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Identifying protein–protein interaction sites in transient complexes with temperature factor, sequence profile and accessible surface area

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Abstract

Transient protein–protein interactions play a vital role in many biological processes, such as cell regulation and signal transduction. A nonredundant dataset of 130 protein chains extracted from transient complexes was used to analyze the features of transient interfaces. It was found that besides the two well-known features, sequence profile and accessible surface area (ASA), the temperature factor (B-factor) can also reflect the differences between interface and the rest of protein surface. These features were utilized to construct support vector machine (SVM) classifiers to identify interaction sites. The results of threefold cross-validation on the nonredundant dataset show that when B-factor was used as an additional feature, the prediction performance can be improved significantly. The sensitivity, specificity and correlation coefficient were raised from 54 to 62%, 41 to 45% and 0.20 to 0.29, respectively. To further illustrate the effectiveness of our method, the classifiers were tested with an independent set of 53 nonhomologous protein chains derived from benchmark 2.0. The sensitivity, specificity and correlation coefficient of the classifier based on the three features were 63%, 45% and 0.33, respectively. It is indicated that our classifiers are robust and can be applied to complement experimental techniques in studying transient protein–protein interactions.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (Grant Nos. 90608020, 30370354, and 90203011), NCET-060651, the National Platform Project of China (Grant No. 2005DKA64001), and the Ministry of Education of China (Grant Nos. 20050487037 and 505010).

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Correspondence to Yanhong Zhou.

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The list of 130 chains and corresponding partner chains (DOC 54 kb)

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Liu, R., Jiang, W. & Zhou, Y. Identifying protein–protein interaction sites in transient complexes with temperature factor, sequence profile and accessible surface area. Amino Acids 38, 263–270 (2010). https://doi.org/10.1007/s00726-009-0245-8

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  • DOI: https://doi.org/10.1007/s00726-009-0245-8

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