Energy minimization and molecular dynamics studies of Asn-102 elastase

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Abstract
Four isomeric forms of the Asn-102 PPE (D 102 N mutant according to the emerging protocol, [Knowles, Science, 236 (1987) 1252–1258]) have been investigated using energy minimization (EM) and molecular dynamics (MD) techniques. MD simulation data for 175 ps are reported for each form (in total 700 ps for about 2500 atoms). The His-57 Nε-protonated forms are calculated to be more stable than the Nδ-protonated ones. The active site region of the most stable form is very similar to that found in the D102N rat trypsin enzyme [Craik et al., Science, 237 (1987) 909–913]. Conformations of the active sites and their hydrogen bond patterns are presented for each of these forms and are compared with the structure of the native enzyme active site. The pH dependent activity of the D102N derivative is discussed.