Destabilizing effect of a fluorouracil extra base in a hybrid RNA duplex compared with bromo and chloro analogues.

In the presence of cobalt, rhodium or iridium hexammine salts, the RNA/DNA hybrid r-GCUUCGGC-d(X)U (with X = F, Cl or Br) crystallizes as a double-stranded helix with four consecutive G-U and C-U mismatches. The deoxy chloro- and bromouracil derivatives are isomorphous, space group C2, unit-cell parameters a = 53.80, b = 19.40, c = 50.31 A, beta = 109.9 degrees, with the same infinite helix arrangement in the packing along the c axis with one extra DNA halogenouracil base included in the stacking. However, the fluorouracil derivative, with unit-cell parameters a = 53.75, b = 19.40, c = 45.84 A, beta = 105.7 degrees, is not isomorphous. The corresponding extra DNA base d(F)U of the second strand is ejected out of the helical stack, leading to a shortening of the c axis. The specific destabilization of the fluorouracil for the duplex building is analyzed in terms of the polarization effect of the halogen atom attached to the 3'-terminal base that modulates its interactions.

Molecular structure of the lipoamide dehydrogenase domain of a surface antigen from Neisseria meningitidis.

The protein p64k from the surface of the Neisseria meningitidis bacteria has been characterized as a two-domain protein. It contains a dihydrolipoamide dehydrogenase domain of 482 residues, involving a FAD prosthetic group as a cofactor, and a smaller lipoic acid binding domain of 86 residues. The two domains are joined by a flexible segment rich in alanine and proline residues. The structure of the dihydrolipoamide dehydrogenase domain was determined by X-ray diffraction. It was solved by a combination of molecular replacement and multiple isomorphous replacement techniques and refined to 2.7 A resolution. In the crystal, the recombinant p64k mimics the functional homo-dimer by using one of the crystallographic 2-fold axes. The reactive disulphide bridge Cys161-Cys166 is in the oxidised state and the FAD is bound in an extended conformation. This main domain contains the major antigenic determinant of the protein, an extended loop of 32 residues at the surface of the protein. A mis-attribution at residue 553 in the sequence has been detected by inspection of electron density maps and the geometry. However, when compared to the other dihydrolipoamide dehydrogenases, there are some significant differences: (1) an unusual number of cis-proline residues and (2) a new motif built around a 2-fold axis by the sulphur atoms of residues Met558, Cys560 and their symmetry related equivalents.

A continuous transition from A-DNA to B-DNA in the 1:1 complex between nogalamycin and the hexamer dCCCGGG.

The antibiotic nogalamycin, a drug with high specificity for TG and CG steps in double-stranded DNA, has been crystallized as a 1:1 complex with the hexamer d(CCCGGG). The antibiotic is inserted at the central CG step of the duplex, with the two sugars oriented in the same direction and with strong interactions with the DNA within the grooves. The amino-glucose residue makes an integral part of a well defined major groove hydration network with van der Waals contacts and several strong hydrogen bonds to the duplex. The nogalose residue resides in the minor groove, making primarily van der Waals contacts. The single site allows an accurate molecular description of the intercalation, without perturbations from end effects observed previously. The local unwinding induced by nogalamycin is completely relaxed 2 base pairs away from the intercalation site. The two strands of the DNA show a continuous deformation from the A to the B form: 1) the cytosines toward the 5' end of the nogalomycin site in each strand have c3'-endo conformations while 5 guanosines toward the 3' ends have c2'-endo conformations; 2) within each strand, the phosphate-phosphate distances increase in a continuous manner from 5.7 A (A-form) to 7.1 A (B-form).

The 1.6 A structure of Kunitz-type domain from the alpha 3 chain of human type VI collagen.

The C-terminal Kunitz-type domain from the alpha 3 chain of human type VI collagen (C5), a single 58 amino acid residue chain with three disulfide bridges, was cloned, expressed and crystallized in a monoclonic form, space group P2(1), with a = 25.7 A, b = 38.2 A, c = 28.8 A and beta = 109 degrees. The structure was resolved by molecular replacement, using Alzheimer's protein precursor inhibitor and bovine pancreatic trypsin inhibitor three-dimensional structures as search models. The molecule with one sulfate ion and 43 associated water molecules was refined by XPLOR to an R-factor of 18.9% at 1.6 A. The molecule was not degraded by trypsin and did not inhibit trypsin or tested serine proteases. As opposed to the other Kunitz family members, C5 demonstrates left-handed chirality of the Cys14-Cys38 disulfide bond. Inversion of the Thr13 carbonyl and bulky side-chains at the interface with trypsin in a model of the C5-trypsin complex may explain the lack of inhibition of trypsin.

