Topoisomerase VI is a chirally-selective, preferential DNA decatenase.

DNA topoisomerase VI (topo VI) is a type IIB DNA topoisomerase found predominantly in archaea and some bacteria, but also in plants and algae. Since its discovery, topo VI has been proposed to be a DNA decatenase; however, robust evidence and a mechanism for its preferential decatenation activity was lacking. Using single-molecule magnetic tweezers measurements and supporting ensemble biochemistry, we demonstrate that Methanosarcina mazei topo VI preferentially unlinks, or decatenates DNA crossings, in comparison to relaxing supercoils, through a preference for certain DNA crossing geometries. In addition, topo VI demonstrates a significant increase in ATPase activity, DNA binding and rate of strand passage, with increasing DNA writhe, providing further evidence that topo VI is a DNA crossing sensor. Our study strongly suggests that topo VI has evolved an intrinsic preference for the unknotting and decatenation of interlinked chromosomes by sensing and preferentially unlinking DNA crossings with geometries close to 90°.

Overscreening, Co-Ion-Dominated Electroosmosis, and Electric Field Strength Mediated Flow Reversal in Polyelectrolyte Brush Functionalized Nanochannels.

Controlling the direction and strength of nanofluidic electrohydrodyanmic transport in the presence of an externally applied electric field is extremely important in a number of nanotechnological applications. Here, we employ all-atom molecular dynamics simulations to discover the possibility of changing the direction of electroosmotic (EOS) liquid flows by merely changing the electric field strength in a nanochannel functionalized with polyelectrolyte (PE) brushes. In exploring this, we have uncovered three facets of nanoconfined PE brush behavior and resulting EOS transport. First, we identify the onset of an overscreening effect: such overscreening refers to the presence of more counterions (Na+) within the brush layer than needed to neutralize the negative brush charges. Accordingly, as a consequence of the overscreening, in the bulk liquid outside the brush layer, there is a greater number of co-ions (Cl-) than counterions in the presence of an added salt (NaCl). Second, this specific ion distribution ensures that the overall EOS flow is along the direction of motion of the co-ions. Such co-ion-dictated EOS transport directly contradicts the notion that EOS flow is always dictated by the motion of the counterions. Finally, for large-enough electric fields, the brush height reduces significantly, causing some of the excess overscreening-inducing counterions to squeeze out of the PE brush layer into the brush-free bulk. As a result, the overscreening effect disappears and the number of co-ions and counterions outside the PE brush layer become similar. Despite that there is an EOS transport, this EOS transport, unlike the standard EOS transport that occurs due to the imbalance of the co-ions and counterions, occurs since a larger residence time of the water molecules in the first solvation shell of the counterions (Na+) ensures a water transport in the direction of motion of the counterions. The net effect is the reversal of the direction of the EOS transport by merely changing the strength of the electric field.

Lipid flip-flop and desorption from supported lipid bilayers is independent of curvature.

Flip-flop of lipids of the lipid bilayer (LBL) constituting the plasma membrane (PM) plays a crucial role in a myriad of events ranging from cellular signaling and regulation of cell shapes to cell homeostasis, membrane asymmetry, phagocytosis, and cell apoptosis. While extensive research has been conducted to probe the lipid flip flop of planar lipid bilayers (LBLs), less is known regarding lipid flip-flop for highly curved, nanoscopic LBL systems despite the vast importance of membrane curvature in defining the morphology of cells and organelles and in maintaining a variety of cellular functions, enabling trafficking, and recruiting and localizing shape-responsive proteins. In this paper, we conduct molecular dynamics (MD) simulations to study the energetics, structure, and configuration of a lipid molecule undergoing flip-flop and desorption in a highly curved LBL, represented as a nanoparticle-supported lipid bilayer (NPSLBL) system. We compare our findings against those of a planar substrate supported lipid bilayer (PSSLBL). Our MD simulation results reveal that despite the vast differences in the curvature and other curvature-dictated properties (e.g., lipid packing fraction, difference in the number of lipids between inner and outer leaflets, etc.) between the NPSLBL and the PSSLBL, the energetics of lipid flip-flop and lipid desorption as well as the configuration of the lipid molecule undergoing lipid flip-flop are very similar for the NPSLBL and the PSSLBL. In other words, our results establish that the curvature of the LBL plays an insignificant role in lipid flip-flop and desorption.

Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches.

Damaged or mismatched DNA bases result in the formation of physical defects in double-stranded DNA. In vivo, defects in DNA must be rapidly and efficiently repaired to maintain cellular function and integrity. Defects can also alter the mechanical response of DNA to bending and twisting constraints, both of which are important in defining the mechanics of DNA supercoiling. Here, we use coarse-grained molecular dynamics (MD) simulation and supporting statistical-mechanical theory to study the effect of mismatched base pairs on DNA supercoiling. Our simulations show that plectoneme pinning at the mismatch site is deterministic under conditions of relatively high force (>2 pN) and high salt concentration (>0.5 M NaCl). Under physiologically relevant conditions of lower force (0.3 pN) and lower salt concentration (0.2 M NaCl), we find that plectoneme pinning becomes probabilistic and the pinning probability increases with the mismatch size. These findings are in line with experimental observations. The simulation framework, validated with experimental results and supported by the theoretical predictions, provides a way to study the effect of defects on DNA supercoiling and the dynamics of supercoiling in molecular detail.

Formation and Properties of a Self-Assembled Nanoparticle-Supported Lipid Bilayer Probed through Molecular Dynamics Simulations.

