Structure of cytosine transport protein CodB provides insight into nucleobase‐cation symporter 1 mechanism

CodB is a cytosine transporter from the Nucleobase‐Cation‐Symport‐1 (NCS1) transporter family, a member of the widespread LeuT superfamily. Previous experiments with the nosocomial pathogen Pseudomonas aeruginosa have shown CodB as also important for the uptake of 5‐fluorocytosine, which has been suggested as a novel drug to combat antimicrobial resistance by suppressing virulence. Here we solve the crystal structure of CodB from Proteus vulgaris, at 2.4 Å resolution in complex with cytosine. We show that CodB carries out the sodium‐dependent uptake of cytosine and can bind 5‐fluorocytosine. Comparison of the substrate‐bound structures of CodB and the hydantoin transporter Mhp1, the only other NCS1 family member for which the structure is known, highlight the importance of the hydrogen bonds that the substrates make with the main chain at the breakpoint in the discontinuous helix, TM6. In contrast to other LeuT superfamily members, neither CodB nor Mhp1 makes specific interactions with residues on TM1. Comparison of the structures provides insight into the intricate mechanisms of how these proteins transport substrates across the plasma membrane.     

Structural Insights into the Lipid A Transport Pathway in MsbA

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Substrate binds in the S1 site of the F253A mutant of LeuT, a neurotransmitter sodium symporter homologue

LeuT serves as the model protein for understanding the relationships between structure, mechanism and pharmacology in neurotransmitter sodium symporters (NSSs). At the present time, however, there is a vigorous debate over whether there is a single high-affinity substrate site (S1) located at the original, crystallographically determined substrate site or whether there are two high-affinity substrates sites, one at the primary or S1 site and the other at a second site (S2) located at the base of the extracellular vestibule. In an effort to address the controversy over the number of high-affinity substrate sites in LeuT, one group studied the F253A mutant of LeuT and asserted that in this mutant substrate binds exclusively to the S2 site and that 1 mM clomipramine entirely ablates substrate binding to the S2 site. Here we study the binding of substrate to the F253A mutant of LeuT using ligand binding and X-ray crystallographic methods. Both experimental methods unambiguously show that substrate binds to the S1 site of the F253A mutant and that binding is retained in the presence of 1 mM clomipramine. These studies, in combination with previous work, are consistent with a mechanism for LeuT that involves a single high-affinity substrate binding site.     

Insights into the ClC-4 transport mechanism from studies of Zn2+ inhibition

The CLC family of chloride channels and transporters is a functionally diverse group of proteins important in a wide range of physiological processes. ClC-4 and ClC-5 are localized to endosomes and seem to play roles in the acidification of these compartments. These proteins were recently shown to function as Cl⁻/H⁺ antiporters. However, relatively little is known about the detailed mechanism of CLC-mediated Cl⁻/H⁺ antiport, especially for mammalian isoforms. We attempted to identify molecular tools that might be useful in probing structure-function relationships in these proteins. Here, we record currents from human ClC-4 (hClC-4) expressed in Xenopus oocytes, and find that Zn²⁺ inhibits these currents, with an apparent affinity of ∼50 μM. Although Cd²⁺ has a similar effect, Co²⁺ and Mn²⁺ do not inhibit hClC-4 currents. In contrast, the effect of Zn²⁺ on the ClC-0 channel, Zn²⁺-mediated inhibition of hClC-4 is minimally voltage-dependent, suggesting an extracellular binding site for the ion. Nine candidate external residues were tested; only mutations of three consecutive histidine residues, located in a single extracellular loop, significantly reduced the effect of Zn²⁺, with one of these making a larger contribution than the other two. An analogous tri-His sequence is absent from ClC-0, suggesting a fundamentally different inhibitory mechanism for the ion on hClC-4. Manipulations that alter transport properties of hClC-4, varying permeant ions as well as mutating the “gating glutamate”, dramatically affect Zn²⁺ inhibition, suggesting the involvement of a heretofore unexplored part of the protein in the transport process.     

