Regensburg 2013 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 8: Posters: Proteins

BP 8.21: Poster

Montag, 11. März 2013, 17:30–19:30, Poster B2

Discerning overall and internal motion of flexible molecules — •Florian Sittel and Gerhard Stock — University of Freiburg

Classical molecular dynamics (MD) simulations allow us to study the structure and dynamics of biomolecules in microscopic detail. To extract the internal molecular motion from an MD trajectory, first the overall motion of the molecule needs to be removed. This procedure is well established in the case that the molecule is almost rigid, i.e. if the vibrational dynamics is well described by small-amplitude motion around an equilibrium structure. In the case of a flexible molecule, however, the transformation does not completely decouple internal and rotational motion due to rotovibrational coupling. In this work, we study the range of validity and applicability of commonly used rotational fitting techniques. To this end, we adopt previously performed MD simulations of polyalanine and villin and compare their conformational distribution in internal and Cartesian coordinates. The study reveals that the free energy landscape of a Cartesian PCA can exhibit remarkable artifacts. Cartesian coordinates on the other hand, may be superior for the study of small-amplitude functional motions in proteins.