Role of Charge Sequence in Polyampholyte Aggregation

We investigate self-association in solutions of polyampholytes (PAs) with all the same, well-defined, sequence placed in moderately poor solvent conditions. By utilizing molecular dynamics (MD) simulations, we examine aggregation for a sequence taken within an ensemble with fixed net charge. As a first approximation, the net charge opposing aggregation is the key control parameter: small net charges lead to massive aggregation while large net charges result in the predominance of unimers. The aggregation behavior for intermediate net charges is highly sensitive to the sequence. The resulting distribution of aggregation numbers clearly indicates this sequence dependence. We provide estimates of the internal energy and free energy of dimerization. The propensity of self-association into dimers correlates with the sequence blockiness, particularly the blockiness of minority charges, and is strongly linked to instability toward microphase separation. The overall free energy variation for increasing cluster size is linear or piecewise linear, depending on the sequence. The incremental change in free energy upon the addition of an extra unimer exhibits a fine structure that is intricately tied to the sequence. The clustering in dilute solution is clearly dictated by not only the overall net charges but also the arrangement of local sequences (blockiness and location of blocks). Analytically considering charge regulation for increasingly larger clusters, we observe moderate charge regulation for small clusters, consistent with MD simulations, and nearly complete counterion localization in the large cluster limit, foreshadowing the macroscopic phase and its interface with the solvent. We also study a PA with a charge sequence mimicking that of intrinsically disordered protein (IDP) integrase (IN), which is weakly charged. The tendency of self-association of this specific sequence is limited when the hydrophobicity of the backbone is marginal but becomes more prominent with a moderate level of hydrophobicity. Our study sheds light on the intricate interplay between charge distribution and sequence characteristics, such as hydrophobicity, in building up the self-association behavior of polyampholytes, offering insights into potential strategies for fine-tuning aggregation properties.