Structures of an unliganded neurophysin and its vasopressin complex: implications for binding and allosteric mechanisms

The structures of des 1-6 bovine neurophysin-II in the unliganded state and as its complex with lysine vasopressin were determined crystallographically at resolutions of 2.4 A and 2.3 A, respectively. The structure of the protein component of the vasopressin complex was, with some local differences, similar to that determined earlier of the full-length protein complexed with oxytocin, but relatively large differences, probably intrinsic to the hormones, were observed between the structures of bound oxytocin and bound vasopressin at Gln 4. The structure of the unliganded protein is the first structure of an unliganded neurophysin. Comparison with the liganded state indicated significant binding-induced conformational changes that were the largest in the loop region comprising residues 50-58 and in the 7-10 region. A subtle binding-induced tightening of the subunit interface of the dimer also was shown, consistent with a role for interface changes in neurophysin allosteric mechanism, but one that is probably not predominant. Interface changes are suggested to be communicated from the binding site through the strands of beta-sheet that connect these two regions, in part with mediation by Gly 23. Comparison of unliganded and liganded states additionally reveals that the binding site for the hormone alpha-amino group is largely preformed and accessible in the unliganded state, suggesting that it represents the initial site of hormone protein recognition. The potential molecular basis for its thermodynamic contribution to binding is discussed.

Comparison of plasma-sprayed hydroxyapatite coatings and hydroxyapatite/tricalcium phosphate composite coatings: in vivo study

This study aimed to compare biological properties, including osteoconduction, osseointegration, and shear strength, between plasma-sprayed hydroxyapatite (HA) and HA/tricalcium phosphate (TCP) coatings, using a transcortical implant model in the femora of canines. After 3 and 12 weeks of implantation, the implants with surrounding bone were assessed histologically in undecalcified sections in backscattered electron images (BEIs) under a scanning electron microscope (SEM). After short-term (3 week) follow-up, both coatings conducted new bone formation and revealed direct bone-to-coating contact. The HA/TCP coating could not enhance early host-to-coating responses. At 12 weeks, serious dissolution of the HA/TCP coatings evidently occurred. By the new bone healing index (NBHI) and apposition index (AI), we found no significant difference between HA/TCP-coated implants and HA-coated implants throughout all implant periods. At 12 weeks of implantation, some particles dissociated from the HA/TCP coating were found within the remodeling canal. After push-out measurements, the shear strength and failure mode of HA/TCP-coated implants were similar to those of HA-coated implants, and no statistical differences were found between either coating. Consequently, this study indicates that HA/TCP coatings have excellent biological response and may be considered suitable bioactive ceramic coatings for short-term clinical use.

[Clinical and experimental study on treatment of infantile mycotic enteritis by jiechang mixture]

OBJECTIVE

To evaluate the therapeutic effect and mechanism of Jiechang Mixture (JCM) in treating infantile mycotic enteritis.

METHODS

The children patients confirmed to be suffered from mycotic enteritis were divided randomly into two groups: the 40 cases in the treated group treated with JCM and the 20 cases in the control group treated with fungicidin. The time of stool forming, diarrhea relieving and fungi vanishing were observed. The promoting effect of JCM on small intestine motility and the inhibition of JCM on Candida albicans in stool culture were studied experimentally.

RESULTS

The time of stool forming, diarrhea relieving and fungi vanishing in the treated group were significantly shorter than those in the control group (P < 0.01), and JCM also showed a better effect in improving clinical symptoms and signs of patients than the control. Results of experimental study showed that JCM could abate the ink evacuation of small intestine in mice. The fungi inhibitory test suggested that Candida albicans was susceptible to JCM.

CONCLUSION

JCM is an effective herbal medicine in treating infantile mycotic enteritis.

