Identifying Functional Sites Based on Prediction of Charged Group Behavior实验方法详情页

Abstract

This protocol describes the implementation and interpretation of THEMATICS, a simple computational predictor of functional information for proteins from the three?dimensional structure. This method is based on the computation of the electrical potential function for the protein and the calculation of the predicted titration curves for each of the titratable groups in the protein. While most of the titratable residues in a protein have predicted titration behavior that fits the Henderson?Hasselbalch equation, the ionizable residues in the active site generally deviate dramatically from the typical behavior. From the calculated titration curves, one identifies those residues that deviate significantly from Henderson?Hasselbalch behavior. A cluster of two or more of such deviant titratable residues in physical proximity is a reliable predictor of active?site location.

Keywords: THEMATICS; protein function prediction; active sites; titration; functional genomics

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Materials

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Figures

Figure 8.6.1 Alanine racemase tyrosines. Predicted titration curves (ensemble average charge C as a function of the pH) for tyrosine residues Y225 (solid squares), Y239 (hollow circles), Y265 (solid triangles), Y269 (hollow triangles), and Y284 (solid diamonds) in one of the two subunits of the alanine racemase dimer.

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Figure 8.6.2 TIM histidines. Predicted titration curves (ensemble average charge C as a function of the pH) for histidine residues H26 (plus signs), H95 (times signs), H100 (asterisks), H115 (hollow squares), H185 (solid squares), H195 (hollow circles), H224 (solid circles), and H248 (hollow triangles) in one of the two subunits of the triosephosphate isomerase (TIM) dimer.

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Figure 8.6.3 HPPK aspartates. Predicted titration curves (ensemble average charge C as a function of the pH) for aspartate residues D49 (hollow squares), D95 (hollow circles), D97 (solid triangles), D117 (hollow triangles), and D153 (hollow diamonds) in HPPK.

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