Structure of mouse L-chain ferritin at 1.6 A resolution.

Cubic F432 crystals of recombinant mouse L-chain apoferritin were obtained by the hanging-drop technique with ammonium sulfate and cadmium sulfate as precipitants. The structure was refined to 2.1 and 1.6 A resolution from data obtained at room temperature and under cryogenic conditions, respectively. The structure of an eight-amino-acid loop insertion in the mouse sequence is found to be highly disordered both at room temperature and at low temperature.

Initiation of DNA replication by DNA polymerases from primers forming a triple helix.

Despite extensive studies on oligonucleotide-forming triple helices, which were discovered in 1957, their possible relevance in the initiation of DNA replication remains unknown. Using sequences forming triple helices, we have developed a DNA polymerisation assay by using hairpin DNA templates with a 3' dideoxynucleotide end and an unpaired 5'-end extension to be replicated. The T7 DNA polymerase successfully elongated nucleotides to the expected size of the template from the primers forming triple helices composed of 9-14 deoxyguanosine-rich residues. The triple helix-forming primer required for this reaction has to be oriented parallel to the homologous sequence of the hairpin DNA template. Substitution of the deoxyguanosine residues by N7 deazadeoxyguanosines in the hairpin of the template prevented primer elongation, suggesting that the formation of a triple helix is a prerequisite for primer elongation. Furthermore, DNA sequencing could be achieved with the hairpin template through partial elongation of the third DNA strand forming primer. The T4 DNA polymerase and the Klenow fragment of DNA polymerase I provided similar DNA elongation to the T7 polymerase-thioredoxin complex. On the basis of published crystallographic data, we show that the third DNA strand primer fits within the catalytic centre of the T7 DNA polymerase, thus underlying this new property of several DNA polymerases which may be relevant to genome rearrangements and to the evolution of the genetic apparatus, namely the DNA structure and replication processes.

Influence of thermal motion on 1H chemical shifts in proteins: the case of bovine pancreatic trypsin inhibitor.

The possible influence of thermal motion on 1H chemical shifts is discussed for a small stable protein, the bovine pancreatic Kunitz trypsin inhibitor (BPTI). The thermal effects on the aromatic side chains and on the backbone are treated separately. The thermal motion of the aromatic side chains is accounted for in terms of their rotation around the C(alpha)-C(beta) bond and the motion of each individual proton is interpreted as a ratio between the amount of ordered and quite disordered states. The influence of hydrogen bonds is introduced as an extra contribution to the chemical shifts of the bonded proton. Their contribution to the chemical shifts resulting from the polarization of the peptide bond is investigated, as is their influence on local flexibility. Finally, the relative importance of each contribution to the chemical shift information is compared.

N-Terminal domain of HTLV-I integrase. Complexation and conformational studies of the zinc finger.

The HTLV-I integrase N-terminal domain [50-residue peptide (IN50)], and a 35-residue truncated peptide formed by residues 9-43 (IN35) have been synthesized by solid-phase peptide synthesis. Formation of the 50-residue zinc finger type structure through a HHCC motif has been proved by UV-visible absorption spectroscopy. Its stability was demonstrated by an original method using RP-HPLC. Similar experiments performed on the 35-residue peptide showed that the truncation does not prevent zinc complex formation but rather that it significantly influences its stability. As evidenced by CD spectroscopy, the 50-residue zinc finger is unordered in aqueous solution but adopts a partially helical conformation when trifluoroethanol is added. These results are in agreement with our secondary structure predictions and demonstrate that the HTLV-I integrase N-terminal domain is likely to be composed of an helical region (residues 28-42) and a beta-strand (residues 20-23), associated with a HHCC zinc-binding motif. Size-exclusion chromatography showed that the structured zinc finger dimerizes through the helical region.

Human T-lymphotrophic virus type I nucleocapsid protein NCp15: structural study and stability of the N-terminal zinc-finger.

