Kinetic mechanisms of crumpled globule formation

Abstract

Homopolymer chain with beads forming pairwise reversible bonds is a well-known model in polymer physics. We studied kinetics of homopolymer chain collapse, which was induced by pairwise reversible bonds formation. We compared kinetic mechanism of this coil-globule transition with the mechanism of collapse in a poor solvent. We discovered, that coil-globule transition occurs sufficiently more homogeneously on different scales, if collapse is induced by pairwise reversible bonds formation. This effect leads to formation of transient structures, which are not similar to the classical pearl-necklace conformations formed during collapse in a poor solvent. However, both types of collapse lead to formation of a metastable state of crumpled globule, which is one of the well-known models of interphase chromatin structure in different organisms. Moreover, we found out that stability and dynamics of this state can be controlled by fraction of reversible bonds and bond lifetime. * petrov.ai15@physics.msu.ru arXiv:1811.05037v2 [cond-mat.soft]

Different Stages of Polymer-Chain Collapse Following Solvent Quenching–Scaling Relations from Dissipative Particle Dynamics Simulations

“…The reduction of the expected value of 1 is likely due to the finite size of the globule. A similar scaling exponent of ≈0.8 has been reported by Petrov et al for the local scale of their collapsed, 2 × 10 4 -bead DPD chains. However, their local scaling parameter showed a strong influence on the choice of the fitting boundaries.…”

“…However, their local scaling parameter showed a strong influence on the choice of the fitting boundaries. On the global scale, the squared spatial distance approached a constant value (∝ n 0 ) . We note that our globular chains with N < 1000 show a behavior similar to the N = 1000 systems, with a faster transition to the terminal plateau.…”

“…The latter was characterized by a distinct ⟨ R 2 ⟩ ∝ n 1/3 scaling . A crumpled globule is not to be confused with a fractal globule (∝ n 2/3 ), a self-similar structure proposed by Grosberg et al that was, to our knowledge, never found in simulations. ,− Both crumpled and fractal globules can only equilibrate in a reptation-like fashion, which is commonly understood as an additional stage in single-chain collapse . In our system, chain crossing is not prohibited.…”

A novel heterogeneous structure formed by a single multiblock copolymer chain

“…On the other hand, a single multiblock copolymer chain with different types of interactions between beads is a promising model of chromatin organization in various organisms [15,18,19]. We have proposed to model interactions between nucleosomes as reversible bonds in our previous works [15,20]. In this study, we introduced a modified version of this model.…”

“…It is known that lysine 16 in histone H4 (histone H4 "tail") can form a complex with acidic region on H2A-H2B histone dimer (the so-called "acidic patch") [21,22]. We may treat this interaction as a reversible bond between two beads representing a nucleosome [15,20]. Each nucleosome has two histone H4 tails and two acidic regions on the H2A-H2B histone dimer.…”