Novel procedure for structure refinement in homology modeling and its application to the human class Mu glutathione S-transferases.

Glutathione S-transferases (GST) are a major class of phase II detoxifying enzymes that conjugate glutathione to electrophiles. Their involvement in the degradation of chemotherapeutic agents, which contributes to drug resistance, makes this family of enzymes potential targets for therapeutic agents. This study generates, by homology modeling, a 3-D structure of three GST human isozymes of the Mu class, M1b-1b, M2-2 and M3-3, using the Rat3-3 GST structure as a template. The high percentage of identity among these enzymes and the lack of insertions and deletions make the system ideally suited to the technique of homology modeling. A novel technique for the modeling of protein structures was applied. The structure of the template was used to generate a low-resolution crystallographic map in which the initial coordinates of the structure to be modeled were placed. The structure was then annealed within this envelope. In addition, a feedback-restrained molecular dynamics procedure was adopted to scale the template restraints during the simulations. Three independent validation procedures were applied. To assess the reliability of the methods, an identical series of simulation steps to those used in the refinement were applied to the template structure (self modeling). Further, a homology structure for the Rat3-3 template was generated, starting from the modeled M1b-1b structure (reverse modeling). To assess the reasonableness of the modeled structures, two recently developed methodologies to verify protein structures based on statistics of the nonbonded interactions were applied. Overall, the structures appear to be consistent.