable conformation with a C1XGAL-N5FADH distance of,1.85 A. Fig. S6b indicates that the increase in the C1XGALN5FADH distance is accompanied with an increase in the CremerPople angle h. This takes the configuration of the sugar ring from 2 T3, for reactants, to E3 for products. It has to be noted that both, the enlargement of the C1XGAL-N5FADH distance and the change in the conformation of the furanose ring, are required to avoid the steric clash between the cofactor and the substrate. The values of i DERTS presented in Stage 4: Formation of UDP-Galf At first sight, this stage could be considered as the reverse of stage 1, except for the fact that the sugar is now in the funarose form. However, as stated in the previous section, the flavin-Galf bond is already very weak when the transference of the proton from O4FADH to N5FADH is completed. Because of this, the barrier 0 for this step is pretty low, 5.8 + 0.2 kcal/mol, and DGr is quite negative, 214.8 + 0.1 kcal/mol. In Fig. S7 we show the evolution of the distances involved in the definition of reaction coordinate z 6 d1.Ne may be the cyclization from the sugar in to the furanose kind. It happens accompanied with the proton transfer from O4XGAL to O4FADH. We located that this step supports the highest barrier on the complete mechanism: 23.four + 0.4 kcal/mol. This agrees with all the measurements of Sobrado et. al. who determined that this formation with the furanose ring is sensible slower than the opening course of action TcUGM. The absolutely free power adjust from the step is two.9 + 0.2 kcal/mol. In Fig. S5 panel a) we show the evolution from the distances involved inside the definition with the reaction coordinate z 4 d8 {d9 {d10, while panel displays the dihedral angles that determine the orientation of the hydroxyl groups at positions 4 and 5. It is observed that, at the beginning of the process, the two hydroxyl groups change their orientation in a concerted way, while O4XGAL and C1XGAL approximate to each other. These movements destroy the H-bond interaction between O5XGAL and O4FADH and, initially, also drive the H atom to be transferred away from O4FADH. However, once the O4XGAL-C1XGAL distance gets short enough, a fine tuning in the orientation of the hydroxyl group at position 4 is observed. This reorientation takes its H atom closer to O4FADH. Initially, while all these rearrangements take place, the H-O4XGAL bond hardly stretches. Only when the O4XGAL-C1XGAL distance gets smaller than 2.3 A, the H-O4XGAL bond starts to weaken. At the transition Galactopyranose/Galactofuranose Tautomerization in Trypanosoma cruzi C-N single bond. Our results thus indicate that the adduct between Galf and FADH becomes rather weak when N5FADH adopts the sp3 hybridization. The enlargement of the C1XGALN5FADH distance was also described by Huang et. al. However, it that case, the final value was somewhat smaller than in our calculations. In order to check the final distance between C1XGAL and N5FADH we re-simulated the transference using longer simulation times for each window, as well as employing larger QM subsystems. However, we consistently obtained the same result. Moreover, the H transference was simulated applying a restriction on the C1XGAL-N5FADH distance, so that it was forced to get values smaller than 1.65 A. These calculations { 0 provided higher DGr and DGr than PubMed ID:http://jpet.aspetjournals.org/content/124/1/16 those obtained without the restriction. Besides, when an unrestricted MD was performed on the products of the restricted transfer, the system spontaneously relaxed to a stable conformation with a C1XGAL-N5FADH distance of,1.85 A. Fig. S6b indicates that the increase in the C1XGALN5FADH distance is accompanied with an increase in the CremerPople angle h. This takes the configuration of the sugar ring from 2 T3, for reactants, to E3 for products. It has to be noted that both, the enlargement of the C1XGAL-N5FADH distance and the change in the conformation of the furanose ring, are required to avoid the steric clash between the cofactor and the substrate. The values of i DERTS presented in Stage 4: Formation of UDP-Galf At first sight, this stage could be considered as the reverse of stage 1, except for the fact that the sugar is now in the funarose form. However, as stated in the previous section, the flavin-Galf bond is already very weak when the transference of the proton from O4FADH to N5FADH is completed. Because of this, the barrier 0 for this step is pretty low, 5.8 + 0.2 kcal/mol, and DGr is quite negative, 214.8 + 0.1 kcal/mol. In Fig. S7 we show the evolution of the distances involved in the definition of reaction coordinate z 6 d1.
