A Comparison of In Vitro Studies between Cobalt(III) and Copper(II) Complexes with Thiosemicarbazone Ligands to Treat Triple Negative Breast Cancer

Metal complexes have gained significant attention as potential anti-cancer agents. The anti-cancer activity of [Co(phen)2(MeATSC)](NO3)3•1.5H2O•C2H5OH 1 (where phen = 1,10-phenanthroline and MeATSC = 9-anthraldehyde-N(4)-methylthiosemicarbazone) and [Cu(acetylethTSC)Cl]Cl•0.25C2H5OH 2 (where acetylethTSC = (E)-N-ethyl-2-[1-(thiazol-2-yl)ethylidene]hydrazinecarbothioamide) was investigated by analyzing DNA cleavage activity. The cytotoxic effect was analyzed using CCK-8 viability assay. The activities of caspase 3/7, 9, and 1, reactive oxygen species (ROS) production, cell cycle arrest, and mitochondrial function were further analyzed to study the cell death mechanisms. Complex 2 induced a significant increase in nicked DNA. The IC50 values of complex 1 were 17.59 μM and 61.26 μM in cancer and non-cancer cells, respectively. The IC50 values of complex 2 were 5.63 and 12.19 μM for cancer and non-cancer cells, respectively. Complex 1 induced an increase in ROS levels, mitochondrial dysfunction, and activated caspases 3/7, 9, and 1, which indicated the induction of intrinsic apoptotic pathway and pyroptosis. Complex 2 induced cell cycle arrest in the S phase, ROS generation, and caspase 3/7 activation. Thus, complex 1 induced cell death in the breast cancer cell line via activation of oxidative stress which induced apoptosis and pyroptosis while complex 2 induced cell cycle arrest through the induction of DNA cleavage.

Structure of apo-azurin from Alcaligenes denitrificans at 1.8 A resolution

The structure of apo-azurin from Alcaligenes denitrificans has been determined at high resolution by X-ray crystallography. Two separate structure analyses have been carried out, (i) on crystals obtained from solutions of apo-azurin and (ii) on crystals obtained by removal of copper from previously formed crystals of holo-azurin. Data to 1.8 A resolution were collected from the apo-azurin crystals, by Weissenberg photography (with image plates) using synchrotron radiation and by diffractometry, and the structure was refined by restrained least-squares methods to a final R value of 0.160 for all data in the range 10.0-1.8 A. The final model of 1954 protein atoms, 246 water molecules (66 half-weighted), four SO(4)(2-) ions, and two low-occupancy (0.13 and 0.15) Cu atoms has r.m.s. deviations of 0.012, 0.045 and 0.013 A from standard bond lengths, angle distances and planar groups. For copper-removed azurin, data to 2.2 A were collected by diffractometry and the structure refined by restrained least squares to a final R value of 0.158 for all data in the range 10.0-2.2 A. The final model of 1954 protein atoms, 264 water molecules, two SO(4)(2-) ions, two low occupancy (0.18 and 0.22) metal atoms and one unidentified atom (modelled as S) has r.m.s. deviations of 0.013, 0.047 and 0.012 A from standard bond lengths, angle distances and planar groups. The two structures are essentially identical to each other and show no significant differences from the oxidized and reduced holo-azurin structures. The ligand side chains move slightly closer together following the removal of copper, with the radius of the cavity between the three strongly binding ligands, His 46, His 117 and Cys 112, shrinking from 1.31 A in reduced azurin to 1.24 A in oxidized azurin and 1.16 A in apo-azurin. There is a suggestion of increased flexibility in one of the copper-binding loops but the structure supports the view that the copper site found in holo-azurin is a stable structure, defined by the constraints of the polypeptide structure even in the absence of a bound metal ion.

Crystal structure and iron-binding properties of the R210K mutant of the N-lobe of human lactoferrin: implications for iron release from transferrins

Lactoferrin (Lf) and serum transferrin (Tf) combine high-affinity iron binding with an ability to release this iron at reduced pH. Lf, however, retains iron to significantly lower pH than Tf, giving the two proteins distinct functional roles. In this paper, we compared the iron-release profiles for human Lf, Tf, and their N-lobe half-molecules Lf(N) and Tf(N) and showed that half of the difference in iron retention at low pH ( approximately 1.3 pH units) results from interlobe interactions in Lf. To probe factors intrinsic to the N-lobes, we further examined the specific role of two basic residues that are proposed to form a pH-sensitive dilysine trigger for iron release in the N-lobe of Tf [Dewan, J. C., Mikami, B., Hirose, M., and Sacchettini, J. C. (1993) Biochemistry 32, 11963-11968] by mutating Arg 210 to Lys in the N-lobe half-molecule Lf(N). The R210K mutant was expressed, purified, and crystallized, and its crystal structure was determined and refined at 2.0-A resolution to a final R factor (R(free)) of 19.8% (25.0%). The structure showed that Lys 210 and Lys 301 in R210K do not form a dilysine interaction like that between Lys 206 and Lys 296 in human Tf. The R210K mutant retained iron to lower pH than Tf(N), consistent with the absence of the dilysine interaction but released iron at approximately 0.7 pH units higher than Lf(N). We conclude that (i) the ability of Lf to retain iron to significantly lower pH than Tf is due equally to interlobe interactions and to the absence in Lfs of an interaction analogous to the dilysine pair in Tfs, even when two lysines are present at the corresponding sequence positions, and (ii) an appropriately positioned basic residue (Arg 210 in human Lf) modulates iron release by inhibiting protonation of the N-lobe iron ligands, specifically His 253.

