High specificity of a phosphate transport protein determined by hydrogen bonds

FbpA--a bacterial transferrin with more to offer

BACKGROUND

Gram negative bacteria require iron for growth and virulence. It has been shown that certain pathogenic bacteria such as Neisseria gonorrhoeae possess a periplasmic protein called ferric binding protein (FbpA), which is a node in the transport of iron from the cell exterior to the cytosol.

SCOPE OF REVIEW

The relevant literature is reviewed which establishes the molecular mechanism of FbpA mediated iron transport across the periplasm to the inner membrane.

MAJOR CONCLUSIONS

Here we establish that FbpA may be considered a bacterial transferrin on structural and functional grounds. Data are presented which suggest a continuum whereby FbpA may be considered as a naked iron carrier, as well as a Fe-chelate carrier, and finally a member of the larger family of periplasmic binding proteins.

GENERAL SIGNIFICANCE

An investigation of the molecular mechanisms of action of FbpA as a member of the transferrin super family enhances our understanding of bacterial mechanisms for acquisition of the essential nutrient iron, as well as the modes of action of human transferrin, and may provide approaches to the control of pathogenic diseases. This article is part of a Special Issue entitled Transferrins: Molecular mechanisms of iron transport and disorders.

NMR studies of anion-induced conformational changes in diindolylureas and diindolylthioureas

The conformational properties of 1,3-diindolylureas and thioureas were studied by a combination of heteronuclear NMR spectroscopy and quantum mechanics calculations. NOE experiments showed that the anti–anti conformer along the C7–N7α bonds was predominant in DMSO-d₆ solution in the absence of anions. Anion-induced changes in the ¹H and ¹⁵N chemical shifts confirm the weak binding of chloride anions with negligible conformational changes. Strong deshielding of ureido protons and moderate deshielding of indole NH was observed upon the addition of acetate, benzoate, bicarbonate and dihydrogen phosphate, which indicated that the predominant hydrogen bond interactions occurred at the urea donor groups. Binding of oxo-anions caused conformational changes along the C7–N7α bonds and the syn–syn conformer was preferred for anion–receptor complexes. The conformational changes upon anion binding are in good agreement with energetic preferences established by ab initio calculations.

Binding of ReO4(-) with an engineered MoO4(2-)-binding protein: towards a new approach in radiopharmaceutical applications

Radiolabeled biomolecules are routinely used for clinical diagnostics. (99m)Tc is the most commonly used radioactive tracer in radiopharmaceuticals. (188)Re and (186)Re are also commonly used as radioactive tracers in medicine. However, currently available methods for radiolabeling are lengthy and involve several steps in bioconjugation processes. In this work we present a strategy to engineer proteins that may selectively recognize the perrhenate (ReO(4)(-)) ion as a new way to label proteins. We found that a molybdate (MoO(4)(2-))-binding protein (ModA) from Escherichia coli can bind perrhenate with high affinity. Using fluorescence and isothermal titration calorimetry measurements, we determined the dissociation constant of ModA for ReO(4)(-) to be 541 nM and we solved a crystal structure of ModA with a bound ReO(4)(-). On the basis of the structure we created a mutant protein containing a disulfide linkage, which exhibited increased affinity for perrhenate (K(d) = 104 nM). High-resolution crystal structures of ModA (1.7 Å) and A11C/R153C mutant (2.0 Å) were solved with bound perrhenate. Both structures show that a perrhenate ion occupies the molybdate binding site using the same amino acid residues that are involved in molybdate binding. The overall structure of the perrhenate-bound ModA is unchanged compared with that of the molybdate-bound form. In the mutant protein, the bound perrhenate is further stabilized by the engineered disulfide bond.

Anion binding properties of the transferrins. Implications for function

BACKGROUND

Since the transferrins have been defined by the highly cooperative binding of Fe(3+) and a carbonate anion to form an Fe-CO(3)-Tf ternary complex, the focus has been on synergistic anion binding. However, there are other types of anion binding with both apotransferrin and diferric transferrin that affect metal binding and release.

SCOPE OF REVIEW

This review covers the binding of anions to the apoprotein, as well as the formation and structure of Fe-anion-transferrin ternary complexes. It also covers interactions between ferric transferrin and non-synergistic anions that appear to be important in vivo.

GENERAL SIGNIFICANCE

The interaction of anions with apotransferrin can alter the effective metal binding constants, which can affect the transport of metal ions in serum. These interactions also play a role in iron release under physiological conditions.

