Journal article Open Access

The opposing effects of isotropic and anisotropic attraction on association kinetics of proteins and colloids

Arthur C. Newton; Ramses Kools; David W. H. Swenson; Peter G. Bolhuis

The association and dissociation of particles via specific anisotropic interactions is a fundamental
process, both in biology (proteins) and in soft matter (colloidal patchy particles). The presence of
alternative binding sites can lead to multiple productive states and also to non-productive “decoy” or
intermediate states. Besides anisotropic interactions, particles can experience non-specific isotropic
interactions. We employ single replica transition interface sampling to investigate how adding a
non-productive binding site or a nonspecific isotropic interaction alters the dimerization kinetics of
a generic patchy particle model. The addition of a decoy binding site reduces the association rate
constant, independent of the site’s position, while adding an isotropic interaction increases it due
to an increased rebinding probability. Surprisingly, the association kinetics becomes non-monotonic
for a tetramer complex formed by multivalent patchy particles. While seemingly identical to twoparticle
binding with a decoy state, the cooperativity of binding multiple particles leads to a kinetic
optimum. Our results are relevant for the understanding and modeling of biochemical networks and
self-assembly processes. Published by AIP Publishing. https://doi.org/10.1063/1.5006485

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