Computational study of restriction endonuclease HincII
| Authors | |
|---|---|
| Year of publication | 2007 |
| Type | Article in Proceedings |
| Conference | Materials Structure, vol. 14, no. 1 (2007), 6th Discussions in Structural Molecular Biology |
| MU Faculty or unit | |
| Citation | |
| Field | Biochemistry |
| Keywords | molecular modeling; restriction endonuclease; HincII |
| Description | We have examined the stability and/or dynamics of protein/DNA complex HincII by computational tools. Although molecular dynamics is not able to follow the reaction mechanism itself, it may serve as a good tool to describe reaction partners or intermediates. We want to describe the structure of the complex to provide detailed view of the active site and relationships in it. The stability of the ions coordination can be seen from our simulations, as well as electrostatics around them. We attempt to bring some ideas about the structure of the active site and possible role of the ions in it. We have found strong electrostatic potential around catalytic aminoacids, which is ballanced by presence of ions. It leads to the idea that B site ion is required at least to stabilize the reaction environment. |
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