108
Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery Poster Session II
53-POS
Board 6
Do Not Call Me α, I Am π-helix
Prasun Kumar
, Manju Bansal.
Indian Institute of Science, Bangalore, India.
Existing secondary structure identification methods identify very few π-helices in the structures
available in Protein Data Bank (PDB). The path traversed by Cα atoms is used to devise a new
method for the identification of secondary structure elements (SSEs) in proteins and is
designated as ASSP (Assignment of Secondary Structure in Proteins). Using ASSP to search a
non-redundant subset of high-resolution and well-refined protein structures comprising of 3582
protein chains, we found total of 574 π-helices with average unit twist and rise being 85.2˚and
1.2 Å respectively. A total of 391 (68%) π-helices were found at the termini of α-helices with a
majority (312) of them being present at the C-termini. The size of the dataset allowed us to
analyze the position wise preference for the commonly occurring 20 amino acids within and
around π-helices. They show certain positional amino acid preferences and these are different
from those of α-helices. Amino acid propensities in π-helices were found to be context
dependent, viz. occurring independently, or at N-terminus, C-terminus or middle of α helices.
They also influence the preference of amino acids in the flanking α-helices. Majority of
interspersed π-helices were found to be conserved across a large number of structures within a
family and introduce a kink or distortion in the neighboring α-helices. In addition to hydrogen
bonds, several other non-bonded interactions contributing to the stability of the π-helices have
also been identified and studied in detail. Finally, functional and structural role of π-helices have
been analyzed. Our analysis indicates that the conformation of the π-helix has evolved to provide
unique structural and functional features within a variety of proteins.
