DPG Phi
Verhandlungen
Verhandlungen
DPG

Dresden 2017 – scientific programme

Parts | Days | Selection | Search | Updates | Downloads | Help

BP: Fachverband Biologische Physik

BP 24: Posters - Protein Structure and Dynamics

BP 24.5: Poster

Tuesday, March 21, 2017, 14:00–16:00, P1A

Identification of reaction coordinates for functional dynamics: understanding the molecular pacman T4 Lysozyme — •Matthias Ernst, Steffen Wolf, and Gerhard Stock — Biomolecular Dynamics, University of Freiburg, Germany

T4 Lysozyme is a model system for both experimental and computational investigations of functional protein dynamics. The major functional dynamics is a hinge-bending motion between its two domains which occurs on a timescale of 10-20µs[1]. Yet, the Free energy landscape based on widely applied reaction coordinates like the radius of gyration or the root mean square deviation to the crystal structure shows a barrier that is much too small to explain this timescale. Hence, there must be mechanistic details that require other reaction coordinates.

Using a combination of distance-based principal component analysis[2] on a 50us long equilibrium trajectory of T4L and inverse targeted molecular dynamics simulations[3], we could identify new reaction coordinates describing local structural rearrangements which act as a locking mechanism. We find two intermediate states on the path between "open" and "closed" which slow down the process. Thus, we propose a hierarchical four-state model that can explain the observed timescales semi-quantitatively.
R.B. Yirdaw and H.S. Mchaourab, Biophys.J. 2012, 103(7), 1525.
M. Ernst, F. Sittel and G. Stock, J.Chem.Phys. 2015, 143, 244114.
J. Schlitter, M. Engels and P. Krüger, J.Mol.Graph. 1994, 12, 84.

100% | Mobile Layout | Deutsche Version | Contact/Imprint/Privacy
DPG-Physik > DPG-Verhandlungen > 2017 > Dresden