Nanoscale Protein Interactions Determine the Mesoscale Dynamic Organisation of Biomembranes

Abstract

Recent advances in experimental biophysical techniques, such as super-resolution microscopy, have given new insights into the complex organization of membrane proteins for length scales of hundreds of nanometers and timescales of milliseconds. Likewise, progress has been made in term of computational models, allowing the creation of biomembrane systems containing molecular detail at the 100 nanometer lengthscale. Thus, it has recently been shown that protein crowding underpins the turnover of bacterial outer membrane proteins, a process that is vital for the adaptation of certain bacteria to new environments1. Nevertheless, experiments as well as computational models have been devoid of a full understanding of protein crowding in both molecular detail and at experimentally observable time and length scales. I will describe how these clusters may be generated for the Outer Membrane Proteins (OMPs) BtuB and OmpF using coarse- grain (CG) Molecular Dynamics (MD) simulations. However, a mesoscale model is necessary to assess the dynamic behaviour of these OMPs at the mesoscale (hundreds of nanometers and millisecond timescales) and to bridge MD simulations and single molecule fluorescence microscopy. From the dynamics and protein interactions observed in our CG-MD simulations, we generate such a mesoscale model, and are able to directly compare in vitro and in silico results by using single molecule tracking analysis on both. Simulations using the mesoscale model reveal that bacterial outer membranes are comprised of protein clusters that present a mesh of moving barriers that can act to confine newly inserted proteins into OMP ‘islands’.