The breakdown of the local thermal equilibrium approximation for a polymer chain during packaging

AT-specific DNA visualization revisits the directionality of bacteriophage λ DNA ejection

In this study, we specifically visualized DNA molecules at their AT base pairs after in vitro phage ejection. Our AT-specific visualization revealed that either end of the DNA molecule could be ejected first with a nearly 50% probability. This observation challenges the generally accepted theory of Last In First Out (LIFO), which states that the end of the phage λ DNA that enters the capsid last during phage packaging is the first to be ejected, and that both ends of the DNA are unable to move within the extremely condensed phage capsid. To support our observations, we conducted computer simulations that revealed that both ends of the DNA molecule are randomized, resulting in the observed near 50% probability. Additionally, we found that the length of the ejected DNA by LIFO was consistently longer than that by First In First Out (FIFO) during in vitro phage ejection. Our simulations attributed this difference in length to the stiffness difference of the remaining DNA within the phage capsid. In conclusion, this study demonstrates that a DNA molecule within an extremely dense phage capsid exhibits a degree of mobility, allowing it to switch ends during ejection.

Interdomain exchange and the flip-flop of cholesterol in ternary component lipid membranes and their effects on heterogeneous cholesterol diffusion

Cell membranes are heterogeneous with a variety of lipids, cholesterol, and proteins and are composed of domains of different compositions. Such heterogeneous environments make the transport of cholesterol complicated: cholesterol not only diffuses within a particular domain but also travels between domains. Cholesterol also flip-flops between upper and lower leaflets such that cholesterol may reside both within leaflets and in the central region between two leaflets. How the presence of multiple domains and the interdomain exchange of cholesterol would affect the cholesterol transport, however, remains elusive. In this study, therefore, we perform molecular dynamics simulations up to 100μs for ternary component lipid membranes, which consist of saturated lipids (dipalmitoylphosphatidylcholine, DPPC), unsaturated lipids (dilinoleylphosphatidylcholine, DIPC), and cholesterol. The ternary component membranes in our simulations form two domains readily: DPPC and DIPC domains. We find that the diffusion of cholesterol molecules is much more heterogeneous and non-Gaussian than expected for binary component lipid membranes of lipids and cholesterol. The non-Gaussian parameter of the cholesterol molecules is about four times larger in the ternary component lipid membranes than in the binary component lipid membranes. Such non-Gaussian and heterogeneous transport of cholesterol arises from the interplay among the interdomain kinetics, the different diffusivity of cholesterol in different domains, and the flip-flop of cholesterol. This suggests that in cell membranes that consist of various domains and proteins, the cholesterol transport can be very heterogeneous. We also find that the mechanism of the interdomain exchange differs for different domains: cholesterol tends to exit the DIPC domain along the central region of the membrane for the DIPC-to-DPPC transition, while the cholesterol is likely to exit the DPPC domain within the membrane leaflet for the DPPC-to-DIPC transition. Also, the interdomain exchange kinetics of cholesterol for the DPPC-to-DIPC transition is up to 7.9 times slower than the DIPC-to-DPPC transition.

History-dependent nonequilibrium conformations of a highly confined polymer globule in a sphere

Chromatin undergoes condensation-decondensation processes repeatedly during its cell lifetime. The spatial organization of chromatin in nucleus resembles the fractal globule, of which structure significantly differs from an equilibrium polymer globule. There have been efforts to develop a polymer globule model to describe the fractal globulelike structure of tightly packed chromatin in nucleus. However, the transition pathway of a polymer toward a globular state has been often ignored. Because biological systems are intrinsically in nonequilibrium states, the transition pathway that the chromatin would take before reaching the densely packaged globule should be of importance. In this study, by employing a simple polymer model and Langevin dynamics simulations, we investigate the conformational transition of a single polymer from a swollen coil to a compact globule. We aim to elucidate the effect of transition pathways on the final globular structure. We show that a fast collapse induces a nonequilibrium structure even without a specific intramolecular interaction and that its relaxation toward an equilibrium globule is extremely slow. Due to a strong confinement, the fractal globule never relaxes into an equilibrium state during our simulations such that the globular structure becomes dependent on the transition pathway.