Original scientific paper

Predicting Membrane Protein Secondary Structure:Preference Functions Method for Finding Optimal Conformational Parameters

Davor Juretić ; Physics Department, Faculty of Science, University of Split, N. Tesle 12, 58000 Split, Croatia
Bono Lučić ; Physics Department, Faculty of Science, University of Split, N. Tesle 12, 58000 Split, Croatia
Nenad Trinajstić ; Physics Department, Faculty of Science, University of Split, N. Tesle 12, 58000 Split, Croatia

Abstract

An automated iterative method is developed for predicting secondary conformation in membrane proteins. The initial set of parameters are a-helix preferences and associated conformational preference functions extracted from the data set of known soluble protein structures. The secondary structure segments are assigned to each of 14 tested membrane proteins by using the prediction method, which evaluates and compares preference functions in the tested protein. A new set of parameters are then calculated which is based on the predicted protein structure from the previous iterative cycle. The method takes advantage of the similarities in local sequence patterns found in the tested proteins. Residues in membrane proteins are predicted with 84% accuracy and with the correlation coefficient for the a-helix structure equal to 0.68, which is a considerably better performance than that of neural network programs or Garnier-Robson’s algorithm.

Keywords

Hrčak ID:

137107

URI

https://hrcak.srce.hr/137107

Publication date:

1.6.1993.

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