Abstract
Residue interaction networks and loop motions are important for catalysis in dihydrofolate reductase (DHFR). Here, we investigate the effects of ligand binding and chain connectivity on network communication in DHFR. We carry out systematic network analysis and molecular dynamics simulations of the native DHFR and 19 of its circularly permuted variants by breaking the chain connections in ten folding element regions and in nine nonfolding element regions as observed by experiment. Our studies suggest that chain cleavage in folding element areas may deactivate DHFR due to large perturbations in the network properties near the active site. The protein active site is near or coincides with residues through which the shortest paths in the residue interaction network tend to go. Further, our network analysis reveals that ligand binding has “network-bridging effects” on the DHFR structure. Our results suggest that ligand binding leads to a modification, with most of the interaction networks now passing through the cofactor, shortening the average shortest path. Ligand binding at the active site has profound effects on the network centrality, especially the closeness.
Highlights
Extensive experimental studies of dihydrofolate reductase (DHFR) have provided rich data toward the structure– function relationship in proteins
Agarwal et al carried out genomic analysis of sequence conservation, kinetic measurements of multiple mutations, and theoretical calculations, observing that nonbonded residue interactions in DHFR form a network of coupled motions that are important for enzyme catalysis [4]
When we look at the closeness centrality, we see that the cuttings in the folding element group cause larger deviation in the bindingrelated regions compared with the native DHFR structures
Summary
Extensive experimental studies of dihydrofolate reductase (DHFR) have provided rich data toward the structure– function relationship in proteins. Based largely on the conformation of the Met-20 loop [3], the three states of the enzymatic reaction process (binding and release of cofactor, substrate, and product) can be defined using available crystal structures (Figure 1). In the closed state (Figure 1, blue), the Met-20 loop packs against the cofactor and seals the active site. Simulations of the closed state indicate changes in the other side of the binding pocket, in the helix region (residues 44 to 50), which binds the cofactor. Agarwal et al carried out genomic analysis of sequence conservation, kinetic measurements of multiple mutations, and theoretical calculations, observing that nonbonded residue interactions in DHFR form a network of coupled motions that are important for enzyme catalysis [4].
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