Validation of Techniques for Structure Prediction and Thermostabilization of a Protein

A Case Study Using the TIM-barrel Enzyme Lactate Oxidase

Abstract

Recently, a variety of methods for protein structure prediction have been developed. However, there are only a limited number of studies where the results have been adequately validated. With this in mind, we have evaluated our previously predicted model of lactate oxidase by comparison with the recently determined crystal structure. In addition, we also analyzed our thermotolerant mutants that were designed on the basis of a predicted model. The validity of these procedures was assessed by comparing the results of rational design against the interpretation of the thermostabilization mechanism. Specifically, we analyzed lactate oxidase (LOX), a useful lactic acid sensor, as an example for validation. LOX was chosen because it has an (β/α)8 barrel (TIM barrel) fold, which constitutes the basic structural framework of numerous important enzymes. We also propose an effective modeling method and thermostabilization technique for the TIM barrel fold.