The pAR5 mutation and the allosteric mechanism of Escherichia coli aspartate carbamoyltransferase.

Mutation pAR5 replaces residues 145'-153' at the C terminus of the regulatory (r) chains of Escherichia coli ATCase by a new sequence of six residues. The mutated enzyme has been shown to lack substrate cooperativity and inhibition by CTP. Solution X-ray scattering curves demonstrate that, in the absence of ligands, its structure is intermediate between the T form and the R form. In the presence of N-phosphonacetyl-L-aspartate, the mutant is similar to the wild type. An examination of the crystal structure of unligated ATCase reveals that the mutated site is at an interface between r and catalytic (c) chains, which exists only in the T allosteric form. A computer simulation by energy minimization suggests that the pAR5 mutation destabilizes this interface and induces minor changes in the tertiary structure of r chains. The resulting lower stability of the T form explains the loss of substrate cooperativity. The lack of allosteric inhibition may be related to a new electrostatic interaction made in mutant r chains between the C-terminal carboxylate and a lysine residue of the allosteric domain.     

Haemoglobin: the surface buried between the alpha 1 beta 1 and alpha 2 beta 2 dimers in the deoxy and oxy structures

Using the newly available refined co-ordinates of deoxy and oxyhaemoglobin, we have re-examined and compared the interfaces between the dimers alpha 1 beta 1 and alpha 2 beta 2. The most extensive monomer-monomer contacts are between alpha 1 and beta 2, and, symmetrically, alpha 2 and beta 1. In oxyhaemoglobin these interfaces bury 700 A2 less protein surface than in deoxyhaemoglobin. The alpha 1 alpha 2 interface involves similar salt bridges in both forms, but in oxyhaemoglobin buries 240 A2 more surface than in deoxyhaemoglobin. There is a loosely packed beta 1 beta 2 interface burying 320 A2 of surface in oxyhaemoglobin; there is no beta 1 beta 2 interface in deoxyhaemoglobin. The greater stability of the deoxy form, in the absence of ligands, can be attributed to a combination of hydrophobic, van der Waals' and electrostatic interactions.     

Voltage-Sensor Transitions of the Inward-Rectifying K+ Channel KAT1 Indicate a Latching Mechanism Biased by Hydration within the Voltage Sensor

