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Statistical mechanics of biomolecular confinement and translocation

Objective

We propose to study the properties of polymers in conditions where confined geometries dramatically reduce the accessible volume. The properties of polymers can change significantly under such conditions, and there are important applications both in materi al science and in biological systems. In the biological world confinement occurs during important processes like the translocation of biopolymers through pores in cell or nucleus membranes, or during the encapsulation in small compartments (misfolded prote ins in chaperonin complexes).We propose to study the fundamental properties of the flow of polymers through such biological pores, which, although complex in the number of parameters involved, are not conceptually complicated. A computer simulation of such a system will then be a powerful tool to understand what the relevant parameters are that determine the system's behavior. The computational methods we will develop are largely inspired by successful techniques from the field of colloid science. In partic ular we combine Stochastic Rotational Dynamics scheme with a coarse grained representation of the biopolymer. For this last point we will extend the recent experience gained on design of configurational changes in protein and of protein-protein interaction s to a continuous representation of the amino acid chain. The model will then provide at the same time a general description of the mechanical action of the confinement, and how it depends on the interactions between the protein and the nanopore/nanocage.

Call for proposal

FP6-2004-MOBILITY-5
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Funding Scheme

EIF - Marie Curie actions-Intra-European Fellowships

Coordinator

THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE
Address
The Old Schools, Trinity Lane
Cambridge
United Kingdom