doi:10.1038/npre.2010.4468.1 Open Source Kinesin-1 Stochastic Simulation and Gliding Assay Tracking Software Lawrence J. Herskowitz1, Anthony L. Salvagno1, Brian P. Josey1, Andy Maloney1 & Steven J. Koch1 Correspondence: (Login to view email address) University of New Mexico, Deptartment of Physics and Astronomy and CHTM PDF (2 MB) Document Type: Poster Date: Received 18 May 2010 19:46 UTC; Posted 19 May 2010 Subjects: Molecular Cell Biology Tags: gliding motility assay kinesin-1 kinesin microtubules stochastic simulation Abstract: Kinesin-1 (conventional kinesin) is a homodimeric motor protein important for axonal transport. It has been well studied through ensemble and single-molecule assays. However, the enzymatic stepping cycle is complex, with many rate constants that are modulated by interaction of the two motor domains. This makes it difficult to predict how changes in a given rate constant may affect observable properties such as processivity, velocity, or stall force. We have written a simulation of kinesin walking using a Stochastic Simulation Algorithm. The model allows for interactions between the heads, and includes states that are not considered part of the normal cycle. This adds to the complexity of the model but also allows for probing rare events, such as those that lead to a finite processivity. Also included are rate constant dependencies on force and concentrations of ATP, ADP, and Pi, which may provide insight into other processes under investigation, such as kinesin backstepping. We intend to use the simulation to aid in interpreting our own gliding motility assay results and to place upper and lower limits on values for rate constants. Our source and executable codes will be freely available. Acknowledgements: This work was supported by the DTRA CB Basic Research Program under Grant No. HDTRA1-09-1-008. Presented at: Thermodynamics and Kinetics of Molecular Motors, 20 May 2010 Discussion Comments: 0 comments Share: (Login to share with a colleague) Additional information License: This document is licensed to the public under the Creative Commons Attribution 3.0 License How to cite this document: Herskowitz, Lawrence, Salvagno, Anthony, Josey, Brian, Maloney, Andy, and Koch, Steven. Open Source Kinesin-1 Stochastic Simulation and Gliding Assay Tracking Software. Available from Nature Precedings (2010) Version info: Other versions of this document in Nature Precedings None. Other versions of this document elsewhere on the web None known.