A novel system of galangin–potassium permanganate–polyphosphoric acid for the determination of tryptophan and its chemiluminescence mechanism

A novel galangin–potassium permanganate (KMnO₄)–polyphosphoric acid (PPA) system was found to have an outstanding response to tryptophan (Trp). Trp determination using this KMnO₄–PPA system was enhanced significantly in the presence of galangin. A highly sensitive flow‐injection chemiluminescence (CL) method to determine Trp was developed based on the CL reaction of galangin–KMnO₄–Trp in PPA media. The presence of galangin, a member of the flavonol class of flavonoid complexes, greatly increased the luminous intensity of Trp in KMnO₄–PPA systems. Under optimized conditions, Trp was determined in the 0.05–10 µg/mL range, with a detection limit (3σ) of 5.0 × 10^?3 µg/mL. The relative standard deviation (RSD) was 1.0% for 11 replicate determinations of 1.0 µg/mL Trp. Two synthetic samples were determined selectively with recoveries of 98.4–100.1% in the presence of other amino acids. The possible mechanism is summarized as follows: excited states of Mn(II)^* and Mn(III ^* types are the main means of generating chemical luminescent species, and Trp concentration and luminescence intensity have a linear relationship, which enables quantitative analysis. Copyright © 2014 John Wiley & Sons, Ltd.     

Insights into the DNA cleavage mechanism of human LINE-1 retrotransposon endonuclease

The human LINE-1 endonuclease (L1-EN) contributes in defining the genomic integration sites of the abundant human L1 and Alu retrotransposons. LINEs have been considered as possible vehicles for gene delivery and understanding the mechanism of L1-EN could help engineering them as genetic tools. We tested the in vitro activity of point mutants in three L1-EN residues--Asp145, Arg155, Ile204--that are key for DNA cleavage, and determined their crystal structures. The L1-EN structure remains overall unaffected by the mutations, which change the enzyme activity but leave DNA cleavage sequence specificity mostly unaffected. To better understand the mechanism of L1-EN, we performed molecular dynamics simulations using as model the structures of wild type EN-L1, of two betaB6-betaB5 loop exchange mutants we have described previously to be important for DNA recognition, of the R155A mutant from this study, and of the homologous TRAS1 endonuclease: all confirm a rigid scaffold. The simulations crucially indicate that the betaB6-betaB5 loop shows an anticorrelated motion with the surface loops betaA6-betaA5 and betaB3-alphaB1. The latter loop harbors N118, a residue that alters DNA cleavage specificity in homologous endonucleases, and implies that the plasticity and correlated motion of these loops has a functional importance in DNA recognition and binding. To further explore how these loops are possibly involved in DNA binding, we docked computationally two DNA substrates to our structure, one involving a flipped-out nucleotide downstream the scissile phosphodiester; and one not. The models for both scenarios are feasible and agree with the hypotheses derived from the dynamic simulations. The reduced cleavage activity we have observed for the I204Y mutant above however, favors the flipped out nucleotide model.     

Insights into nonspecific binding of homeodomains from a structure of MATalpha2 bound to DNA

The 2.1-A resolution crystal structure of the MATalpha2 homeodomain bound to DNA reveals the unexpected presence of two nonspecifically bound alpha2 homeodomains, in addition to the two alpha2 homeodomains bound to canonical alpha2 binding sites. One of the extra homeodomains makes few base-specific contacts, while the other extra homeodomain binds to DNA in a previously unobserved manner. This unusually bound homeodomain is rotated on the DNA, making possible major groove contacts by side-chains that normally do not contact the DNA. This alternate docking may represent one way in which homeodomains sample nonspecific DNA sequences.     