Glucocorticoid-remediable aldosteronism and pregnancy

Glucocorticoid-remediable aldosteronism (GRA) is a hereditary form of primary hyperaldosteronism that presents with hypokalemia and hypertension from childhood onward. GRA is characterized by the ectopic production of aldosterone in the cortisol-producing zona fasciculata under the regulation of adrenocorticotrophic hormone. Despite the early age of onset, no previous reports of pregnancy and GRA exist. Therefore, we set out to describe the maternal and fetal outcomes of pregnancy in women with GRA. Data regarding the blood pressure and pregnancy outcomes were collected in a retrospective chart review of prenatal and hospital records of 35 pregnancies in 16 women with genetically proven GRA. A total of 6% of pregnancies in women with GRA (GRA+) were complicated by preeclampsia. The published rates of preeclampsia in general obstetric populations vary from 2.5% to 10%. Despite the lack of an apparent increase in the rate of preeclampsia, GRA+ women with chronic hypertension had a high rate (39%) of pregnancy-aggravated hypertension. Starting with a higher baseline blood pressure, maternal blood pressure plotted over the time course of pregnancy followed a quadratic curve similar to that previously described in normal pregnancy. Mean gestational age at delivery was 39.1 weeks. Mean birth weight, excluding the 3 sets of twins, was 3219 g. However, infants of GRA+ mothers with pregnancy-aggravated hypertension tended to have lower birth weights than those that did not (3019 g versus 3385 g, respectively; P=0.08). The primary cesarean section rate was 32%, which is approximately double that seen in other general or hypertensive obstetric populations. In summary, GRA+ women did not seem to have an increased risk of preeclampsia. However, GRA+ women with chronic hypertension seem to be at an increased risk for an exacerbation of their hypertension during pregnancy.

The structure of the exo-beta-(1,3)-glucanase from Candida albicans in native and bound forms: relationship between a pocket and groove in family 5 glycosyl hydrolases

A group of fungal exo-beta-(1,3)-glucanases, including that from the human pathogen Candida albicans (Exg), belong to glycosyl hydrolase family 5 that also includes many bacterial cellulases (endo-beta-1, 4-glucanases). Family members, despite wide sequence variations, share a common mechanism and are characterised by possessing eight invariant residues making up the active site. These include two glutamate residues acting as nucleophile and acid/base, respectively. Exg is an abundant secreted enzyme possessing both hydrolase and transferase activity consistent with a role in cell wall glucan metabolism and possibly morphogenesis. The structures of Exg in both free and inhibited forms have been determined to 1.9 A resolution. A distorted (beta/alpha)8 barrel structure accommodates an active site which is located within a deep pocket, formed when extended loop regions close off a cellulase-like groove. Structural analysis of a covalently bound mechanism-based inhibitor (2-fluoroglucosylpyranoside) and of a transition-state analogue (castanospermine) has identified the binding interactions at the -1 glucose binding site. In particular the carboxylate of Glu27 serves a dominant hydrogen-bonding role. Access by a 1,3-glucan chain to the pocket in Exg can be understood in terms of a change in conformation of the terminal glucose residue from chair to twisted boat. The geometry of the pocket is not, however, well suited for cleavage of 1,4-glycosidic linkages. A second glucose site was identified at the entrance to the pocket, sandwiched between two antiparallel phenylalanine side-chains. This aromatic entrance-way must not only direct substrate into the pocket but also may act as a clamp for an acceptor molecule participating in the transfer reaction.

Crystal structure of hemopexin reveals a novel high-affinity heme site formed between two beta-propeller domains

The ubiquitous use of heme in animals poses severe biological and chemical challenges. Free heme is toxic to cells and is a potential source of iron for pathogens. For protection, especially in conditions of trauma, inflammation and hemolysis, and to maintain iron homeostasis, a high-affinity binding protein, hemopexin, is required. Hemopexin binds heme with the highest affinity of any known protein, but releases it into cells via specific receptors. The crystal structure of the heme-hemopexin complex reveals a novel heme binding site, formed between two similar four-bladed beta-propeller domains and bounded by the interdomain linker. The ligand is bound to two histidine residues in a pocket dominated by aromatic and basic groups. Further stabilization is achieved by the association of the two beta-propeller domains, which form an extensive polar interface that includes a cushion of ordered water molecules. We propose mechanisms by which these structural features provide the dual function of heme binding and release.

On the molecular-replacement problem in the presence of merohedral twinning: structure of the N-terminal half-molecule of human lactoferrin

The structure of a hemihedrally twinned protein crystal with two molecules in the asymmetric unit was solved by molecular replacement. The protein, a site-specific mutant of the N-terminal half-molecule of human lactoferrin, is able to undergo an internal rigid-body domain motion. Therefore, determining the structure required the independent positioning of four protein domains. The molecular-replacement solutions were obtained using a conventional real-space rotation function, and a translation function based on the linear correlation coefficient. Once the molecules were positioned, it was necessary to assign them to the appropriate twin domain. Several methods for doing this are described, one of which leads to a determination of the volume of each twin domain. In the appendix to the paper we discuss the interpretation of the self-rotation function in the presence of merohedral twinning.

Structure of human apolactoferrin at 2.0 A resolution. Refinement and analysis of ligand-induced conformational change

The three-dimensional structure of a form of human apolactoferrin, in which one lobe (the N-lobe) has an open conformation and the other lobe (the C-lobe) is closed, has been refined at 2.0 A resolution. The refinement, by restrained least-squares methods, used synchrotron radiation X-ray diffraction data combined with a lower resolution diffractometer data set. The final refined model (5346 protein atoms from residues 1-691, two Cl- ions and 363 water molecules) gives a crystallographic R factor of 0.201 (Rfree = 0. 286) for all 51305 reflections in the resolution range 10.0-2.0 A. The conformational change in the N-lobe, which opens up the binding cleft, involves a 54 degrees rotation of the N2 domain relative to the N1 domain. This also results in a small reorientation of the two lobes relative to one another with a further approximately 730 A2 of surface area being buried as the N2 domain contacts the C-lobe and the inter-lobe helix. These new contacts also involve the C-terminal helix and provide a mechanism through which the conformational and iron-binding status of the N-lobe can be signalled to the C-lobe. Surface-area calculations indicate a fine balance between open and closed forms of lactoferrin, which both have essentially the same solvent-accessible surface. Chloride ions are bound in the anion-binding sites of both lobes, emphasizing the functional significance of these sites. The closed configuration of the C-lobe, attributed in part to weak stabilization by crystal packing interactions, has important implications for lactoferrin dynamics. It shows that a stable closed structure, essentially identical to that of the iron-bound form, can be formed in the absence of iron binding.

