Heterogeneous distribution of components in the biological membrane is critical in the process of cell polarization. However, little is known about the mechanisms that can generate and maintain the heterogeneous distribution of the membrane components. Here, we report that the propagating wave patterns of the bacterial Min proteins can impose steric pressure on the membrane, resulting in transport and directional accumulation of the component in the membrane. Therefore, the membrane component waves represent transport of the component in the membrane that is caused by the steric pressure gradient induced by the differential levels of binding and dissociation of the Min proteins in the propagating waves on the membrane surface. The diffusivity, majorly influenced by the membrane anchor of the component, and the repulsed ability, majorly influenced by the steric property of the membrane component, determine the differential spatial distribution of the membrane component. Thus, transportation of the membrane component by the Min proteins follows a simple physical principle, which resembles a linear peristaltic pumping process, to selectively segregate and maintain heterogeneous distribution of materials in the membrane.

No abstract

Helicases are biomolecular motors that unwind nucleic acids, and their regulation is essential for proper maintenance of genomic integrity. E. coli Rep helicase, whose primary role is to help restart stalled replication, serves as a model for Superfamily I helicases. Rep-like helicases contain a flexible subdomain (2B) that regulates their activity; however, the mechanism of control is not well understood. While a monomer of Rep cannot unwind duplex DNA, complete removal of 2B activates the motor for unwinding, though not as processively as locking 2B into one conformation. Here we investigate the behavior of a 2B-deletion variant (RepD2B) in relation to wild-type Rep. Using a single-molecule optical tweezers assay, we show that DNA unwinding by RepD2B monomer is more processive than by wtRep oligomer. Additionally, we find that RepD2B can switch between strands and form a single-stranded DNA loop, both of which limit unwinding. By exploring the effect of force and DNA geometry on helicase activity, we further show that the behaviors mentioned above are highly influenced by duplex stability. In light of our results, we propose a new model for regulation of unwinding by Rep-like helicases. DNA from neutrophil cells is released into the blood stream to forms neutrophil extracellular traps (NETs), as an immune response response to trap circulating pathogens. The mechanosensitive blood-coagulation adhesive protein, von Willebrand Factor (VWF), has been recently identified to interact with DNA of NETs and suggested to play a key stabilization role of such traps during inflammation. Nevertheless, the molecular nature, structural stability, and biological implications of this interaction remained to be elucidated. Here, we addressed this question by performing Brownian Dynamics and Molecular Dynamics simulations. Our simulations revealed an interesting mode of binding in which a specific region in VWF, namely a helix 4 (H4) in its A1 domain, acts as the specific binding site for DNA. In turn, DNA offers multiple unspecific binding sites for the A1 domain. Three arginines of the H4 were identified as key residues anchoring VWF to DNA. Furthermore, simulations varying the ionic strength and extensive in silico mutational studies pointed to electrostatic attraction as the main driving force governing the VWF-DNA interaction. Our data predicts a naturally-occurring mutation of one of the arginines to significantly destabilize the VWF-DNA interaction, a prediction that is currently under experimental validation. Moreover, our data attribute the partial diminish in binding of platelets to VWF, not to competition of DNA and platelets for the same binding site at A1, but rather, to partial unspecific steric preclusion of the platelet binding site upon binding of DNA to VWF. All together, our study provides the molecular basis for the stabilization of DNA-based NETs by VWF, with potential implications during inflammation. . RNA-DNA hybrids are functionally essential structures involved in numerous protein-dependent processes suc...

Heterogeneous distribution of components in the biological membrane is critical in the process of cell polarization. However, little is known about the mechanisms that can generate and maintain the heterogeneous distribution of the membrane components. Here we report that the propagating wave patterns of the bacterial Min proteins can impose corresponding steric pressure on the membrane to establish a directional accumulation of the membrane components, resulting in segregation of the components in the membrane. The diffusivity, influenced by the membrane anchor of the component, and the repulsed ability, influenced by the steric property of the soluble region of the component and molecular crowding, determine the differential spatial distribution of the component in the membrane. Thus, transportation of the membrane components by the Min proteins follows a simple physical principle, which resembles a linear peristaltic pumping process, to selectively segregate and maintain heterogeneous distribution of materials in the membrane.

Phosphorylation of AHL10, one of the AT-hook family of plant-specific DNA binding proteins, is critical for growth suppression during moderate severity drought (low water potential) stress. To understand how AHL10 phosphorylation determines drought response, we identified putative AHL10 interacting proteins and further characterized interaction with RRP6L1, a protein involved in epigenetic regulation. RRP6L1 and AHL10 mutants, as well as ahl10-1rrp6l1-2, had similar phenotype of increased growth maintenance during low water potential. Conversely, loss of AHL13, which is homologous to AHL10 and phosphorylated at similar C-terminal site, blocked the enhanced growth maintenance of ahl10-1. Chromatin precipitation demonstrated that RRP6L1 chromatin association increased during low water potential stress and was dependent upon AHL10 phosphorylation. Transcriptome analyses showed that AHL10 and RRP6L1 have concordant effects on expression of stress- and development-related genes. Stress signaling can act via AHL10 phosphorylation to control the chromatin association of the key regulatory protein RRP6L1. AHL10 and RRP6L1 interaction in meristem cells is part of a mechanism to down-regulate growth during low water potential stress. AHL10 and AHL13 are not redundant but rather have distinct roles, likely as part of AHL hetero-complexes.