Structural Modeling and Molecular Dynamics Simulation of the Actin Filament
Please always quote using this URN:urn:nbn:de:0296-matheon-11076
- Actin is a major structural protein of the eukaryotic cytoskeleton and enables cell motility. Here, we present a model of the actin filament (F-actin) that incorporates the global structure of the recently published model by Oda et al. but also conserves internal stereochemistry. A comparison is made using molecular dynamics simulation of the model with other recent F- actin models. A number of structural determents such as the protomer propeller angle, the number of hydrogen bonds and the structural variation among the protomers are analyzed. The MD comparison is found to reflect the evolution in quality of actin models over the last six years. In addition, simulations of the model are carried out in states with both ADP or ATP bound and local hydrogen-bonding differences characterized. The results point to the significance of a direct interaction of Gln137 with ATP for activation of ATPase activity after the G-to-F-actin transition.
Author: | Thomas Splettstoesser, Kenneth C. Holmes, Frank Noe, Jeremy C. Smith |
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URN: | urn:nbn:de:0296-matheon-11076 |
Referee: | Christof Schütte |
Document Type: | Preprint, Research Center Matheon |
Language: | English |
Date of first Publication: | 2012/02/27 |
Release Date: | 2012/02/27 |
Institute: | Research Center Matheon |
Freie Universität Berlin | |
MSC-Classification: | 62-XX STATISTICS / 62Mxx Inference from stochastic processes / 62M05 Markov processes: estimation |
Preprint Number: | 932 |