Allosteric communication in dihydrofolate reductase: Signaling network and pathways for closed to occluded transition and back

Escherichia coli dihydrofolate reductase (DHFR) catalyzes the reduction of dihydrofolate to tetrahydrofolate. During the catalytic cycle, DHFR undergoes conformational transitions between the closed (CS) and occluded (OS) states that, respectively, describe whether the active site is closed or occluded by the Met20 loop. The CS -> OS and the reverse transition may be viewed as allosteric transitions. Using a sequence-based approach, we identify a network of residues that represents the allostery wiring diagram. Many of the residues in the allostery wiring diagram, which are dispersed throughout the adenosine-binding domain as well as the loop domain, are not conserved. Several of the residues in the network have been previously shown by NMR experiments, mutational studies, and molecular dynamics simulations to be linked to equilibration conformational fluctuations of DHFR. To further probe the nature of events that occur during conformational fluctuations, we use a self-organized polymer model to monitor the kinetics of the CS -> OS and the reverse transitions. During the CS -> OS transition, coordinated changes in a number of residues in the loop domain enable the Met:20 loop to slide along the alpha-helix in the adenosine-binding domain. Sliding is triggered by pulling of the Met20 loop by the beta G-pH loop and the pushing action of the beta G-OH loop. The residues that facilitate the Met20 loop motion are part of the network of residues that transmit allosteric signals during the CS -> OS transition. Replacement of M16 and G121, whose C-alpha atoms are about 4.3 angstrom in the CS, by a disulfide cross-link impedes that CS -> OS transition. The order of events in the OS -> CS transition is not the reverse of the forward transition. The contact Glu18-Ser49 in the OS persists until the sliding of the Met20 loop is nearly complete. The ensemble of structures in the transition state in both the allosteric transitions is heterogeneous. The most probable transition-state structure resembles the OS(CS) in the CS -> OS (OS -> CS) transition, which is in accord with the Hammond postulate. Structures resembling the OS (CS) are present as minor (similar to 1-3%) components in equilibrated CS(OS) structures. (c) 2007 Elsevier Ltd. All rights reserved.