An 18-residue peptide, corresponding to the minimum sequence of the N-terminal zinc-finger domain in the nucleocapsid of human T-lymphotrophic virus type I, was synthesized by a solid-phase method and fully characterized. Its ability to complex metal ions (Co(2+) and Zn(2+)) was clearly established by UV-visible spectroscopy and MS. The stability of these complexes was investigated by an original method with HPLC chromatography. Our results show that, even in the presence of air, the Zn(2+) complex is highly stable. In contrast, the Co(2+) complex undergoes a relatively fast degradation due to an intramolecular oxidation leading to the formation of a disulphide bridge between two cysteine residues. The (1)H-NMR analysis indicates that Zn(2+) binds to the Ndelta atom of the histidine residue rather than to the Nepsilon atom. Two-dimensional NMR techniques were used to determine the solution structure of the zinc-finger, illustrated by the existence of turns in the overall conformation.

Crystallization and preliminary X-ray diffraction data of mouse L-chain apoferritin crystals.

Crystals of recombinant mouse L-chain apoferritin were obtained by the hanging-drop technique using ammonium sulfate as precipitant. Two crystal forms were observed in the same drop. The crystals belong to either the P2 monoclinic or to the P42(1)2 tetragonal space group. The monoclinic crystals diffracted to beyond 2.4 A resolution but were systematically twinned, while the tetragonal crystals diffracted to beyond 2.9 A. These crystallization conditions in the absence of metal salts should facilitate the study of the interaction between L-chain ferritins and heavy metals, particularly the iron core.

Release of the cyano moiety in the crystal structure of N-cyanomethyl-N-(2-methoxyethyl)-daunomycin complexed with d(CGATCG).

Doxorubicin is among the most widely used anthracycline in cancer chemotherapy. In an attempt to avoid the cardiotoxicity and drug resistance of doxorubicin therapy, several analogues were synthesized. The cyanomorpholinyl derivative is the most cytotoxic. They differ greatly from their parent compound in their biological and pharmacological properties, inducing cross-links in drug DNA complexes. The present study concerns N-cyanomethyl-N-(2-methoxyethyl)-daunomycin (CMDa), a synthetic analogue of cyanomorpholino-daunomycin. Compared to doxorubicin, CMDa displays a cytotoxic activity on L1210 leukemia cells at higher concentration but is effective on doxorubicin resistant cells. The results of fluorescence quenching experiments as well as the melting temperature (DeltaTm = 7.5 degrees C) studies are consistent with a drug molecule which intercalates between the DNA base pairs and stabilizes the DNA double helix. The crystal structure of CMDa complexed to the hexanucleotide d(CGATCG) has been determined at 1.5 A resolution. The complex crystallizes in the space group P41212 and is similar to other anthracycline-hexanucleotide complexes. In the crystal state, the observed densities indicate the formation of N-hydroxymethyl-N-(2-methoxyethyl)-daunomycin (HMDa) with the release of the cyano moiety without DNA alkylation. The formation of this degradation compound is discussed in relation with other drug modifications when binding to DNA. Comparison with two other drug-DNA crystal structures suggests a correlation between a slight change in DNA conformation and the nature of the amino sugar substituents at the N3' position located in the minor groove.

Expression, purification, crystallization and preliminary X-ray diffraction results from Campylobacter jejuni ferritin.

The prokaryotic ferritin gene of Campylobacter jejuni was overexpressed in Escherichia coli under control of the bacteriophage T7 promoter and the protein (Cj-FTN) purified. Preliminary crystallization experiments have been performed using the hanging-drop vapour-diffusion method with ammonium sulfate as the precipitant. Diffraction studies show the crystals belong to the I432 space group (a = 151.52 A). Structure solution by molecular replacement is in progress while crystal quality improvement is carried out.

Structure of a monoclinic crystal from of cyctochrome b1 (Bacterioferritin) from E. coli.

