Prediction of the disulfide-bonding state of cysteine in proteins

The bonding states of cysteine play important functional and structural roles in proteins. In particular, disulfide bond formation is one of the most important factors influencing the three-dimensional fold of proteins. Proteins of known structure were used to teach computer-simulated neural networks rules for predicting the disulfide-bonding state of a cysteine given only its flanking amino acid sequence. Resulting networks make accurate predictions on sequences different from those used in training, suggesting that local sequence greatly influences cysteines in disulfide bond formation. The average prediction rate after seven independent network experiments is 81.4% for disulfide-bonded and 80.0% for non-disulfide-bonded scenarios. Predictive accuracy is related to the strength of network output activities. Network weights reveal interesting position-dependent amino acid preferences and provide a physical basis for understanding the correlation between the flanking sequence and a cysteine's disulfide-bonding state. Network predictions may be used to increase or decrease the stability of existing disulfide bonds or to aid the search for potential sites to introduce new disulfide bonds.