The dependence of the rate on polymer mass was examined for the reaction of four sulfhydryl-directed poly(ethylene glycol) reagents with cysteine residues located in the lumen of the staphylococcal ␣-hemolysin pore. The logarithms of the apparent rate constants for a particular site in the lumen were proportional to N, the number of repeat units in a polymer chain. The proportionality constant was ؊(a͞D) 5/3 , where a is the persistence length of the polymer (Ϸ3.5Å) and D is the diameter of the pore. Despite some incongruencies with the assumptions of the derivation, the result suggests that the polymers partition into the lumen of the pore according to the simple scaling law of Daoud and de Gennes, c pore͞csolution ؍ exp(؊N(a͞D) 5/3 ). Therefore, the measured reaction rates yield an estimate of the diameter of the pore and might be applied to determine the approximate dimensions of cavities within other similar proteins.T he interactions of polymers with proteinaceous channels and pores has been studied extensively (1, 2). The osmotic effects of polymers on the voltage-dependent anion channel of mitochondria (VDAC) and other channels have been examined (1,(3)(4)(5). Polymer partitioning into pores from concentrated solutions has been investigated in studies of single-channel conductance (6), access resistance (7,8), and single-channel noise (2,(8)(9)(10). The movement of nucleic acids through pores has been examined through their effects on single-channel conductance (11)(12)(13)(14). The effects of covalently attached polymers on the properties of channels and pores have also been investigated (15)(16)(17).Given the interest in this area, it is of fundamental importance to understand how polymers partition from dilute solution into protein pores. This problem has received attention by theoreticians. Notably, scaling theory has been used to estimate partition coefficients (18,19). Specifically, Daoud and de Gennes (20) found the partition coefficient (⌸) for polymers into a tube to bewhere c is the concentration, N is the number of units in a polymer chain, a is the persistence length of the polymer, and D is the diameter of the pore. This relation applies to a narrow tube both where the Flory radius of the polymer R F Ͼ D (20) and where R F Ϸ D (21, 22). It requires that the free energy of confinement of each segment (''blob'') of the polymer within the pore is k B T, where k B is the Boltzmann constant and T the absolute temperature. Interestingly, the scaling relation has not been subjected to extensive experimental examination. Several studies have shown that Ϫln ⌸ is linearly dependent on N (18, 23), but the appropriateness of the scaling coefficient Ϫ(a͞D) 5/3 has received less attention. Here, we analyze how poly(ethylene glycol) (PEG) molecules partition into the pore formed by staphylococcal ␣-hemolysin (␣HL). The dimensions of the ␣HL pore have been determined by crystallography ( Fig. 1; ref. 24). Importantly for the present study, the transmembrane portion of the pore is a -barrel measuring Ϸ20...