Structure of a mispaired RNA double helix at 1.6-A resolution and implications for the prediction of RNA secondary structure.

The nonamer r(GCUUCGGC)dBrU, where dBrU is 5-bromo-2'-deoxyuridine, contains the tetraloop sequence UUCG. It crystallizes in the presence of Rh(NH3)6Cl3. In solution the oligomer is expected to form a hairpin loop but the x-ray structure analysis, to a resolution of 1.6 A, indicates an eight-base-pair A-RNA duplex containing a central block of two G.U and two C.U pairs. Self-pairs which approximate to Watson-Crick geometry are also formed in the extended crystal structure between symmetry-related BrU residues and are part of infinite double-helical stacks. The G.U pair is a wobble base pair analogous to the G.T pair found in DNA fragments. The C.U mismatch involves one hydrogen-bonded contact between the bases and a bridging water molecule which ensures a good fit of the base pair in the RNA helix. The BrU.BrU pair is held by two hydrogen bonds in an orientation which is compatible with duplex geometry. The structure observed within the crystal has some parallels with the structure of globular RNAs, and the presence of stable, noncanonical base pairs has implications for the prediction of RNA secondary structure.

Crystal structure of a catalytic antibody Fab with esterase-like activity.

BACKGROUND: Antibodies with catalytic properties can be prepared by eliciting an antibody response against 'transition state analog' haptens. The specificity, rate and number of reaction cycles observed with these antibodies more closely resemble the properties of enzymes than any of the many other known enzyme-mimicking systems. RESULTS: We have determined to 3 A resolution the first X-ray structure of a catalytic antibody Fab. This antibody catalyzes the hydrolysis of a p-nitrophenyl ester. In conjunction with binding studies in solution, this structure of the uncomplexed site suggests a model for transition state fixation where two tyrosines mimic the oxyanion binding hole of serine proteases. A comparison with the structures of known Fabs specific for low molecular weight haptens reveals that this catalytic antibody has an unusually long groove at its combining site. CONCLUSION: Since transition state analogs contain elements of the desired product, product inhibition is a severe problem in antibody catalysis. The observation of a long groove at the combining site may relate to the ability of this catalytic antibody to achieve multiple cycles of reaction.

Structure determination of a dimeric form of erabutoxin-b, crystallized from a thiocyanate solution.

Erabutoxin-b, M(r) = 6861.1, a single 62 amino-acid chain folded by four disulfide bridges, was crystallized in a new orthorhombic form by using thiocyanate as crystallizing agent. The space group is P2(1)2(1)2(1) with a = 53.36 (4), b = 40.89 (4), c = 55.71 (5) A, V = 121533.1 A and Z = 8. X-ray diffraction data were recorded at the LURE synchrotron facility (lambda = 1.405 A). The structure was solved by molecular replacement and shows a dimeric association through an anti-parallel beta-sheet around the twofold non-crystallographic axis. The two independent molecules, one SCN- ion and 97 associated water molecules were refined by molecular dynamics and annealing techniques to R = 19.6% (10,913 Fobs, resolution 5-1.7 A). The thiocyanate ion is located at the interface of the dimer and close to the non-crystallographic twofold axis.

Three-dimensional structure of Fab R19.9, a monoclonal murine antibody specific for the p-azobenzenearsonate group.

The crystal structure of Fab R19.9, derived from an anti-p-azobenzenearsonate monoclonal antibody, has been determined and refined to 2.8-A resolution by x-ray crystallographic techniques. Monoclonal antibody R19.9 (IgG2b kappa) shares some idiotopes with a major idiotype (CRIA) associated with A/J anti-p-azobenzenearsonate antibodies. The amino acid sequences of the variable (V) parts of the heavy (VH) and light (VL) polypeptide chains of monoclonal antibody R19.9 were determined through nucleotide sequencing of their mRNAs. The VL region is very similar to that of CRIA-positive anti-p-azobenzenearsonate antibodies as is VH, except for its third complementarity-determining region, which is three amino acids longer; it makes a loop, unique to R19.9, that protrudes into the solvent. A large number of tyrosine residues in the complementarity-determining region of VH and VL, with their side chains pointing towards the solvent, may have an important function in antigen binding.

