Proton binding sites and conformational analysis of H+K(+)-ATPase

The interaction of Na+, K+, and phosphate with the gastric H,K-ATPase. Kinetics of E1-E2 conformational changes assessed by eosin fluorescence measurements

H,K-ATPase and Na,K-ATPase show the highest degree of sequence similarity among all other members of the P-type ATPases family. To explore their common features in terms of ligand binding, we evaluated conformational transitions due to the binding of Na⁺, K⁺ and Pi in the H,K-ATPase, and compared the results with those obtained for the Na,K-ATPase. This work shows that eosin fluorescence time courses provide a reasonably precise method to study the kinetics of the E1-E2 conformational changes in the H,K-ATPase. We found that, although Na⁺ shifts the equilibrium toward the E1 conformation and seems to compete with H⁺ in ATPase activity assays, it was neither possible to isolate a Na⁺-occluded state, nor to reveal an influx of Na⁺ related to H,K-ATPase activity. The high rate of the E2K → E1 transition found for the H,K-ATPase, which is not compatible with the presence of a K⁺-occluded form, agrees with the negligible level of occluded Rb⁺ (used as a K⁺ congener) found in the absence of added ligands. The use of vanadate and fluorinated metals to induce E2P-like states increased the level of occluded Rb⁺ and suggests that-during dephosphorylation-the probability of K⁺ to remain occluded increases from the E2P-ground to the E2P-product state. From kinetic experiments we found an unexpected increase in the values of k_obs for E2P formation with [Pi]; consequently, to obey the Albers-Post model, the binding of Pi to the E2 state cannot be a rapid-equilibrium reaction.

Measurement of Autoantibodies to Gastric H+,K+-ATPase (ATP4A/B) Using a Luciferase Immunoprecipitation System (LIPS)

The Luciferase Immuno Precipitation System (LIPS) enables the detection of specific serum antibodies by immunoprecipitation of recombinant antigens tagged with a luciferase reporter. Here we describe LIPS assays for the quantification of autoantibodies to the H+, K+-ATPase A (ATP4A) and B (ATP4B) subunits, two serological markers of autoimmune atrophic gastritis and pernicious anemia. In particular, we will describe the expression of luciferase-tagged recombinant ATP4A and ATP4B, their immunoprecipitation with test sera, the recovery and washing of immune-complexes with a protein-A coated resin, and the quantification of autoantibodies by addition of a luciferase substrate and the measurement of the light output from captured luciferase-tagged antigens.

Luminescent Immunoprecipitation System (LIPS) for Detection of Autoantibodies Against ATP4A and ATP4B Subunits of Gastric Proton Pump H+,K+-ATPase in Atrophic Body Gastritis Patients

OBJECTIVES

Circulating autoantibodies targeting the H+/K+-ATPase proton pump of gastric parietal cells are considered markers of autoimmune gastritis, whose diagnostic accuracy in atrophic body gastritis, the pathological lesion of autoimmune gastritis, remains unknown. This study aimed to assess autoantibodies against ATP4A and ATP4B subunits of parietal cells H+, K+-ATPase in atrophic body gastritis patients and controls.

METHODS

One-hundred and four cases with atrophic body gastritis and 205 controls were assessed for serological autoantibodies specific for ATP4A or ATP4B subunits using luminescent immunoprecipitation system (LIPS). Recombinant luciferase-reporter-fused-antigens were expressed by in vitro transcription-translation (ATP4A) or after transfection in Expi293F cells (ATP4B), incubated with test sera, and immune complexes recovered using protein-A-sepharose. LIPS assays were compared with a commercial enzyme immunoassay (EIA) for parietal cell autoantibodies.