Two high-resolution crystal structures of the recombinant N-lobe of human transferrin reveal a structural change implicated in iron release

The N-lobe of human serum transferrin (hTF/2N) has been expressed in baby hamster kidney cells and crystallized in both orthorhombic (P212121) and tetragonal (P41212) space groups. Both crystal forms diffract to high resolution (1.6 and 1.8 A, respectively) and have been solved by molecular replacement. Subsequent refinement resulted in final models for the structure of hTF/2N that had crystallographic R-factors of 18.1 and 19.7% for the two crystal forms, respectively; these models represent the highest-resolution transferrin structures determined to date. The hTF/2N polypeptide has a folding pattern similar to those of other transferrins, including the presence of a deep cleft that contains the metal-binding site. In contrast to other transferrins, both crystal forms of hTF/2N display disorder at the iron-binding site; model building suggests that this disorder consists of alternative conformations of the synergistically bound carbonate anion, the side chain for Arg-124, and several solvent molecules. Subsequent refinement revealed that conformation A has an occupancy of 0.63-0. 65 and corresponds to the structure of the iron-binding site found in other transferrins. The alternative conformation B has an occupancy of 0.35-0.37; in this structure, the carbonate has rotated 30 degrees relative to the iron and the side chain for Arg-124 has moved to accommodate the new carbonate position. Several water molecules appear to stabilize the carbonate anion in the two conformations. These structures are consistent with the protonation of the carbonate and resulting partial removal of the anion from the metal; these events would occur prior to cleft opening and metal release.

Intracranial aneurysm and hemorrhagic stroke in glucocorticoid-remediable aldosteronism

There are anecdotal reports of early cerebrovascular complications occurring in patients with glucocorticoid-remediable aldosteronism (GRA). The issue has never been systematically evaluated. In this study, we retrospectively reviewed the International Registry for GRA to see if there was an association between cerebrovascular complications and GRA. We searched the records of 376 patients from 27 genetically proven GRA pedigrees for premature death or cerebrovascular complications. Each case was subsequently verified through the referring physician, or autopsy reports. The number of complications occurring in patients with proven GRA were compared to GRA negative subjects from the same pedigrees. There were 18 cerebrovascular events in 15 patients with proven GRA (n=167) and none in the GRA negative group (n=194; P<.001). There were an additional 15 events in 15 subjects that were suspected of having GRA based on clinical history. Seventy percent of events were hemorrhagic strokes; the overall case fatality rate was 61%. The mean (+/- SD) age at the time of the initial event was 31.7+/-11.3 years. In total, 48% of all GRA pedigrees and 18% of all GRA patients had cerebrovascular complications, which is similar to the frequency of aneurysm in adult polycystic kidney disease. GRA is associated with high morbidity and mortality from early onset of hemorrhagic stroke and ruptured intracranial aneurysms. Screening for intracranial aneurysm with magnetic resonance angiography is advised for patients with genetically proven GRA.

Three-dimensional structure of diferric bovine lactoferrin at 2.8 A resolution

The three-dimensional structure of diferric bovine lactoferrin (bLf) has been determined by X-ray crystallography in order to investigate the factors that influence iron binding and release by transferrins. The structure was solved by molecular replacement, using the coordinates of diferric human lactoferrin (hLf) as a search model, and was refined with data to 2.8 A resolution by simulated annealing (X-PLOR) and restrained least squares (TNT). The final model comprises 5310 protein atoms (residues 5 to 689), 124 carbohydrate atoms (from ten monosaccharide units, in three glycan chains), 2 Fe3+, 2 CO32- and 50 water molecules. This model gives an R-factor of 0.232 for 21440 reflections in the resolution range 30.0 to 2.8 A. The folding of the bLf molecule is essentially the same as that of hLf, but bLf differs in the extent of closure of the two domains of each lobe, and in the relative orientations of the two lobes. Differences in domain closure are attributed to amino acid changes in the interface, and differences in lobe orientations to slightly altered packing of two hydrophobic patches between the lobes. Changed interdomain interactions may explain the lesser iron affinity of bLf, compared with hLf, and two lysine residues behind the N-lobe iron site of bLf offer new insights into the "dilysine trigger" mechanism proposed for iron release by transferrins. The bLf structure is also notable for several well-defined oligosaccharide units which demonstrate the structural factors that stabilise carbohydrate structure. One glycan chain, attached to Asn545, appears to contribute to interdomain interactions and may modulate iron release from the C-lobe.

Crystal structure of the streptococcal superantigen SPE-C: dimerization and zinc binding suggest a novel mode of interaction with MHC class II molecules

Bacterial superantigens are small proteins that have a very potent stimulatory effect on T lymphocytes through their ability to bind to both MHC class II molecules and T-cell receptors. We have determined the three-dimensional structure of a Streptococcal superantigen, SPE-C, at 2.4 A resolution. The structure shows that SPE-C has the usual superantigen fold, but that the surface that forms a generic, low-affinity MHC-binding site in other superantigens is here used to create a SPE-C dimer. Instead, MHC class II binding occurs through a zinc binding site that is analogous to a similar site in staphylococcal enterotoxin A. Consideration of the SPE-C dimer suggests a novel mechanism for promotion of MHC aggregation and T-cell activation.