Aldehyde dehydrogenase. Maintaining critical active site geometry at motif 8 in the class 3 enzyme

Alignment of all known, diverse members of the aldehyde dehydrogenase (ALDH) extended family revealed only two strictly conserved, nonglycine residues, a glutamate and a phenylalanine residue. Both occur in one of the highly conserved 'motif' segments and both occupy strategic locations in the tertiary structure at the bottom of the catalytic funnel. In class 3 ALDH, these are Glu333 and Phe335. In addition, Asp247, which is not highly conserved but is characteristic of class 3 ALDHs, hydrogen bonds the main chain between Glu333 and Phe335. These three residues were mutated conservatively. Michaelis constants determined for both NAD/propanal and NADP/benzaldehyde substrate pairs show all three residues to be crucial to effective catalysis, and suggest that the hydrogen bond to Asp247 is a key element in maintaining precise geometry of key elements at the active site.

The 2.0 A structure of human ferrochelatase, the terminal enzyme of heme biosynthesis

Human ferrochelatase (E.C. 4.99.1.1) is a homodimeric (86 kDa) mitochondrial membrane-associated enzyme that catalyzes the insertion of ferrous iron into protoporphyrin to form heme. We have determined the 2.0 A structure from the single wavelength iron anomalous scattering signal. The enzyme contains two NO-sensitive and uniquely coordinated [2Fe-2S] clusters. Its membrane association is mediated in part by a 12-residue hydrophobic lip that also forms the entrance to the active site pocket. The positioning of highly conserved residues in the active site in conjunction with previous biochemical studies support a catalytic model that may have significance in explaining the enzymatic defects that lead to the human inherited disease erythropoietic protoporphyria.

Structure of the Ca2+-regulated photoprotein obelin at 1.7 A resolution determined directly from its sulfur substructure

The crystal structure of the photoprotein obelin (22.2 kDa) from Obelia longissima has been determined and refined to 1.7 A resolution. Contrary to the prediction of a peroxide, the noncovalently bound substrate, coelenterazine, has only a single oxygen atom bound at the C2-position. The protein-coelenterazine 2-oxy complex observed in the crystals is photo-active because, in the presence of calcium ion, bioluminescence emission within the crystal is observed. This structure represents only the second de novo protein structure determined using the anomalous scattering signal of the sulfur substructure in the crystal. The method used here is theoretically different from that used for crambin in 1981 (4.72 kDa) and represents a significant advancement in protein crystal structure determination.

Shifting the NAD/NADP preference in class 3 aldehyde dehydrogenase

Among pyridine-nucleotide-dependent oxidoreductases, the class 3 family of aldehyde dehydrogenases (ALDHs) is unusual in its ability to function with either NAD or NADP. This is all the more surprising because an acidic residue, Glu140, coordinates the adenine ribose 2' hydroxyl. In many NAD-dependent dehydrogenases a similarly placed carboxylate is thought to be responsible for exclusion of NADP. The corresponding residue in most (approximately 71%) sequences in the ALDH extended family is also Glu, and most of these are NAD-specific enzymes. Site-directed mutagenesis was performed on this residue in rat class 3 ALDH. Our results indicate that this residue contributes to tighter binding of NAD in the native enzyme, but suggest that additional factors must contribute to the ability to utilize NADP. Mutagenesis of an adjacent basic residue (Lys137) indicates that it is even more essential for binding both coenzymes, consistent with its conservation in nearly all ALDHs (> 98%).

Cell science and protein crystal growth research for the International Space Station

The recent National Research Council report, Future Biotechnology Research on the International Space Station, evaluates NASA's plans for research in cell science and protein crystal growth to be conducted on the International Space Station. This report concludes that the NASA biotechnology programs have the potential to significantly impact relevant scientific fields and to increase understanding and insight into fundamental biological issues. In order to realize the potential impacts, NASA must focus its research programs by selecting specific questions related to gravitational forces' role in cell behavior and by using the microgravity environment as a tool to determine the structure of macromolecules with important biological implications. Given the time and volume constraints associated with space-based experiments, instrumentation to be used on the space station must be designed to maximize the productivity of researchers, and NASA's recruitment of investigators and support for space station experiments should aim to encourage and facilitate cutting-edge research.

