Expression, characterization and crystallization of the Fv fragment of mouse antibody 3B62 from the secondary immune response.

Affinity of antibodies increases in the course of the immune response. Mouse anti-nitrophenol antibody 3B62 from the secondary immune response shows higher affinity than the primary-response antibodies. An expression system for the 3B62 Fv fragment was constructed by introducing coding regions for the V(L) and V(H) into the genome of the methylotrophic yeast Pichia pastoris. Each of the coding regions was placed downstream of the coding region for the secretion signal of the yeast alpha-factor. The alpha-factor signals were cleaved off from the expressed proteins and the Fv was secreted as a heterodimer consisting of the V(L) and V(H) domains. The binding constant of the expressed Fv against the (4-hydroxy-5-iodo-3-nitrophenyl)acetate ligand was comparable to that of the Fab fragment. Crystals of the Fv were obtained in the presence of the ligand and diffracted X-rays to 1.8 A resolution. The crystals belong to the monoclinic space group P2(1), with unit-cell parameters a = 46.48 (9), b = 34.99 (4), c = 77.76 (17) A, beta = 101.47 (14) degrees, and contain one Fv molecule per asymmetric unit.

A strong constant magnetic field affects muscle tension development in bullfrog neuromuscular preparations.

Effects of a constant magnetic field (CMF) of 0.65 T on muscle tension over 9 h were studied in the neuromuscular preparation of the bullfrog sartorius muscle. Tension was developed every 30 min by stimulation of the sciatic nerve (nerve stimulation) or of the sartorius muscle itself (muscle stimulation). In sciatic nerve stimulation, tension decreased rapidly for the first 3-4 h at a similar rate in both test (exposed to CMF) and control muscles. However, the rate of decrease became smaller and almost leveled off after 3-4 h in the test muscles, whereas tension continued to decrease monotonically in control muscles. The slope of the decrease for these later periods was significantly different between the test and the control conditions. Accordingly, tension was larger in test than in control muscles. In muscle stimulation, tension decreased monotonically from the start of experiments in control muscles, while tension in test muscles maintained their initial values for almost 3 h. Thereafter they started to decrease with a similar rate to the control. Hence, tension was always larger in test than in control muscles. A similar pattern of temporal change was observed for the rate of rise of the maximum tension for nerve or muscle stimulation. However, a significant difference was detected only in the case of muscle stimulation. The present results showed that a strong CMF of 0.65 T had biological effects on tension development of the bullfrog sartorius muscle by stimulation of the sciatic nerve as well as by stimulation of muscle itself. The presence of a small AC magnetic field component leaves open the possibility of an AC, rather than a CMF effect.

Crystallization and preliminary X-ray analysis of a bacterial lysozyme produced by Streptomyces globisporus.

The extracellular bacteriolytic enzyme produced by Streptomyces globisporus shows a beta-1,4-N,6-O-diacetylmuramidase activity as well as a beta-1,4-N-acetylmuramidase activity. Crystals of this enzyme have been obtained by the hanging-drop vapour-diffusion method using polyethylene glycol as a precipitant. They belong to the tetragonal space group P4(1)2(1)2, with unit-cell parameters a = 63.11 (4), c = 121.1 (1) A, diffract to at least 2.0 A resolution and are suitable for high-resolution structure analysis. The crystal structure was solved by molecular replacement using lysozyme produced by S. erythraeus as a search model. The structure refinement is now in progress.

Crystal structure of the low-humidity form of aspartame sweetener.

The low-humidity IB crystal form of aspartame (L-alphaaspartyl-L-phenylalanine methyl ester) is prepared via humidity-induced transition from the highly hydrated IA crystal form and is used widely as a sweetener. The crystal structure of the low-humidity IB form is determined at 1.05 A resolution (0.476 A(-1) in maximum sintheta/lambda) from an extremely fine fibrous crystal using synchrotron radiation. There are three aspartame molecules and two water molecules in the asymmetric unit of the monoclinic space group P2(1). Each aspartame molecule adopts an almost identical extended conformation which is commonly observed in other crystal forms of aspartame. Three aspartame molecules are assembled into a triangular trimer, and trimer units are stacked along the b-axis via hydrogen-bonding and electrostatic interactions in the main chains and also via hydrophobic contacts in the phenyl side-chains. Six trimer units are related by pseudo 6(1)-screw axis symmetry and form a hydrophilic channel at their center. The hydrophilic channel in the IB form contains only four water molecules in the unit cell, compared with 16 in the IA form. Although the IB form exhibits a trimer structure similar to that of the IA form, one aspartame molecule is rotated by approximately equals 20 degrees from the orientation in the IA form. This arrangement of the molecule implies that the humidity-induced transition is accompanied by a flapping motion of its methyl ester group. These structural differences may imply the stepwise transition from the IA to the IB forms.