X-ray diffraction studies of an anti-azophenylarsonate antibody and of an antigen-antibody complex.

X-ray crystallographic studies of the Fab fragments of two murine monoclonal antibodies of predefined specificity are under way. Diffracted X-ray intensities of the crystalline native Fab fragment of an anti-azophenylarsonate antibody and of three heavy atom derivatives have been measured to a resolution of 3.5 A. A preliminary 6-A resolution electron density map has been obtained. The 6-A resolution structure of an antigen-antibody (hen lysozyme-Fab) complex has been determined. There are close contacts between the antigen and the antibody over a large contact area, about 20 X 25 A. At least two segments of the polypeptide chain of lysozyme, of about 10 amino acids each (positions 19-27 and 116-129), are involved in the contacts, as well as all six complementarity-determining regions of the antibody. No gross conformational changes are observed in the antigen at this resolution, although there are some smaller local changes in areas in contact with the antibody and elsewhere. The effects of amino acid substitutions on antigen recognition by the monoclonal anti-hen lysozyme antibody were investigated using different, closely related lysozymes. These effects can be readily explained in terms of the three-dimensional model presented here. A 3.5-A resolution electron density map has been calculated and is currently under study.

Crystallization of the fab fragments of monoclonal anti-p-azophenylarsonate antibodies and their complexes with haptens.

We report on the preparation, crystallization, and preliminary x-ray crystallographic study of Fab fragments from monoclonal anti-p-azophenylarsonate antibodies. Several crystalline forms were obtained with the Fab fragment from the R19.9 monoclonal antibody as well as with the complex between the hapten p-aminobenzenearsonic acid and Fab R19.9. The crystals of this hapten-Fab complex are similar to but not always isomorphous with the native Fab crystals. All the native and complex crystals were obtained using polyethylene glycol 6000 as crystallizing agent. Some of these crystalline forms diffract to a 2-A resolution or beyond and are suitable for high resolution x-ray diffraction analysis. A possible interpretation of hapten binding to crystalline Fab fragments from R19.9 and from the R9.3 monoclonal anti-p-azophenylarsonate antibody, implying conformational changes, is discussed.

Preliminary crystallographic study of the complex between the Fab fragment of a monoclonal anti-lysozyme antibody and its antigen.

Preliminary crystallographic data are given for the complex between the Fab fragment of a monoclonal anti-lysozyme antibody and its antigen. This crystalline complex was found by screening a number of Fab-lysozyme complexes prepared from monoclonal anti-lysozyme antibodies produced by hybrids of BALB/c immune spleen cells with a non-secreting mouse hybrid myeloma line. The complex crystallizes in the monoclinic space group P21 with a = 55.5 (+/- 0.1) A, b = 143.5 (+/- 0.3) A, c = 49.1 (+/- 0.1) A, beta = 120 degrees 20' (+/- 10'). X-ray photographs show reflections extending to a resolution of 2.7 A. The crystals are suitable for high-resolution X-ray diffraction studies.

Preliminary crystallographic study of the Fab fragment of a monoclonal anti-phenylarsonate antibody.

Preliminary crystallographic data are given for the Fab fragment of a monoclonal anti-p-phenylarsonate antibody. This crystalline Fab fragment was found by screening a number of monoclonal anti-arsonate antibodies obtained from hybrids of A/J immune spleen cells with a non-secreting mouse myeloma line. The protein crystallizes in the monoclinic space group P21 with a = 86.2 +/- 0.1 A, b = 80.4 +/- 0.2 A, c = 75.8 +/- 0.1 A, beta = 90.3 +/- 0.1 degrees. Precession photographs show X-ray reflections extending to a resolution of 3 A.

Structure of the body-centered cubic phase of lipid systems.

A new model is proposed for the structure of the body-centered cubic phase of lipid systems. Infinite rods of polar groups (and water) are arranged with axes parallel to the four cubic [unk]1 1 1[unk] directions. The hydrocarbon chains fill the space between the rods to form a continuous matrix. With this unified topology, the model explains satisfactorily the x-ray diffraction patterns of strontium soaps, lecithin, galactolipids, potassium soaps, and hexadecyltrimethylammonium bromide and explains the transition between cubic/H(II) phases. The paradoxical thermal effects on the lipid cubic phase, in particular the decrease of unit cell dimensions with increasing temperature, can be explained with the proposed model by mechanisms similar to those used for the monodimensional and bidimensional (mesomorphic) phases.