Spatial structure and the mechanism of tyrosine phenol-lyase and tryptophan indole-lyase

Bacterial tyrosine phenol-lyase [EC 4.1.99.2] and tryptophan indole-lyase [EC 4.1.99.1] are pyridoxal 5′-phosphate dependent β-eliminating lyases that catalyze the reversible decomposition of L-tyrosine and L-tryptophan to pyruvate, ammonia, and phenol or indole, respectively. This review considers the three-dimensional structures of the holoenzymes of tyrosine phenol-lyase and tryptophan indole-lyase and several enzyme-inhibitor complexes that model distinct reaction stages of the β-elimination of L-tyrosine. The structural basis of the influence of monovalent cations on enzymatic activity is discussed. Studies of the spectral and catalytic properties of mutant enzymes made it possible to elucidate the catalytic functions of a number of amino acid residues and to conclude that the acid-base properties of the catalytic groups are optimal for catalysis in the hydrophobic active sites of tyrosine phenol-lyase and tryptophan indol-lyase and differ from those in water solutions. A study of the mechanisms of labilization of the Cα proton of the bound amino acids and activation of the leaving groups of the substrates during the catalytic process demonstrated that the reaction proceeds via concerted, rather than stepwise, pathways in certain cases.     

Insights into the decoding mechanism from recent ribosome structures

During the decoding process, tRNA selection by the ribosome is far more accurate than expected from codon-anticodon pairing. Antibiotics such as streptomycin and paromomycin have long been known to increase the error rate of translation, and many mutations that increase or lower accuracy have been characterized. Recent crystal structures show that the specific recognition of base-pairing geometry leads to a closure of the domains of the small subunit around cognate tRNA. This domain closure is likely to trigger subsequent steps in tRNA selection. Many antibiotics and mutations act by making the domain closure more or less favourable. In conjunction with recent cryoelectron microscopy structures of the ribosome, a comprehensive structural understanding of the decoding process is beginning to emerge.     

Responses of growth performance and tryptophan metabolism to oxidative stress induced by diquat in weaned pigs

During many pathological conditions, the tryptophan concentration in blood may be reduced. However, the effects of oxidative stress on tryptophan metabolism remain unknown. In this study, we investigated the effects of oxidative stress on growth performance and tryptophan metabolism in weaned pigs. A total of 24 weaned pigs were assigned to one of three treatments that included pigs fed ad libitum (control), pigs challenged with diquat at a dose of 10 mg/kg BW and fed ad libitum (oxidative stress) or pigs pair-fed to receive the same amount of feed as the diquat-challenged pigs. The trial lasted for 7 days. The growth performance and activities of antioxidant enzymes were declined in diquat-challenged pigs. The diquat challenge decreased the tryptophan concentration in serum and the 5-hydroxytryptamine concentration in the hypothalamus, and increased large neutral amino acids, kynurenine (Kyn) and malondialdehyde in serum. The 544-bp porcine partial mRNA sequence of the tryptophan 2,3-dioxygenase (TDO) gene was obtained according to the conserved region in the human gene sequence. In addition, the oxidative stress induced by the diquat challenge stimulated TDO-relative mRNA abundance in the liver and γ-glutamyl transpeptidase activity in intestinal mucosa, but did not affect the mRNA levels of Na+-neutral amino acid transporter B0. These results suggested that oxidative stress induced by diquat depressed growth performance and increased metabolism of tryptophan via Kyn pathway that upregulated TDO mRNA expression in weaned pigs.     

Structural dynamics of the monoamine transporter homolog LeuT from accelerated conformational sampling and channel analysis

The bacterial leucine transporter LeuT retains significant secondary structure similarities to the human monoamine transporters (MAT) such as the dopamine and serotonin reuptake proteins. The primary method of computational study of the MATs has been through the use of the crystallized LeuT structure. Different conformations of LeuT can give insight into mechanistic details of the MAT family. A conformational sampling performed through accelerated molecular dynamics simulations testing different combinations of the leucine substrate and bound sodium ions revealed seven distinct conformational clusters. Further analysis has been performed to target salt‐bridge residues R30–D404, Y108–F253, and R5–D369 and transmembrane domains on both the seven isolated structures and the total trajectories. In addition, solvent accessibility of LeuT and its substrate binding pockets has been analyzed using a program for calculating channel radii. Occupation of the Na2 site stabilizes the outward conformation and should bind to the open outward conformation before the leucine and Na1 sodium while two possible pathways were found to be available for intracellular transport. Proteins 2014; 82:2289–2302. © 2014 Wiley Periodicals, Inc.     

