113Cd nuclear magnetic resonance of Cd(II) alkaline phosphatases

113Cd NMR spectra of 113Cd(II)-substituted Escherichia coli alkaline phosphatase have been recorded over a range of pH values, levels of metal site occupancy, and states of phosphorylation. Under all conditions resonances attributable to cadmium specifically bound at one or more of the three pairs of metal-binding sites (A, B, and C sites) are detected. By following changes in both the 113Cd and 31P NMR spectra of 113Cd(II)2 alkaline phosphatase during and after phosphorylation, it has been possible to assign the cadmium resonance that occurs between 140 and 170 ppm to Cd(II) bound to the A or catalytic site of the enzyme and the resonance occurring between 51 and 76 ppm to Cd(II) bound to B site, which from x-ray data is located 3.9 A from the A site. The kinetics of phosphorylation show that cadmium migration from the A site of one subunit to the B site of the second subunit follows and is a consequence of phosphate binding, thus precluding the migration as a sufficient explanation for half-of-the-sites reactivity. Rather, there is evidence for subunit-subunit interaction rendering the phosphate binding sites inequivalent. Although one metal ion, at A site, is sufficient for phosphate binding and phosphorylation, the presence of a second metal ion at B site greatly enhances the rate of phosphorylation. In the absence of phosphate, occupation of the lower affinity B and C sites produces exchange broadening of the cadmium resonances. Phosphorylation abolishes this exchange modulation. Magnesium at high concentration broadens the resonances to the point of undetectability. The chemical shift of 113Cd(II) in both A and B sites (but not C site) is different depending on the state of the bound phosphate (whether covalently or noncovalently bound) and gives separate resonances for each form. Care must be taken in attributing the initial distribution of cadmium or phosphate in the reconstituted enzyme to that of the equilibrium species in samples reconstituted from apoenzyme. Both 113Cd NMR and 31P NMR show that some conformational changes consequent to metal ion or phosphate binding require several days before the final equilibrium species is formed.     

Kinetic Intermediates en Route to the Final Serpin-Protease Complex: STUDIES OF COMPLEXES OF α1-PROTEASE INHIBITOR WITH TRYPSIN*

Serpin protein protease inhibitors inactivate their target proteases through a unique mechanism in which a major serpin conformational change, resulting in a 70-Å translocation of the protease from its initial reactive center loop docking site to the opposite pole of the serpin, kinetically traps the acyl-intermediate complex. Although the initial Michaelis and final trapped acyl-intermediate complexes have been well characterized structurally, the intermediate stages involved in this remarkable transformation are not well understood. To better characterize such intermediate steps, we undertook rapid kinetic studies of the FRET and fluorescence perturbation changes of site-specific fluorophore-labeled derivatives of the serpin, α₁-protease inhibitor (α₁PI), which report the serpin and protease conformational changes involved in transforming the Michaelis complex to the trapped acyl-intermediate complex in reactions with trypsin. Two kinetically resolvable conformational changes were observed in the reactions, ascribable to (i) serpin reactive center loop insertion into sheet A with full protease translocation but incomplete protease distortion followed by, (ii) full conformational distortion and movement of the protease and coupled serpin conformational changes involving the F helix-sheet A interface. Kinetic studies of calcium effects on the labeled α₁PI-trypsin reactions demonstrated both inactive and low activity states of the distorted protease in the final complex that were distinct from the intermediate distorted state. These studies provide new insights into the nature of the serpin and protease conformational changes involved in trapping the acyl-intermediate complex in serpin-protease reactions and support a previously proposed role for helix F in the trapping mechanism.     

Sampling Rhyparida nitida Clark (Coleoptera: Chrysomelidae) and symptoms of their damage on sugarcane

Sampling statistics were determined for larvae, pupae and adults of the chrysomelid Rhyparida nitida associated with sugarcane in Australia and for symptoms of their damage. Iwao's patchiness regression was inappropriate for modelling the mean–variance relationships of the insect counts. Taylor's power law was used to model these data and relationships were developed for counts of small, medium and large larvae, all larvae combined, pupae and adults. The mean–variance relationships of counts of live shoots and shoots killed by larvae of R. nitida were modelled using Iwao's patchiness regression; Taylor's power law was not appropriate to either data set. Relationships to determine sample sizes for fixed levels of precision and fixed-precision-level stop lines for sequential sampling of the different stages and live and dead shoots were also developed. Neither the ln(x + 1) transformation nor the Healy and Taylor transformation consistently standardised the mean–variance relationships of insect counts and the appropriate transformation should be selected on a case-by-case basis. Counts of both live and dead shoots were adequately transformed by the Iwao and Kuno transformation.     