Crystals of E. coli cytochrome b1, alias bacterioferritin, were grown fr om a low ionic strength solution. The resulting monoclniic P21 structure was solved by molecular replacement and refined using noncrystallographi c symmetries applied to the fundamental unit, consisting of two protein subunits and a single haem. From the Patterson self-rotation results it was shown that the asymmetric unit of the monoclinic crystal consists of 12 such dimers and corresponds to a complete, nearly spherical, molecule of bacterioferritin (M4 = 450 kDa) of 432 point-group symmetry. It is thus the most symmetrical cytochrome. As previously determined for the tetragonal form, the haem is located in a special position on a local twofold axis of the dimer. A bimetal centre is also observed within the four-helix bundle of each monomer; a metal-binding site is located on the fourfold axis.

Expression, purification, crystallization and preliminary X-ray diffraction analysis of human uroporphyrinogen decarboxylase.

A recombinant human uroporphyrinogen decarboxylase (E.C. 4.1.1.37, UROD) has been expressed in Escherichia coli and purified to homogeneity. Crystals grew by the hanging-drop vapor-diffusion technique from a starting solution containing 1.5 mg ml-1 protein. The crystals belong to the trigonal space group P3121 or its enantiomer P3221 and diffract to 3 A resolution. The unit-cell parameters are a = b = 103.4, c = 75.7 A and gamma = 120 degrees. The asymmetric unit contains one molecule. Preliminary structural predictions suggest for the protein a TIM-barrel type tertiary structure.

Evidence of new cadmium binding sites in recombinant horse L-chain ferritin by anomalous Fourier difference map calculation.

We refined the structure of the tetragonal form of recombinant horse L-chain apoferritin to 2.0 A and we compared it with that of the cubic form previously refined to the same resolution. The major differences between the two structures concern the cadmium ions bound to the residues E130 at the threefold axes of the molecule. Taking advantage of the significant anomalous signal (f" = 3.6 e-) of cadmium at 1.375 A, the wavelength used here, we performed anomalous Fourier difference maps with the refined model phases. These maps reveal the positions of anomalous scatterers at different locations in the structure. Among these, some are found near residues that were known previously to bind metal ions, C48, E57, C126, D127, E130, and H132. But new cadmium binding sites are evidenced near residues E53, E56, E57, E60, and H114, which were suggested to be involved in the iron loading process. The quality of the anomalous Fourier difference map increases significantly with noncrystallographic symmetry map averaging. Such maps reveal density peaks that fit the positions of Met and Cys sulfur atoms, which are weak anomalous scatterers (f" = 0.44 e-).

Remarkable ability of horse spleen apoferritin to demetallate hemin and to metallate protoporphyrin IX as a function of pH.

In previous studies it has been shown that reaction of crystalline horse spleen apoferritin with hemin leads to a protoporphyrin IX-apoferritin complex [Précigoux et al. (1994) Acta Crystallogr. D50, 739-743]. We show here the following. (i) Hemin binds to two classes of sites in horse spleen apoferritin at pH 8, each with a binding stoichiometry of 0.5 hemin/subunit; protoporphyrin IX also binds to horse spleen apoferritin with an apparent binding stoichiometry of 1 molecule of protoporphyrin IX/subunit. (ii) When Fe(III)-protoporphyrin IX binds to apoferritin, there is a pH-dependent loss of the metal ion, extremely slow at alkaline pH values (half-time of weeks) and much more rapid at acidic pH values (half-time of seconds below pH 5.0); maximum rates of demetallation are found at pH 4.0, and at lower pH values they decrease. (iii) Chemical modification of 11 carboxyl groups/subunit in horse spleen apoferritin does not affect hemin binding at alkaline pH values; however, it prevents hemin demetallation at acidic pH values. (iv) Hemin that has been demetallated at acidic pH values can be remetallated by increasing the pH; the rate of remetallation is greater at more alkaline pH values. (v) When around 20 atoms of iron/molecule are incorporated into horse spleen apoferritin and protoporphyrin IX is then bound, iron can subsequently be transferred to the porphyrin at pH 8.0. A mechanism is proposed to explain demetallation of heme, involving attack on the tetrapyrrole nitrogens of the protoporphyrin IX-Fe by protons derived from protein carboxylic acid groups and subsequent complexation of the iron by the corresponding carboxylates and binding of protoporphyrin IX to a preformed pocket in the inner surface of the apoferritin protein shell. The cluster of carboxylates involved is situated at the entrance to the pocket in which the protoporphyrin IX molecule is bound and has been previously identified as the site of iron incorporation into L-chain apoferritins. This appears to be the first example of iron removal and incorporation into porphyrins under relatively mild physiological conditions.