ABC transporter architecture and mechanism: implications from the crystal structures of BtuCD and BtuF

ABC transporters are ubiquitous membrane proteins that facilitate unidirectional substrate translocation across the lipid bilayer. Over the past five years, new crystal structures have advanced our understanding of how ABC transporters couple adenosine triphosphate (ATP) hydrolysis to substrate transport. In the following, we will briefly review the results of these structural investigations and outline their mechanistic implications.     

Insights into the catalytic mechanism of cofactor-independent phosphoglycerate mutase from X-ray crystallography,simulated dynamics and molecular modeling

Phosphoglycerate mutases catalyze the isomerization of 2 and 3-phosphoglycerates, and are essential for glucose metabolism in most organisms. Here, we further characterize the 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (iPGM) from Bacillus stearothermophilus by determination of a high-resolution (1.4A) crystal structure of the wild-type enzyme and the crystal structure of its S62A mutant. The mutant structure surprisingly showed the replacement of one of the two catalytically essential manganese ions with a water molecule, offering an additional possible explanation for its lack of catalytic activity. Crystal structures invariably show substrate phosphoglycerate to be entirely buried in a deep cleft between the two iPGM domains. Flexibility analyses were therefore employed to reveal the likely route of substrate access to the catalytic site through an aperture created in the enzyme's surface during certain stages of the catalytic process. Several conserved residues lining this aperture may contribute to orientation of the substrate as it enters. Factors responsible for the retention of glycerate within the phosphoenzyme structure in the proposed mechanism are identified by molecular modeling of the glycerate complex of the phosphoenzyme. Taken together, these results allow for a better understanding of the mechanism of action of iPGMs. Many of the results are relevant to a series of evolutionarily related enzymes. These studies will facilitate the development of iPGM inhibitors which, due to the demonstrated importance of this enzyme in many bacteria, would be of great potential clinical significance.     

A structural and functional analysis of the glycosyltransferase BshA from Staphylococcus aureus: Insights into the reaction mechanism and regulation of bacillithiol production

Bacillithiol is a glucosamine‐derived antioxidant found in several pathogenic Gram‐positive bacteria. The compound is involved in maintaining the appropriate redox state within the cell as well as detoxifying foreign agents like the antibiotic fosfomycin. Bacillithiol is produced via the action of three enzymes, including BshA, a retaining GT‐B glycosyltransferase that utilizes UDP‐N‐acetylglucosamine and l ‐malate to produce N‐acetylglucosaminyl‐malate. Recent studies suggest that retaining GT‐B glycosyltransferases like BshA utilize a substrate‐assisted mechanism that goes through an S_Ni‐like transition state. In a previous study, we relied on X‐ray crystallography as well as computational simulations to hypothesize the manner in which substrates would bind the enzyme, but several questions about substrate binding and the role of one of the amino acid residues persisted. Another study demonstrated that BshA might be subject to feedback inhibition by bacillithiol, but this phenomenon was not analyzed further to determine the exact mechanism of inhibition. Here we present X‐ray crystallographic structures and steady‐state kinetics results that help elucidate both of these issues. Our ligand‐bound crystal structures demonstrate that the active site provides an appropriate steric and geometric arrangement of ligands to facilitate the substrate‐assisted mechanism. Finally, we show that bacillithiol is competitive for UDP‐N‐acetylglucosamine with a K_i value near 120–130 μM and likely binds within the BshA active site, suggesting that bacillithiol modulates BshA activity via feedback inhibition. The work presented here furthers our understanding of bacillithiol metabolism and can aid in the development of inhibitors to counteract resistance to antibiotics such as fosfomycin.     