Mutagenesis of the histidine ligand in human lactoferrin: iron binding properties and crystal structure of the histidine-253-->methionine mutant

The contribution of the conserved His ligand to iron binding in transferrins has been addressed by site-directed mutagenesis and X-ray crystallographic analysis. His 253 in the N-terminal half-molecule of human lactoferrin, LfN (residues 1-333), has been changed to Gly, Ala, Pro, Thr, Leu, Phe, Met, Tyr, Glu, Gln, and Cys by oligonucleotide-directed mutagenesis. The proteins have been expressed in baby hamster kidney cells, at high levels, and purified. The results show that the His ligand is essential for the stability of the iron binding site. All of the substitutions destabilized iron binding irrespective of whether the replacements were potential iron ligands or not. Iron was lost below pH approximately 6 for the Cys, Glu, and Tyr mutants and below pH 7 or higher for the others, compared with pH 5.0 for LfN. The destabilization is attributed to both steric and electronic effects. The importance of electronic effects has been shown by the crystal structure of the H253M mutant, which has been determined at an effective resolution of 2.5 A and refined to a final R factor of 0.173. The iron atom is changed from six-coordinate to five-coordinate; the Met 253 side chain is not bound to iron even though there appears to be no steric barrier. This is attributed to the poorer affinity of the thioether ligand for Fe(III) compared with imidazole nitrogen. The decreased stability of the iron binding is attributed solely to the loss of the His ligand as the protein conformation and interdomain interactions are unchanged.

Anion binding by transferrins: importance of second-shell effects revealed by the crystal structure of oxalate-substituted diferric lactoferrin

Proteins of the transferrin family bind, with high affinity, two Fe3+ ions and two CO3(2)- ions but can also bind other metal ions and other anions. In order to find out how the protein structure and its two binding sites adapt to the binding of larger anions, we have determined the crystal structure of oxalate-substituted diferric lactoferrin at 2.4 A resolution. The final model has a crystallographic R-factor of 0.196 for all data in the range 8.0-2.4 A. Substitution of oxalate for carbonate does not produce any significant change in the polypeptide folding or domain closure. Both binding sites are perturbed, however, and the effects are different in each. In the C-lobe site the oxalate ion is bound to iron in symmetric 1,2-bidentate fashion whereas in the N-lobe the anion coordination is markedly asymmetric. The difference arises because in each site substitution of the larger anion causes displacement of the arginine that forms one wall of the anion binding site; the movement is different in each case, however, because of different interactions with "second shell" amino acid residues in the binding cleft. These observations provide an explanation for the site inequivalences that accompany the substitution of non-native anions and cations.

Three-Dimensional Structure of Cytochrome c' from Two Alcaligenes Species and the Implications for Four-Helix Bundle Structures

The three-dimensional structures of two cytochromes c' have been determined in order to analyse the common features of proteins of this family and their relationship with other four-helix bundle structures. The structure of cytochrome c' from Alcaligenes sp was determined by molecular replacement supplemented with the iron anomalous scattering and the use of a single isomorphous heavy-atom derivative, and was refined using synchrotron data to 1.8 A resolution. The final model, comprising 956 protein atoms (one monomer) and 89 water molecules, has a final R value of 0.188 for all data in the range 20.0-1.8 A resolution (14 673 reflections). The structure of the cytochrome c' from Alcaligenes denitrificans is isomorphous and essentially identical (r.m.s. deviation for all atoms 0.36 A). Although its amino-acid sequence has not been determined chemically, only four differences from that of Alcaligenes sp cytochrome c' were identified by the X-ray analysis. The final model for Alcaligenes denitrificans cytochrome c', comprising 953 protein atoms and 75 water molecules, gave a final R factor of 0.167 for all data in the range 20.0-2.15 A (8220 reflections). The cytochrome c' monomer forms a classic four-helix bundle, determined by the packing of hydrophobic side chains around the enclosed haem group. There are very few cross-linking hydrogen bonds between the helices, the principal side-chain hydrogen bonding involving one of the haem propionates and a conserved Arg residue. The cytochrome c' dimer is created by a crystallographic twofold axis. Monomer-monomer contacts primarily involve the two A helices, with size complementarity of side chains in a central solvent-excluded portion of the interface and hydrogen bonding at the periphery. Both species have a pyroglutamic acid N-terminal residue. The haem iron is five-coordinate, 0.32 A out of the haem plane towards the fifth ligand, His120. The unusual magnetic properties of the Fe atom may be linked to a conserved basic residue, Arg124, adjacent to His120.

The crystal structure of a major secreted aspartic proteinase from Candida albicans in complexes with two inhibitors

BACKGROUND

Infections caused by Candida albicans, a common fungal pathogen of humans, are increasing in incidence, necessitating development of new therapeutic drugs. Secreted aspartic proteinase (SAP) activity is considered an important virulence factor in these infections and might offer a suitable target for drug design. Amongst the various SAP isozymes, the SAP2 gene product is the major form expressed in a number of C. albicans strains.

RESULTS

The three-dimensional structures of SAP2 complexed with the tight-binding inhibitor A70450 (a synthetic hexapeptide analogue) and with the general aspartic proteinase inhibitor pepstatin A (a microbial natural product) have been determined to 2.1 A and 3.0 A resolution, respectively. Although the protein structure retains the main features of a typical aspartic proteinase, it also shows some significant differences, due mainly to several sequence insertions and deletions (as revealed by homology modelling), that alter the shape of the binding cleft. There is also considerable variation in the C-terminal structural domain.

CONCLUSIONS

The differences in side chains, and in the conformations adopted by the two inhibitors, particularly at their P4, P3 and P'2 positions (using standard notation for protease-inhibitor residues), allows the A70450 structure to complement, more accurately, that of the substrate-binding site of SAP2. Some differences in the binding clefts of other SAP isoenzymes may be deduced from the SAP2 structure.