Crystal structure of the 64M-2 antibody Fab fragment in complex with a DNA dT(6-4)T photoproduct formed by ultraviolet radiation.

DNA photoproducts with (6-4) pyrimidine-pyrimidone adducts formed by ultraviolet radiation are implicated in mutagenesis and cancer, particularly skin cancer. The crystal structure of the Fab fragment of the murine 64M-2 antibody specific to DNA T(6-4)T photoproducts is determined as a complex with dT(6-4)T, a (6-4) pyrimidine-pyrimidone photodimer of dTpT, at 2.4 A resolution to a crystallographic R-factor of 0.199 and an R(free) value of 0.279. The 64M-2 Fab molecule is in an extended arrangement with an elbow angle of 174 degrees, and its five complementarity-determining regions, except L2, are involved in the ligand binding. The bound dT(6-4)T ligand adopting a ring structure with (6-4) linked 5' thymine-3' pyrimidone bases is fully accommodated in an antigen-binding pocket of about 15 Ax10 A. The 5'-thymine and 3'-pyrimidone bases are in half-chair and planar conformations, respectively, and are nearly perpendicular to each other. The 5'-thymine base is hydrogen-bonded to Arg95H and Ser96H, and is in van der Waals contact with Tyr100iH. The 3'-pyrimidone base is hydrogen-bonded to His35H, and is in contact with Trp33H. Three water molecules are located at the interface between the bases and the Fab residues. Hydrogen bonds involving these water molecules also contribute to Fab recognition of the dT(6-4)T bases. The sugar-phosphate backbone connecting the bases is surrounded by residues His27dL, Tyr32L, Ser92L, Trp33H, and Ser58H, but is not hydrogen-bonded to these residues.

Mechanism of superoxide dismutase-like activity of Fe(II) and Fe(III) complexes of tetrakis-N,N,N',N'(2-pyridylmethyl)ethylenediamine.

The superoxide dismutase (SOD) activity of iron(II) tetrakis-N,N,N',N'(2-pyridylmethyl)ethylenediamine complex (Fe-TPEN) was reexamined using a pulse radiolysis method. In our previous study (J. Biol. Chem., 264, 9243-9249 (1989)), we reported that this complex has a potent SOD activity in a cyt. c (cytochrome c)-based system (IC50 = 0.8 microM) and protects E. coli cells against paraquat toxicity. The present pulse radiolysis experiment revealed that Fe(II)TPEN reacts stoichiometrically with superoxide to form Fe(III)TPEN with a second-order rate constant of 3.9 x 10(6) M-1 S-1 at pH 7.1, but superoxide did not reduce Fe(III)TPEN to Fe(II)TPEN. The reaction of Fe(III)TPEN and superoxide was biphasic. In the fast reaction, an adduct (Fe(III)TPEN-superoxide complex) was formed at the second-order rate constant of 8.5 x 10(5) M-1 S-1 at pH 7.4. In the slow one, the adduct reacted with another molecule of the adduct, regenerating Fe(III)TPEN. In the cyt. c method with catalase, this Fe(III)TPEN-superoxide complex showed cyt. c oxidation activity, which had led to overestimation of its SOD activity. Based on the titration data, the main species of complex in aqueous media at neutral pH was indicated to be Fe(III)TPEN(OH-). A spectral change after the reduction with hydrated electron indicates that the OH- ion coordinates directly to Fe(III) by displacing one of the pyridine rings. The X-ray analysis of [Fe(II)TPEN]SO4 supported this structure. From the above results we propose a novel reaction mechanism of FeTPEN and superoxide which resembles a proton catalyzed dismuting process, involving Fe(III)TPEN-superoxide complex.

Complex formation of double-stranded DNA (6-4) photoproducts and anti-(6-4) photoproduct antibody Fabs.