Crystallization and preliminary X-ray analysis of the Clostridium thermocellum cellulosome xylanase Z feruloyl esterase domain

Feruloyl esterases cleave ferulic acid from arabinoxylan and pectin. Feruloyl groups are believed to crosslink the polysaccharide chain within the polymer and to link hemicellulose to lignin, which may play a role in controlling the growth of plants. The Clostridium thermocellum cellulosome xylanase Z feruloyl esterase was expressed in Escherichia coli, purified and crystallized. The crystals diffract to 2.4 A resolution and belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 43.14, b = 63.77, c = 79.57 A. Assuming one molecule per asymmetric unit, the Matthews coefficient is calculated to be 1.87 A(3) Da(-1), which corresponds to a solvent content of 34%.

Crystallization and preliminary X-ray diffraction analysis of the mitochondrial transcription factor sc-mtTFB from Saccharomyces cerevisiae

Eukaryotic mitochondria contain a distinct mini-chromosome. In yeast, transcription of the mitochondrial genome is mediated by a nuclear-encoded RNA polymerase consisting of a single polypeptide core enzyme and a specificity factor termed sc-mtTFB which bears some similarity to bacterial sigma-factors. sc-mtTFB from Saccharomyces cerevisiae has been cloned, expressed, purified and crystallized. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 89.7, b = 44.6, c = 98.9 A, beta = 110 degrees. Based on one molecule per asymmetric unit, the solvent content is estimated to be 48%. Small crystals of dimensions 0.01 x 0.05 x 0.13 mm diffract to at least 2.7 A resolution on a rotating-anode X-ray source.

[Determination of ibandronate by high performance ion exchange chromatography]

A method for the determination of Ibandronate by high performance ion exchange chromatography is reported. Ibandronate can form a complex compound with the copper ion added in the mobile phase. The complex can be detected at UV 240 nm. The effects of pH of mobile phase and concentration of methanol to the retention time were studied. Concentration of 10% methanol and pH 2.5 were suitable for the detection in less than 5 min. The flow rate was 1.0 mL/min. The relative standard deviation of peak area was 0.8%. The linear correlation was observed from 300 mg/L to 1,500 mg/L of Ibandronate (r = 0.9989). The lowest detectable concentration of Ibandronate was 6 mg/L. The method is simple, rapid and reproducible.

Preparation and preliminary study of crystals of the recombinant calcium-regulated photoprotein obelin from the bioluminescent hydroid Obelia longissima

Crystals of recombinant obelin, the Ca(2+)-regulated photoprotein from the marine hydroid Obelia longissima, have been grown from sodium citrate solutions. Crystals grow as hexagonal light-yellow rods (0.1 x 0.1 x 1.0 mm) which diffract to beyond 1.8 A with synchrotron radiation of 1.0 A wavelength. The crystals have a primitive hexagonal lattice with unit-cell parameters a = 81.55, c = 86.95 A. The asymmetric unit contains two molecules. This represents the successful preparation of single crystals of a photoprotein obelin which have promising diffraction properties.

Low-salt crystallization of T7 RNA polymerase: a first step towards the transcription bubble complex

DNA-dependent RNA polymerase is the key enzyme responsible for the biosynthesis of RNA, a process known as transcription. This process, which decodes the genetic information from DNA, is one of the most significant events in a biological system. The crystallization of both native and a chimeric T7/T3 RNAP using high salt conditions has been reported previously but these conditions proved unsuitable for DNA-RNAP complex formation since at high salt concentrations the DNA binding affinity to RNAP is reduced. A search for low-salt crystallization conditions has yielded new low-salt crystals of native T7-RNAP, a chimeric T7-RNAP (T7/T3 RNAP) which contains the T3 promoter recognition sequence, and a T7-RNAP containing an N-terminal histidine tag. The crystals, which are better suited for DNA-RNAP complex formation, belong to space group P3121 with a = 136, c = 156 A, contain a single molecule per asymmetric unit and diffract to 2.7 A resolution. Packing analysis shows that the new low-salt crystals have packing contacts similar to those observed in the high-salt T7-RNAP crystals reported previously. The diffraction anisotropicity observed in crystals of T7 RNAP is explained in term of crystal packing.