Structure of human diferric lactoferrin refined at 2.2 Å resolution

The three-dimensional structure of the diferric form of human lactoferrin has been refined at 2.2 A resolution, using synchrotron data combined with a lower resolution (3.2 A) diffractometer data set. Following restrained least-squares refinement and model rebuilding the final model comprises 5330 protein atoms (691 residues), 2Fe(3+) and 2CO(3)(2-) ions, 469 solvent molecules and 98 carbohydrate atoms (eight sugar residues). Root-mean-square deviations from standard geometry are 0.015 A for bond lengths and 0.038 A for angle (1-3) distances, and the final crystallographic R-factor is 0.179 for all 39 113 reflections in the resolution range 8.0-2.2 A. A close structural similarity is seen between the two lobes of the molecule, with differences mainly in loops and turns. The two binding sites are extremely similar, the only apparent differences being a slightly more asymmetric bidentate binding of the carbonate ion to the metal, and a slightly longer Fe-O bond to one of the Tyr ligands, in the N-lobe site relative to the C-lobe site. Distinct differences are seen in the interactions made by two cationic groups, Arg210 and Lys546, behind the iron site, and these may influence the stability of the two metal sites. Analysis of interdomain and interlobe interactions shows that these are few in number which is consistent with the known flexibility of the molecule with respect to domain and lobe movements. Internal water molecules are found in discrete sites and in two large clusters (in the two interdomain clefts) and one tightly bound water molecule is present 3.8 A from the Fe atom in each lobe. The carbohydrate is weakly defined and has been modelled to a limited extent; two sugar residues of the N-lobe glycan and six of the C-lobe glycan. Only one direct protein-carbohydrate contact can be found.

Use of iron anomalous scattering with multiple models and data sets to identify and refine a weak molecular replacement solution: structure analysis of cytochromec' from two bacterial species

The structure of cytochrome c' from two bacterial species, Alcaligenes sp and Alcaligenes denitrificans, have been determined from X-ray diffraction data to 3.0 A resolution using the anomalous scattering of the single Fe atom in each to identify and refine a weak molecular-replacement solution. Molecular-replacement studies, with the program AMORE, used two isomorphous data sets (from the two species), two independent search models (the cytochromes c' from Rhodospirillum molischianum and Rhodospirillum rubrum), both with and without side chains, and two different resolution ranges (10.0-4.0 and 15.0-3.5A) to generate a large number of potential solutions. No single solution stood out and none appeared consistently. The Fe-atom position in each structure was then determined from its anomalous-scattering contribution and all molecular- replacement solutions were discarded which did not (i) place the Fe atom correctly and (ii) orient the molecule such that a crystallographic twofold axis generated a dimer like those of the two search models. Finally, electron-density maps phased solely by the Fe-atom anomalous scattering were calculated. As these were combined and subjected to solvent flattening and histogram matching (with the program SQUASH), correlation with the remaining molecular-replacement solutions identified one as correct and enabled it to be improved and subjected to preliminary refinement. The correctness of the solution is confirmed by parallel isomorphous-replacement studies.

The three-dimensional structure of PNGase F, a glycosylasparaginase from Flavobacterium meningosepticum

BACKGROUND

Peptide:N-glycosidase F (PNGase F) is an enzyme that catalyzes the complete removal of N-linked oligosaccharide chains from glycoproteins. Often called an endoglycosidase, it is more correctly termed an amidase or glycosylasparaginase as cleavage is at the asparagine-sugar amide linkage. The enzyme is widely used in structure-function studies of glycoproteins.

RESULTS

We have determined the crystal structure of PNGase F at 1.8 A resolution. The protein is folded into two domains, each with an eight-stranded antiparallel beta jelly roll configuration similar to many viral capsid proteins and also found, in expanded form, in lectins and several glucanases. Two potential active site regions have been identified, both in the interdomain region and shaped by prominent loops from one domain. Exposed aromatic residues are a feature of one site.

CONCLUSIONS

The finding that PNGase F is based on two jelly roll domains suggests parallels with lectins and other carbohydrate-binding proteins. These proteins either bind sugars on the concave face of the beta-sandwich structure (aided by loops) or amongst the loops themselves. Further analysis of the function and identification of the catalytic site should lead to an understanding of both the specificity of PNGase F and possibly also the recognition processes that identify glycosylation sites on proteins.

Structure of copper- and oxalate-substituted human lactoferrin at 2.0 Å resolution

The three-dimensional structure of human dicupric monooxalate lactoferrin, Cu(2)oxLf, has been determined to 2.0 A resolution, using X-ray diffraction data collected by diffractometry to 2.5 A resolution, and oscillation photography on a synchrotron source to 2.0 A resolution. Difference electron-density maps calculated between Cu(2)oxLf and both dicupric lactoferrin, Cu(2)Lf, and diferric lactoferrin, Fe(2)Lf, showed that the oxalate had replaced a carbonate in the C-terminal binding site, and that, relative to Cu(2)Lf, there were no significant differences in the N-terminal site. The structure was then refined crystallographically by restrained least-squares methods. The final model, in which the r.m.s. deviation in bond distances is 0.017 A, contains 5314 protein atoms (691 residues), two Cu(2+) ions, one bicarbonate ion, one oxalate ion, 325 solvent molecules and one sugar residue. The crystallographic R factor of 0.193 is for 46 134 reflections in the range 8.0 to 2.0 A resolution. The oxalate ion is coordinated to copper in a 1,2-bidentate fashion, and the added bulk of the anion results in the rearrangement of the side chains of nearby arginine and tyrosine residues. No other major alterations in the molecule can be observed, the overall protein structure being the same as that for Cu(2)Lf and Fe(2)Lf.

Three-dimensional structure of lactoferrin in various functional states

The three-dimensional structures of various forms of lactoferrin, determined by high resolution crystallographic studies, have been compared in order to determine the relationship between structure and biological function. These comparisons include human apo and diferric lactoferrins, metal and anion substituted lactoferrins, the N-terminal half molecule of human lactoferrin, and bovine diferric lactoferrin. The structures themselves define the nature and location of the iron binding sites and allow anti-bacterial and putative receptor-binding regions to be mapped on to the molecular surface. The structural comparisons show that small internal adjustments can allow the accommodation of different metals and anions without altering the overall molecular structure, whereas large-scale conformational changes are associated with metal binding and release, and smaller, but significant, movements accompany species variations. The results also focus on differences in flexibility between the two lobes, and on the importance of interactions in the inter-lobe region in modulating iron release from the N-lobe and in possibly enabling binding at one site to be signalled to the other.