Specificity of Binding of the Low Density Lipoprotein Receptor-related Protein to Different Conformational States of the Clade E Serpins Plasminogen Activator Inhibitor-1 and Proteinase Nexin-1

The low density lipoprotein receptor-related protein (LRP) is the principal clearance receptor for serpins and serpin-proteinase complexes. The ligand binding regions of LRP consist of clusters of cysteine-rich ∼40-residue complement-like repeats (CR), with cluster II being the principal ligand-binding region. To better understand the specificity of binding at different sites within the cluster and the ability of LRP to discriminate in vivo between uncomplexed and proteinase-complexed serpins, we have systematically examined the affinities of plasminogen activator inhibitor-1 (PAI-1) and proteinase nexin-1 (PN-1) in their native, cleaved, and proteinase-complexed states to (CR)₂ and (CR)₃ fragments of LRP cluster II. A consistent blue shift of the CR domain tryptophan fluorescence suggested a common mode of serpin binding, involving lysines on the serpin engaging the acidic region around the calcium binding site of the CR domain. High affinity binding of non-proteinase-complexed PAI-1 and PN-1 occurred to all fragments containing three CR domains (3–59 nm) and most that contain only two CR domains, although binding energies to different (CR)₃ fragments differed by up to 18% for PAI-1 and 9% for PN-1. No detectable difference in affinity was seen between native and cleaved serpin. However, the presence of proteinase in complex with the serpin enhanced affinity modestly and presumably nonspecifically. This may be sufficient to give preferential binding of such complexes in vivo at the relevant physiological concentrations.The low density lipoprotein receptor-related protein (LRP)² is a member of the LDL receptor family of mosaic-like receptors (1). Ligand binding occurs to regions composed of multiple copies of a ∼40-residue cysteine-rich, calcium-binding domain, termed variously CR (for complement-like repeat) or Ldl-A. In the case of LDLR, there is a single cluster of seven CR domains, whereas in LRP, there are four clusters (designated I–IV) composed of 2, 8, 10, and 11 CR domains, respectively. Unlike LDLR, which has a very limited range of protein ligands, LRP is known to bind and internalize a very wide range of structurally unrelated proteins, including serpins and their proteinase complexes, and activated forms of the panproteinase inhibitor α₂-macroglobulin (α₂M) (2). Cluster II is the principal ligand-binding region, although many of the ligands to this cluster have also been reported to bind to cluster IV (2). That the wider range of ligands for LRP is not solely related to the much greater number of CR domains compared with LDLR is shown by the quite wide range of ligands for VLDLR, which, like LDLR, has only a single cluster of CR domains, albeit of eight rather than seven domains.Given that serpins are able to undergo a number of conformational transitions, most notably as a result of formation of complexes during proteinase inhibition, many early studies on the in vivo receptor-mediated clearance of serpins focused on the relative rates of clearance of the different conformational forms (3–5). It was shown for several serpins that their complexes with proteinase were cleared much more rapidly than native, cleaved, or latent forms. This led to the idea that a neoepitope is formed in the complex (6). From comparison of the internalization properties of PAI-1 complexes with different proteinases, it was further suggested that the neoepitope is localized to the serpin moiety, thus implying that the conformation of the serpin in the serpin-proteinase complex is sufficiently different to permit discrimination between complexed and uncomplexed serpin by the clearance receptor (7). However, the determination of x-ray structures of the serpin α₁PI with two different proteinases showed that the serpin moiety is almost identical in conformation to cleaved α₁PI (8, 9). Studies on other serpin-proteinase complexes, including those of PAI-1 with four different proteinases, all suggested equivalent structures for the complexes and hence no major conformational difference for the serpin moiety compared with the cleaved form (10, 11). Although the consequence of binding of serpins in their various conformational forms appears to result only in internalization and degradation, the consequences for binding of activated α₂Ms are more complex. In addition to internalization, there is also good evidence for signal transduction, resulting in a range of intracellular changes, such as increase in Ca²⁺ and phosphorylation (12–14).Given these variations in ligand-receptor interaction (namely the wide versus narrow specificity of LRP and LDLR, the apparent discrimination by LRP between different serpin conformational states, and the different cellular consequences of binding serpins and activated α₂Ms to LRP), it is of great interest to understand the molecular level basis for these behaviors. We have already shown that the receptor binding domain of α₂M, which contains the full binding region of the intact protein, shows a 30-fold preference for binding to one region of cluster II of LRP compared with an adjacent region (15). With the goal of determining whether there is comparable selectivity for serpins, we have now examined the binding of two closely related serpins, PAI-1 and PN-1, in different conformational states, to overlapping fragments of cluster II from LRP. We found that the serpin ligands bound tightly to many regions of cluster II, although with up to 12-fold difference in K_d for binding of PAI-1 to different (CR)₃ fragments and up to 5-fold difference for PN-1. Most importantly, we found that, for both PAI-1 and PN-1, native and cleaved conformations bound with similar affinities, and, for PAI-1, the higher affinity of proteinase-complexed versus non-complexed serpin arose solely from a small additional, most likely nonspecific, binding contribution from the proteinase.     