Comparison of the structures of the cubic and tetragonal forms of horse-spleen apoferritin.

Horse-spleen apoferritin is known to crystallize in three different space groups, cubic F432, tetragonal P42(1)2 and orthorhombic P2(1)2(1)2. A structure comparison of the cubic and tetragonal forms is presented here. Both crystal forms were obtained by the vapor-diffusion technique and data were collected at 2.26 A (cubic crystal) and 2.60 A (tetragonal crystal) resolution. Two main differences were observed between these crystal structures: (i) whereas intermolecular contacts only involve salt-bridge type interactions via cadmium ions in the cubic structure, two types of interactions are observed in the tetragonal crystal (cadmium-ion-mediated salt bridges and hydrogen-bonding interactions) and (ii) cadmium ions bound in the threefold axes of ferritin molecules exhibit lower site-occupation factors in the tetragonal structure than in the cubic one.

Parallel and antiparallel (G.GC)2 triple helix fragments in a crystal structure.

Nucleic acid triplexes are formed by sequence-specific interactions between single-stranded polynucleotides and the double helix. These triplexes are implicated in genetic recombination in vivo and have application to areas that include genome analysis and antigene therapy. Despite the importance of the triple helix, only limited high-resolution structural information is available. The x-ray crystal structure of the oligonucleotide d(GGCCAATTGG) is described; it was designed to contain the d(G middle dotGC)2 fragment and thus provide the basic repeat unit of a DNA triple helix. Parameters derived from this crystal structure have made it possible to construct models of both parallel and antiparallel triple helices.

Formation of (C.G)*G triplets in a B-DNA duplex with overhanging bases.

Crystallization of a DNA double helix with overhanging bases at the 5'-ends of both strands, results in the formation of two crystallographically independent (C.G)*G triplets. In a previous report [Van Meervelt, Vlieghe, Dautant, Gallois, Précigoux & Kennard (1995). Nature (London), 374, 742-744] the unique molecular packing of the duplex and the Hoogsteen hydrogen-bond pattern and parallel backbone orientation of the guanine-containing strands in the triplets was described. The fine structural details and hydration of the d(GCGAATTCG) crystal structure refined to 2.05 A (R = 0.168, 86 water molecules, two Mg(2+) cations) are now presented. Helical parameters, stacking effects, the geometry at the duplex-triplex junction, and the hydration of the minor groove are discussed and compared with related theoretical and crystal structures.

Preliminary X-ray diffraction studies of the tetragonal form of native horse-spleen apoferritin.

Horse-spleen ferritin is known to crystallize in three different space groups, cubic F432, orthorhombic P2(1)2(1)2 and tetragonal P42(1)2, but only the cubic form has been fully investigated. Crystals of the tetragonal form of apoferritin have been obtained, by the vapour-diffusion technique, which diffract beyond 3.0 A. The unit-cell dimensions are a = b = 146.63, c = 152.94 A. The orientation of the non-crystallographic symmetry axes of the apoferritin molecule (24 subunits of 174 amino acids each, arranged in a 432 point symmetry rhombododecahedron) has been determined by a self-rotation Patterson function. The asymmetric unit is made of six subunits and was positioned by molecular replacement.