Domain closure in lactoferrin. Two hinges produce a see-saw motion between alternative close-packed interfaces

Lactoferrin is an iron transport protein. Upon binding iron, the two domains in the N-terminal half of the molecule move together. Previous work has shown that this domain closure involves two hinges. Using the newly refined structure of the open form, the structural mechanism underlying this motion is analyzed here in detail. Upon closure the domains rotate 54 degrees essentially as rigid bodies. The axis of rotation passes through the two beta-strands linking the domains. These strands contain hinges in the sense that three large torsion angle changes are responsible for the bulk of the motion while smaller torsion angle changes in neighboring residues are responsible for the remainder of the motion. The rotation axes of these three torsion angle changes are nearly parallel to the axis of the overall 54 degrees rotation, so the local motion in the hinges can be directly related to the overall motion. A crucial feature of the hinge residues is that they have very few packing constraints on their main-chain atoms. The domains make different packing contacts with each other in the open and closed forms. These contacts form two interdomain interfaces arranged on either side of the hinges. Pivoting about the hinges produces a see-saw motion between the two interfaces. That is, when the domains close down, residues in the interface on one side of the hinges become buried and close-packed and residues on the other side become exposed. The situation is reversed when the domains open up. Lactoferrin provides a particularly clear example of the general features of hinged domain motion. It is compared to other instances of hinged domain closure and contrasted with instances of shear domain closure, where the overall motion is a summation of many small sliding motions between close-packed segments of polypeptide.

Structure of the recombinant N-terminal lobe of human lactoferrin at 2.0 A resolution

The three-dimensional structure of the N-terminal half-molecule of human lactoferrin, LfN, prepared by recombinant DNA methods, has been determined by X-ray crystallography at 2.0 A resolution. The protein is in its iron-bound form and is deglycosylated. X-ray diffraction data were obtained by diffractometry to 3.2 A resolution and synchrotron data collection, using Weissenberg photography with imaging plates, to 1.8 A resolution. The structure was solved by molecular replacement, using the N-lobe of native diferric human lactoferrin (Lf) as search model. Restrained least squares refinement (program TNT) has resulted in a model structure with an R-factor of 0.184 for all data 34,180 (reflections) in the resolution range 8.0 to 2.0 A. The model comprises 2490 protein atoms (residues 4 to 327), 1 Fe3+, 1 CO3(2-) and 180 solvent molecules, all regarded as water. The structure of LfN is essentially the same as that of the N-lobe of intact Lf, being folded into two similar alpha/beta domains, with the Fe3+ and CO3(2-) bound in a specific site in the interdomain cleft. These details are not affected by either deglycosylation or expression in a non-native system. At the C terminus, however, the conformation of residues 321 to 333 is changed. Whereas in Lf residues 321 to 332 form a helix crossing between the domains at the back of the iron site, in LfN residues 321 to 326 have an extended conformation, forming a third interdomain beta-strand, and residues 328 to 333 appear disordered. The conformational change is attributed to the loss of stabilizing interactions from the C-lobe and is mediated by two Gly residues, at positions 321 and 323. It is further proposed that the conformational change is responsible for the more facile iron release properties of LfN, by its effect on the hinge mechanism and increased solvent exposure of residues near the back of the iron site. Other details of the polypeptide chain conformation and the binding site have also been analysed. Two cis-proline residues are found at positions 71 and 142. The bidentate binding of the CO3(2-) to the metal ion is unambiguous, and a network of hydrogen bonds in and around the binding site links the two domains. Clearly-defined amino-aromatic hydrogen bonds are found for Arg210, near the metal site, and some 31 internal water molecules have been identified, 15 of them in essentially discrete sites, and 16 in a cluster filling a cavity in the interdomain cleft.

Preliminary crystallographic studies of the amino terminal half of human lactoferrin in its iron-saturated and iron-free forms

The amino terminal half of human lactoferrin (LfN) produced from transfected baby hamster kidney cells has been crystallized in its iron-saturated and iron-free forms. The crystals of glycosylated LfN and deglycosylated LfN are monoclinic, space group C2, with cell dimensions a = 133.0 A, b = 58.3 A, c = 58.3 A, alpha = 90.0 degrees, beta = 114.7 degrees, gamma = 90.0 degrees, and one molecule per asymmetric unit. Crystals of apo LfN have also been prepared using deglycosylated protein. These crystals are tetragonal, space group P4(1)2(1)2 (or P4(3)2(1)2), with cell dimensions of a = b = 58.4 A and c = 217.2 A and one molecule per asymmetric unit. Both the iron-saturated and the iron-free crystals are suitable for high resolution X-ray analysis.

Metal substitution in transferrins: the crystal structure of human copper-lactoferrin at 2.1-A resolution

The structural consequences of binding a metal other than iron to a transferrin have been examined by crystallographic analysis of human copper-lactoferrin, Cu2Lf. X-ray diffraction data were collected from crystals of Cu2Lf, using a diffractometer, to 2.6-A resolution, and oscillation photography on a synchrotron source, to 2.1-A resolution. The structure was refined crystallographically, by restrained least-squares methods, starting with a model based on the isomorphous diferric structure from which the ligands, metal ions, anions, and solvent molecules had been deleted. The final model, comprising 5321 protein atoms (691 residues), 2 Cu2+ ions, 2 (bi)carbonate ions, and 308 solvent molecules has good stereochemistry (rms deviation of bond lengths from standard values of 0.018 A) and gives a crystallographic R value of 0.196 for 43,525 reflections in the range 7.5-2.1-A resolution. The copper coordination is different in the two binding sites. In the N-terminal site, the geometry is square pyramidal, with equatorial bonds to Asp 60, Tyr 192, His 253, and a monodentate anion and a longer apical bond to Tyr 92. In the C-terminal site, the geometry is distorted octahedral, with bonds to Asp 395, Tyr 435, Tyr 528, and His 597 and an asymmetrically bidentate anion. The protein structure is the same as for the diferric protein, Fe2Lf, demonstrating that the closure of the protein domains over the metal is the same in each case irrespective of whether Fe3+ or Cu2+ is bound and that copper could be transported and delivered to cells equally well as iron. The differences in metal coordination are achieved by small movements of the metal ion and anion within each binding site, which do not affect the protein structure.

