Ultra-high resolution X-ray structure of orthorhombic bovine pancreatic Ribonuclease A at 100K.

The crystal structure of orthorhombic Bovine Pancreatic Ribonuclease A has been determined to 0.85 Å resolution using low temperature, 100 K, synchrotron X-ray data collected at 16000 keV (λ = 0.77 Å). This is the first ultra-high-resolution structure of a native form of Ribonuclease A to be reported. Refinement carried out with anisotropic displacement parameters, stereochemical restraints, inclusion of H atoms in calculated positions, five [Formula: see text] moieties, eleven ethanol molecules and 293 water molecules, converged with final R values of R1(Free) = 0.129 (4279 reflections) and R1 = 0.112 (85,346 reflections). The refined structure was deposited in the Protein Data Bank as structure 7p4r. Conserved waters, using four high resolution structures, have been investigated. Cluster analysis identified clusters of water molecules that are associated with the active site of Bovine Ribonuclease A. Particular attention has been paid to making detailed comparisons between the present structure and other high quality Bovine Pancreatic Ribonuclease A X-ray crystal structures with special reference to the deposited classic monoclinic structure 3RN3 Howlin et al. (Acta Crystallogr A 45:851-861, 1989). Detailed studies of various aspects of hydrogen bonding and conformation have been carried out with particular reference to active site residues Lys-1, Lys-7, Gln-11, His-12, Lys-41, Asn-44, Thr-45, Lys-66, His-119 and Ser-123. For the two histidine residues in the active site the initial electron density map gives a clear confirmation that the position of His-12 is very similar in the orthorhombic structure to that in 3RN3. In 3RN3 His-119 exhibited poor electron density which was modelled and refined as two distinct sites, A (65%) and B (35%) but with respect to His-119 in the present ultra-high resolution orthorhombic structure there is clear electron density which was modelled and refined as a single conformation distinct from either conformation A or B in 3RN3. Other points of interest include Serine-32 which is disordered at the end of the sidechain in the present orthorhombic form but has been modelled as a single form in 3RN3. Lysine-66: there is density indicating a possible conformation for this residue. However, the density is relatively weak, and the conformation is unclear. Three types of amino acid representation in the ultra-high resolution electron density are examined: (i) sharp with very clearly resolved features, for example Lys-37; (ii) well resolved but clearly divided into two conformations which are well behaved in the refinement, both having high quality geometry, for example Tyr-76; (iii) poor density and difficult or impossible to model, an example is Lys-31 for which density is missing except for Cß. The side chains of Gln-11, His-12, Lys-41, Thr-45 and His-119 are generally recognised as being closely involved in the enzyme activity. It has also been suggested that Lys-7, Asp-44, Lys-66, Phe-120, Asp-121 and Ser-123 may also have possible roles in this mechanism. A molecular dynamics study on both structures has investigated the conformations of His-119 which was modelled as two conformations in 3RN3 but is observed to have a single clearly defined conformation in the present orthorhombic structure. MD has also been used to investigate Lys-31, Lys-41 and Ser32. The form of the Ribonuclease A enzyme used in both the present study and in 3RN3 (Howlin et al. in Acta Crystallogr A 45:851-861, 1989) includes a sulphate anion which occupies approximately the same location as the [Formula: see text] phosphate group in protein nucleotide complexes (Borkakoti et al. in J Mol Biol 169:743-755, 1983). The present structure contains 5 [Formula: see text] groups SO41151-SO41155 two of which, SO41152 and SO41153 are disordered, SO41152 being in the active site, and 11 EtOH molecules, EOH A 201-EOH A 211 all of which have good geometry. H atoms were built into the EtOH molecules geometrically. Illustrations of these features in the present structure are included here. The sulphates are presumably present in the material purchased for use in the present study. 293 water molecules are included in the present structure compared to 134 in 3RN3 (Howlin et al. in Acta Crystallogr A 45:851-861, 1989).

