Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data

and Computer Simulations

Poster Abstracts

28-POS

Board 28

Molecular Dynamics Simulations of Kinesin Eg5 using a Structure Based Model

Jose C. Flores-Canales

1,2

, Keehyoung Joo

1,2

, Steven P. Gross

3,1

, Jooyoung Lee

1,2

Korea Institute for Advanced Study, Seoul, South Korea,

Korea Institute for Advanced Study,

Seoul, South Korea,

University of California, Irvine, Irvine, CA, USA.

Eg5 belongs to the kinesins family of molecular motors, which move along microtubules by

using the energy of ATP hydrolysis. Eg5 has an essential role in mitotic cell division, and as

such, disruption of its function has a considerable interest for development of new drugs for

oncogenic treatment. While usually a tetramer, here we studied a truncated Eg5 dimer, consisting

of two catalytic domains, each of which is joined by a neck linker to one terminus of a coiled-

coil domain. Based on multiple experiments, it is generally believed that kinesins move along

microtubules using a hand over hand mechanism, involving the binding of ATP to the

nucleotide-binding region, ATP hydrolysis, and subsequent release of ADP. Importantly, these

changes are coupled to the docking state of the neck-linker structural motif. Docking of the latter

transmits mechanical force between the two catalytic domains. However, this model does not

provide a detailed dynamic description of the coupling between multiple states of the neck-linker

and nucleotide-binding region. In this work, we present a structure based model and molecular

dynamics (MD) simulations of Eg5.

Eg5’s X-ray structures in ATP- and ADP-bound states have suggested that conformational

changes in the nucleotide-binding site are coupled to both the generation of force and to motion

along microtubules. To gain insight on the coupling of ligand binding and generation of force,

we have carried out multiple independent MD runs of the transition from the ATP- to ADP-

bound state. We constructed a dual-basin structure-based model using Lorentzian restrains.

Analysis shows that there is a weak coupling of switch I and the neck-linker. Furthermore,

principal component analysis shows that there are multiple pathways of transition from ATP- to

ADP-bound state. An interpretation of this pathway diversity for Eg5 is provided.