%0 Journal Article %J Protein Engineering %D 2001 %T Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY-YIG superfamily member, using NMR restraints and Monte Carlo dynamics %A Janusz M. Bujnicki %A Piotr Rotkiewicz %A Andrzej Koliński %A Leszek Rychlewski %K Algorithms %K Binding Sites %K Biomolecular %K Endodeoxyribonucleases %K Endodeoxyribonucleases: chemistry %K Models %K Molecular %K Monte Carlo Method %K Nuclear Magnetic Resonance %K Protein Structure %K Sequence Alignment %K Tertiary %X Using a recent version of the SICHO algorithm for in silico protein folding, we made a blind prediction of the tertiary structure of the N-terminal, independently folded, catalytic domain (CD) of the I-TevI homing endonuclease, a representative of the GIY-YIG superfamily of homing endonucleases. The secondary structure of the I-TevI CD has been determined using NMR spectroscopy, but computational sequence analysis failed to detect any protein of known tertiary structure related to the GIY-YIG nucleases (Kowalski et al., Nucleic Acids Res., 1999, 27, 2115-2125). To provide further insight into the structure-function relationships of all GIY-YIG superfamily members, including the recently described subfamily of type II restriction enzymes (Bujnicki et al., Trends Biochem. Sci., 2000, 26, 9-11), we incorporated the experimentally determined and predicted secondary and tertiary restraints in a reduced (side chain only) protein model, which was minimized by Monte Carlo dynamics and simulated annealing. The subsequently elaborated full atomic model of the I-TevI CD allows the available experimental data to be put into a structural context and suggests that the GIY-YIG domain may dimerize in order to bring together the conserved residues of the active site. %B Protein Engineering %V 14 %P 717–721 %8 oct %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/11739889