The Kv-like (potassium voltage-dependent) K⁺ channels at the plasma membrane, including the inward-rectifying KAT1 K⁺ channel of Arabidopsis (Arabidopsis thaliana), are important targets for manipulating K⁺ homeostasis in plants. Gating modification, especially, has been identified as a promising means by which to engineer plants with improved characteristics in mineral and water use. Understanding plant K⁺ channel gating poses several challenges, despite many similarities to that of mammalian Kv and Shaker channel models. We have used site-directed mutagenesis to explore residues that are thought to form two electrostatic countercharge centers on either side of a conserved phenylalanine (Phe) residue within the S2 and S3 α-helices of the voltage sensor domain (VSD) of Kv channels. Consistent with molecular dynamic simulations of KAT1, we show that the voltage dependence of the channel gate is highly sensitive to manipulations affecting these residues. Mutations of the central Phe residue favored the closed KAT1 channel, whereas mutations affecting the countercharge centers favored the open channel. Modeling of the macroscopic current kinetics also highlighted a substantial difference between the two sets of mutations. We interpret these findings in the context of the effects on hydration of amino acid residues within the VSD and with an inherent bias of the VSD, when hydrated around a central Phe residue, to the closed state of the channel.Plant cells utilize the potassium ion (K⁺) to maintain hydrostatic (turgor) pressure, to drive irreversible cell expansion for growth, and to facilitate reversible changes in cell volume during stomatal movements. Potassium uptake and its circulation throughout the plant relies both on high-affinity, H⁺-coupled K⁺ transport (Quintero and Blatt, 1997; Rubio et al., 2008) and on K⁺ channels to facilitate K⁺ ion transfer across cell membranes. Uptake via K⁺ channels is thought to be responsible for roughly 50% of the total K⁺ content of the plant under most field conditions (Spalding et al., 1999; Rubio et al., 2008; Amtmann and Blatt, 2009). K⁺ channels confer on the membranes of virtually every tissue distinct K⁺ conductances and regulatory characteristics (Véry and Sentenac, 2003; Dreyer and Blatt, 2009). Their characteristics are thus of interest for engineering directed to manipulating K⁺ flux in many aspects of plant growth and cellular homeostasis. The control of K⁺ channel gating has been identified as the most promising target for the genetic engineering of stomatal responsiveness (Lawson and Blatt, 2014; Wang et al., 2014a), based on the recent development of quantitative systems models of guard cell transport and metabolism (Chen et al., 2012b; Hills et al., 2012; Wang et al., 2012). By contrast, modifying the expression and, most likely, the population of native K⁺ channels at the membrane was found to have no substantial effect on stomatal physiology (Wang et al., 2014b).The Kv-like K⁺ channels of the plant plasma membrane (Pilot et al., 2003; Dreyer and Blatt, 2009) share a number of structural features with the Kv superfamily of K⁺ channels characterized in animals and Drosophila melanogaster (Papazian et al., 1987; Pongs et al., 1988). The functional channels assemble from four homologous subunits and surround a central transmembrane pore that forms the permeation pathway (Daram et al., 1997). Each subunit comprises six transmembrane α-helices, designated S1 to S6, and both N and C termini are situated on the cytosolic side of the membrane (Uozumi et al., 1998). The pore or P loop between the S5 and S6 α-helices incorporates a short α-helical stretch and the highly conserved amino acid sequence TxGYGD, which forms a selectivity filter for K⁺ (Uozumi et al., 1995; Becker et al., 1996; Nakamura et al., 1997). The carbonyl oxygen atoms of these residues in all four K⁺ channel subunits face inward to form coordination sites for K⁺ ions between them (Doyle et al., 1998; Jiang et al., 2003; Kuo et al., 2003; Long et al., 2005) and a multiple-ion pore (Thiel and Blatt, 1991) such that K⁺ ions pass through the selectivity filter as if in free solution. The plant channels are also sensitive to a class of neurotoxins that exhibit high specificity in binding around the mouth of the channel pore (Obermeyer et al., 1994).These K⁺ channels also share a common gating mechanism. Within each subunit, the first four α-helices form a quasiindependent unit, the voltage sensor domain (VSD), with the S4 α-helix incorporating positively charged (Arg or Lys) residues regularly positioned across the lipid bilayer and transmembrane electric field. Voltage displaces the S4 α-helix within the membrane and couples rotation of the S5 and S6 α-helices lining the pore, thereby opening or closing the channel (Sigworth, 2003; Dreyer and Blatt, 2009). For outward-rectifying channels, such as the mammalian Kv1.2 and the D. melanogaster Shaker K⁺ channels, an inside-positive electric field drives the positively charged, S4 α-helix outward (the up position), which draws on the S4-S5 linker to open the pore. This simple expedient of a lever and string secures current flow in one direction by favoring opening at positive, but not negative, voltages. This same model applies to the Arabidopsis (Arabidopsis thaliana) Kv-like K⁺ channels, including outward rectifiers that exhibit sensitivity to external K⁺ concentration (Blatt, 1988; Blatt and Gradmann, 1997; Johansson et al., 2006), and it serves equally in the gating of inward-rectifying K⁺ channels such as KAT1, which gates open at negative voltages (Dreyer and Blatt, 2009).Studies of KAT1 gating (Latorre et al., 2003; Lai et al., 2005) have indicated that the S4 α-helix of the channel most likely undergoes very similar conformational changes with voltage as those of the mammalian and Shaker K⁺ channels. These findings conform with the present understanding of the evolution of VSD structure (Palovcak et al., 2014) and the view of a common functional dynamic to its molecular design. It is likely, therefore, that a similar electrostatic network occurs in KAT1 to stabilize the VSD. Crucially, however, experimental evidence in support of such a network has yet to surface. Electrostatic countercharges and the hydration of amino acid side chains between the α-helices within the VSDs of mammalian and Shaker K⁺ channel models are important for the latch-like stabilization of the so-called down and up states of these channels (Tao et al., 2010; Pless et al., 2011). Nonetheless, some studies (Gajdanowicz et al., 2009; Riedelsberger et al., 2010) have pointed to subtle differences in the structure of KAT1 that relate to the VSD.We have explored the electrostatic network of the KAT1 VSD through site-directed mutagenesis to manipulate the voltage dependence of KAT1, combining these studies with molecular dynamic simulations previously shown to accommodate the plant VSDs and their hydration during gating transitions (Gajdanowicz et al., 2009; Garcia-Mata et al., 2010). We report here that gating of KAT1 is sensitive to manipulations affecting a set of electrostatic charge transfer centers. These findings conform in large measure to the mammalian and Shaker models. However, virtually all manipulations affecting a highly conserved, central Phe favor the up state of the VSD and the closed KAT1 channel, whereas mutations affecting the electrostatic networks on either side of this Phe favor the down state of the VSD and the open channel. These and additional observations suggest that hydration within the VSD is a major determinant of KAT1 gating.     

