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?