Insights into the antineoplastic mechanism of Chelidonium majus via systems pharmacology approach

Background: The antineoplastic activity of Chelidonium majus has been reported, but its mechanism of action (MoA) is unsuspected. The emerging theory of systems pharmacology may be a useful approach to analyze the complicated MoA of this multi-ingredient traditional Chinese medicine (TCM). Methods: We collected the ingredients and related compound-target interactions of C. majus from several databases. The bSDTNBI (balanced substructure-drug-target network-based inference) method was applied to predict each ingredient’s targets. Pathway enrichment analysis was subsequently conducted to illustrate the potential MoA, and prognostic genes were identified to predict the certain types of cancers that C. majus might be beneficial in treatment. Bioassays and literature survey were used to validate the in silico results. Results: Systems pharmacology analysis demonstrated that C. majus exerted experimental or putative interactions with 18 cancer-associated pathways, and might specifically act on 13 types of cancers. Chelidonine, sanguinarine, chelerythrine, berberine, and coptisine, which are the predominant components of C. majus, may suppress the cancer genes by regulating cell cycle, inducing cell apoptosis and inhibiting proliferation. Conclusions: The antineoplastic MoA of C. majus was investigated by systems pharmacology approach. C. majus exhibited promising pharmacological effect against cancer, and may consequently be useful material in further drug development. The alkaloids are the key components in C. majus that exhibit anticancer activity.     

Insights into interstitial flow,shear stress,and mass transport effects on ECM heterogeneity in bioreactor-cultivated engineered cartilage hydrogels

Interstitial flow in articular cartilage is secondary to compressive and shear deformations during joint motion and has been linked with the well-characterized heterogeneity in structure and composition of its extracellular matrix. In this study, we investigated the effects of introducing gradients of interstitial flow on the evolution of compositional heterogeneity in engineered cartilage. Using a parallel-plate bioreactor, we observed that Poiseuille flow stimulation of chondrocyte-seeded agarose hydrogels led to an increase in glycosaminoglycan and type II collagen deposition in the surface region of the hydrogel exposed to flow. Experimental measurements of the interstitial flow fields based on the fluorescence recovery after photobleaching technique suggested that the observed heterogeneity in composition is associated with gradients in interstitial flow in a boundary layer at the hydrogel surface. Interestingly, the interstitial flow velocity profiles were nonlinearly influenced by flow rate, which upon closer examination led us to the original observation that the apparent hydrogel permeability decreased exponentially with increased interfacial shear stress. We also observed that interstitial flow enhances convective mass transport irrespective of molecular size within the boundary layer near the hydrogel surface and that the convective contribution to transport diminishes with depth in association with interstitial flow gradients. The implications of the nonlinearly inverse relationship between the interfacial shear stress and the interstitial flux and permeability and its consequences for convective transport are important for tissue engineering, since porous scaffolds comprise networks of Poiseuille channels (pores) through which interstitial flow must navigate under mechanical stimulation or direct perfusion.     

Biochemical mechanisms leading to tryptophan 2,3-dioxygenase activation

Tryptophan 2,3-dioxygenase (TDO) is the first enzyme in the tryptophan oxidation pathway. It is a hemoprotein and its heme prosthetic group is present as a heme-ferric (heme-Fe(3+)) form that is not active. To be able to oxidize tryptophan, the heme-Fe(3+) form of the enzyme must be reduced to a heme-ferrous (heme-Fe(2+)) form and this study describes conditions that promote TDO activation. TDO is progressively activated upon mixing with tryptophan in a neutral buffer, which leads to an impression that tryptophan is responsible for TDO activation. Through extensive analysis of factors resulting in TDO activation during incubation with tryptophan, we conclude that tryptophan indirectly activates TDO through promoting the production of reactive oxygen species. This consideration is supported by the virtual elimination of the initial lag phase when either pre-incubated tryptophan solution was used as the substrate or a low concentration of superoxide or hydrogen peroxide was incorporated into the freshly tryptophan and TDO mixture. However, accumulation of these reactive oxygen species also leads to the inactivation of TDO, so that both TDO activation and inactivation proceed with the specific outcome depending greatly on the concentrations of superoxide and hydrogen peroxide. As a consequence, the rate of TDO catalysis varies depending upon the proportion of the active to inactive forms of the enzyme, which is in a dynamic relationship in the reaction mixture. These data provide some insight towards elucidating the molecular regulation of TDO in vivo.