Biophysics and Physics of Soft Active Matter
Theory and Mechanistic Modeling
Internship position (M2) available
Kinetic study of defect creation during microtubule polymerization
Project Description:
The goal of this internship is to conduct a theoretical kinetic study of topological defect creation in polymerizing microtubules.
Microtubules (MTs) are central structures in living cells, involved in cell division, migration, and intracellular transport. A complete understanding of the mechanisms regulating their dynamics and stability is a central issue in cell biology and a key challenge for human health. MTs are hollow cylindrical structures where tubulin dimers associate in a head-to-tail fashion into protofilaments, 13 of which form a tube by lateral association.
MTs grow by adding tubulin dimers to their extremities. It has been
know since the 1990's that the MT lattice contains topological
defects, the most prominent being dislocations [1]. However, recently it was discovered that monomer
vacancies [2], which engender so-called multi-seam
structures, are much more prevalent than dislocations. Currently, we
have no knowledge under which conditions monomer vacancies are created
during MT tip growth, as all models stipulate the head-to-tail
association of new dimers to existing protofilaments at the MT
extremity. The goal of this internship is to simulate MT tip growth
using a previously developed kinetic Monte Carlo and to determine the
lattice parameters (lattice binding energy and anisotropy) under which
monomer vacancies and multiseam structures can be formed. The obtained
lattice parameters are then critically compared to values found in the
literature.
With this project we expect to gain (i) a first understanding of the conditions of defect formation in the growing MT tip and (ii) narrow down MT lattice parameters, which vary hugely in the literature.
References:
[1] Chrétien, D., Metoz, F., Verde, F., Karsenti, E. and Wade,
R. H. Lattice defects in microtubules: protofilament numbers vary
within individual microtubules. J. Cell Biol. 117, 1031–1040 (1992).
[2] Guyomar, C., Bousquet, C., Ku, S., Heumann, J.M., Guilloux, G.,
Gaillard, N., Heichette, C., Duchesne, L., Steinmetz, M.O., Gibeaux,
R., and Chrétien, D. et al. Changes in seam number and location induce holes within microtubules
assembled from porcine brain tubulin and in xenopus egg cytoplasmic extracts. eLife 11, e83021 (2022).
Working environment:
The MC2 (Mécanique des Cellules en Milieu Complexe)
team at the LIPhy conducts interdisciplinary research at the interface of mechanics, physics, and life sciences, using experimental and theoretical approaches at different scales.
We offer an
interdisciplinary research environment with a close collaboration
between experimentalists and theoreticians. Grenoble is a dynamic city
with a big university (Université Grenoble-Alpes) and host to several
big research facillities (CNRS, CEA, ILL, ESRF,...). Its unique
location in the heart of the french Alpes makes it the ideal place for
outdoor activities.
Requirements:
The successful applicant has a background in physics or life sciences
with a strong interest in deciphering complex biological systems and
mathematical modeling. Excellent written and oral communication skills
(English) are desirable. Interested candidates are invited to email me
as soon as possible. Previous experience in modeling and scientific programing (C, C++, Python) would be appreciated but is not required.