Translocation of flexible and tensioned ssDNA through in silico designed hydrophobic nanopores with two constrictions

ABSTRACTProtein-inspired nanopores with hydrophobic constriction regions have previously been shown to offer some promise for DNA sequencing. Here we explore a series of pores with two hydrophobic constrictions. The impact of nanopore radius, the nature of residues that define the constriction region and the flexibility of the ssDNA is explored. Our results show that aromatic residues slow down DNA translocation, and in the case of short DNA strands, they cause deviations from a linear DNA conformation. When DNA is under tension, translocation is once again slower when aromatic residues are present in the constriction. However, the lack of flexibility in the DNA backbone provides a narrower window of opportunity for the DNA bases to be retained inside the pore via interaction with the aromatic residues, compared to more flexible strands. Consequently, there is more variability in translocation rates for strands under tension. DNA entry into the pores is correlated to pore width, but no such correlation between width and translocation rate is observed.

Reverse genetics-based biochemical studies of the ribosomal exit tunnel constriction region in eukaryotic ribosome stalling: spatial allocation of the regulatory nascent peptide at the constriction

A number of regulatory nascent peptides have been shown to regulate gene expression by causing programmed ribosome stalling during translation. Nascent peptide emerges from the ribosome through the exit tunnel, and one-third of the way along which β-loop structures of ribosomal proteins uL4 and uL22 protrude into the tunnel to form the constriction region. Structural studies have shown interactions between nascent peptides and the exit tunnel components including the constriction region. In eukaryotes, however, there is a lack of genetic studies for the involvement of the constriction region in ribosome stalling. Here, we established transgenic Arabidopsis lines that carry mutations in the β-loop structure of uL4. Translation analyses using a cell-free translation system derived from the transgenic Arabidopsis carrying the mutant ribosome showed that the uL4 mutations reduced the ribosome stalling of four eukaryotic stalling systems, including those for which stalled structures have been solved. Our data, which showed differential effects of the uL4 mutations depending on the stalling systems, explained the spatial allocations of the nascent peptides at the constriction that were deduced by structural studies. Conversely, our data may predict allocation of the nascent peptide at the constriction of stalling systems for which structural studies are not done.

Small Molecule Permeation Across Membrane Channels: Chemical Modification to Quantify Transport Across OmpF

Biological channels facilitate the exchange of small molecules across membranes, but surprisingly there is a lack of general tools for the identification and quantification of transport (i.e., translocation and binding). Analyzing the ion current fluctuation of a typical channel with its constriction region in the middle does not allow a direct conclusion on successful transport. For this, we created an additional barrier acting as a molecular counter at the exit of the channel. To identify permeation, we mainly read the molecule residence time in the channel lumen as the indicator whether the molecule reached the exit of the channel. As an example, here we use the well-studied porin, OmpF, an outer membrane channel from <i>E. coli</i>. Inspection of the channel structure suggests that aspartic acid at position 181 is located below the constriction region (CR) and we subsequently mutated this residue to cysteine, where else cysteine free and functionalized it by covalent binding with 2-sulfonatoethyl methanethiosulfonate (MTSES) or the larger glutathione (GLT) blockers. Using the dwell time as the signal for transport, we found that both mono-arginine and tri-arginine permeation process is prolonged by 20% and 50% respectively through OmpF_E181CMTSES, while the larger sized blocker modification OmpF_E181CGLT drastically decreased the permeation of mono-arginine by 9-fold and even blocked the pathway of the tri-arginine. In case of the hepta-arginine as substrate, both chemical modifications led to an identical ‘blocked’ pattern observed by the dwell time of ion current fluctuation of the OmpF_wt. As an instance for antibiotic permeation, we analyzed norfloxacin, a fluoroquinolone antimicrobial agent. The modulation of the interaction dwell time suggests possible successful permeation of norfloxacin across OmpF_wt. This approach may discriminate blockages from translocation events for a wide range of substrates. A potential application could be screening for scaffolds to improve the permeability of antibiotics.