DNA (6-4) photoproducts are major constituents of ultraviolet-damaged DNAs. We prepared double-stranded (ds) (6-4) DNA photoproducts and analyzed formation of their complexes with anti-(6-4) photoproduct antibody Fabs. Elution profiles of the mixtures of ds-(6-4) DNAs and Fabs from anion-exchange and gel-filtration columns indicate that Fab 64M-2 deprives 14mer ds-(6-4) DNA of single-stranded (ss) (6-4) DNA and shows no interaction with 18 mer ds-(6-4) DNA (A18). Fab 64M-5 with an approximately 100-fold higher affinity than Fab 64M-2 forms a complex with the ds-(6-4) DNA (A18), but partly dissociates another 18 mer ds-(6-4) DNA (A18-3), with a lowered G-C content, into ss-DNAs. From these results, antibody 64M-5 possibly accommodates the T(6-4)T photolesion moiety of the ds-(6-4) DNA (A18) by flipping out the moiety from its neighboring segments.

Recognition and cleavage of double-stranded DNA by yeast VMA1-derived endonuclease.

DNA endonuclease derived from the yeast VMA1-gene product recognizes and cleaves 31 base-pairs of double-stranded DNA (dsDNA). Mixtures of the endonuclease (VDE) with a full DNA substrate consisting of 34 base-pairs, with nicked substrates each having a nick in either DNA chain, and with cleaved substrates each having a cleaved-off chain are prepared. Molecular weights (MWs) of eluted peaks from gel filtration columns were estimated from elution profiles in the presence of Mg2+ ions. Each mixture exhibited an elute peak at about 63k MW, larger than the MW of VDE unbound to dsDNA. This indicates that VDE and dsDNA substrates form stable complexes. The mixture of VDE either with the full substrate or with the nicked substrate having a nick in the anti-sense chain eluted an additional 25k-MW peak, which presumably corresponds to a cleaved product. The complex of VDE with the full substrate was eluted at 62k-MW location in the absence of Mg2+ ions and yielded a single crystal. Stable complexes of VDE either with the dsDNA substrates or with the cleaved products are obtainable.

Crystal structures of the 64M-2 and 64M-3 antibody Fabs complexed with DNA (6-4) photoproducts.

Crystal structures of the 64M-2 antibody Fab fragment complexed with DNA photoproducts of dT(6-4)T and dTT(6-4)TT, and of the 64M-3 Fab fragment complexed with dT(6-4)T were determined. The 5'-thymine base of the bound dT(6-4)T ligand is in a half-chair conformation, and its base plane is nearly perpendicular to the planar 3'-pyrimidone base. The 64M-2 and 64M-3 Fabs have a common structure suitable for accommodating the dT(6-4)T ligand. In each of the antigen binding sites of the 64M-2 and 64M-3 Fabs, basic residues of His 35H and Arg 95H are located at the bottom of the binding pocket, and are hydrogen-bonded to the base moieties of dT(6-4)T. Two water molecules are involved in the interactions that intervene between the base moieties and the binding site. Aromatic residues of Trp 33H and Tyr 100iH form a side-wall of the pocket and are in van der Waals interactions with the base moieties. The Trp 33H side-chain is placed in parallel to the 3'-pyrimidone base, and the Tyr 100iH side-chain is nearly perpendicular to the 5'-thymine base. His 27dL, Tyr 32L, Leu 93L, and Ser 58H forming another side-wall are located in the vicinity of the sugar-phosphate backbone. In the 64M-2 Fab complex with dTT(6-4)TT, 5'- and 3'-side phosphate groups are also involved in interaction with Fab residues.

Three-dimensional structure of Escherichia coli glutathione S-transferase complexed with glutathione sulfonate: catalytic roles of Cys10 and His106.

Cytosolic glutathione S-transferase is a family of multi-functional enzymes involved in the detoxification of a large variety of xenobiotic and endobiotic compounds through glutathione conjugation. The three-dimensional structure of Escherichia coli glutathione S-transferase complexed with glutathione sulfonate, N-(N-L-gamma-glutamyl-3-sulfo-L-alanyl)-glycine, has been determined by the multiple isomorphous replacement method and refined to a crystallographic R factor of 0.183 at 2.1 A resolution. The E. coli enzyme is a globular homodimer with dimensions of 58 Ax56 Ax52 A. Each subunit, consisting of a polypeptide of 201 amino acid residues, is divided into a smaller N-terminal domain (residues 1 to 80) and a larger C-terminal one (residues 89 to 201). The core of the N-terminal domain is constructed by a four-stranded beta-sheet and two alpha-helices, and that of the C-terminal one is constructed by a right-handed bundle of four alpha-helices. Glutathione sulfonate, a competitive inhibitor against glutathione, is bound in a cleft between the N and C-terminal domains. Therefore, the E. coli enzyme conserves overall constructions common to the eukaryotic enzymes, in its polypeptide fold, dimeric assembly, and glutathione-binding site. In the case of the eukaryotic enzymes, tyrosine and serine residues near the N terminus are located in the proximity of the sulfur atom of the bound glutathione, and are proposed to be catalytically essential. In the E. coli enzyme, Tyr5 and Ser11 corresponding to these residues are not involved in the interaction with the inhibitor, although they are located in the vicinity of catalytic site. Instead, Cys10 N and His106 Nepsilon2 atoms are hydrogen-bonded to the sulfonate group of the inhibitor. On the basis of this structural study, Cys10 and His106 are ascribed to the catalytic residues that are distinctive from the family of the eukaryotic enzymes. We propose that glutathione S-transferases have diverged from a common origin and acquired different catalytic apparatuses in the process of evolution.

