Lateral Distribution of Charged Species along a Polyelectrolyte Probed with a Fluorescence Blob Model

Method-Unifying View of Loop-Formation Kinetics in Peptide and Protein Folding

Protein folding can be described as a probabilistic succession of events in which the peptide chain forms loops closed by specific amino acid residue contacts, herein referred to as loop nodes. To measure loop rates, several photophysical methods have been introduced where a pair of optically active probes is incorporated at selected chain positions and the excited probe undergoes contact quenching (CQ) upon collision with the second probe. The quenching mechanisms involved triplet-triplet energy transfer, photoinduced electron transfer, and collision-induced fluorescence quenching, where the fluorescence of Dbo, an asparagine residue conjugated to 2,3-diazabicyclo[2.2.2]octane, is quenched by tryptophan. The discrepancy between the loop rates afforded from these three CQ techniques has, however, remained unresolved. In analyzing this discrepancy, we now report two short-distance FRET methods where Dbo acts as an energy acceptor in combination with tryptophan and naphtylalanine, two donors with largely different fluorescence lifetimes of 1.3 and 33 ns, respectively. Despite the different quenching mechanisms, the rates from FRET and CQ methods were, surprisingly, of comparable magnitude. This combination of FRET and CQ data led to a unifying physical model and to the conclusion that the rate of loop formation in folding reactions varies not only with the kind and number of residues that constitute the chain but also in particular with the size and properties of the residues that constitute the loop node.

The chain conformation and relaxation dynamics of poly(acrylic acid)-graft-poly(ethylene oxide)-graft-dodecyl in water: effect of side-chains and distribution of counterions

We present a study on the dielectric behavior of aqueous solution of an amphiphilic copolymer, poly(acrylic acid)-graft-poly(ethylene oxide)-graft-dodecyl (PAA-g-PEO-g-dodecyl), in the frequency range of 40 Hz to 110 MHz at varying concentrations and temperatures.

Effect of sequence on the ionization behavior of a series of amphiphilic polypeptides

The behavior of five polypeptides made of hydrophilic and pH-responsive aspartic acid (Asp) and hydrophobic phenylalanine (Phe), which had been prepared by stitching together short well-defined sequences of Asp and Phe, was studied as a function of pH. The effect of pH on these polypeptides referred to as (Asp3Phe1)n, (Asp2Phe1)n, (Asp1Phe1)n, (Asp1Phe2)n, and (Asp1Phe3)n varied dramatically depending on their constituting sequence. The more hydrophobic polypeptides (Asp1Phe2)n and (Asp1Phe3)n behaved as if the Asp's were isolated from each other and showed an apparent pKa (pKa(app)) that remained constant with level of ionization (α = [Asp(-)]/[Asp]total) and equaled 5.4 and 6.4, respectively. The more hydrophilic polypeptides (Asp3Phe1)n and (Asp2Phe1)n behaved like weak polyacids showing a linear increase in pKa(app) with increasing α. The pKa(app) of (Asp1Phe1)n showed a trend as a function of α intermediate between the Asp-rich and Phe-rich polypeptides, behaving as if the Asp's were isolated at low α values (<0.35) but acting as a weak polyacid for large α values (>0.35). The effect that α, and thus the charge density of the polypeptides, had on the collapse and aggregation of the polypeptides was characterized by conducting static light scattering and fluorescence measurements. Static light scattering measurements demonstrated that all polypeptides precipitated and aggregated in solution at a critical charge density of 0.2. Fluorescence measurements with pyrene indicated that this behavior was due to the formation of Phe aggregates in water. Together, these experiments provide a complete description of how pH affects the behavior of a series of unique amphiphilic polypeptides designed with a well-defined sequence.

Dielectric relaxations of poly(acrylic acid)-graft-poly(ethylene oxide) aqueous solution: analysis coupled with scaling approach and hydrogen-bonding complex

Dielectric properties of poly(acrylic acid)-graft-poly(ethylene oxide) (PAA-g-PEO) aqueous solution were measured as a function of concentration and temperature over a frequency range of 40 Hz to 110 MHz. After subtracting the contribution of electrode polarization, three relaxation processes were observed at about 20 kHz, 220 kHz, and 4 MHz, and they are named low-, mid- and high-frequency relaxation, respectively. The relaxation parameters of these three relaxations (dielectric increment Δε and relaxation time τ) showed scaling relations with the polyelectrolyte concentration. The mechanisms of the three relaxations were concluded in light of the scaling theory: The relaxations of low- and mid frequency were attributed to the fluctuation of condensed counterions, while the high-frequency relaxation was ascribed to the fluctuation of free counterions. Based on the dielectric measurements of varying temperatures, the thermodynamic parameters (enthalpy change ΔH and entropy change ΔS) of the three relaxations were calculated and these relaxation processes were also discussed from the microscopic thermodynamical view. In addition, the impacts of PEO side chains on the conformation of PAA-g-PEO chains were discussed. PEO side chains greatly strengthen the hydrogen-bonding interactions between PAA-g-PEO chains, resulting in the chains overlapping at a very low concentration and the formation of a hydrogen-bonding complex. Some physicochemical parameters of PAA-g-PEO molecules were calculated, including the overlap concentration, the effective charge of the chain, the friction coefficient, and the diffusion coefficient of hydrogen counterions.