Ribonucleotide reductases (RNRs) reduce ribonucleotides to deoxyribonucleotides. Their overall activity is stimulated by ATP and downregulated by dATP via a genetically mobile ATP cone domain mediating the formation of oligomeric complexes with varying quaternary structures. The crystal structure and solution X-ray scattering data of a novel dATP-induced homotetramer of the Pseudomonas aeruginosa class I RNR reveal the structural bases for its unique properties, namely one ATP cone that binds two dATP molecules and a second one that is non-functional, binding no nucleotides. Mutations in the observed tetramer interface ablate oligomerization and dATP-induced inhibition but not the ability to bind dATP. Sequence analysis shows that the novel type of ATP cone may be widespread in RNRs. The present study supports a scenario in which diverse mechanisms for allosteric activity regulation are gained and lost through acquisition and evolutionary erosion of different types of ATP cone.
The ability of cationic-rich and anionic-rich mixtures of CTAB (cetyltrimethylammonium bromide) and SDS (sodium dodecyl sulfate) for dispersing of carbon nanotubes (CNTs) in aqueous media has been studied through both the experimental and molecular dynamics simulation methods. Compared to the pure CTAB and SDS, these mixtures are more effective with the lower concentrations and more individual CNTs, reflecting a synergistic effect in these mixtures. The synergistic effects observed in mixed surfactant systems are mainly due to the electrostatic attractions between surfactant heads. In addition, the surface charge related to the colloidal stability of mixed surfactant-covered nanotubes has been characterized by means of ζ-potential measurements. The results indicate that the hydrophobic interactions between surfactant tails also give rise to the higher adsorption of surfactant molecules. Furthermore, molecular dynamics (MD) simulations have been performed to provide insight about the structure of surfactant aggregates onto nanotubes and to attempt an explanation of the experimental results. The MD simulation results indicate that the random and disordered adsorption of mixed surfactants onto carbon nanotubes may be preferred for a low surfactant concentration. Our research may provide experimental and theoretical bases for using mixed surfactants to disperse CNTs, which can open an avenue for new applications of mixed surfactants.
After publication of the original article, three errors were discovered in Figure 2 and its legend. In Figure 2A, the dATP curve was described as red and the dGTP curve as blue; in fact, the dATP curve is blue and the dGTP curve is red. In Figure 2C, the dATP and dGTP curves were colored incorrectly, i.e., dATP in red and dGTP in blue. This was inconsistent with the coloring of the other panels. Finally, in the legend for Figure 2E, the colors of the curves were also wrongly described, as in Figure 2A. The figure and legend have been corrected in the online version of the article, and the corrected figure and legend are also printed below. These errors do not affect the interpretation of the data. The authors apologize for any confusion this may have caused.
Copper (Cu) is one of the most abundant trace metals in all organisms, involved in a plethora of cellular processes. Yet elevated concentrations of the element are harmful, and interestingly prokaryotes are more sensitive for environmental Cu stress than humans. Various transport systems are present to maintain intracellular Cu homeostasis, including the prokaryotic plasmidencoded multiprotein pco operon, which is generally assigned as a defense mechanism against elevated Cu concentrations. Here we structurally and functionally characterize the outer membrane component of the Pco system, PcoB, recovering a 2.0 Å structure, revealing a classical β-barrel architecture. Unexpectedly, we identify a large opening on the extracellular side, linked to a considerably electronegative funnel that becomes narrower towards the periplasm, defining an ion-conducting pathway as also supported by metal binding quantification via inductively coupled plasma mass spectrometry and molecular dynamics (MD) simulations. However, the structure is partially obstructed towards the periplasmic side, and yet flux is permitted in the presence of a Cu gradient as shown by functional characterization in vitro. Complementary in vivo experiments demonstrate that isolated PcoB confers increased sensitivity towards Cu. Aggregated, our findings indicate that PcoB serves to permit Cu import. Thus, it is possible the Pco system physiologically accumulates Cu in the periplasm as a part of an unorthodox defense mechanism against metal stress. These results point to a previously unrecognized principle of Ping Li and Niloofar Nayeri contributed equally.
Measurement of protein-facilitated copper flux across biological membranes is a considerable challenge. Here, we demonstrate a straightforward microfluidic-derived approach for visualization and measurement of membranous Cu flux. Giant unilamellar vesicles, reconstituted with the membrane protein of interest, are prepared, surface-immobilized, and assessed using a novel quencher–sensor reporter system for detection of copper. With the aid of a syringe pump, the external buffer is exchanged, enabling consistent and precise exchange of solutes, without causing vesicle rupture or uneven local metal concentrations brought about by rapid mixing. This approach bypasses common issues encountered when studying heavy metal-ion flux, thereby providing a new platform for in vitro studies of metal homeostasis aspects that are critical for all cells, health, and disease.
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