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Protein Science (2008), 17:72-78. Published by Cold Spring Harbor Laboratory Press. Copyright © 2008 The Protein Society
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Identification of transient hub proteins and the possible structural basis for their multiple interactions

Miho Higurashi1, Takashi Ishida1, and Kengo Kinoshita1,2

1 Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
2 Structure and Function of Biomolecules, SORST JST, Kawaguchi, Saitama 332-0012, Japan

(RECEIVED August 27, 2007; FINAL REVISION October 5, 2007; ACCEPTED October 5, 2007)

Proteins that can interact with multiple partners play central roles in the network of protein–protein interactions. They are called hub proteins, and recently it was suggested that an abundance of intrinsically disordered regions on their surfaces facilitates their binding to multiple partners. However, in those studies, the hub proteins were identified as proteins with multiple partners, regardless of whether the interactions were transient or permanent. As a result, a certain number of hub proteins are subunits of stable multi-subunit proteins, such as supramolecules. It is well known that stable complexes and transient complexes have different structural features, and thus the statistics based on the current definition of hub proteins will hide the true nature of hub proteins. Therefore, in this paper, we first describe a new approach to identify proteins with multiple partners dynamically, using the Protein Data Bank, and then we performed statistical analyses of the structural features of these proteins. We refer to the proteins as transient hub proteins or sociable proteins, to clarify the difference with hub proteins. As a result, we found that the main difference between sociable and nonsociable proteins is not the abundance of disordered regions, in contrast to the previous studies, but rather the structural flexibility of the entire protein. We also found greater predominance of charged and polar residues in sociable proteins than previously reported.

Keywords: hub protein; protein–protein interaction; transient interaction; three-dimensional structure; intrinsic disorder


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 Nucleic Acids ResHome page
M. Higurashi, T. Ishida, and K. Kinoshita
PiSite: a database of protein interaction sites using multiple binding states in the PDB
Nucleic Acids Res., October 4, 2008; (2008) gkn659v1.
[Abstract] [Full Text] [PDF]


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