engleski

Protein Secondary Structure Conformations and Associated Hydrophobicity Scale

We have developed conformational preference functions and a hierarchy of algorithms that can evaluate the success of each hydrophobicity scale in predicting protein secondary conformation. The results of such evaluation are shown for fiftyfive different scales with respect to their ability to predict alpha- helix, beta-sheet and coil structure in three testing sets of proteins: five integral membrane proteins, twelve alpha-class and sixteen beta-class soluble proteins. Our scale of conformational parameters is the best predictor of secondary structure segments in membrane proteins and alpha-class proteins. The success rate and correlation coefficient for alpha-helix conformation in membrane proteins are 76% and 0.46 respectively, which is superior to the performance measures attained with other prediction schemes. Evaluation of solution hydrophobicity scales, often used to predict transmembrane segments in membrane proteins, indicated absence of correlation in prediction of helix segments and experimental results for the conformation of membrane proteins. Such scales have better performance (correlation coefficient around 0.30) in predicting sheet conformation in the beta-class proteins.

amino-acid-residues ; photosynthetic reaction center ; globular-proteins ; alpha-helices ; rhodopseudomonas-viridis ; energetic approach ; membrane-proteins ; side-chains ; beta-sheet ; prediction

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