Berlin 2015 – scientific programme

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BP: Fachverband Biologische Physik

BP 17: Posters: Protein structure and dynamics

BP 17.5: Poster

Monday, March 16, 2015, 17:30–19:30, Poster A

Dimensionality reduction of protein dynamics by employing distance and contact analysis — •Matthias Ernst and Gerhard Stock — University of Freiburg, 79104 Freiburg, Germany

To describe and understand protein dynamics, a reduction of the 3N-6 dimensional space of the N atoms involved is crucial. A commonly employed way to reduce dimensionality is principal component analysis (PCA), a linear transformation which removes linear correlations of the coordinates by diagonalizing their covariance matrix. As PCA results depends strongly on the type of coordinates, use of internal coordinates like dihedral angles (dPCA[1]) instead of cartesian atomic coordinates often provides higher resolution, especially for large-amplitude motion e.g. found in folding systems[2]. In contrast to dihedral angles which mainly reflect the behaviour of neighbouring residues in a protein, distances between pairs of atoms also contain information about residues further apart in the primary sequence.

We employ and classify different types of PCA for dimension reduction by quantities based on information theory and on their structural resolution. We show that analysis based on contact distances support the findings gained by dPCA and facilitate interpretation and visualization of the folding process by highlighting which contacts contribute to the folding transitions.

[1] Y. Mu, P. H. Nguyen, and G. Stock, Proteins 2005, 58, 45.

[2] F. Sittel, A. Jain and G. Stock, J. Chem. Phys. 2014, 141, 014111.