Small Molecule Permeation Across Membrane Channels: Chemical Modification to Quantify Transport Across OmpF

Biological channels facilitate the exchange of small molecules across membranes, but surprisingly there is a lack of general tools for the identification and quantification of transport (i.e., translocation and binding). Analyzing the ion current fluctuation of a typical channel with its constriction region in the middle does not allow a direct conclusion on successful transport. For this, we created an additional barrier acting as a molecular counter at the exit of the channel. To identify permeation, we mainly read the molecule residence time in the channel lumen as the indicator whether the molecule reached the exit of the channel. As an example, here we use the well-studied porin, OmpF, an outer membrane channel from <i>E. coli</i>. Inspection of the channel structure suggests that aspartic acid at position 181 is located below the constriction region (CR) and we subsequently mutated this residue to cysteine, where else cysteine free and functionalized it by covalent binding with 2-sulfonatoethyl methanethiosulfonate (MTSES) or the larger glutathione (GLT) blockers. Using the dwell time as the signal for transport, we found that both mono-arginine and tri-arginine permeation process is prolonged by 20% and 50% respectively through OmpF_E181CMTSES, while the larger sized blocker modification OmpF_E181CGLT drastically decreased the permeation of mono-arginine by 9-fold and even blocked the pathway of the tri-arginine. In case of the hepta-arginine as substrate, both chemical modifications led to an identical ‘blocked’ pattern observed by the dwell time of ion current fluctuation of the OmpF_wt. As an instance for antibiotic permeation, we analyzed norfloxacin, a fluoroquinolone antimicrobial agent. The modulation of the interaction dwell time suggests possible successful permeation of norfloxacin across OmpF_wt. This approach may discriminate blockages from translocation events for a wide range of substrates. A potential application could be screening for scaffolds to improve the permeability of antibiotics.

Omp35, a New Enterobacter aerogenes Porin Involved in Selective Susceptibility to Cephalosporins

ABSTRACT In Enterobacter aerogenes, β-lactam resistance often involves a decrease in outer membrane permeability induced by modifications of porin synthesis. In ATCC 15038 strain, we observed a different pattern of porin production associated with a variable antibiotic susceptibility. We purified Omp35, which is expressed under conditions of low osmolality and analyzed its pore-forming properties in artificial membranes. This porin was found to be an OmpF-like protein with high conductance values. It showed a noticeably higher conductance compared to Omp36 and a specific location of WNYT residues in the L3 loop. The importance of the constriction region in the porin function suggests that this organization is involved in the level of susceptibility to negative large cephalosporins such as ceftriaxone by bacteria producing the Omp35 porin subfamily.

Molecular characterization of the secondary constriction region (qh) of human chromosome 9 with pericentric inversion

Pericentric inversion of the secondary constriction region (qh) of human chromosome 9 is a frequent occurrence. This structural alteration is regarded as a normal familial variant, termed heteromorphism, and is inherited in a Mendelian fashion without any apparent phenotypic consequences. We characterized the qh region of chromosome 9 from five individuals using a series of molecular cytogenetic techniques. Four out of the five individuals have an additional area composed of alphoid DNA sequences on the inverted chromosome 9 while one case was found to have an apparently intact alphoid DNA sequence. Although the direct function(s) of alphoid DNA sequences remain unclear, the centromeric breakage involving these sequences in inverted chromosome 9 raises a series of questions pertaining to the monocentric, dicentric and pseudodicentric nature of pericentric inversions. Nevertheless, these findings have prompted us to suggest that the structural organization of alphoid DNA sequences of the centromeric region of chromosome 9 are apparently “breakage prone” and may be associated with a higher incidence of pericentric inversions. Furthermore, the hierarchical organization of various satellite DNA families (alpha-satellite, beta-satellite and satellite III) within the primary and secondary constriction regions of chromosomes 9 are elucidated here.

The specification of metameric order in the insect Callosobruchus maculatus Fabr. (Coleoptera)

Eggs of the pea-beetle Callosobruchus were divided into two at different stages of development. Both fragments were allowed to develop into partial larvae. The segment patterns of normal and partial larvae are described using cuticular markers of cell differentiation. To study the contribution of cytological damage to the segment gap phenomenon three different types of constriction were performed: complete and incomplete permanent constriction and complete temporary constriction. Changes in the structure of the egg can produce absence of segments resulting from two different effects. First, partial absence of segments results from a decreased egg circumference in the constriction region and involves the disturbance of a morphogenetic process (dorsal closure). Secondly, cytological damage can result in a gap between two arrays of segments. The loss of segments in the gap occurred in two different ways. In a spatial segment gap the two arrays of segments were physically discontinuous, whereas in a non-spatial gap the segments bordering the gap were juxtaposed in a physically continuous cuticle. The extent to which the gap phenomenon can be attributed to cytological damage is discussed. We also discuss, on the basis of certain dorsal defects, a possible stepwise specification of the dorsal transverse cuticular pattern.