Two-Dimensional Triblock Peptide Assemblies for the Stabilization of Pickering Emulsions with pH Responsiveness.

A variety of two-dimensional (2D) nanomaterials, including graphene oxide and clays, are known to stabilize Pickering emulsions to fabricate structures for functions in sensors, catalysts, and encapsulation. We introduce here a novel Pickering emulsion using self-assembled amphiphilic triblock oligoglycine as the emulsifier. Peptide amphiphiles are more responsive to environmental changes (e.g., pH, temperature, and ionic strength) than inorganic 2D materials, which have a chemically rigid, in-plane structure. Noncovalent forces between the peptide molecules change with the environment, thereby imparting responsiveness. We provide new evidence that the biantennary oligoglycine, Gly4-NH-C10H20-NH-Gly4, self-assembles into 2D platelet structures, denoted as tectomers, in solution at a neutral buffered pH using small-angle X-ray scattering and molecular dynamics simulations. The molecules are stacked in the platelets with a linear conformation, rather than in a U-shape. We discovered that the lamellar oligoglycine platelets adsorbed at an oil/water interface and stabilized oil-in-water emulsions. This is the first report of 2D oligoglycine platelets being used as a Pickering stabilizer. The emulsions showed a strong pH response in an acidic environment. Thus, upon reducing the pH, the protonation of the terminal amino groups of the oligoglycine induced disassembly of the lamellar structure due to repulsive electrostatic forces, leading to emulsion destabilization. To demonstrate the application of the material, we show that a model active ingredient, ß-carotene, in the oil is released upon decreasing the pH. Interestingly, in pH 9 buffer, the morphology of the oil droplets evolved over time, as the oligoglycine stabilizer created progressively a thicker interfacial layer. This demonstration opens a new route to use self-assembled synthetic peptide amphiphiles to stabilize Pickering emulsions, which can be significant for biomedical and pharmaceutical applications.

Single ion free energy calculation in ASIC1: the importance of the HG loop.

Acid Sensing Ion Channels (ASICs) are one of the most studied channels of the Epithelial Sodium Channel/Degenerin (ENaC/DEG) superfamily. They are responsible for excitatory responses following acidification of the extracellular medium and are involved in several important physiological roles. The ASIC1 subunit can form a functional homotrimeric channel and its structure is currently the most characterised of the whole ENaC/DEG family. Here we computed the free energy profiles for single ion permeation in two different structures of ASIC1 using both Na+ and Cl- as permeating ions. The first structure is the open structure of the channel from the PDB entry 4NTW, and the second structure is the closed structure with the re-entrant loop which contains the highly conserved 'HG' motif form PDB entry 6VTK. Both structures show cation selective free energy profiles, however the profiles of the permeating Na+ differ significantly between the two structures. Indeed, whereas there is only a small energetically favorable (-0.5 kcal mol-1) location for Na+ in the open channel (4NTW) near the end of the pore, we observed a clear ion binding site (-7.8 kcal mol-1) located in between the 'GAS' belt and the 'HG' loop for the channel containing the re-entrant loop (6VTK). Knowing that the 'GAS' motif was determined as the selectivity filter, our results support previous observations while addressing the importance of the 'HG' motif for the interactions between the pore and the permeating cations.

Ion Selectivity in the ENaC/DEG Family: A Systematic Review with Supporting Analysis.

The Epithelial Sodium Channel/Degenerin (ENaC/DEG) family is a superfamily of sodium-selective channels that play diverse and important physiological roles in a wide variety of animal species. Despite their differences, they share a high homology in the pore region in which the ion discrimination takes place. Although ion selectivity has been studied for decades, the mechanisms underlying this selectivity for trimeric channels, and particularly for the ENaC/DEG family, are still poorly understood. This systematic review follows PRISMA guidelines and aims to determine the main components that govern ion selectivity in the ENaC/DEG family. In total, 27 papers from three online databases were included according to specific exclusion and inclusion criteria. It was found that the G/SxS selectivity filter (glycine/serine, non-conserved residue, serine) and other well conserved residues play a crucial role in ion selectivity. Depending on the ion type, residues with different properties are involved in ion permeability. For lithium against sodium, aromatic residues upstream of the selectivity filter seem to be important, whereas for sodium against potassium, negatively charged residues downstream of the selectivity filter seem to be important. This review provides new perspectives for further studies to unravel the mechanisms of ion selectivity.

