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

COMP 190

Vagmita Pabuwal, vpabuwal@mail.usp.edu, Department of Chemistry and Biochemistry, University of Sciences in Philadelphia, 600 South, 43rd Street, Philadelphia, PA 19104 and Zhijun Li, z.li@usp.edu, Department of Bioinformatics and Computer Science, University of Sciences in Philadelphia, 600 south 43rd street, philadelphia, PA 19104.
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.
 

Poster Session
6:00 PM-8:00 PM, Tuesday, August 18, 2009 Walter E. Washington Convention Center -- Ballroom A, Poster

Division of Computers in Chemistry

The 238th ACS National Meeting, Washington, DC, August 16-20, 2009