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PEDS Advance Access published online on December 2, 2008
Protein Engineering Design and Selection, doi:10.1093/protein/gzn074
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org

Comparative analysis of the packing topology of structurally important residues in helical membrane and soluble proteins

Vagmita Pabuwal1 and Zhijun Li1,2,3,4

1Departments of Chemistry and Biochemistry 2Bioinformatics and Computer Science, University of the Sciences in Philadelphia, Philadelphia, PA 19104, USA 3Institute for Translational Medicine and Therapeutics, University of the Pennsylvania, Philadelphia, PA 19104, USA

4 To whom correspondence should be addressed. E-mail: z.li{at}usp.edu

Elucidating the distinct topology of residue packing in transmembrane proteins is essential for developing high-quality computational tools for their structure prediction. Network approaches transforming a protein’s three-dimensional structure into a network have proven useful in analyzing various aspects of protein structures. Residues with high degree of connectivity as identified through network analysis are considered to be important for the stability of a protein’s folded structure. It is thus of interest to study the packing topology of these structurally important residues in membrane proteins. In this work, we systematically characterized the importance and the spatial topology of these highly connected residues in helical membrane and helical soluble proteins from several aspects. A representative helical membrane protein and two helical soluble protein structure data sets were compiled and analyzed. Results of analyses indicate that the highly connected amino acid residues in membrane proteins are more scattered peripherally and more exposed to the membrane than in soluble proteins. Accordingly, they are less densely connected with each other in membrane proteins than in soluble proteins. Together with the knowledge of a centralized function site for many membrane proteins, these findings suggest a structure–function model that is distinguishable from soluble proteins.

Keywords: hub-residue/membrane protein/network/residue packing

Received August 29, 2008; revised October 24, 2008; accepted November 12, 2008.


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