Purification, crystallization and preliminary X-ray analysis of Drosophila melanogaster ferrochelatase

Ferrochelatase (protoheme ferrolyase, E.C. 4.99.1.1), the terminal enzyme in the heme biosynthetic pathway, catalyzes the insertion of ferrous iron into protoporphyrin IX to form protoheme. In eukaryotes, the protein is associated with the inner surface of the inner mitochondrial membrane, and in higher animals the enzyme contains a [2Fe-2S] cluster. This cluster is highly sensitive to NO and is coordinated by four Cys residues whose spacing in the primary sequence is unique. Ferrochelatase from Drosophila melanogaster has been expressed in Escherichia coli with an amino-terminal six-histidine tag and purified to homogeneity. The protein has been crystallized with the [2Fe-2S] cluster intact. The crystals belong to space group I422, with unit-cell dimensions a = b = 158.1, c = 171.2 A and two molecules in the asymmetric unit, and diffract to 3. 0 A resolution.

Structural basis of neurophysin hormone specificity: Geometry, polarity, and polarizability in aromatic ring interactions

The structural origins of the specificity of the neurophysin hormone-binding site for an aromatic residue in peptide position 2 were explored by analyzing the binding of a series of peptides in the context of the crystal structure of liganded neurophysin. A new modeling method for describing the van der Waals surface of binding sites assisted in the analysis. Particular attention was paid to the unusually large (5 kcal/mol) difference in binding free energy between Phe and Leu in position 2, a value representing more than three times the maximum expected based on hydrophobicity alone, and additionally remarkable since modeling indicated that the Leu side chain was readily accommodated by the binding pocket. Although evidence was obtained of a weak thermodynamic linkage between the binding interactions of the residue 2 side chain and of the peptide alpha-amino group, two factors are considered central. (1) The bound Leu side chain can establish only one-third of the van der Waals contacts available to a Phe side chain. (2) The bound Phe side chain appears to be additionally stabilized relative to Leu by more favorable dipole and induced dipole interactions with nonaromatic polar and sulfur ligands in the binding pocket, as evidenced by examination of its interactions in the pocket, analysis of the detailed energetics of transfer of Phe and Leu side chains from water to other phases, and comparison with thermodynamic and structural data for the binding of residue 1 side chains in this system. While such polar interactions of aromatic rings have been previously observed, the present results suggest their potential for significant thermodynamic contributions to protein structure and ligand recognition.

Pharmacology study of the neutral myocardial imaging agent technetium-99m-N(NOEt)2

OBJECTIVE

The biological properties of a new neutral myocardial imaging agent 99mTcN(NOEt)2 were evaluated.

METHODS

Blood clearance in rabbits, biodistribution in rats, and initial myocardial imaging in dogs were performed.

RESULTS

Radiochemical purity of 99mTcN(NOEt)2 was more than 90% and stable for 6 h at room temperature. Blood disappearance was analyzed with a biexponential model and T1/2(alpha) = 2.53 min, T1/2(beta) = 330 min and CI = 378 ml/h were obtained. Biodistribution studies demonstrated that 99mTcN(NOEt)2 localized selectively in the rat myocardium. Cardiac uptakes were 4.69, 4.20, 3.95 and 3.43% ID/g at 5, 30, 60 and 90 min postinjection, respectively. The mean heart-to-lung activity ratios were 1.69, 2.40 and 2.55 at 10 min, 30 min and 60 min postinjection, respectively.

CONCLUSION

Technetium-99m-N(NOEt)2 exhibited favorable stability and biological properties. Further study in humans is required.

