PMID: 9552160Apr 29, 1998Paper

Prediction of the three-dimensional structure of proteins using the electrostatic screening model and hierarchic condensation

Proteins
F Avbelj, L Fele

Abstract

We describe a method for predicting the three-dimensional (3-D) structure of proteins from their sequence alone. The method is based on the electrostatic screening model for the stability of the protein main-chain conformation. The free energy of a protein as a function of its conformation is obtained from the potentials of mean force analysis of high-resolution x-ray protein structures. The free energy function is simple and contains only 44 fitted coefficients. The minimization of the free energy is performed by the torsion space Monte Carlo procedure using the concept of hierarchic condensation. The Monte Carlo minimization procedure is applied to predict the secondary, super-secondary, and native 3-D structures of 12 proteins with 28-110 amino acids. The 3-D structures of the majority of local secondary and super-secondary structures are predicted accurately. This result suggests that control in forming the native-like local structure is distributed along the entire protein sequence. The native 3-D structure is predicted correctly for 3 of 12 proteins composed mainly from the alpha-helices. The method fails to predict the native 3-D structure of proteins with a predominantly beta secondary structure. We suggest that the hie...Continue Reading

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Citations

Jan 24, 2007·Protein Science : a Publication of the Protein Society·Franc Avbelj, Simona Golic Grdadolnik
Sep 15, 2000·Journal of Molecular Biology·K F Fischer, S Marqusee

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