Asymmetric introgression between sympatric molestus and pipiens forms of Culex pipiens (Diptera: Culicidae) in the Comporta region, Portugal

Background  

Culex pipiens L. is the most widespread mosquito vector in temperate regions. This species consists of two forms, denoted molestus and pipiens, that exhibit important behavioural and physiological differences. The evolutionary relationships and taxonomic status of these forms remain unclear. In northern European latitudes molestus and pipiens populations occupy different habitats (underground vs. aboveground), a separation that most likely promotes genetic isolation between forms. However, the same does not hold in southern Europe where both forms occur aboveground in sympatry. In these southern habitats, the extent of hybridisation and its impact on the extent of genetic divergence between forms under sympatric conditions has not been clarified. For this purpose, we have used phenotypic and genetic data to characterise Cx. pipiens collected aboveground in Portugal. Our aims were to determine levels of genetic differentiation and the degree of hybridisation between forms occurring in sympatry, and to relate these with both evolutionary and epidemiological tenets of this biological group.     

Solution structure of the viral receptor domain of Tva and its implications in viral entry

Tva is the cellular receptor for subgroup A avian sarcoma and leukosis virus (ASLV-A). The viral receptor function of Tva is determined by a 40-residue, cysteine-rich motif called the LDL-A module. Here we report the solution structure of the LDL-A module of Tva, determined by nuclear magnetic resonance (NMR) spectroscopy. Although the carboxyl terminus of the Tva LDL-A module has a structure similar to those of other reported LDL-A modules, the amino terminus adopts a different conformation. The LDL-A module of Tva does not contain the signature antiparallel beta-sheet observed in other LDL-A modules, and it is more flexible than other reported LDL-A modules. The LDL-A structure of Tva provides mechanistic insights into how a simple viral receptor functions in retrovirus entry. The side chains of H38 and W48 of Tva, which have been identified as viral contact residues by mutational analysis, are solvent exposed, suggesting that they are directly involved in EnvA binding. However, the side chain of L34, another potential viral contact residue identified previously, is buried inside of the module and forms the hydrophobic core with other residues. Thus L34 likely stabilizes the Tva structure but is not a viral interaction determinant. In addition, we propose that the flexible amino-terminal region of Tva plays an important role in determining specificity in the Tva-EnvA interaction.     

alpha1-Proteinase inhibitor forms initial non-covalent and final covalent complexes with elastase analogously to other serpin-proteinase pairs, suggesting a common mechanism of inhibition

Despite several concordant structural studies on the initial non-covalent complex that serpins form with target proteinases, a recent study on the non-covalent complex between the serpin alpha(1)-proteinase inhibitor (alpha(1)PI) and anhydroelastase concluded that translocation of the proteinase precedes cleavage of the reactive center loop and formation of the acyl ester. Because this conclusion is diametrically opposite to those of the other structural studies on serpin-proteinase pairs, we proceeded to examine this specific serpin-proteinase complex by the same successful NMR approach used previously on the alpha(1)PI-Pittsburgh-S195A trypsin pair. Both non-covalent complex with anhydroelastase and covalent complex with active elastase were made with (15)N-alanine-labeled wild-type alpha(1)PI. The heteronuclear single quantum correlation spectroscopy (HSQC) NMR spectrum of the non-covalent complex showed that the entire reactive center loop remained exposed, and the serpin body maintained a conformation indistinguishable from that of native alpha(1)PI, indicating no movement of the proteinase and no insertion of the reactive center loop into beta-sheet A. In contrast, the HSQC NMR spectrum of the covalent complex showed that the reactive center loop had fully inserted into beta-sheet A, indicating that translocation of the proteinase had occurred. These results agree with previous NMR, fluorescence resonance energy transfer, and x-ray crystallographic studies and suggest that a common mechanism is employed in formation of serpin-proteinase complexes. We found that preparations of anhydroelastase that are not appropriately purified contain material that can regenerate active elastase over time. It is likely that the material used by Mellet and Bieth contained such active elastase, resulting in mistaken attribution of the behavior of covalent complex to that of the non-covalent complex.     