Increased phosphorylation of DARPP-32 by D1 agonistic action of l-stepholidine in the 6-OHDA-lesioned rat striatum

In order to explore the characteristics of l-stepholidine (SPD) activating the postsynaptic D(1) receptors, the effects of SPD on DARPP-32 phosphorylation in vivo with back-phosphorylation assay and on the postsynaptic D(1) receptor densities with radioligand assay were observed in the striatum of 6-OHDA-lesioned rat. The results showed that following subcutaneously administration of 20 or 40 mg/kg SPD for 21 d, (32)P phosphate incorporation into the DARPP-32 protein in the denervated striatum showed a 50% reduction (P<0.01) vs the intact striatum, indicating an increase of DARPP-32 phosphorylation in vivo in the denervated striatum. However,the D(1) receptor B(max) was decreased from 385.0+/-26.1 to 319.7+/-20.1 fmol/mg protein. It is suggested that D(1) agonist action of SPD decreases the D(1) receptor density but increases the phosphorylation of DARPP-32 in the striatum of 6-OHDA-lesioned rat, which may be responsible for the regulation of D(1) receptor signal transduction in brain neurons.

Relationships within the aldehyde dehydrogenase extended family

One hundred-forty-five full-length aldehyde dehydrogenase-related sequences were aligned to determine relationships within the aldehyde dehydrogenase (ALDH) extended family. The alignment reveals only four invariant residues: two glycines, a phenylalanine involved in NAD binding, and a glutamic acid that coordinates the nicotinamide ribose in certain E-NAD binary complex crystal structures, but which may also serve as a general base for the catalytic reaction. The cysteine that provides the catalytic thiol and its closest neighbor in space, an asparagine residue, are conserved in all ALDHs with demonstrated dehydrogenase activity. Sixteen residues are conserved in at least 95% of the sequences; 12 of these cluster into seven sequence motifs conserved in almost all ALDHs. These motifs cluster around the active site of the enzyme. Phylogenetic analysis of these ALDHs indicates at least 13 ALDH families, most of which have previously been identified but not grouped separately by alignment. ALDHs cluster into two main trunks of the phylogenetic tree. The largest, the "Class 3" trunk, contains mostly substrate-specific ALDH families, as well as the class 3 ALDH family itself. The other trunk, the "Class 1/2" trunk, contains mostly variable substrate ALDH families, including the class 1 and 2 ALDH families. Divergence of the substrate-specific ALDHs occurred earlier than the division between ALDHs with broad substrate specificities. A site on the World Wide Web has also been devoted to this alignment project.

Structural modeling of the pro-ocytocin-neurophysin precursor

The hormonal precursor pro-ocytocin-neurophysin is activated by selective cleavage at Arg2-Ala13, producing mature ocytocin and neurophysin. To understand the cleavage mechanism better, and in particular the recognition of the cleavage site, it is necessary to characterize the three-dimensional structure of the precursor molecule. Here we combine a variety of experimental data with molecular modeling and dynamics calculations to derive possible precursor conformations. In the models obtained, the N-terminus of the precursor, corresponding to the ocytocin segment, is hydrogen bonded in a pocket of the neurophysin moiety in a similar manner to a crystallographically obtained non-covalent complex between the two molecules. The calculations suggest that although the ocytocin segment is relatively flexible, it adopts a stable, broad loop structure in the vicinity of the cleavage region, which may constitute the structural element recognized by the cleaving enzyme. The calculations also suggest a possible widening of the distance between the two neurophysin domains in the precursor relative to that in the non-covalent neurophysin-ocytocin complex.

