Seminar on polymers under local active forces: a simplified stochastic model for motor-induced translocations by Laura Natali from Università di Roma “La Sapienza”, Nexus, 22 January 2020

Polymers under local active forces: a simplified stochastic model for motor-induced translocations.
Seminar by Laura Natali from the University of Rome “La Sapienza”, Rome, Italy.

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 [1]. Exploiting the translocation process, we can acquire information about the target proteins’ structure, such as the intermediate configurations between the folded and denatured structures [2]. 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 [3]. 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 [4], 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 [5], 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 [6] 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.

References:

  1. J. Nivala, D. B. Marks and M. Akeson, Nature Biotechnol., 2013, 31, 247
  2. M. Bacci, M. Chinappi, C. M. Casciola and F. Cecconi, J. Phys.Chem. B, 2012, 116, 4255–4262
  3. L. Caprini and U. M. B. Marconi, Soft matter, 2018, 14, 9044–9054.
  4. P. E. Rouse, J. Chem. Phys., 1953, 21, 1272.
  5. T. A. Baker and R. T. Sauer, Biochimica et Biophysica Acta (BBA) – Molecular Cell Research, 2012, 1823, 15–28.
  6. 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

Hillevi Wachtmeister joins the Soft Matter Lab

Hillevi Wachtmeister joined the Soft Matter Lab on 21 January 2020.

Hillevi Wachtmeister is a Master student in Physics at Chalmers University of Technology.

During her Master thesis work she will work on characterizing and tracking different particles and micro organisms using deep learning. She is supervised by Daniel Midtvedt.

Harshith Bachimanchi joins the Soft Matter Lab

Harshith Bachimanchi starts his PhD at the Physics Department of the University of Gothenburg on 20th January 2020.

Harshith has a Master degree in physics from the Indian Institute of Science Education and Research, Pune, India, where he submitted a Master thesis in optics, whose results can be found here.

In his PhD, he will focus on microscopy and deep learning.

Start-up “Lucero” Semi-finalist in SPIE Startup Challenge

Our idea Lucero, has reached the semi-final for the SPIE Start-up challenge, where will pitch in front of a jury at Photonics West in San Francisco, CA, USA on the 4th of February 2020.

Lucero will compete, among other 41 semifinalists, for cash prizes and business support.

In addition, Lucero was awarded one of the three Early Stage Entrepreneurship Travel Grants to attend the semi-final.

The start-up is aiming to make cutting-edge laser technology easy to use and available to anyone by combining it with commercial microscope. The product and software combo utilizes optical tweezers in a brand-new way – and bridges the gap between physics and other scientific fields that would greatly benefit from easier access to this tool.

In December, Lucero was ranked among the best 5 business ideas in West Sweden.

Team components: Christopher Jacklin, Rich Zapata Rosas, Felix Mossberg, Falko Schmidt, Alejandro Diaz Tormo and Martin Mojica-Benavides.

Links: Lucero Homepage