MAJOR CONCLUSIONS

Apotransferrin binds a variety of anions with no special selectivity for carbonate. The selectivity for carbonate as a synergistic anion is associated with the iron binding reaction. Conformational changes in the binding of the synergistic carbonate and competition from non-synergistic anions both play a role in intracellular iron release. Anion competition also occurs in serum and reduces the effective metal binding affinity of Tf. Lastly, anions bind to allosteric sites (KISAB sites) on diferric transferrin and alter the rates of iron release. The KISAB sites have not been well-characterized, but kinetic studies on iron release from mutant transferrins indicate that there are likely to be multiple KISAB sites for each lobe of transferrin. This article is part of a Special Issue entitled Transferrins: Molecular mechanisms of iron transport and disorders.

Mechanisms of protein-ligand association and its modulation by protein mutations

Protein-ligand interactions are essential for nearly all biological processes, and yet the biophysical mechanism that enables potential binding partners to associate before specific binding occurs remains poorly understood. Fundamental questions include which factors influence the formation of protein-ligand encounter complexes, and whether designated association pathways exist. To address these questions, we developed a computational approach to systematically analyze the complete ensemble of association pathways. Here, we use this approach to study the binding of a phosphate ion to the Escherichia coli phosphate-binding protein. Various mutants of the protein are considered, and their effects on binding free-energy profiles, association rates, and association pathway distributions are quantified. The results reveal the existence of two anion attractors, i.e., regions that initially attract negatively charged particles and allow them to be efficiently screened for phosphate, which is subsequently specifically bound. Point mutations that affect the charge on these attractors modulate their attraction strength and speed up association to a factor of 10 of the diffusion limit, and thus change the association pathways of the phosphate ligand. It is demonstrated that a phosphate that prebinds to such an attractor neutralizes its attraction effect to the environment, making the simultaneous association of a second phosphate ion unlikely. This study suggests ways in which structural properties can be used to tune molecular association kinetics so as to optimize the efficiency of binding, and highlights the importance of kinetic properties.

Parallel Evolution and Horizontal Gene Transfer of the pst Operon in Firmicutes from Oligotrophic Environments

The high affinity phosphate transport system (pst) is crucial for phosphate uptake in oligotrophic environments. Cuatro Cienegas Basin (CCB) has extremely low P levels and its endemic Bacillus are closely related to oligotrophic marine Firmicutes. Thus, we expected the pst operon of CCB to share the same evolutionary history and protein similarity to marine Firmicutes. Orthologs of the pst operon were searched in 55 genomes of Firmicutes and 13 outgroups. Phylogenetic reconstructions were performed for the pst operon and 14 concatenated housekeeping genes using maximum likelihood methods. Conserved domains and 3D structures of the phosphate-binding protein (PstS) were also analyzed. The pst operon of Firmicutes shows two highly divergent clades with no correlation to the type of habitat nor a phylogenetic congruence, suggesting horizontal gene transfer. Despite sequence divergence, the PstS protein had a similar 3D structure, which could be due to parallel evolution after horizontal gene transfer events.

Phosphate transporters in renal, gastrointestinal, and other tissues

Inorganic phosphate (Pi) is essential for all living organisms. Bound to organic molecules, Pi fulfills structural, metabolic, and signaling tasks. Therefore, cell growth and maintenance depends on efficient transport of Pi across cellular membranes into the intracellular space. Uptake of Pi requires energy because the substrate is transported against its electrochemical gradient. Till recently, 2 major families of physiologically relevant Pi-specific transporters have been identified: the solute carrier families Slc34 and Slc20. Interestingly, phylogenetic links can be detected between prokaryotic and eukaryotic transporters in both families. Because less complex model organisms are often instrumental in establishing paradigms for protein function in human beings, a brief assessment of Slc34 and Slc20 phylogeny is of interest.

Rotaxanes capable of recognising chloride in aqueous media

A new, versatile chloride-anion-templating synthetic pathway is exploited for the preparation of a series of eight new [2]rotaxane host molecules, including the first sulfonamide interlocked system. (1)H NMR spectroscopic titration investigations demonstrate the rotaxanes' capability to selectively recognise the chloride anion in competitive aqueous solvent media. The interlocked host's halide binding affinity can be further enhanced and tuned through the attachment of electron-withdrawing substituents and by increasing its positive charge. A dicationic rotaxane selectively binds chloride in 35% water, wherein no evidence of oxoanion binding is observed. NMR spectroscopy, X-ray structural analysis and computational molecular dynamics simulations are used to account for rotaxane formation yields, anion binding strengths and selectivity trends.