RESULTS

ATP4A and ATP4B autoantibody titers were higher in cases compared to controls (P<0.0001). The area under the receiver-operating characteristic curve was 0.98 (95% CI 0.965-0.996) for ATP4A, and 0.99 (95% CI 0.979-1.000) for ATP4B, both higher as compared with that of EIA: 0.86 (95% CI 0.809-0.896), P<0.0001. Sensitivity-specificity were 100-89% for ATP4A and 100-90% for ATP4B assay. Compared with LIPS, EIA for parietal cell autoantibodies showed a lower sensitivity (72%, P<0.0001) at a similar specificity (92%, P=0.558).

CONCLUSIONS

Positivity to both, ATP4A and ATP4B autoantibodies is closely associated with atrophic body gastritis. Both assays had the highest sensitivity, at the cost of diagnostic accuracy (89 and 90% specificity), outperforming traditional EIA. Once validated, these LIPS assays should be valuable screening tools for detecting biomarkers of damaged atrophic oxyntic mucosa.

FDA approved drugs complexed to their targets: evaluating pose prediction accuracy of docking protocols

Efficient drug discovery programs can be designed by utilizing existing pools of knowledge from the already approved drugs. This can be achieved in one way by repositioning of drugs approved for some indications to newer indications. Complex of drug to its target gives fundamental insight into molecular recognition and a clear understanding of putative binding site. Five popular docking protocols, Glide, Gold, FlexX, Cdocker and LigandFit have been evaluated on a dataset of 199 FDA approved drug-target complexes for their accuracy in predicting the experimental pose. Performance for all the protocols is assessed at default settings, with root mean square deviation (RMSD) between the experimental ligand pose and the docked pose of less than 2.0 Å as the success criteria in predicting the pose. Glide (38.7 %) is found to be the most accurate in top ranked pose and Cdocker (58.8 %) in top RMSD pose. Ligand flexibility is a major bottleneck in failure of docking protocols to correctly predict the pose. Resolution of the crystal structure shows an inverse relationship with the performance of docking protocol. All the protocols perform optimally when a balanced type of hydrophilic and hydrophobic interaction or dominant hydrophilic interaction exists. Overall in 16 different target classes, hydrophobic interactions dominate in the binding site and maximum success is achieved for all the docking protocols in nuclear hormone receptor class while performance for the rest of the classes varied based on individual protocol.

The nucleotide, inhibitor, and cation binding sites of P-type II ATPases

P-type ATPases constitute a ubiquitous superfamily of cation transport enzymes, responsible for carrying out actions of paramount importance in biology such as ion transport and expulsion of toxic ions from cells. The harmonized toggling of gates in the extra- and intracellular domains explain the phenomenon of specific cation binding in selective physiological states. A quantitative understanding of the fundamental aspects of ion transport mechanism and regulation of P-type ATPases requires detailed knowledge of thermodynamical, structural, and functional properties. Computational studies have made significant contributions to our understanding of biological ion pumps. Various 3D structures of Ca(2+) -ATPase between E1 and E2 transition states have given a impetus to the theorists to work on the Na(+) K(+) - and H(+) K(+) -ATPase to address important questions about their function. The current review delineates the importance of cation, nucleotide, and inhibitor binding domains, with a focus on the therapeutic potential and biological relevance of the three P-type II ATPases. This will give an insight into the ion selectivity and their conduction across the transmembrane helices of P-type II ATPases, which may pave the way to a range of fundamental questions about the mechanism and aid in the efforts of structure- and analog-based drug design.

Virtual screening filters for the design of type II p38 MAP kinase inhibitors: a fragment based library generation approach