Molecular replacement solution of the structure of apolactoferrin, a protein displaying large-scale conformational change

The crystal structure of an orthorhombic form of human apolactoferrin (ApoLf) has been determined from 2.8 A diffractometer data by molecular replacement methods. A variety of search models derived from the diferric lactoferrin structure (Fe2Lf) were used to obtain a consistent solution to the rotation function. An R-factor search gave the correct translational solution and the model was refined by rigid-body least-squares refinement (program CORELS). Only three of the four domains were located correctly by this procedure, however; the fourth was finally placed correctly by rotating it manually onto three strands of electron density which were recognized as part of its central beta-sheet. The final model, refined by restrained least-squares methods to an R factor of 0.214 for data in the resolution range 10.0 to 2.8 A, shows a large domain movement in the N-terminal half of the molecule (a 54 degree rotation of domain N2) and smaller domain movements elsewhere, when compared with Fe2Lf. A feature of the crystal structure is that although the ApoLf and Fe2Lf unit cells appear very similar, their crystal packing and molecular structures are quite different.

Structure, function and flexibility of human lactoferrin

X-ray structure analyses of four different forms of human lactoferrin (diferric, dicupric, an oxalate-substituted dicupric, and apo-lactoferrin), and of bovine diferric lactoferrin, have revealed various ways in which the protein structure adapts to different structural and functional states. Comparison of diferric and dicupric lactoferrins has shown that different metals can, through slight variations in the metal position, have different stereochemistries and anion coordination without any significant change in the protein structure. Substitution of oxalate for carbonate, as seen in the structure of a hybrid dicupric complex with oxalate in one site and carbonate in the other, shows that larger anions can be accommodated by small side-chain movements in the binding site. The multidomain nature of lactoferrin also allows rigid body movements. Comparison of human and bovine lactoferrins, and of these with rabbit serum transferrin, shows that the relative orientations of the two lobes in each molecule can vary; these variations may contribute to differences in their binding properties. The structure of apo-lactoferrin demonstrates the importance of large-scale domain movements for metal binding and release and suggests that in solution an equilibrium exists between open and closed forms, with the open form being the active binding species. These structural forms are shown to be similar to those seen for bacterial periplasmic binding proteins, and lead to a common model for the various steps in the binding process.

Apolactoferrin structure demonstrates ligand-induced conformational change in transferrins

Proteins of the transferrin family, which contains serum transferrin and lactoferrin, control iron levels in higher animals through their very tight (Kapp approximately 10(20)) but reversible binding of iron. These bilobate molecules have two binding sites, one per lobe, each housing one Fe3+ and the synergistic CO3(2-) ion. Crystallographic studies of human lactoferrin and rabbit serum transferrin in their iron-bound forms have characterized their binding sites and protein structure. Physical studies show that a substantial conformational change accompanies iron binding and release. We have addressed this phenomenon through crystal structure analysis of human apolactoferrin at 2.8 A resolution. In this structure the N-lobe binding cleft is wide open, following a domain rotation of 53 degrees, mediated by the pivoting of two helices and flexing of two interdomain polypeptide strands. Remarkably, the C-lobe cleft is closed, but unliganded. These observations have implications for transferrin function and for binding proteins in general.

Structure of human lactoferrin: crystallographic structure analysis and refinement at 2.8 A resolution

The structure of human lactoferrin has been refined crystallographically at 2.8 A (1 A = 0.1 nm) resolution using restrained least squares methods. The starting model was derived from a 3.2 A map phased by multiple isomorphous replacement with solvent flattening. Rebuilding during refinement made extensive use of these experimental phases, in combination with phases calculated from the partial model. The present model, which includes 681 of the 691 amino acid residues, two Fe3+, and two CO3(2-), gives an R factor of 0.206 for 17,266 observed reflections between 10 and 2.8 A resolution, with a root-mean-square deviation from standard bond lengths of 0.03 A. As a result of the refinement, two single-residue insertions and one 13-residue deletion have been made in the amino acid sequence, and details of the secondary structure and tertiary interactions have been clarified. The two lobes of the molecule, representing the N-terminal and C-terminal halves, have very similar folding, with a root-mean-square deviation, after superposition, of 1.32 A for 285 out of 330 C alpha atoms; the only major differences being in surface loops. Each lobe is subdivided into two dissimilar alpha/beta domains, one based on a six-stranded mixed beta-sheet, the other on a five-stranded mixed beta-sheet, with the iron site in the interdomain cleft. The two iron sites appear identical at the present resolution. Each iron atom is coordinated to four protein ligands, 2 Tyr, 1 Asp, 1 His, and the specific Co3(2-), which appears to bind to iron in a bidentate mode. The anion occupies a pocket between the iron and two positively charged groups on the protein, an arginine side-chain and the N terminus of helix 5, and may serve to neutralize this positive charge prior to iron binding. A large internal cavity, beyond the Arg side-chain, may account for the binding of larger anions as substitutes for CO3(2-). Residues on the other side of the iron site, near the interdomain crossover strands could provide secondary anion binding sites, and may explain the greater acid-stability of iron binding by lactoferrin, compared with serum transferrin. Interdomain and interlobe interactions, the roles of charged side-chains, heavy-atom binding sites, and the construction of the metal site in relation to the binding of different metals are also discussed.

