A major problem in structural biology is the recognition of errors in experimental and theoretical models of protein structures. The ProSA program (Protein Structure Analysis) is an established tool which has a large user base and is frequently employed in the refinement and validation of experimental protein structures and in structure prediction and modeling. The analysis of protein structures is generally a difficult and cumbersome exercise. The new service presented here is a straightforward and easy to use extension of the classic ProSA program which exploits the advantages of interactive web-based applications for the display of scores and energy plots that highlight potential problems spotted in protein structures. In particular, the quality scores of a protein are displayed in the context of all known protein structures and problematic parts of a structure are shown and highlighted in a 3D molecule viewer. The service specifically addresses the needs encountered in the validation of protein structures obtained from X-ray analysis, NMR spectroscopy and theoretical calculations. ProSA-web is accessible at https://prosa.services.came.sbg.ac.at.

ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins.

P-glycoprotein (P-gp) detoxifies cells by exporting hundreds of chemically unrelated toxins but has been implicated in multidrug resistance (MDR) in the treatment of cancers. Substrate promiscuity is a hallmark of P-gp activity, thus a structural description of poly-specific drug-binding is important for the rational design of anticancer drugs and MDR inhibitors. The x-ray structure of apo P-gp at 3.8 angstroms reveals an internal cavity of ∼6000 angstroms cubed with a 30 angstrom separation of the two nucleotide-binding domains. Two additional P-gp structures with cyclic peptide inhibitors demonstrate distinct drug-binding sites in the internal cavity capable of stereoselectivity that is based on hydrophobic and aromatic interactions. Apo and drug-bound P-gp structures have portals open to the cytoplasm and the inner leaflet of the lipid bilayer for drug entry. The inward-facing conformation represents an initial stage of the transport cycle that is competent for drug binding.

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Structure of P-glycoprotein reveals a molecular basis for poly-specific drug binding.

Summary: High-affinity iron acquisition is mediated by siderophore-dependent pathways in the majority of pathogenic and nonpathogenic bacteria and fungi. Considerable progress has been made in characterizing and understanding mechanisms of siderophore synthesis, secretion, iron scavenging, and siderophore-delivered iron uptake and its release. The regulation of siderophore pathways reveals multilayer networks at the transcriptional and posttranscriptional levels. Due to the key role of many siderophores during virulence, coevolution led to sophisticated strategies of siderophore neutralization by mammals and (re)utilization by bacterial pathogens. Surprisingly, hosts also developed essential siderophore-based iron delivery and cell conversion pathways, which are of interest for diagnostic and therapeutic studies. In the last decades, natural and synthetic compounds have gained attention as potential therapeutics for iron-dependent treatment of infections and further diseases. Promising results for pathogen inhibition were obtained with various siderophore-antibiotic conjugates acting as “Trojan horse” toxins and siderophore pathway inhibitors. In this article, general aspects of siderophore-mediated iron acquisition, recent findings regarding iron-related pathogen-host interactions, and current strategies for iron-dependent pathogen control will be reviewed. Further concepts including the inhibition of novel siderophore pathway targets are discussed.

/pdf/siderophore-based-iron-acquisition-and-pathogen-control-2r9qlb86av.pdf

Siderophore-Based Iron Acquisition and Pathogen Control

Large amounts of antibiotics used for human therapy, as well as for farm animals and even for fish in aquaculture, resulted in the selection of pathogenic bacteria resistant to multiple drugs. Multidrug resistance in bacteria may be generated by one of two mechanisms. First, these bacteria may accumulate multiple genes, each coding for resistance to a single drug, within a single cell. This accumulation occurs typically on resistance (R) plasmids. Second, multidrug resistance may also occur by the increased expression of genes that code for multidrug efflux pumps, extruding a wide range of drugs. This review discusses our current knowledge on the molecular mechanisms involved in both types of resistance.

Multidrug Resistance in Bacteria

Inwardly rectifying K+ (Kir) channels allow K+ to move more easily into rather than out of the cell. They have diverse physiological functions depending on their type and their location. There are ...

Inwardly Rectifying Potassium Channels: Their Structure, Function, and Physiological Roles

Multidrug transporters of the ABC family facilitate the export of diverse cytotoxic drugs across cell membranes. This is clinically relevant, as tumour cells may become resistant to agents used in chemotherapy. To understand the molecular basis of this process, we have determined the 3.0 A crystal structure of a bacterial ABC transporter (Sav1866) from Staphylococcus aureus. The homodimeric protein consists of 12 transmembrane helices in an arrangement that is consistent with cross-linking studies and electron microscopic imaging of the human multidrug resistance protein MDR1, but critically different from that reported for the bacterial lipid flippase MsbA. The observed, outward-facing conformation reflects the ATP-bound state, with the two nucleotide-binding domains in close contact and the two transmembrane domains forming a central cavity—presumably the drug translocation pathway—that is shielded from the inner leaflet of the lipid bilayer and from the cytoplasm, but exposed to the outer leaflet and the extracellular space. Multidrug efflux transporters cause serious problems in cancer chemotherapy and in the treatment of bacterial infections. A puzzling aspect of their biology is how a single transporter can recognize and transport such a wide variety of structurally dissimilar compounds. The publication of the crystal structures of two quite different multidrug efflux transporters will help to solve the mystery. In the first study, the structure of AcrB — a multidrug efflux transporter from E. coli — was determined. Its three constituent subunits were captured at different steps in the transport cycle: prior to substrate binding, substrate-bound, and post-extrusion. The voluminous multidrug binding pocket handles multiple substrates via multi-site binding. The second study determined the structure of an ATP-driven multidrug transporter from S. aureus. The clinical relevance of this 'ABC' family of transporters derives from the fact that they catalyse the extrusion of various cytotoxic compounds used in cancer therapy. The structure, with the transporter in the outward-facing conformation, is a useful model of human homologues and may initiate the rational design of drugs aimed at interfering with the extrusion of agents used in chemotherapy.

Structure of a bacterial multidrug ABC transporter

Structure and mechanism of ABC transporter proteins

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/j.febslet.2007.01.073

Structure of the multidrug ABC transporter Sav1866 from Staphylococcus aureus in complex with AMP‐PNP

Structure of the mu-opioid receptor-Giprotein complex.

ATP-binding cassette (ABC) transporters are integral membrane proteins that move diverse substrates across cellular membranes. ABC importers catalyse the uptake of essential nutrients from the environment, whereas ABC exporters facilitate the extrusion of various compounds, including drugs and antibiotics, from the cytoplasm. How ABC transporters couple ATP hydrolysis to the transport reaction has long remained unclear. The recent crystal structures of four complete ABC transporters suggest that a key step of the molecular mechanism is conserved in importers and exporters. Whereas binding of ATP promotes an outward-facing conformation, the release of the hydrolysis products ADP and phosphate promotes an inward-facing conformation. This basic scheme can in principle explain ATP-driven drug export and binding protein-dependent nutrient uptake.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2958.2007.05792.x

Roger J. P. Dawson

Papers

Structure of a bacterial multidrug ABC transporter

Structure and mechanism of ABC transporter proteins

Structure of the multidrug ABC transporter Sav1866 from Staphylococcus aureus in complex with AMP‐PNP

Structure of the mu-opioid receptor-Giprotein complex.

Uptake or extrusion: crystal structures of full ABC transporters suggest a common mechanism.