Epithelium Expressing the E7 Oncoprotein of HPV16 Attracts Immune-Modulatory Dendritic Cells to the Skin and Suppresses Their Antigen-Processing Capacity

Antigen presenting cells (APCs) in skin can promote either antigen-specific effector functions or antigen tolerance, and thus determine clearance or persistence of cutaneous viral infections. Human papillomavirus (HPV) infections can persist in squamous epithelium in immunocompetent individuals, and some persisting HPV infections, particularly with HPV16, promote malignant epithelial transformation. Here, we investigate whether local expression of the HPV16 protein most associated with malignant transformation, HPV16-E7, affects the phenotype and function of APC subsets in the skin. We demonstrate an expanded population of Langerhans cells in HPV16-E7 transgenic skin with distinct cell surface markers which express immune-modulatory enzymes and cytokines not expressed by cells from non transgenic skin. Furthermore, HPV16-E7 transgene expression in keratinocytes attracts new APC subsets to the epidermis. In vivo migration and transport of antigen to the draining lymph node by these APCs is markedly enhanced in HPV16-E7 expressing skin, whereas antigen-processing, as measured by proteolytic cleavage of DQ-OVA and activation of T cells in vivo by APCs, is significantly impaired. These data suggest that local expression of HPV16-E7 in keratinocytes can contribute to persisting infection with this oncogenic virus, by altering the phenotype and function of local APCs.     

Prevalence and Phylogenetic Analysis of Hepatitis B in Captive and Wild-Living Pileated Gibbons (Hylobates pileatus) in Cambodia

International Journal of Primatology - The risk of transmitting novel pathogens from released animals to wild conspecifics is an important consideration for reintroduction initiatives. Apart from...     

Nucleophilic activation by positioning in phosphoryl transfer catalyzed by nucleoside diphosphate kinase

The nonenzymatic reaction of ATP with a nucleophile to generate ADP and a phosphorylated product proceeds via a dissociative transition state with little bond formation to the nucleophile. Consideration of the dissociative nature of the nonenzymatic transition state leads to the following question: To what extent can the nucleophile be activated in enzymatic phosphoryl transfer? We have addressed this question for the NDP kinase reaction. A mutant form of the enzyme lacking the nucleophilic histidine (H122G) can be chemically rescued for ATP attack by imidazole or other exogenous small nucleophiles. The ATP reaction is 50-fold faster with the wild-type enzyme, which has an imidazole nucleophile positioned for reaction by a covalent bond, than with H122G, which employs a noncovalently bound imidazole nucleophile [(kcat/KM)ATP]. Further, a 4-fold advantage for imidazole positioned in the nucleophile binding pocket created by the mutation is suggested from comparison of the reaction of H122G and ATP with an imidazole versus a water nucleophile, after correction for the intrinsic reactivities of imidazole and water toward ATP in solution. X-ray structural analysis shows no detectable rearrangement of the residues surrounding His 122 upon mutation to Gly 122. The overall rate effect of approximately 10(2)-fold for the covalent imidazole nucleophile relative to water is therefore attributed to positioning of the nucleophile with respect to the reactive phosphoryl group. This is underscored by the more deleterious effect of replacing ATP with AlphaTauPgammaS in the wild-type reaction than in the imidazole-rescued mutant reaction, as follows. For the wild-type, AlphaTauPgammaS presumably disrupts positioning between nucleophile and substrate, resulting in a large thio effect of 300-fold, whereas precise alignment is already disrupted in the mutant because there is no covalent bond to the nucleophile, resulting in a smaller thio effect of 10-fold. In summary, the results suggest a catalytic role for activation of the nucleophile by positioning in phosphoryl transfer catalyzed by NDP kinase.     

Crystal structure of yeast allantoicase reveals a repeated jelly roll motif

Allantoicase (EC 3.5.3.4) catalyzes the conversion of allantoate into ureidoglycolate and urea, one of the final steps in the degradation of purines to urea. The mechanism of most enzymes involved in this pathway, which has been known for a long time, is unknown. In this paper we describe the three-dimensional crystal structure of the yeast allantoicase determined at a resolution of 2.6 A by single anomalous diffraction. This constitutes the first structure for an enzyme of this pathway. The structure reveals a repeated jelly roll beta-sheet motif, also present in proteins of unrelated biochemical function. Allantoicase has a hexameric arrangement in the crystal (dimer of trimers). Analysis of the protein sequence against the structural data reveals the presence of two totally conserved surface patches, one on each jelly roll motif. The hexameric packing concentrates these patches into conserved pockets that probably constitute the active site.