Modeling the AKR/Opt-1 complex:

Methodology

Processing and rendering of the data used to generate the models.

Amino acids 2 to 61 of AKR were threaded using the data generated from the crystal structure of yeast TALE homeodomain protein MATá2 complexed to its recognition element. The amino acid sequence from position 2 to 61 of the AKR homeodomain (GenBank accession no. U25353) was submitted to SWISSPROT server at http://expasy.hcuge.ch/swissmod/SWISS-MODEL.html in FASTA format. This server threaded the á-carbons of AKR using the coordinates derived from the crystal structure of the MATá2 homeodomain complexed to DNA (MMDB ID 3857, PDB ID 1YRN). The resultant structure was then docked to a fragment of double-stranded DNA that was generated using Sybyl v6.4 software (Tripos Inc., St. Louis), as guided by the MATá2/DNA complex structure. The DNA sequence used was that of the optimal binding element of AKR, Opt-1 (5’-CTCTATGACAGATCT-3’, the hexanucleotide core binding element is underlined). Following energy minimization the homeodomain/DNA complex was analysed using Procheck, a program that checks the stereochemical quality of protein structures [Laskowski, RA, Macarthur, MW, Moss, DS, and Thornton, JM PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr. 1993, 26:283-291]. The figures derived from this model were generated using the Molscript and Raster3D programs [Kraulis, PJ. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr. 1991, 24:946-950. 4-16; Merrit, EA and Bacon, DJ Raster3D: photorealistic molecular graphics. Methods Enzymol. 1997, 277:505-524]. The surface model depicting the putative hydrophobic pocket of AKR was generated using GRASP [Nicholls, A., Sharp, K. A., and Honig, B. Protein folding and association: insights from interfacial and thermodynamic properties of hydrocarbons. Proteins 1991, 11:281-296].

Here is a sampling of these figures

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