Molecular dynamics simulations of microtubules in the external electric field

Dnr:

SNIC 2017/3-28

Type:

SNAC Small

Principal Investigator:

Alexandr Nasedkin

Affiliation:

Chalmers tekniska högskola

Start Date:

2017-03-02

End Date:

2018-04-01

Primary Classification:

10603: Biofysik

Webpage:

Allocation

Abstract

Microtubules form cellular cytoskeleton, they support structure of the cell, involved in intracellular transport and cell division, ultimately control cell ageing and degeneration. Microtubules attracted a lot of research interest in the past decades. For example, microtubules proved to be promising targets in cancer treatment. A number of microtubule-binding drugs were developed to suppress certain cancer cell division. Another approach to control cell development is to apply external stimuli affecting cell signaling and internal transport. It is believed that microtubules transfer signals by mechanical transduction and polarization. However, little is known about mechanical wave propagation across the microtubule. Even less information is available concern polarization events which accompany protein structural changes. Individual microtubule is a cylinder-like structure, which walls are consist of specific protein - tubulin. Tubulin molecule is evolutionary designed to bind sidewise with its copy. The binding could be at different angles, which provides diversity in microtubule sizes (from 9 to 17 units in the radial cross-section). Moreover, tubulin surface is charged and the molecule has a large dipole moment. This feature of tubulin also diversifies electric properties of microtubules. Recently our group proposed to use X-ray solution scattering measurements (SAXS/WAXS) to monitor structural changes induced by electric field excitation. This computation project should support the ongoing experimental work and analysis of the collected data. Aims for this computational project: 1. Molecular dynamics (MD) simulation of tubulin protein in the oscillating electric field (MHz to GHz frequency range). It is unknown how the oscillating electric field changes a number of physical properties of tubulin in and if its structure is affected. To test this we aim to set a series of short MD simulations. We aim to use GROMACS simulation package. Configuring and running such simulations will, most probably, encounter several know-hows. However, we believe to succeed in this field since my previous experience with GROMACS. 2. Proof-of-concept microtubule MD simulations in GROMACS. We aim to run test simulations of the microtubule. We believe that even a very short (ps-range) would be very helpful in analyzing recently collected X-ray scattering data. Moreover, MD simulations of such a system contribute positively to computational experience within the group.