We have carried out coarse-grained molecular dynamics (MD) simulations to study the self-assembly procedure of a system of randomly placed lipid molecules, water beads, and a nanoparticle (NP). The self-assembly results in the formation of the nanoparticle-supported lipid bilayer (NPSLBL), with the self-assembly mechanism being driven by events such as the formation of small lipid clusters, merging of the lipid clusters in the vicinity of the NP to form NP-embedded vesicle with a pore, and collapsing of that pore to eventually form the equilibrated NPSLBL system overcoming a large free-energy barrier. Subsequently, we quantify the properties and the configurations of this NPSLBL system. We reveal that unlike our proposition of an equal number of lipid molecules occupying the inner and outer leaflets in a recent report studying the properties of a preassembled lipid bilayer, the equilibrated self-assembled NPSLBL system demonstrates a much larger number of lipid molecules occupying the outer leaflet as compared to the inner leaflet. Second, the thickness of the water layer entrapped between the NP and the inner leaflet shows similar values as predicted by experiments and our previous study. Finally, we reveal that, similar to our previous study, the diffusivity of the lipid molecules in the outer leaflet is larger than that in the inner leaflet but, due to higher temperature employed during our simulations, are even larger than that predicted by our previous study.

Nanovesicles Versus Nanoparticle-Supported Lipid Bilayers: Massive Differences in Bilayer Structures and in Diffusivities of Lipid Molecules and Nanoconfined Water.

We carry out molecular dynamics (MD) simulations to compare the equilibrium architecture and properties of nanoparticle-supported lipid bilayers (NPSLBLs) with the free vesicles of similar dimensions. Three key differences emerge. First, we witness that for a free vesicle, a much larger number of lipid molecules occupy the outer layer as compared to the inner layer; on the other hand, for the NPSLBL the number of lipid molecules occupying the inner and outer layers is identical. Second, we witness that the diffusivities of the lipid molecules occupying both the inner and the outer layers of the free vesicles are identical, whereas for the NPSLBLs the diffusivity of the lipid molecules in the outer layer is more than twice the diffusivity of the lipid molecules in the inner layer. Finally, the NPSLBLs entrap nanoscopic thin water film between the inner lipid layer and the NP and the diffusivity of this water film is nearly 1 order of magnitude smaller than the diffusivity of the bulk water; on the other hand, the water inside the free vesicles has a diffusivity that is only slightly lower than that of the bulk water. Our findings, possibly the first probing the atomistic details of the NPSLBLs, are anticipated to shed light on the properties of this important nanomaterial with applications in a large number of disciplines ranging from drug and gene delivery to characterizing curvature-sensitive molecules.

Ion at Air-Water Interface Enhances Capillary Wave Fluctuations: Energetics of Ion Adsorption.

Recent simulations provide the energetics of ion adsorption at the air-water (a/w) interface: The presence of the ion at the interface suppresses the fluctuations of the capillary waves (CWs) reducing the entropy and displaces the weakly interacting water molecules to the bulk causing a reduction in the enthalpy. Here, we provide atomistic simulation-based evidence that the inferences of the existing studies stem from considering a small simulation volume that pins the CWs. For an appropriate size of the simulation system, an ion at the a/w interface enhances the CW fluctuations. Furthermore, we discover that the characteristics of the waves governing these enhanced CW fluctuations ensure a significant decrease in the pressure-volume work causing the enthalpy decrease, while the same wave characteristics of the CWs become responsible for an entropy decrease. Overall, the paper revisits the free energy picture of this fundamental problem of ion adsorption at the a/w interface.

Lubrication in polymer-brush bilayers in the weak interpenetration regime: Molecular dynamics simulations and scaling theories.

We conduct molecular dynamics (MD) simulations and develop scaling laws to quantify the lubrication behavior of weakly interpenetrated polymer brush bilayers in the presence of an external shear force. The weakly interpenetrated regime is characterized by 1

Polyelectrolyte brush bilayers in weak interpenetration regime: Scaling theory and molecular dynamics simulations.

We employ molecular dynamics (MD) simulations and develop scaling theories to quantify the equilibrium behavior of polyelectrolyte (PE) brush bilayers (BBLs) in the weakly interpenetrated regime, which is characterized by d_{0}

Compression of polymer brushes in the weak interpenetration regime: scaling theory and molecular dynamics simulations.

We employ scaling theory and Molecular Dynamics (MD) simulations to probe the compression of the semi-dilute polymer brush bilayers (BBLs) in the weak interpenetration (IP) regime. Such a regime is characterized by two layers of interacting polymer brushes grafted on opposing planar surfaces having a separation dg, such that d0 < dg < 2d0, with d0 being the unperturbed brush height. Currently, scaling theories are known for polymer BBLs with a much larger degree of IP (i.e., dg < d0) - in such regimes, the brush height can be quantified by the corresponding IP length δ. On the other hand, we show that in the weak IP regime, the brush height is not solely dictated by δ. We develop new scaling theories to show that δ in this weak IP regime is different from that in the strong IP regime. Secondly, we establish that the compressed brush height in this weakly IP regime can be described as d ∼ Nχ with χ < 1 and varying monotonically with dg/d0. MD simulations are carried out to quantify δ and χ and the results match excellently with our new scaling theory predictions. Finally, we establish that our scaling theory can reasonably predict the experimentally witnessed variation of the interaction energy dictating the compressive force between the interpenetrating brushes in this weakly IP regime.