Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

Structural and Functional Significance of Polypeptide phi, psi outliers

High-resolution X-ray crystal structures in the Protein Data Base typically present one or more residues with dihedral angles phi and psi of the polypeptide backbone that deviate from sterically allowed and energetically favored regions of the Ramachandran map. Previous analyses (Gunasekaran et al., 1996; Pal et al., 2002) indicated that the deviations cluster in phi, psi space and that certain small polar residue types are overrepresented among these outliers. These findings suggest that local interactions may compensate for unfavorable backbone energies. Some outliers are preserved in independently solved structures deposited in the database, suggesting functional relevance. The substantial expansion of the database since the time of the previous analyses prompted renewed evaluation of phi, psi outliers. Preliminary results of this analysis will be presented together with an evaluation of whether the dataset is currently large enough to address the following questions. What is the frequency of outlier residue types? Do local interactions define structural motifs? Is there a relationship between structural motifs and residue type? Do enzymes differ from non-enzyme proteins in frequency, identity, or local interactions of outliers? Are local interactions energetically compensatory?

References and Footnotes
  1. Gunasekaran, K., Ramakrishnan C., Balaram P. (1996) J. Mol. Biol. 264, 191?198.
  2. Pal, D., Chakrabarti, P. (2002) Biopolymers 63, 195?206.

Harish Balasubramanian1
Kenneth Gunasekera2
Jannette Carey1

1 Chemistry Department
Princeton University
Princeton NJ 08544-1009
2 Mount Sinai High School
Long Island, NY