Novel channel enzyme fusion proteins confer arsenate resistance

Steady exposure to environmental arsenic has led to the evolution of vital cellular detoxification mechanisms. Under aerobic conditions, a two-step process appears most common among microorganisms involving reduction of predominant, oxidized arsenate (H(2)As(V)O(4)(-)/HAs(V)O(4)(2-)) to arsenite (As(III)(OH)(3)) by a cytosolic enzyme (ArsC; Escherichia coli type arsenate reductase) and subsequent extrusion via ArsB (E. coli type arsenite transporter)/ACR3 (yeast type arsenite transporter). Here, we describe novel fusion proteins consisting of an aquaglyceroporin-derived arsenite channel with a C-terminal arsenate reductase domain of phosphotyrosine-phosphatase origin, providing transposable, single gene-encoded arsenate resistance. The fusion occurred in actinobacteria from soil, Frankia alni, and marine environments, Salinispora tropica; Mycobacterium tuberculosis encodes an analogous ACR3-ArsC fusion. Mutations rendered the aquaglyceroporin channel more polar resulting in lower glycerol permeability and enhanced arsenite selectivity. The arsenate reductase domain couples to thioredoxin and can complement arsenate-sensitive yeast strains. A second isoform with a nonfunctional channel may use the mycothiol/mycoredoxin cofactor pool. These channel enzymes constitute prototypes of a novel concept in metabolism in which a substrate is generated and compartmentalized by the same molecule. Immediate diffusion maintains the dynamic equilibrium and prevents toxic accumulation of metabolites in an energy-saving fashion.

Cryptand-like anion receptors

The design of supramolecular hosts for anions began with simple diaza bicycles, named katapinands, and has evolved over the last 40 years to a number of elegantly designed receptors capable of binding many different anions. About the same time the term cryptand appeared in reference to another bicyclic compound that was selective for alkaline-earth ions. Since the first report these simple bicycles, a vast arena of hosts has appeared, including acyclic, monocyclic, and other multicyclic supramolecular receptors. Studies of these systems have revealed considerable information about anion coordination chemistry, including the fact that many of these complexes mimic their transition-metal corollaries in terms of coordination numbers. However, for anions interactions occur via H-bonding most often, rather than the coordinate covalent or dative bonds observed in transition-metal coordination. This critical review examines the design of enclosed, primarily bicyclic cryptands as hosts for anions, with a small scattering of higher polyhedra when deemed appropriate to the discussion. In order to show the development (evolution) of the field, key examples of early work will be noted and compared with more recent developments (136 references).

Anion binding in covalent and self-assembled molecular capsules

This critical review describes selected examples extracted from the extensive literature generated during the past 42 years on the topic of anion binding in molecular capsules. The goal of including anions in molecular capsules emerges from the idea of incorporating the traits exhibited by biological receptors into synthetic ones. At the outset of this research area the capsules were unimolecular. The scaffold of the receptor was designed to covalently link a series of functional groups that could converge into a cavity and to avoid its collapse. The initial examples involved the encapsulation of one monoatomic spherical anion. With time, the cavity size of the receptor was increased and encapsulation of polyatomic anions and co-encapsulation became a reality. Synthetic economy fueled the use of aggregates of self-complementary molecules rather than one large molecule as capsules. The main purpose of this review is to give a general overview of the topic which might be of interest to supramolecular or non supramolecular chemists alike (149 references).

Functional characterization of Synechocystis sp. strain PCC 6803 pst1 and pst2 gene clusters reveals a novel strategy for phosphate uptake in a freshwater cyanobacterium

