Inter-filament Attractions Narrow the Length Distribution of Actin Filaments

We show that the exponential length distribution that is typical of actin filaments under physiological conditions dramatically narrows in the presence of (i) crosslinker proteins (ii) polyvalent counterions or (iii) depletion mediated attractions. A simple theoretical model shows that in equilibrium, short-range attractions enhance the tendency of filaments to align parallel to each other, eventually leading to an increase in the average filament length and a decrease in the relative width of the distribution of filament lengths.Comment: 5 pages, 4 figure

Hydration interactions: aqueous solvent effects in electric double layers

A model for ionic solutions with an attractive short-range pair interaction between the ions is presented. The short-range interaction is accounted for by adding a quadratic non-local term to the Poisson-Boltzmann free energy. The model is used to study solvent effects in a planar electric double layer. The counter-ion density is found to increase near the charged surface, as compared with the Poisson-Boltzmann theory, and to decrease at larger distances. The ion density profile is studied analytically in the case where the ion distribution near the plate is dominated only by counter-ions. Further away from the plate the density distribution can be described using a Poisson-Boltzmann theory with an effective surface charge that is smaller than the actual one.Comment: 11 Figures in 13 files + LaTex file. 20 pages. Accepted to Phys. Rev. E. Corrected typos and reference

A Transcript Cleavage Factor of Mycobacterium tuberculosis Important for Its Survival

After initiation of transcription, a number of proteins participate during elongation and termination modifying the properties of the RNA polymerase (RNAP). Gre factors are one such group conserved across bacteria. They regulate transcription by projecting their N-terminal coiled-coil domain into the active center of RNAP through the secondary channel and stimulating hydrolysis of the newly synthesized RNA in backtracked elongation complexes. Rv1080c is a putative gre factor (MtbGre) in the genome of Mycobacterium tuberculosis. The protein enhanced the efficiency of promoter clearance by lowering abortive transcription and also rescued arrested and paused elongation complexes on the GC rich mycobacterial template. Although MtbGre is similar in domain organization and shares key residues for catalysis and RNAP interaction with the Gre factors of Escherichia coli, it could not complement an E. coli gre deficient strain. Moreover, MtbGre failed to rescue E. coli RNAP stalled elongation complexes, indicating the importance of specific protein-protein interactions for transcript cleavage. Decrease in the level of MtbGre reduced the bacterial survival by several fold indicating its essential role in mycobacteria. Another Gre homolog, Rv3788 was not functional in transcript cleavage activity indicating that a single Gre is sufficient for efficient transcription of the M. tuberculosis genome

Modeling electrolytically top gated graphene

We investigate doping of a single-layer graphene in the presence of electrolytic top gating. The interfacial phenomena is modeled using a modified Poisson-Boltzmann equation for an aqueous solution of simple salt. We demonstrate both the sensitivity of graphene's doping levels to the salt concentration and the importance of quantum capacitance that arises due to the smallness of the Debye screening length in the electrolyte.Comment: 7 pages, including 4 figures, submitted to Nanoscale Research Letters for a special issue related to the NGC 2009 conference (http://asdn.net/ngc2009/index.shtml

Long Range Hydration Effects in Electrolytic Free Suspended Black Films

The force law within free suspended black films made of negatively charged Aerosol-OT (AOT) with added LiCl or CsCl is studied accurately using X-ray reflectivity (ca. 1{\AA}). We find an electrolyte concentration threshold above which a substantial additional repulsion is detected in the LiCl films, up to distances of 100 {\AA}. We interpret this phenomenon as an augmentation of the Debye screening length, due to the local screening of the condensed hydrophilic counterions by the primary hydration shell.Comment: 4 pages, 4 figures, to be published Phys. Rev. Let

Counterion adsorption on flexible polyelectrolytes: comparison of theories

Counterion adsorption on a flexible polyelectrolyte chain in a spherical cavity is considered by taking a "permuted" charge distribution on the chain so that the "adsorbed" counterions are allowed to move along the backbone. We compute the degree of ionization by using self-consistent field theory (SCFT) and compare with the previously developed variational theory. Analysis of various contributions to the free energy in both theories reveals that the equilibrium degree of ionization is attained mainly as an interplay of the adsorption energy of counterions on the backbone, the translational entropy of the small ions, and their correlated density fluctuations. Degree of ionization computed from SCFT is significantly lower than that from the variational formalism. The difference is entirely due to the density fluctuations of the small ions in the system, which are accounted for in the variational procedure. When these fluctuations are deliberately suppressed in the truncated variational procedure, there emerges a remarkable quantitative agreement in the various contributing factors to the equilibrium degree of ionization, in spite of the fundamental differences in the approximations and computational procedures used in these two schemes. Nevertheless, since the significant effects from density fluctuations of small ions are not captured by the SCFT, and due to the close agreement between SCFT and the other contributing factors in the more transparent variational procedure, the latter is a better computational tool for obtaining the degree of ionization

