Molecular motors are a wide class of enzymes that can transport even large macromolecules by converting chemical into mechanical energy, through the process of ATP-hydrolysis. Among those, active nanopore translocation is a common mechanism to carry proteins across biological membranes. The phospholipid bilayer is impenetrable for the folded protein, that requires to be unfolded and pulled across channels such as alpha-hemolysin . Exploiting the translocation process, we can acquire information about the target proteins’ structure, such as the intermediate configurations between the folded and denatured structures . Here follows the interest in modeling the motor proteins complex in a simple simulation setup.
First of all, we characterized the active polymer’s features in free space and subsequently, we confined it inside a nanopore model. The study in free space aims to investigate how activity affects both the global and the local polymer properties. The chosen model for the active force is an Active Ornstein-Uhlenbeck Particle, a model closely related to Active Brownian Particles . The presence of the catalytic head affects the end-to-end distance of the polymer, which describes its degree of compactness. The active chain can be studied through the Rouse mode decomposition , which allowed us to analyze the dependence of the second moment of the end-to-end distance as a function of the persistence time of the activity. We considered also the distance between consecutive monomers, which provides an insight into the local effects of the active force and how it is transmitted along the chain.
In this work, we were inspired by an experiment employing the ClpXP complex , a protein-degradation machine responsible for unfolding and digesting malfunctioning proteins through unidirectional transport across the nanopore. In the model we propose, we enclose the polymer chain in a confining potential, simulating the effect of the nanopore. The energy generated by the molecular motor translocates the polymers, which means they cross the pore from side to side. In our setup, the effect of the molecular motor  is represented as a potential barrier combined with a region that makes active the monomers that are crossing it. The translocation pathways have a step-wise profile typical of their biological counterparts.
- J. Nivala, D. B. Marks and M. Akeson, Nature Biotechnol., 2013, 31, 247
- M. Bacci, M. Chinappi, C. M. Casciola and F. Cecconi, J. Phys.Chem. B, 2012, 116, 4255–4262
- L. Caprini and U. M. B. Marconi, Soft matter, 2018, 14, 9044–9054.
- P. E. Rouse, J. Chem. Phys., 1953, 21, 1272.
- T. A. Baker and R. T. Sauer, Biochimica et Biophysica Acta (BBA) – Molecular Cell Research, 2012, 1823, 15–28.
- L. Caprini, U. Marini Bettolo Marconi, A. Puglisi and A. Vulpiani, J. Chemi. Phys., 2019, 150, 024902.
Place: Nexus room, Fysik Origo, Fysik
Time: 22 January, 2020, 11:00