Automated determination of interhelical angles for protein alpha helices from coordinate data Robert Fraser, James Stewart, Janice Glasgow Queen's University.

Automated determination of interhelical angles for proteinalpha helices from coordinate

data

Robert Fraser, James Stewart, Janice Glasgow

Queen's University School of Computing, Kingston, ON

• Protein Structure

• Contact Maps

• Helix Packing Models

• Proposed Method

• Results

The HUGE picture

• Sequence Structure

• Structure Function

• I’m working on a tiny bit of the first step

Protein Structure

• Different levels of structure• We’re interested in alpha helices

Used with permission from Petsko, G.A. and D. Ringe, Protein Structure and Function, 2004

Contact Maps

• Distance map represents full 3D structure• Contact map is a binary version• 10Ǻ threshold used here

Knobs and Holes

• Steric surface of the molecule

Two surfaces to a helix

Sign is important

Angle method

• if (da × db) · (b0 – a0) > 0

• then the top vector is rotated clockwise• else the top vector is rotated counter-clockwise• Clockwise negative sign

Comparison to observed values

Results

• 4.1° +/- 3.2° of observed data

• 3.6° +/- 1.9° after removing an outlier

Acknowledgements

• Kelly Fraser• Janice Glasgow • James Stewart• Henk Meijer • Mehdi Hedjazi• Alan Ableson• Eduardo Zuviria • Tony Kuo

Thank you

• Questions?