Shape Fluctuations of Random Polyampholyte and Intrinsically Disordered Protein Sequences

Charged polymers with quenched charge sequences adopt pearl-necklace structures due to the interplay between charge disorder and thermal fluctuations. Partially globular pearl necklace conformations from random (+/-) sequences are intrinsically heterogeneous and exhibit various structures characterized by different numbers of pearls. On the basis of the molecular dynamics simulations of random model polyampholytes (PAs), we study dynamics of pearls and associated conformational heterogeneity in pearl structures. Fast nucleation/dissolution of small pearls controls the dynamics of the number of pearls, which is well described by first order kinetic equations. Most of the individual sequences we considered have a rather stable number of large pearls. Only a few sequences allow for fast switchings in the number of large pearls following complex processes (trajectories in parameter space) going through states with different numbers of pearls. Processes are most complex in the tail of the switching time distribution. The specific sequences of two intrinsically disordered proteins (IDPs) are studied along the same lines. Our study shows the resemblance in shape fluctuations between the IDP sequences and the fast-switching PA sequences.

Automated summary

Charged polymers with random charge sequences form pearl-necklace structures, with dynamics of pearls controlled by nucleation/dissolution processes. Most sequences have a stable number of large pearls, while a few exhibit fast-switching behavior. Similar shape fluctuations are observed in intrinsically disordered protein (IDP) sequences.