Crystallization and preliminary X-ray analysis of an orthorhombic form of horse-spleen apoferritin.

Horse-spleen apofemtin crystallizes in two different space groups: cubic F432 and tetragonal P42(1)2 while its iron-containing analogue is known to present a cubic and an orthorhombic form. Up to now, only the structure of the cubic form has been fully investigated by X-ray diffraction, although some information concerning the molecular packing of the two other forms was deduced from analysis of X-ray photographs. While growing cubic crystals of horse-spleen apoferritin with Pt-mesoporphyrin IX, we obtained one crystal, with a diffraction limit of 2.4 A, belonging to the orthorhombic P2(1)2(1)2 space group, with unit-cell dimensions a = 181.6, b = 128.9, c = 128.9 A. The orientation of the non-crystallographic axes of the molecule was determined by self-rotation Patterson function and the structure was determined by the molecular-replacement method. The asymmetric unit consists of half an apoferritin molecule. Refinement of the structure is in progress, some preliminary results of the molecular packing are given.

Structural investigation of the complexation properties between horse spleen apoferritin and metalloporphyrins.

Crystallographic studies of L-chain horse spleen apoferritin (HSF) co-crystallized with Pt-hematoporphyrin IX and Snprotoporphyrin IX have brought significant new insights into structure-function relationships in ferritins. Interactions of HSF with porphyrins are discussed. Structural results show that the nestling properties into HSF are dependent on the porphyrin moiety. (Only protoporphyrin IX significantly interacts with the protein, whereas hematoporphyrin IX does not.) These studies additionally point out the L-chain HSF ability to demetalate metalloporphyrins, a result which is of importance in looking at the iron storage properties of ferritins. In both compound investigated (whether the porphyrin reaches the binding site or not), the complexation appears to be concomitant with the extraction of the metal from the porphyrin. To analyze further the previous results, a three-dimensional alignment of ferritin sequences based on available, crystallographic coordinates, including the present structures, is given. It confirms a high degree of homology between these members of the ferritin family and thus allows us to emphasize observed structural differences: 1) unlike L-chain HSF, H-chain human ferritin presents no preformed binding site; and 2) despite the absence of axial ligands, and due to the demetalation, L-chain HSF is able to host protoporphyrin at a similar location to that naturally found in bacterioferritin.

Chemical synthesis of a 7 kDa insect gonadotropic neurohormone.

An original insect neurohormone of 65 residues was synthesized by the solid-phase methodology using t-Boc strategy and Boc-Val-PAM-resin. The purification, conducted by several steps of liquid chromatography having mass, polarity or charge as separative criteria, yielded the product with the correct molecular weight of 6922 Da determined by mass spectrometry. The synthetic peptide had both the same affinity for the anti-native neurohormone serum and the same biological activity as the native neurohormone.

High-resolution structure of a DNA helix forming (C.G)*G base triplets.

Triple helices result from interaction between single- and double-stranded nucleic acids. Their formation is a possible mechanism for recombination of homologous gene sequences in nature and provides, inter alia, a basis for artificial control of gene activity. Triple-helix motifs have been extensively studied by a variety of techniques, but few high-resolution structural data are available. The only triplet structures characterized so far by X-ray diffraction were in protein-DNA complexes studied at about 3 A resolution. We report here the X-ray analysis of a DNA nonamer, d(GCGAATTCG), to a resolution of 2.05 A, in which the extended crystal structure contains (C.G)*G triplets as a fragment of triple helix. The guanosine-containing chains are in a parallel orientation. This arrangement is a necessary feature of models for homologous recombination which results ultimately in replacement of one length of DNA by another of similar sequence. The present-structure agrees with many published predictions of triplex organization, and provides an accurate representation of an element that allows sequence-specific association between single- and double-stranded nucleic acids.