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Document Type

Open Access Dissertation

Degree Name

Doctor of Philosophy (PhD)

Degree Program

Physics

Year Degree Awarded

2018

Month Degree Awarded

September

First Advisor

V. Adrian Parsegian

Subject Categories

Biological and Chemical Physics

Abstract

The cell interior, enclosed by membrane barriers, is a condensed solution of inorganic ions, polymers, carbohydrates, polynucleotides, and a large number of other organic molecules. Within cells, transport of metabolites and biopolymers, such as polynucleotides and proteins, occurs partly through specific transmembrane pores (mesoscopic ion channels) spanning cellular compartments. Examples of such functions are translocation of matrix RNA molecules from cell nucleus through nuclear pore complexes, ejection of viral genome from bacterial virus capsids into host bacterial cells, and translocation of protein factors across toxin channels in biological membranes. All these processes, that occur in the cellular milieu, are mediated by complex membrane structures and must be affected by molecular crowding. However, the effects of crowding are insufficiently addressed. Particular effects of certain types of molecular ``crowders'' have only begun to be understood. Partially they stem from the dramatic complexity of the cellular translocation machinery, which makes direct observation of crowding phenomena extremely challenging. In addressing pore-assisted metabolite transport, a simplified experimental system with isolated protein channels in artificial membranes has been a useful model to probe and to assess crowding effects of such transport. In the experimental scheme employed here, a single pore is spontaneously assembled into an artificial bilayer separating two voltage-clamped electrolyte compartments. As the electric field is applied across the pore, the resulting ion current can be detected with high precision; interference of channel-passing or channel-excluded polymers with the ion flow gives a sensitive report on the studied phenomena of molecular crowding. In the absence of a field, polymers partition ``passively'' into the pores, a direct result of the ``osmotic stress'' induced by the polymers (crowders) themselves.

Here, we study partitioning of polymers from a non-ideal binary mixture composed of polymers of different molecular weights going into structurally different ion channels. This is based on the assumption that in a two-component polymer mixture, one component that is preferentially excluded from the channel cavity will "actively" force the other component into the channel cavity. In order to assess the extent to which our results are useful in understanding concrete examples of ion-conducting aqueous pores and size-dependent forced partitioning into these pores.

We describe the equation of state of a polymer mixture by its osmotic pressure, study the effects of polymer crowding on electrolyte solutions, investigate the partitioning of polymers from such mixtures into structurally different ion channels.

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