Dynamics and Free Energy of Polymers Partitioning into a Nanoscale Pore

Abstract

Membrane-bound proteinaceous nanoscale pores allow us to simultaneously observe the thermodynamic and kinetic properties of differently sized polymers within their confines. We determine the dynamic partitioning of poly(ethylene glycol) (PEG) into the pore formed by Staphylococcus aureus α-toxin and evaluate the free energy of polymer confinement by measuring polymer-induced changes to the pore's ionic conductance. The free energy deduced from the partition coefficient has a sharper dependence on polymer length (or weight) than scaling theory predicts. Moreover, the polymer-induced conductance fluctuations show a striking nonmonotonic dependence on the polymer molecular weight. The movement of polymer inside the pore is characterized by a diffusion coefficient that is orders of magnitude smaller than that for polymer in the bulk aqueous solution, which suggests that PEG has an attractive interaction with the pore. Using an ad-hoc approach, we show that a simple molecular weight-dependent modification of the polymer's diffusion coefficient accounts for these results, but only qualitatively. Given that PEG associates with hydrophobic regions in proteins, we also conclude that, contrary to the conventional view of ion channels, the aqueous cavity of the α-toxin pore's interior is, to some extent, hydrophobic.

Probing the role of water in protein conformation and function

“…The extra cost of forming the cavity in the presence of large solute will be the extra osmotic pressure imparted by it multiplied by the volume of water from which the large solute is prevented access. If the cavity is a membrane channel, the gating properties of that channel can bear a complex relation to the full complement of solutes surrounding it Bezrukov et al 1994Bezrukov et al , 1996.…”

Probing single nanometer-scale pores with polymeric molecular rulers

“…For example, scanning cysteine mutagenesis and covalent chemical modification were used to identify amino acid side chains that line the pore of the nicotinic acetylcholine receptor channel, 5 the Staphylococcus aureus ␣-hemolysin ͑␣HL͒ channel, [6][7][8][9][10][11][12][13][14] and the active form of Bacillus anthracis protective antigen ͑i.e., PA 63 ͒. 15,16 Nonelectrolyte water soluble polymers have been used to deduce channel structural features.…”

“…In addition, Krasilnikov and others used PEGs to estimate the radii of ion channels from the ability of size-selected PEGs to partition into the channel pore. 11,[19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36] Protein translocation across membranes, which plays a key role in many biological processes, can be facilitated by ion channels. [37][38][39] Other biomolecules can be detected as they transport through ion channels.…”

Dynamics of Polymer Decompression: Expansion, Unfolding, and Ejection

“…[3,4,5] The second case of interest is encountered in the field of confined polymers [6]. A recent advance in nanoscale fabrications and single-chain experiments allows one to manipulate and observe individual polymers, thereby facilitating a number of potential applications in biological as well as nanoscale sciences [7,8,9,10,11,12]. The aim of the present Letter is to provide a unified framework to describe decompression processes engaged in such situations.…”