Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations - September 10-14, 2014, Istanbul, Turkey

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.

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