Synechocystis sp. strain PCC 6803 possesses two putative ABC-type inorganic phosphate (P(i)) transporters with three associated P(i)-binding proteins (PBPs), SphX (encoded by sll0679), PstS1 (encoded by sll0680), and PstS2 (encoded by slr1247), organized in two spatially discrete gene clusters, pst1 and pst2. We used a combination of mutagenesis, gene expression, and radiotracer uptake analyses to functionally characterize the role of these PBPs and associated gene clusters. Quantitative PCR (qPCR) demonstrated that pstS1 was expressed at a high level in P(i)-replete conditions compared to sphX or pstS2. However, a P(i) stress shift increased expression of pstS2 318-fold after 48 h, compared to 43-fold for pstS1 and 37-fold for sphX. A shift to high-light conditions caused a transient increase of all PBPs, whereas N stress primarily increased expression of sphX. Interposon mutagenesis of each PBP demonstrated that disruption of pstS1 alone caused constitutive expression of pho regulon genes, implicating PstS1 as a major component of the P(i) sensing machinery. The pstS1 mutant was also transformation incompetent. (32)P(i) radiotracer uptake experiments using pst1 and pst2 deletion mutants showed that Pst1 acts as a low-affinity, high-velocity transporter (K(s), 3.7 + or - 0.7 microM; V(max), 31.18 + or - 3.96 fmol cell(-1) min(-1)) and Pst2 acts as a high-affinity, low-velocity system (K(s), 0.07 + or - 0.01 microM; V(max), 0.88 + or - 0.11 fmol cell(-1) min(-1)). These P(i) ABC transporters thus exhibit differences in both kinetic and regulatory properties, the former trait potentially dramatically increasing the dynamic range of P(i) transport into the cell, which has potential implications for our understanding of the ecological success of this key microbial group.

Colorimetric and fluorescence sensing of fluoride anions with potential salicylaldimine based schiff base receptors

Salicylaldimine based schiff base receptors with different substituents showing fluorescent enhancement in the presence of fluoride anion was visualized through naked eye as well as by change in spectral properties (UV-vis and fluorescent techniques). The reason for such fluorescence enhancement may be due to hydrogen bond interaction between receptor recognition site and fluoride anion. Such a hydrogen bond interaction creates a six-membered transition state, which avoids quenching processes. To support this, fluorescence enhancement factor (FEF) was calculated and it was found to be more (FEF=652) for -NO(2) substituted receptor compared to other receptors.

Elucidation of the phosphate binding mode of DING proteins revealed by subangstrom X-ray crystallography

PfluDING is a bacterial protein isolated from Pseudomonas fluorescens that belongs to the DING protein family, which is ubiquitous in eukaryotes and extends to prokaryotes. DING proteins and PfluDING have very similar topologies to phosphate Solute Binding Proteins (SBPs). The three-dimensional structure of PfluDING was obtained at subangstrom resolution (0.88 and 0.98 A) at two different pH's (4.5 and 8.5), allowing us to discuss the hydrogen bond network that sequesters the phosphate ion in the binding site. From this high resolution data, we experimentally elucidated the molecular basis of phosphate binding in phosphate SBPs. The phosphate ion is tightly bound to the protein via 12 hydrogen bonds between phosphate oxygen atoms and OH and NH groups of the protein. The proton on one oxygen atom of the phosphate dianion forms a 2.5 A low barrier hydrogen bond with an aspartate, with the energy released by forming this strong bond ensuring the specificity for the dianion even at pH 4.5. In particular, contrary to previous theories on phosphate SBPs, accurate electrostatic potential calculations show that the binding cleft is positively charged. PfluDING structures reveal that only dibasic phosphate binds to the protein at both acidic and basic phosphate, suggesting that the protein binding site environment stabilizes the HPO(4)(2-) form of phosphate.

For whom the bell tolls? DING proteins in health and disease

DING proteins, identified mainly by their eponymous N-terminal sequences, are ubiquitous in living organisms. Amongst bacteria, they are common in pseudomonads, and have been characterised with respect to genetics and structure. They form part of a wider family of phosphate-binding proteins, with emerging roles in phosphate acquisition and pathogenicity. Many DING proteins have been isolated in eukaryotes, in which they have been associated with very diverse biological activities, often in the context of possible signalling roles. Disease states in which DING proteins have been implicated include rheumatoid arthritis, lithiasis, atherosclerosis, some tumours and tumour-associated cachexia, and bacterial and viral adherence. Complete genetic and structural characterisation of eukaryotic DING genes and proteins is still lacking, though the phosphate-binding site seems to be conserved. Whether as bacterial proteins related to bacterial pathogenicity, or as eukaryotic components of biochemical signalling systems, DING proteins require further study.

The DING family of proteins: ubiquitous in eukaryotes, but where are the genes?

