2014/06/04 by Nina Müller, Jan Kierfeld · 5 citations
Biochemistry, Genetics and Molecular Biology · Chemistry · Physics and Astronomy · #Chemistry #Computational chemistry #Microtubule and mitosis dynamics #Molecular dynamics #Molecular mechanics #Photosynthetic Processes and Mechanisms #Physics #Protist diversity and phylogeny #Statistical physics #cond-mat.soft #physics.bio-ph #q-bio.SC
paper · pdf · doi:10.1088/1478-3975/11/4/046001
published in Physical Biology 11(4), 046001 (IOP Publishing)
openalex publication_date 2014/06/04 · arxiv created 2014/06/05 · arxiv updated 2014/12/12 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05
We introduce a model for microtubule (MT) mechanics containing lateral bonds between dimers in neighboring protofilaments, bending rigidity of dimers, and repulsive interactions between protofilaments modeling steric constraints to investigate the influence of mechanical forces on hydrolysis and catastrophes. We use the allosteric dimer model, where tubulin dimers are characterized by an equilibrium bending angle, which changes from 0° to 22° by hydrolysis of a dimer. This also affects the lateral interaction and bending energies and, thus, the mechanical equilibrium state of the MT. As hydrolysis gives rise to conformational changes in dimers, mechanical forces also influence the hydrolysis rates by mechanical energy changes modulating the hydrolysis rate. The interaction via the MT mechanics then gives rise to correlation effects in the hydrolysis dynamics, which have not been taken into account before. Assuming a dominant influence of mechanical energies on hydrolysis rates, we investigate the most probable hydrolysis pathways both for vectorial and random hydrolysis. Investigating the stability with respect to lateral bond rupture, we identify initiation configurations for catastrophes along the hydrolysis pathways and values for a lateral bond rupture force. If we allow for rupturing of lateral bonds between dimers in neighboring protofilaments above this threshold force, our model exhibits avalanche-like catastrophe events.