Paper Citing NAMD - Abstract
Patriche, Simona; Matsushita, Shinji; Banu, Mihaela; Epureanu, Bogdan I.; Adachi, Taiji
Atomistic Mechano-Chemical Modeling of Kinesins
BIOINSPIRATION, BIOMIMETICS, AND BIOREPLICATION, 7975 Art. No. 797519, 2011
This work is concerned with the dynamics of motor proteins. In particular, we discuss the development of computational analysis tools for predicting the dynamics of molecular motors such as certain types of kinesin. The ability to model and predict how these biomolecular machines work forms the critical link to biotechnological device development, including lab-on-a-chip applications and many others. The focus of this research is on the identification and modeling of nonlinear dynamic phenomena caused by coupled thermal, chemical, and mechanical fields. A mechanistic model of kinesin has been developed recently at the University of Michigan. This model accounts for transient dynamics and uses parameters which have to be identified from experimental data and/or from first principles. In this work, accurate atomistic simulations using a monomeric human kinesin structure (PDB ID: 1MKJ, 2.70 Angstroms resolution) is used instead of experimental data to obtain key nano-scale properties of the motor protein. The approach allows an accurate bridging between nano-scale processes occurring over pico seconds and micron- or millimeter-scale processes occurring over seconds.