PstS and DING proteins are members of a superfamily of secreted, high-affinity phosphate-binding proteins. Whereas microbial PstS have a well-defined role in phosphate ABC transporters, the physiological function of DING proteins, named after their DINGGG N termini, still needs to be determined. PstS and DING proteins co-exist in some Pseudomonas strains, to which they confer a highly adhesive and virulent phenotype. More than 30 DING proteins have now been purified, mostly from eukaryotes. They are often associated with infections or with dysregulation of cell proliferation. Consequently, eukaryotic DING proteins could also be involved in cell-cell communication or adherence. The ubiquitous presence in eukaryotes of proteins structurally and functionally related to bacterial virulence factors is intriguing, as is the absence of eukaryotic genes encoding DING proteins in databases. DING proteins in eukaryotes could originate from unidentified commensal or symbiotic bacteria and could contribute to essential functions. Alternatively, DING proteins could be encoded by eukaryotic genes sharing special features that prevent their cloning. Both hypotheses are discussed.

(Thio)urea organocatalysis--what can be learnt from anion recognition?

The present critical review outlines the close relationship and mutual interplay between molecular recognition, active site considerations in enzyme catalysis involving anions, and organocatalysis utilizing explicit hydrogen bonding. These interconnections are generally not made although, as we demonstrate, they are quite apparent as exemplified with pertinent examples in the field of (thio)urea organocatalysis. Indeed, the concepts of anion binding or binding with negatively (partially) charged heteroatoms is key for designing new organocatalytic transformations. Utilizing anions through recognition with hydrogen-bonding organocatalysts is still in its infancy but bears great potential. In turn, the discovery and mechanistic elucidation of such reactions is likely to improve the understanding of enzyme active sites (108 references).

Protein design provides lead(II) ion biosensors for imaging molecular fluxes around red blood cells

Metalloprotein design and semiconductor nanoparticles have been combined to generate a reagent for selective fluorescence imaging of Pb(2+) ions in the presence red blood cells. A biosensor system based on semiconductor nanoparticles provides the photonic properties for small molecule measurement in and around red blood cells. Metalloprotein design was used to generate a Pb(2+) ion selective receptor from a protein that is structurally homologous to a protein used previously in this biosensing system. Parameters for the Pb(2+) ion binding site were derived from crystallographic structures of low molecular weight Pb(2+) ion complexes that contain a stereoactive lone pair. When the designed protein was produced and attached to ZnS-coated CdSe nanoparticles, two Pb(NO(3))(2)-associated binding events were observed (2-fold emission decrease; K(A1) = 1 x 10(9) M(-1); K(A2) = 3.5 x 10(6) M(-1)). The fluorescence response had a 100 pM Pb(NO(3))(2) detection limit, while no response was observed with Ca(2+) ions (10 mM), Zn(2+) ions (100 muM), or Cd(2+) ions (100 muM). Metal ion selectivity presumably comes from the coordination geometry selected to favor lone pair formation on Pb(2+) ions and electrostatically disfavor tetrahedral coordination. Replacement of ZnS-coated CdSe with ZnS-coated InGaP nanoparticles provided similar biosensors (100 pM limit of detection; K(A1) = 1 x 10(9) M(-1); K(A2) = 1 x 10(7) M(-1)) but with excitation/emission wavelengths longer than the major absorbance of red blood cell hemoglobin (>620 nm). The InGaP nanoparticle-based biosensors provided a 5 nM Pb(NO(3))(2) detection limit in the presence of red blood cells. The modularity of the biosensor system provides exchangeable Pb(2+) ion detection around red blood cells.

Structure, function, and evolution of bacterial ATP-binding cassette systems

SUMMARY

ATP-binding cassette (ABC) systems are universally distributed among living organisms and function in many different aspects of bacterial physiology. ABC transporters are best known for their role in the import of essential nutrients and the export of toxic molecules, but they can also mediate the transport of many other physiological substrates. In a classical transport reaction, two highly conserved ATP-binding domains or subunits couple the binding/hydrolysis of ATP to the translocation of particular substrates across the membrane, through interactions with membrane-spanning domains of the transporter. Variations on this basic theme involve soluble ABC ATP-binding proteins that couple ATP hydrolysis to nontransport processes, such as DNA repair and gene expression regulation. Insights into the structure, function, and mechanism of action of bacterial ABC proteins are reported, based on phylogenetic comparisons as well as classic biochemical and genetic approaches. The availability of an increasing number of high-resolution structures has provided a valuable framework for interpretation of recent studies, and realistic models have been proposed to explain how these fascinating molecular machines use complex dynamic processes to fulfill their numerous biological functions. These advances are also important for elucidating the mechanism of action of eukaryotic ABC proteins, because functional defects in many of them are responsible for severe human inherited diseases.