Random forest classification for predicting lifespan-extending chemical compounds.

Ageing is a major risk factor for many conditions including cancer, cardiovascular and neurodegenerative diseases. Pharmaceutical interventions that slow down ageing and delay the onset of age-related diseases are a growing research area. The aim of this study was to build a machine learning model based on the data of the DrugAge database to predict whether a chemical compound will extend the lifespan of Caenorhabditis elegans. Five predictive models were built using the random forest algorithm with molecular fingerprints and/or molecular descriptors as features. The best performing classifier, built using molecular descriptors, achieved an area under the curve score (AUC) of 0.815 for classifying the compounds in the test set. The features of the model were ranked using the Gini importance measure of the random forest algorithm. The top 30 features included descriptors related to atom and bond counts, topological and partial charge properties. The model was applied to predict the class of compounds in an external database, consisting of 1738 small-molecules. The chemical compounds of the screening database with a predictive probability of ≥ 0.80 for increasing the lifespan of Caenorhabditis elegans were broadly separated into (1) flavonoids, (2) fatty acids and conjugates, and (3) organooxygen compounds.

A Novel Approach to Atomistic Molecular Dynamics Simulation of Phenolic Resins Using Symthons.

Materials science is beginning to adopt computational simulation to eliminate laboratory trial and error campaigns-much like the pharmaceutical industry of 40 years ago. To further computational materials discovery, new methodology must be developed that enables rapid and accurate testing on accessible computational hardware. To this end, the authors utilise a novel methodology concept of intermediate molecules as a starting point, for which they propose the term 'symthon'[a] rather than conventional monomers. The use of symthons eliminates the initial monomer bonding phase, reducing the number of iterations required in the simulation, thereby reducing the runtime. A novel approach to molecular dynamics, with an NVT (Canonical) ensemble and variable unit cell geometry, was used to generate structures with differing physical and thermal properties. Additional script methods were designed and tested, which enabled a high degree of cure in all sampled structures. This simulation has been trialled on large-scale atomistic models of phenolic resins, based on a range of stoichiometric ratios of formaldehyde and phenol. Density and glass transition temperature values were produced, and found to be in good agreement with empirical data and other simulated values in the literature. The runtime of the simulation was a key consideration in script design; cured models can be produced in under 24 h on modest hardware. The use of symthons has been shown as a viable methodology to reduce simulation runtime whilst generating accurate models.

An aza-nucleoside, fragment-like inhibitor of the DNA repair enzyme alkyladenine glycosylase (AAG).

The DNA repair enzyme AAG has been shown in mice to promote tissue necrosis in response to ischaemic reperfusion or treatment with alkylating agents. A chemical probe inhibitor is required for investigations of the biological mechanism causing this phenomenon and as a lead for drugs that are potentially protective against tissue damage from organ failure and transplantation, and alkylative chemotherapy. Herein, we describe the rationale behind the choice of arylmethylpyrrolidines as appropriate aza-nucleoside mimics for an inhibitor followed by their synthesis and the first use of a microplate-based assay for quantification of their inhibition of AAG. We finally report the discovery of an imidazol-4-ylmethylpyrrolidine as a fragment-sized, weak inhibitor of AAG.

A selective and easily recyclable dimer based on a calix[4]pyrrole derivative for the removal of mercury(ii) from water.