Kinetic analysis of binding interaction between the subgroup A Rous sarcoma virus glycoprotein SU and its cognate receptor Tva: calcium is not required for ligand binding

Tva is the receptor for subgroup A Rous sarcoma virus, and it contains a single LDL-A module which is the site of virus interaction. In this study, we expressed the entire extracellular region of Tva (referred to as Ecto-Tva) as a GST fusion protein and characterized its refolding properties. We demonstrated that the correct folding of the Ecto-Tva protein, like that of the Tva LDL-A module, is calcium dependent. We used the IAsys system to measure the kinetics of binding between the surface (SU) subunit of the viral glycoprotein and Tva in real time. We found that the Ecto-Tva protein and the Tva LDL-A module displayed similar affinities for SU, providing direct evidence that the LDL-A module of Tva is the only viral interaction domain of the receptor. Furthermore, misfolded Tva proteins displayed lower binding affinities to SU, largely due to a decrease in their association rates, suggesting that a high association rate between SU and Tva is crucial for efficient virus-host interaction. Furthermore, we found that calcium did not influence the overall binding affinity between Tva and SU. These results indicate that, although calcium is important in facilitating correct folding of the LDL-A module of Tva, it is not essential for ligand binding. Thus, these results may have broad implications for the mechanism of protein folding and ligand recognition of the LDL receptor and other members of the LDL receptor superfamily.     

Characterization of the LDL-A module mutants of Tva,the subgroup A Rous sarcoma virus receptor,and the implications in protein folding

Tva is the cellular receptor for subgroup A Rous sarcoma virus (RSV-A), and the viral receptor function is solely determined by a 40-residue motif called the LDL-A module of Tva. In this report, an integral approach of molecular, biochemical, and biophysical techniques was used to examine the role of a well-conserved tryptophan of the LDL-A module of Tva in protein folding and ligand binding. We show that substitution of tryptophan by glycine adversely affected the correct folding of the LDL-A module of Tva, with only a portion giving a calcium-binding conformation. Furthermore, we show that the misfolded LDL-A conformations of Tva could not efficiently bind to its ligand. These results indicate that this conserved tryptophan in the LDL-A module of Tva plays an important role in correct protein folding and ligand recognition. Furthermore, these results suggest that the familial hypercholesterolemia (FH) French Canadian-4 mutation is likely caused by protein misfolding of low-density lipoprotein receptor, thus explaining the defect for this class of FH.     

Structural similarity of the covalent complexes formed between the serpin plasminogen activator inhibitor-1 and the arginine-specific proteinases trypsin, LMW u-PA, HMW u-PA, and t-PA: use of site-specific fluorescent probes of local environment

We have used two fluorescent probes, NBD and dansyl, attached site-specifically to the serpin plasminogen activator inhibitor-1 (PAI-1) to address the question of whether a common mechanism of proteinase translocation and full insertion of the reactive center loop is used by PAI-1 when it forms covalent SDS-stable complexes with four arginine-specific proteinases, which differ markedly in size and domain composition. Single-cysteine residues were incorporated at position 119 or 302 as sites for specific reporter labeling. These are positions approximately 30 A apart that allow discrimination between different types of complex structure. Fluorescent derivatives were prepared for each of these variants using both NBD and dansyl as reporters of local perturbations. Spectra of native and cleaved forms also allowed discrimination between direct proteinase-induced changes and effects solely due to conformational change within the serpin. Covalent complexes of these derivatized PAI-1 species were made with the proteinases trypsin, LMW u-PA, HMW u-PA, and t-PA. Whereas only minor perturbations of either NBD and dansyl were found for almost all complexes when label was at position 119, major perturbations in both wavelength maximum (blue shifts) and quantum yield (both increases and decreases) were found for all complexes for both NBD and dansyl at position 302. This is consistent with all four complexes having similar location of the proteinase catalytic domain and hence with all four using the same mechanism of full-loop insertion with consequent distortion of the proteinase wedged in at the bottom of the serpin.