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Analysis of Hot Region Organization in Hub Proteins

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Abstract

Protein interaction maps constructed from binary interactions reveal that some proteins are highly connected to others (acting as hub proteins), whereas some others have a few interactions (at the edges of the map). This paper addresses hub proteins from a structural point: interfaces. It investigates how hot spots are organized in hub proteins (hot regions). We annotate interfaces as the ones between two date-hubs (DD), two party hubs (PP), and two non-hubs (NN). We investigate the physico-chemical properties of these three types of interfaces focusing on the accessible surface area distribution, hot region organization, and amino acid composition differences. Results reveal that there are significant differences between DD and PP interfaces. More of the hot spots are organized into the hot regions in DD interfaces compared to PP ones. A high fraction of the interfaces are covered by hot regions in DD interfaces. There are more distinct hot regions in DDs. Since the same (or overlapping) DD interfaces should be used repeatedly, different hot regions can be used to bind to different partners. Further, these hot region characteristics can be used to predict whether a given hub interface is involved in a DD or a PP interface type with 80% accuracy.

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Acknowledgments

We thank Nurcan Tuncbag for providing Protein G complexes. This project has been supported by TUBITAK (Research Grant No 109T343 and 109E207).

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Authors and Affiliations

  1. Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Rumeli Feneri Yolu, 34450, Sariyer Istanbul, Turkey

    Engin Cukuroglu, Attila Gursoy & Ozlem Keskin

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  1. Engin Cukuroglu
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  2. Attila Gursoy
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  3. Ozlem Keskin
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Correspondence to Ozlem Keskin.

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Associate Editor Michael S. Detamore oversaw the review of this article.

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Cukuroglu, E., Gursoy, A. & Keskin, O. Analysis of Hot Region Organization in Hub Proteins. Ann Biomed Eng 38, 2068–2078 (2010). https://doi.org/10.1007/s10439-010-0048-9

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  • DOI: https://doi.org/10.1007/s10439-010-0048-9

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