A recyclable mercury(ii) selective dimer based on a calix[4]pyrrole derivative has been synthesised and characterised by mass and FT-IR spectrometry, Scanning Electron Microscopy (SEM) and Energy Dispersive X-ray (EDX). Information regarding the ability of the dimer to interact with metal cations was obtained from FTIR and SEM-EDX analyses. A striking feature of micrographs of the loaded dimer is the change of morphology with the cation. Based on these results, optimal conditions for removing cations from water were assessed under different experimental conditions. Results obtained demonstrate that the removal process is fast. Capacity values and selectivity factors show that the dimer is selective for Hg(ii) in single and multiple component metal solutions relative to other cations. Single-ion transfer Gibbs energies from water to a solvent containing common functionalities to those of the dimer were used to assess the counter-ion effect on the removal process. Agreement is found between these data and energy calculations derived from molecular simulation studies. Studies on polluted water in the presence of normal water components in addition to toxic metal cations are reported. Further experimental work on wastewater from the mining industry is in progress.

Automated drug design of kinase inhibitors to treat Chronic Myeloid Leukemia.

Medicinal chemistry has in the past been dominated by learned insights from experienced organic chemists. However, with the advent of computer based methods, computer aided drug design has become prominent. We have compared here the ability of locally sourced expert medicinal chemists to purely automated methods and found that the automated method produces a better potential candidate drug than the expert input. The example chosen is based on inhibitors to Abl-kinase and the successful anti-leukaemic drug imatinib. The proposed molecule is a simple modification of nilotinib and has a docking energy of 4.2 kJ/mol better than the best intuitive molecule.

Examining the Influence of Anion Nucleophilicity on the Polymerisation Initiation Mechanism of Phenyl Glycidyl Ether.

The reaction of phenyl glycidyl ether (PGE) with 1-ethyl-3-methylimidazolium acetateand 1-ethyl-3-methylimidazolium thiocyanate to initiate the polyetherification reaction wasexamined using thermal and spectral analysis techniques. The influence of the nucleophilicity of theanions on the deprotonation of the 1-ethyl-3-methylimidazolium cation determined the reactionpathway. The thermal degradation of the ionic liquid liberated the acetate ion and led, subsequently,to the deprotonation of the acidic proton in the imidazole ring. Thus, polymerisation of PGEoccurred via a carbene intermediate. The more nucleophilic thiocyanate anion was not sufficientlybasic to deprotonate the 1-ethyl-3-methylimidazolium cation, and thus proceeded through directreaction with the PGE, unless the temperature was elevated and a competing carbene mechanismensued.

Calix[4]arene urea derivatives: The pathway from fundamental studies to the selective removal of fluorides and phosphates from water.

Wet processes of phosphoric acids produce untreated wastewater containing large amounts of fluoride leading to serious environmental problems. This paper reports fundamental studies on two lower rim functionalised calix[4]arene based receptors namely 5, 11, 17, 23 tetra-tert-butyl, 25, 27 bis [diethylphenylurea]ethoxy, 26, 28 dihydroxycalix[4]arene, 1 and 25, 27 bis[diethylphenylurea]ethoxy, 26, 28 dihydroxycalix[4]arene, 2 and their ionic interactions. It is shown that these receptors only interact with fluoride and phosphate in acetonitrile. Their receptive properties are higher for phosphate (2:1 anion:receptor complex) relative to fluoride (1:1 complex). However, thermodynamics shows that these receptors are more selective for fluoride relative to phosphate in the formation of the 1:1 complex. The pathway from fundamental studies to the use of these receptors for removing these anions from water has been tested. The receptive properties of 1 for phosphate are held when the extraction involves aqueous solutions containing individual ions. However, in mixtures containing both anions, the kinetics of the process and the selectivity of 1 for fluoride predominate and as a result, fluoride is better extracted than phosphate. The counter-ion effect on the removal process is assessed from Molecular Simulation studies. The removal of fluoride from phosphate is discussed taking into account existing technologies.

Exploring Structure⁻Property Relationships in Aromatic Polybenzoxazines Through Molecular Simulation.

