E. Fadrná
1, J. Fukal1, and J. Koča1,2 

1National Centre of Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno
2Department of Organic Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno


Restriction endonuclease HincII cleaves DNA at GTPyPuAC sequence. X-ray structure of Hinc II/DNA complex was determined with the central sequence GTCGAC in DNA 13mer [1] and in complex with Ca2+ ions [2] which serves as an inhibitor. Magnesium is an essential cofactor for this enzyme. Cleavage leads to inversion of configuration at the scissille phosphate and results in two DNA fragments with 3'-OH and a 5'-phosphate.

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.

Exploring molecular tunnels brings some explanation of the ion transport between active sites and bulk solvent. Although electrostatics can strongly control this process (and maybe refuse it), this possibility of ion exchange is still there. However, negative electrostatic potential is concentrated around active sites and around DNA (due to phosphates) and the ions may get inside during the early stage of folding.

Computational tools can provide a deeper insight into the structure and dynamics of the  protein/DNA complex active site and can describe experimentally unknown features of the complex. Also the role of possible mutations in DNA or protein can be usefull in evaluation of activity and prediction of complex dynamics.


 [1] N.C. Horton, L.F. Dorner & J.J. Perona, Nature Structural Biology, 9 (2002), 42-47.

[2] Ch. Etzkorn & N.C. Horton, Biochemistry, 43 (2004), 13256-13270.