Crystal and Molecular Structures of Two Isomorphous Solvates of the Macrolide Antibiotic Borrelidin: Absolute Configuration Determination by Incorporation of a Chiral Solvent in the Crystal Lattice

Crystal structures of two isomorphous solvates of the macrolide antibiotic borrelidin [ borrelidin 3-methylbutan-1-ol (A) and borrelidin (S)-2-methylbutan-1-ol (B)] have been determined from X-ray diffractometer data recorded at 294 and 152 K respectively. Crystals are monoclinic, space group P21, with a 13.501(2), b 12.000(2), c 11.863(2) � , β 110.76(1)� [(A); T = 294 K], and a 13.565(2), b 11.646(2), c 11 .376(3) �, β 109.76(1)� [(B); T = 152 K], (Z = 2). The structures were solved by direct-methods procedures and refined by full-matrix least-squares analysis to conventional R-factors of 0.061 [(A), 2676 reflections] and 0.048 [(B), 2851 reflections]. The absolute configuration of borrelidin follows from the known chirality of the (S)-2-methylbutan-1-ol solvent in (B), and is 3S,4S,6S,8R,1OS,11R,17S,18R,22R. The unusual structural and stereochemical features of borrelidin are discussed in relation to other macrolide antibiotics.

Structure of human lactoferrin at 3.2-A resolution

The three-dimensional structure of human milk lactoferrin, a member of the transferrin family, has been determined crystallographically at 3.2-A resolution. The molecule has two-fold internal homology. The N- and C-terminal halves form two separate globular lobes, connected by a short alpha-helix, and carry one iron-binding site each. Each lobe has the same folding, based on two domains of similar supersecondary structure, with the iron site at the domain interface. Each iron atom is coordinated by four protein ligands: two tyrosines, one histidine, and one aspartate. A probable CO3(2-) (or HCO3-) ion is suggested by the electron density, bound to iron and adjacent to an arginine side chain and a helix N terminus. The protein folding and location of the binding sites show marked similarities with those of other binding proteins, notably the sulfate-binding protein from Salmonella typhimurium.

Preliminary crystallographic studies on bovine lactoferrin

The purification of bovine lactoferrin, its crystallization at low ionic strength, and preliminary X-ray crystallographic data are reported. The crystals, which grow from a two-phase system, are radiation-stable and suitable for a medium-resolution X-ray analysis. They are orthorhombic, space group P2(1)2(1)2(1), with cell dimensions a = 138.4 A, b = 87.1 A, c = 73.6 A, and one protein molecule in the asymmetric unit.

The solution conformation of the peptide antibiotic thiostrepton: a 1H NMR study

The majority of the 84 protons in the 1H NMR spectrum of thiostrepton at 300 MHz were unambiguously assigned on the basis of double resonance experiments under different conditions of solvent, temperature and 2H-exchange by comparison with the known crystal structure determined by Anderson et al.1) Evidence is presented to suggest that the side chain, the nature of which remained undefined on X-ray analysis, is comprised of two dehydroalanine residues which supports the conclusions reached by Tori et al.2) on the basis of 13C NMR spectroscopy. These two residues are missing in thiostrepton A2, a minor artifact. All available 1H NMR evidence suggests thiostrepton to have a similar conformation in deuterochloroform solution to that found in the crystal form.

Structure of azurin from Alcaligenes denitrificans at 2.5 A resolution

The structure of the blue copper protein, azurin, from Alcaligenes denitrificans has been determined from an electron density map at a nominal resolution of 3.0 A. Four isomorphous heavy-atom derivatives, prepared with KAu(CN)2, uranyl acetate, Hg(NH3)2Cl2 and KAu(CN)2 + uranyl acetate (a double derivative) were used to calculate phases by the method of isomorphous replacement. The overall figure of merit was 0.61. The two molecules in the asymmetric unit are related by an approximate 2-fold axis. Independent interpretations of the density were made for the two molecules, and the structures have since been partially refined. After 12 refinement cycles, using the Hendrickson-Konnert restrained least-squares program, the R factor is 0.318 for data to 2.5 A resolution and there are no major conformational differences between the two molecules. Refinement is continuing. Eight extended strands of the polypeptide chain form a beta-barrel structure whose topology is the same as that of plastocyanin and the alternative folding proposed for Pseudomonas aeruginosa azurin. As in the latter two proteins, the copper atom forms three short bonds, with His-46 N delta 1, His117 N delta 1 and Cys112 S gamma, and one longer bond, with Met121 S delta, these four ligands forming a very distorted tetrahedron. A possible additional interaction, between copper and the carbonyl oxygen of Gly45, cannot be discounted at the present stage of the analysis. A surface hydrophobic patch, around the edge of the imidazole ring of His117 appears the most likely electron transfer locus. The sequences of azurin and plastocyanin have been aligned and the homology between the two proteins is discussed.

Synthetic plant growth regulators. V. The synthesis and crystal structure of a hybrid gibberellin-helminthosporic acid

(3aRS,4RS,6RS,8aSR)-5-Methyleneoctahydro-4H-3a,6-methanoazulene-4-carboxylic acid (7) has been synthesized and a detailed comparison made between its molecular structure and that of gibberellic acid (4). Indane-5-carboxylic acid (8) was converted by an alternating sequence of reduction and isomerization into the hydrindene acid (11). The diazomethyl ketone derived from (11) was transformed to cyclopropyl ketone (12) which was reduced by Li/NH3 with stereochemical inversion at the β-carbon to give a 1:3 mixture of ketones (13) and (14) respectively. Ketone (14) was then converted into the title acid (7) by a standard procedure. ��� Molecules of (7) crystallize in space group P2/c with a 7.782(1), b 11.055(1), c 14.559(3) Ǻ, β 116.05(1)°. The structure was solved by direct methods and refined by full-matrix least squares to a final R value of 0.053.