In this work, we introduce the development and application of a three-step scoring and filtering procedure for the design of type II p38 MAP kinase leads using allosteric fragments extracted from virtual screening hits. The design of the virtual screening filters is based on a thorough evaluation of docking methods, DFG-loop conformation, binding interactions and chemotype specificity of the 138 p38 MAP kinase inhibitors from Protein Data Bank bound to DFG-in and DFG-out conformations using Glide, GOLD and CDOCKER. A 40 ns molecular dynamics simulation with the apo, type I with DFG-in and type II with DFG-out forms was carried out to delineate the effects of structural variations on inhibitor binding. The designed docking-score and sub-structure filters were first tested on a dataset of 249 potent p38 MAP kinase inhibitors from seven diverse series and 18,842 kinase inhibitors from PDB, to gauge their capacity to discriminate between kinase and non-kinase inhibitors and likewise to selectively filter-in target-specific inhibitors. The designed filters were then applied in the virtual screening of a database of ten million (10⁷) compounds resulting in the identification of 100 hits. Based on their binding modes, 98 allosteric fragments were extracted from the hits and a fragment library was generated. New type II p38 MAP kinase leads were designed by tailoring the existing type I ATP site binders with allosteric fragments using a common urea linker. Target specific virtual screening filters can thus be easily developed for other kinases based on this strategy to retrieve target selective compounds.

Selective monovalent cation association and exchange around Keplerate polyoxometalate macroanions in dilute aqueous solutions

The interaction between water-soluble Keplerate polyoxometalate {Mo(72)Fe(30)} macroions and small countercations is explored by laser light scattering, anomalous small-angle X-ray scattering (ASAXS), and isothermal titration calorimetry (ITC) techniques. The macroions are found to be able to select the type of associated counterions based upon the counterions' valence state and hydrated size, when multiple types of additional cations are present in solution (even among different monovalent cations). The preference goes to the cations with higher valences or smaller hydrated sizes if the valences are identical. This counterion exchange process changes the magnitude of the macroion-counterion interaction and, thus, is reflected in the dimension of the self-assembled {Mo(72)Fe(30)} blackberry supramolecular structures. The hydrophilic macroions exhibit a competitive recognition of various monovalent counterions in dilute solutions. A critical salt concentration (CSC) for each type of cation exists for the blackberry formation of {Mo(72)Fe(30)} macroions, above which the blackberry size increases significantly with the increasing total ionic strength in solution. The CSC values are much smaller for cations with higher valences and also decrease with the cations' hydrated size for various monovalent cations. The change of blackberry size corresponding to the change of ionic strength in solution is reversible.

Cation-aromatic database

Cation-aromatic database (CAD) is a publicly available web-based database that aims to provide further understanding of interaction between a cation and the pi interactions. A tool to identify the interactions in a user-given protein is also added to the database. CAD is freely accessible via the Internet at http://203.199.182.73/gnsmmg/databases/cad/.

IR Spectrum of the H5O2+ Cation in the Context of Proton Disolvates L−H+−L

The H(5)O(2)(+) ion has been studied in chlorocarbon, benzene, and weakly coordinating anion environments to bridge the gap between the gas-phase and traditional condensed-phase investigations. Symmetrical cations of the type [H(5)O(2)(+) x 4Solv] are formed via H-bonding with the terminal O-H groups. In the infrared spectrum, the nu(s)OH and nu(as)OH vibrations behave in a manner similar to those of common water molecules: the stronger is the H-bonding interaction with the surroundings, the lower is the frequency shift. A consistent pattern of IR bands from the central O-H(+)-O group is identified, regardless of the strength of the interaction of H(5)O(2)(+) with its environment. Three intense bands develop: a (860-995 cm-1), b (1045-1101 cm(-1)), and c (1672-1700 cm(-1)), as well as two weak bands, d ( approximately 1300 cm(-1)) and e ( approximately 1400-1500 cm(-1)). These fingerprint bands are highly characteristic for vibrations of O-H-O group irrespective of formal charge. They are seen in symmetrical proton disolvates of the type L-H(+)-L, where L is an O-atom donor (alcohol, ether, ketone, phosphate, etc.), and in [A-H-A](-) acid salts (A(-) = oxyanion). The commonality is equivalency of the two O-atoms, a short O...O distance (ca. 2.40 Angstrom), and a flat-bottomed potential well for the bridging proton, that is, a short, strong, low-barrier H-bond. Assignments for bands a-e are suggested in an attempt to resolve inconsistencies between experimental and calculated data.