Translocation, Rejection and Trapping of Polyampholytes

Kinetics of Polyampholyte Dimerization: Influence of Charge Sequences

Polyampholytes (PAs) exhibit complex behaviors in various environments influenced by their charge distribution. This study focuses on the kinetics of dimerization of PAs, aiming to elucidate the underlying mechanisms and clarify relevant characteristics of the charge sequence. We focus on PAs with non-zero net charges, employing molecular dynamics simulations and theoretical analyses to examine how charge sequences influence the rates of dimer formation and dissociation. Our findings reveal that the charge sequence of tails and the blockiness of the minority charge group markedly influence the kinetics of dimerization: large blockiness and tails with a high number of majority-type charges slow down the dissociation of dimers. Additionally, the presence of an extended (central) block of the majority charge promotes structural diversity. Within dimer states, blocks alternate between intra- and inter-chain contacts. The duration times in the dimer states are significantly longer than the typical dwell times of block inter-contacts, with a notable extension when multiple blocks are engaged. Intrinsically disordered proteins (IDPs) play crucial roles in cellular functions, primarily due to their ability to undergo rapid conformational changes and form transient complexes. These properties largely depend on the sequence of charged residues. We provide insights into the fundamental principles governing the structural and dynamical properties of polyampholytic IDP, emphasizing the importance of sequence-specific effects on both aggregation and dissociation.

Translocation of Hydrophobic Polyelectrolytes under Electrical Field: Molecular Dynamics Study

We studied the translocation of polyelectrolyte (PE) chains driven by an electric field through a pore by means of molecular dynamics simulations of a coarse-grained HP model mimicking high salt conditions. Charged monomers were considered as polar (P) and neutral monomers as hydrophobic (H). We considered PE sequences that had equally spaced charges along the hydrophobic backbone. Hydrophobic PEs were in the globular form in which H-type and P-type monomers were partially segregated and they unfolded in order to translocate through the narrow channel under the electric field. We provided a quantitative comprehensive study of the interplay between translocation through a realistic pore and globule unraveling. By means of molecular dynamics simulations, incorporating realistic force fields inside the channel, we investigated the translocation dynamics of PEs at various solvent conditions. Starting from the captured conformations, we obtained distributions of waiting times and drift times at various solvent conditions. The shortest translocation time was observed for the slightly poor solvent. The minimum was rather shallow, and the translocation time was almost constant for medium hydrophobicity. The dynamics were controlled not only by the friction of the channel, but also by the internal friction related to the uncoiling of the heterogeneous globule. The latter can be rationalized by slow monomer relaxation in the dense phase. The results were compared with those from a simplified Fokker-Planck equation for the position of the head monomer.