Modeling zinc sulfhydryl bonds in zinc fingers

Molecular dynamics simulations have been carried out employing three different model descriptions of the zinc sulfhydryl interactions in class II fingers. One bonded and two nonbonded models were studied. Two variant structures of the glucocorticoid receptor DNA-binding; domain and a NMR structure from a fragment of methionyl-tRNA synthetase were subjected to long-time MD simulations with these models. Our analysis is focused on comparison with experimental and quantum mechanical data, concerning the local Zn-finger and overall structural and dynamic properties for these models. All models performed M ell, but the nonbonded models appeared to reproduce the protein dynamics in better agreement with experimental data than does the bonded description. (C) 2001 John Wiley & Sons, Inc.