A series of commercial difunctional benzoxazine monomers are characterized using thermal and thermo-mechanical techniques before constructing representative polymer networks using molecular simulation techniques. Good agreement is obtained between replicate analyses and for the kinetic parameters obtained from differential scanning calorimetry data (and determined using the methods of Kissinger and Ozawa). Activation energies range from 85 to 108 kJ/mol (Kissinger) and 89 to 110 kJ/mol (Ozawa) for the uncatalyzed thermal polymerization reactions, which achieve conversions of between 85% and 97%. Glass transition temperatures determined from differential scanning calorimetry and dynamic mechanical thermal analysis are comparable, ranging from BA-a (151 °C, crosslink density 3.6 × 10-3 mol cm-3) containing the bisphenol A moiety to BP-a, based on a phenolphthalein bridge (239 to 256 °C, crosslink density 5.5 to 18.4 × 10-3 mol cm-3, depending on formulation). Molecular dynamics simulations of the polybenzoxazines generally agree well with empirical data, indicating that representative networks have been modelled.

'Phoenix polymers': fire induced nanohardness in fibril-forming aromatic cyanate esters.

For the first time we present nanoindentation analysis of charred, cured aromatic cyanate esters, which exhibit outstanding mechanical properties when analysed under applied loads of 0.1-300 mN. Following charring (900 °C for 10 minutes to achieve graphitised structures), the samples display a remarkable combination of a modulus of elasticity of around 25 GPa and nanohardness of 300 kgf mm-2, making them some 30-40% stiffer than bone and practically as hard as tooth enamel. At the same time we find that under the same conditions the chars are highly resilient, displaying complete elastic recovery with very little plastic deformation. When cured in the presence of copper(ii) acetylacetonate (200 ppm) in dodecylphenol (1% w/v active copper suspension) to form a polycyanurate, compound (2) forms a dense, consolidated structure compared with compound (1) under the same conditions. At high magnification, the presence of a nanoscale, fibrillar structure is observed, accounting for the high resilience.

Ultra-high resolution X-ray structures of two forms of human recombinant insulin at 100 K.

The crystal structure of a commercially available form of human recombinant (HR) insulin, Insugen (I), used in the treatment of diabetes has been determined to 0.92 Å resolution using low temperature, 100 K, synchrotron X-ray data collected at 16,000 keV (λ = 0.77 Å). Refinement carried out with anisotropic displacement parameters, removal of main-chain stereochemical restraints, inclusion of H atoms in calculated positions, and 220 water molecules, converged to a final value of R = 0.1112 and Rfree = 0.1466. The structure includes what is thought to be an ordered propanol molecule (POL) only in chain D(4) and a solvated acetate molecule (ACT) coordinated to the Zn atom only in chain B(2). Possible origins and consequences of the propanol and acetate molecules are discussed. Three types of amino acid representation in the electron density are examined in detail: (i) sharp with very clearly resolved features; (ii) well resolved but clearly divided into two conformations which are well behaved in the refinement, both having high quality geometry; (iii) poor density and difficult or impossible to model. An example of type (ii) is observed for the intra-chain disulphide bridge in chain C(3) between Sγ6-Sγ11 which has two clear conformations with relative refined occupancies of 0.8 and 0.2, respectively. In contrast the corresponding S-S bridge in chain A(1) shows one clearly defined conformation. A molecular dynamics study has provided a rational explanation of this difference between chains A and C. More generally, differences in the electron density features between corresponding residues in chains A and C and chains B and D is a common observation in the Insugen (I) structure and these effects are discussed in detail. The crystal structure, also at 0.92 Å and 100 K, of a second commercially available form of human recombinant insulin, Intergen (II), deposited in the Protein Data Bank as 3W7Y which remains otherwise unpublished is compared here with the Insugen (I) structure. In the Intergen (II) structure there is no solvated propanol or acetate molecule. The electron density of Intergen (II), however, does also exhibit the three types of amino acid representations as in Insugen (I). These effects do not necessarily correspond between chains A and C or chains B and D in Intergen (II), or between corresponding residues in Insugen (I). The results of this comparison are reported. Graphical abstract Conformations of PheB25 and PheD25 in three insulin structures: implications for biological activity? Insulin residues PheB25 and PheD25 are considered to be important for insulin receptor binding and changes in biological activity occur when these residues are modified. In porcine insulin and Intergen (II) PheB25 adopts conformation B and PheD25 conformation D. However, unexpectedly PheB25 in Insugen (I) human recombinant insulin adopts two distinct conformations corresponding to B and D, Figure 1 and PheD25 adopts a single conformation corresponding to B not D, Figure 2. Conformations of this residue in the ultra-high resolution structure of Insugen (I) are therefore unique within this set. Figures were produced with Biovia, Discovery Studio 2016.

