Berlin 2012 – scientific programme

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BP: Fachverband Biologische Physik

BP 1: Proteins I

BP 1.6: Talk

Monday, March 26, 2012, 11:00–11:15, H 1058

Characterization of Free Energy Landscape of Villin Headpiece with Principal Components Analysis by Parts (pPCA) — •Abhinav Jain and Gerhard Stock — Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg.

The free-energy landscape of flexible small peptides and nucleic acids can be quite complex, showing numerous metastable conformational states. On the other hand, various computational studies of proteins have given a comparatively simple picture of their energy landscape which is surprising at higher energies where the protein can reversibly fold and unfold. A method to analyze molecular dynamics (MD) simulations of protein folding is proposed, which is based on a principal component analysis (PCA) of the protein’s backbone dihedral angles.[1] Adopting extensive MD simulations of the villin headpiece by Pande and co-workers [2], it is shown that “PCA by parts” allows us to characterize the free-energy landscape of the protein with unprecedented detail.
Jain; Hegger; Stock. J. Phys. Chem. Lett. 2010, 1, 2769 - 2773
Ensign; Kasson; Pande. J. Mol. Biol. 2007, 374, 806 - 816.