Self-Consistent Field study of Polyelectrolyte Brushes

We formulate a self-consistent field theory for polyelectrolyte brushes in the presence of counterions. We numerically solve the self-consistent field equations and study the monomer density profile, the distribution of counterions, and the total charge distribution. We study the scaling relations for the brush height and compare them to the prediction of other theories. We find a weak dependence of the brush height on the grafting density.We fit the counterion distribution outside the brush by the Gouy-Chapman solution for a virtual charged wall. We calculate the amount of counterions outside the brush and find that it saturates as the charge of the polyelectrolytes increases

Escherichia coli ItaT is a Type II Toxin that Inhibits Translation by Acetylating Isoleucyl-tRNAIle

Prokaryotic toxin-antitoxin (TA) modules are highly abundant and are involved in stress response and drug tolerance. The most common type II TA modules consist of two interacting proteins. The type II toxins are diverse enzymes targeting various essential intracellular targets. The antitoxin binds to cognate toxin and inhibits its function. Recently, TA modules whose toxins are GNAT-family acetyltransferases were described. For two such systems, the target of acetylation was shown to be aminoacyl-tRNA: the TacT toxin targets aminoacylated elongator tRNAs, while AtaT targets the amino acid moiety of initiating tRNAMet. We show that the itaRT gene pair from Escherichia coli encodes a TA module with acetyltransferase toxin ItaT that specifically and exclusively acetylates Ile-tRNAIle thereby blocking translation and inhibiting cell growth. ItaT forms a tight complex with the ItaR antitoxin, which represses the transcription of itaRT operon. A comprehensive bioinformatics survey of GNAT acetyltransferases reveals that enzymes encoded by validated or putative TA modules are common and form a distinct branch of the GNAT family tree. We speculate that further functional analysis of such TA modules will result in identification of enzymes capable of specifically targeting many, perhaps all, aminoacyl tRNAs

Partially Annealed Disorder and Collapse of Like-Charged Macroions

Charged systems with partially annealed charge disorder are investigated using field-theoretic and replica methods. Charge disorder is assumed to be confined to macroion surfaces surrounded by a cloud of mobile neutralizing counterions in an aqueous solvent. A general formalism is developed by assuming that the disorder is partially annealed (with purely annealed and purely quenched disorder included as special cases), i.e., we assume in general that the disorder undergoes a slow dynamics relative to fast-relaxing counterions making it possible thus to study the stationary-state properties of the system using methods similar to those available in equilibrium statistical mechanics. By focusing on the specific case of two planar surfaces of equal mean surface charge and disorder variance, it is shown that partial annealing of the quenched disorder leads to renormalization of the mean surface charge density and thus a reduction of the inter-plate repulsion on the mean-field or weak-coupling level. In the strong-coupling limit, charge disorder induces a long-range attraction resulting in a continuous disorder-driven collapse transition for the two surfaces as the disorder variance exceeds a threshold value. Disorder annealing further enhances the attraction and, in the limit of low screening, leads to a global attractive instability in the system.Comment: 21 pages, 2 figure

Mechanism of Translation Inhibition by Type II GNAT Toxin AtaT2

Type II toxin-antitoxins systems are widespread in prokaryotic genomes. Typically, they comprise two proteins, a toxin, and an antitoxin, encoded by adjacent genes and forming a complex in which the enzymatic activity of the toxin is inhibited. Under stress conditions, the antitoxin is degraded liberating the active toxin. Though thousands of various toxin-antitoxins pairs have been predicted bioinformatically, only a handful has been thoroughly characterized. Here, we describe the AtaT2 toxin from a toxin-antitoxin system from Escherichia coli O157:H7. We show that AtaT2 is the first GNAT (Gcn5-related N-acetyltransferase) toxin that specifically targets charged glycyl tRNA. In vivo, the AtaT2 activity induces ribosome stalling at all four glycyl codons but does not evoke a stringent response. In vitro, AtaT2 acetylates the aminoacyl moiety of isoaccepting glycyl tRNAs, thus precluding their participation in translation. Our study broadens the known target specificity of GNAT toxins beyond the earlier described isoleucine and formyl methionine tRNAs, and suggest that various GNAT toxins may have evolved to specifically target other if not all individual aminoacyl tRNAs