CINF 66 |
| 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 10 folding-element regions and in 9 non-folding element regions as observed by experiment. Our studies suggest that even though the cutting in the folding element area may not destroy the protein structure, chain cleavage in these regions may de-activate DHFR due to large perturbations in the network properties near the active site. Protected areas are often associated with protein folding; however, our study indicates that chain connection in protected areas may also be important for network interactions. Further, our network analysis reveals that ligand binding has “network bridging effects” on the DHFR structure. The protein active site is near or coincides with residues through which the shortest paths in residue interaction network tend to go. 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. This work was supported by grant 2 G12 RR003048 from the RCMI Program, Division of Research Infrastructure, National Center for Research Resources, NIH |
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Advances in 3-D Pharmacaphores and 3-D Searching
2:00 PM-5:30 PM, Tuesday, March 27, 2007 Hyatt Regency McCormick -- 12 B, Oral
Division of Chemical Information |