A calix[4]arene derivative and its selective interaction with drugs (clofibric acid, diclofenac and aspirin).

The synthesis and characterisation of a partially substituted calix[4]arene, namely, 5,11,17,23-tetra-tert-butyl,25,27-bis[aminoethoxy] 26,28-dihydroxycalix[4]arene are reported. Its interaction with commonly used pharmaceuticals (clofibric acid, diclofenac and aspirin) was investigated by spectroscopic (1H NMR and UV), electrochemical (conductance measurements) and thermal (titration calorimetry) techniques. It is concluded on the basis of the experimental work and molecular simulation studies that the receptor interacts selectively with these drugs. Preliminary studies on the selective extraction of these pharmaceuticals from water by the calix receptor are reported and the potential for a carrier mediated sensor based on this ligand for 'on site' monitoring of pharmaceuticals is discussed.

p22phox C242T Single-Nucleotide Polymorphism Inhibits Inflammatory Oxidative Damage to Endothelial Cells and Vessels.

BACKGROUND: The NADPH oxidase, by generating reactive oxygen species, is involved in the pathophysiology of many cardiovascular diseases and represents a therapeutic target for the development of novel drugs. A single-nucleotide polymorphism, C242T of the p22(phox) subunit of NADPH oxidase, has been reported to be negatively associated with coronary heart disease and may predict disease prevalence. However, the underlying mechanisms remain unknown. METHODS AND RESULTS: With the use of computer molecular modeling, we discovered that C242T single-nucleotide polymorphism causes significant structural changes in the extracellular loop of p22(phox) and reduces its interaction stability with Nox2 subunit. Gene transfection of human pulmonary microvascular endothelial cells showed that C242T p22(phox) significantly reduced Nox2 expression but had no significant effect on basal endothelial O2 (.-) production or the expression of Nox1 and Nox4. When cells were stimulated with tumor necrosis factor-α (or high glucose), C242T p22(phox) significantly inhibited tumor necrosis factor-α-induced Nox2 maturation, O2 (.-) production, mitogen-activated protein kinases and nuclear factor κB activation, and inflammation (all P<0.05). These C242T effects were further confirmed using p22(phox) short-hairpin RNA-engineered HeLa cells and Nox2(-/-) coronary microvascular endothelial cells. Clinical significance was investigated by using saphenous vein segments from non-coronary heart disease subjects after phlebotomies. TT (C242T) allele was common (prevalence of ≈22%) and, in comparison with CC, veins bearing TT allele had significantly lower levels of Nox2 expression and O2 (.-) generation in response to high-glucose challenge. CONCLUSIONS: C242T single-nucleotide polymorphism causes p22(phox) structural changes that inhibit endothelial Nox2 activation and oxidative response to tumor necrosis factor-α or high-glucose stimulation. C242T single-nucleotide polymorphism may represent a natural protective mechanism against inflammatory cardiovascular diseases.

Developing (Quantitative Structure Property Relationships) QSPR Techniques to Predict the Char Formation of Polybenzoxazines.