The structure of glutamine-binding protein complexed with glutamine at 1.94 A resolution: comparisons with other amino acid binding proteins

The crystal structure of the glutamine-binding protein (GlnBP) complexed with its ligand (Gln) was determined and refined to 1.94 A resolution. This ellipsoidal protein has two globular domains and is approximately 52 Ax40 Ax35 A in size. The glutamine ligand is located in the cleft between the two domains and stablized by hydrogen bondings and ionic interactions with Asp10, Gly68, Thr70, Ala67, Asp157, Arg75, Lys115, Gly119 and His156. The aliphatic portion of the glutamine ligand is sandwiched in a hydrophobic pocket formed between Phe13 and Phe50 and has 21 van der Waals contacts with GlnBP. Lys115 and His156, that are unique to GlnBP among amino acid binding proteins, apparently contribute to the ligand binding specificity of GlnBP. Asp10 is within 3 A of Lys115. These two residues are over 10 A apart in the ligand-free form of the GlnBP. In addition, GlnBP-Gln exhibits a large-scale movement of the two hinges connecting the two globular domains upon ligand binding. The most significant changes are 41.1 degrees in the phi angle of Gly89 and 34.3 degrees in the psi angle of Glu181 from the first and the second hinge of the protein, respectively. Besides the original six hydrogen bonds, three extra hydrogen bonds can be observed between the two hinge strands upon ligand binding. A hydrogen bond network connects the large domain to the second hinge and a second hydrogen bond network coalesces the small domain to the same strand, both via interaction with the glutamine ligand. Although the two strands of the hinge connecting the domains do not directly participate in the ligand binding, Gln183 and Tyr185 from the second hinge may be involved in the cascade of the conformational change that is induced by ligand binding.

Enhancement of (-)-stepholidine on protein phosphorylation of a dopamine- and cAMP-regulated phosphoprotein in denervated striatum of oxidopamine-lesioned rats

AIM

To study effects of (-)-stepholidine (SPD) on the phosphorylation of a dopamine- and cAMP-regulated phosphoprotein (DARPP-32) in the striatum of oxidopamine-lesioned rats.

METHODS

The amount of dephospho-DARPP-32 was measured by a back-phosphorylation assay.

RESULTS

In the striatum of control rats, SPD per se had no effect on the phosphorylation of DARPP-32, but it antagonized the decrease by 28% of dephospho-DARPP-32 induced by the D1 agonist SK&F-38393. In the denervated striatum of oxidopamine-lesioned rats, SPD decreased the amount of dephospho-DARPP-32 by 44%. The effect of SPD was completely counteracted by the concomitant administration of the D1 antagonist Sch-23390.

CONCLUSION

SPD exhibits D1 agonistic action on DARPP-32 phosphorylation in the denervated striatum of oxidopamine-lesioned rats, but it acts as a D1 antagonist in normal striatum.

In vitro and in vivo mechanical evaluations of plasma-sprayed hydroxyapatite coatings on titanium implants: the effect of coating characteristics

This study was undertaken to evaluate the effect of coating characteristics on the mechanical strengths of the plasma-sprayed HA-coated Ti-6Al-4V implant system both in vitro and in vivo. Two types of HA coatings (HACs) with quite different microstructures, concentrations of impurity-phases, and indices-of-crystallinity were used. In vitro testings were done by measuring the bonding-strength at the Ti-6Al-4V-HAC interface, with HACs that had and had not been immersed in a pH-buffered, serum-added simulated body fluid (SBF). The shear-strength at the HAC-bone interface was investigated in a canine transcortical femoral model after 12 and 24 weeks of implantation. The results showed a bonding degradation of approximately 32% or higher of the original strength after 4 weeks of immersion in SBF, and this predominantly depended on the constructed microstructure of the HACs. After the push-out measurements, it was demonstrated that the HACs with higher bonding-strength in vitro would correspondingly result in significantly higher shear-strength at each implant period in vivo. Nevertheless, there were no substantial histological variations between the two types of HACs evaluated. The most important point elucidated in this study was that, among coating characteristics, the microstructure was the key factor in influencing the mechanical stability of the HACs both in vitro and in vivo. As a consequence, a denser HAC was needed to ensure mechanical stability at both interfaces.