Predicting Free Energy Contribution to the Conformational Stability of Folded Proteins From the Residue Sequence with Radial Basis Function Networks

Rita Casadio, Mario Compiani , Piero Fariselli and Francesco Vivarelli

Radial basis function neural networks are trained on a data base comprising 38 globular proteins of well resolved crystallographic structure and the corresponding free energy contributions to the overall protein stability (as computed partially from chrystallographic analysis and partially with multiple regression from experimental thermodynamic data by Ponnuswamy and Gromiha (1994)). Starting from the residue sequence and using as input code the percentage of each residue and the total residue number of the protein, it is found with a cross-validation method that neural networks can optimally predict the free energy contributions due to hydrogen bonds, hydrophobic interactions and the unfolded state. Terms due to electrostatic and disulfide bonding free energies are poorly predicted. This is so also when other input codes, including the percentage of secondary structure type of the protein and/or residue-pair information are used. Furthermore, trained on the computed and/or experimental DG values of the data base, neural networks predict a conformational stability ranging from about 10 to 20 kcal/mol rather independently of the residue sequence, with an average error per protein of about 9 kcal/mol.

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