This study uses the Molecular Operating Environment software (MOE) to generate models to calculate the char yield of polybenzoxazines (PBz). A series of benzoxazine (Bz) monomers were constructed to which a variety of parameters relating to the structure (e.g., water accessible surface, negative van der Waals surface area and hydrophobic volume, etc.) were obtained and a quantitative structure property relationships (QSPR) model was generated. The model was used to generate data for new Bz monomers with desired properties and a comparison was made of predictions based on the QSPR model with the experimental data. This study shows the quality of predictive models and confirms how useful computational screening is prior to synthesis.

Docking and DFT studies on ligand binding to Quercetin 2,3-dioxygenase.

Simple molecular docking calculations on quercetin, kojic acid and diethylcarbamatodithoic acid using the software package MOE are shown to be close to the geometries reported in the X-ray crystal structures of the protein co-crystallized with the respective ligands. Furthermore, DFT optimization of the docked conformations is shown to reproduce the essential features of previous studies on quercetin, showing that docking can be used to provide good starting structures for mechanistic study. The flavone ligand, lacking the hydroxyl group of the quercetin is shown by docking to be unable to approach closely the copper atom, indicating the necessity of the presence of the hydroxyl group and providing a prediction of the likely binding environment of this ligand.

Size and molecular flexibility affect the binding of ellagitannins to bovine serum albumin.

Binding to bovine serum albumin of monomeric (vescalagin and pedunculagin) and dimeric ellagitannins (roburin A, oenothein B, and gemin A) was investigated by isothermal titration calorimetry and fluorescence spectroscopy, which indicated two types of binding sites. Stronger and more specific sites exhibited affinity constants, K1, of 10(4)-10(6) M(-1) and stoichiometries, n1, of 2-13 and dominated at low tannin concentrations. Weaker and less-specific binding sites had K2 constants of 10(3)-10(5) M(-1) and stoichiometries, n2, of 16-30 and dominated at higher tannin concentrations. Binding to stronger sites appeared to be dependent on tannin flexibility and the presence of free galloyl groups. Positive entropies for all but gemin A indicated that hydrophobic interactions dominated during complexation. This was supported by an exponential relationship between the affinity, K1, and the modeled hydrophobic accessible surface area and by a linear relationship between K1 and the Stern-Volmer quenching constant, K(SV).

Molecular insights of p47phox phosphorylation dynamics in the regulation of NADPH oxidase activation and superoxide production.

Phagocyte superoxide production by a multicomponent NADPH oxidase is important in host defense against microbial invasion. However inappropriate NADPH oxidase activation causes inflammation. Endothelial cells express NADPH oxidase and endothelial oxidative stress due to prolonged NADPH oxidase activation predisposes many diseases. Discovering the mechanism of NADPH oxidase activation is essential for developing novel treatment of these diseases. The p47(phox) is a key regulatory subunit of NADPH oxidase; however, due to the lack of full protein structural information, the mechanistic insight of p47(phox) phosphorylation in NADPH oxidase activation remains incomplete. Based on crystal structures of three functional domains, we generated a computational structural model of the full p47(phox) protein. Using a combination of in silico phosphorylation, molecular dynamics simulation and protein/protein docking, we discovered that the C-terminal tail of p47(phox) is critical for stabilizing its autoinhibited structure. Ser-379 phosphorylation disrupts H-bonds that link the C-terminal tail to the autoinhibitory region (AIR) and the tandem Src homology 3 (SH3) domains, allowing the AIR to undergo phosphorylation to expose the SH3 pocket for p22(phox) binding. These findings were confirmed by site-directed mutagenesis and gene transfection of p47(phox-/-) coronary microvascular cells. Compared with wild-type p47(phox) cDNA transfected cells, the single mutation of S379A completely blocked p47(phox) membrane translocation, binding to p22(phox) and endothelial O2(·-) production in response to acute stimulation of PKC. p47(phox) C-terminal tail plays a key role in stabilizing intramolecular interactions at rest. Ser-379 phosphorylation is a molecular switch which initiates p47(phox) conformational changes and NADPH oxidase-dependent superoxide production by cells.