Succinimide and isoaspartate residues in the crystal structures of hen egg-white lysozyme complexed with tri-N-acetylchitotriose.

The isomerization of Asp101 to isoaspartate autocatalytically proceeds via a succinimide intermediate in hen egg-white lysozyme at a mildly acidic condition. The crystal structures of succinimide and isoaspartate forms of the lysozyme proteins, each complexed with a tri-N-acetylchitotriose ligand, have been determined at 1.8 A resolution, and distinctively elucidate coplanar cyclic aminosuccinyl and beta-linked isoaspartyl residues. Compared with the liganded native protein with normal Asp101, succinimide 101 protrudes toward the ligand, and isoaspartate 101 extends away from the ligand. The formations of these residues caused the loss of three hydrogen-bonds between the ligand and the side-chains of Asp101 and Asn103 along with 0.5 A displacement of the ligand location.

Probing novel elements for protein splicing in the yeast Vma1 protozyme: a study of replacement mutagenesis and intragenic suppression.

Protein splicing is a compelling chemical reaction in which two proteins are produced posttranslationally from a single precursor polypeptide by excision of the internal protein segment and ligation of the flanking regions. This unique autocatalytic reaction was first discovered in the yeast Vma1p protozyme where the 50-kD site-specific endonuclease (VDE) is excised from the 120-kD precursor containing the N- and G-terminal regions of the catalytic subunit of the vacuolar H(+)-ATPase. In this work, we randomized the conserved valine triplet residues three amino acids upstream of the C-terminal splicing junction in the Vma1 protozyme and found that these site-specific random mutations interfere with normal protein splicing to different extents. Intragenic suppressor analysis has revealed that this particular hydrophobic triplet preceding the C-terminal splicing junction genetically interacts with three hydrophobic residues preceding the N-terminal splicing junction. This is the first evidence showing that the N-terminal portion of the V-ATPase subunit is involved in protein splicing. Our genetic evidence is consistent with a structural model that correctly aligns two parallel beta-strands ascribed to the triplets. This model delineates spatial interactions between the two conserved regions both residing upstream of the splicing junctions.

Protein splicing in the yeast Vma1 protozyme: evidence for an intramolecular reaction.

Protein splicing is an autocatalytic reaction of a single polypeptide in which a spliced intervening sequence is excised out and the two external regions are ligated with the peptide bond to yield two mature proteins. We examined the reaction mechanism using a folding-dependent in vitro protein splicing system. Protein splicing proceeds at an optimal pH of 7 and is an intramolecular reaction. The reaction is not inhibited by potential protease inhibitors, suggesting that its mechanism is different from those catalyzed by known proteases.

Identification of three core regions essential for protein splicing of the yeast Vma1 protozyme. A random mutagenesis study of the entire Vma1-derived endonuclease sequence.

The translation product of the VMA1 gene of Saccharomyces cerevisiae undergoes protein splicing, in which the intervening region is autocatalytically excised and the franking regions are ligated. The splicing reaction is catalyzed essentially by the in-frame insert, VMA1-derived endonuclease (VDE), which is a site-specific endonuclease to mediate gene homing. Previous mutational analysis of the splicing reaction has been concentrated extensively upon the splice junctions. However, it still remains unknown which amino acid residues are crucial for the splicing reaction within the entire region of VDE and its neighboring elements. In this work, a polymerase chain reaction-based random mutagenesis strategy was used to identify such residues throughout the overall intervening sequence of the VMA1 gene. Splicing-defective mutant proteins were initially screened using a bacterial expression system and then analyzed further in yeast cells. Mutations were mapped at the N- and C-terminal splice junctions and around the N-terminal one-third of VDE. We identified four potent mutants that yielded aberrant products with molecular masses of 200, 90, and 80 kDa. We suggest that the conserved His362, newly identified as the essential residue for the splicing reaction, contributes to the first cleavage at the N-terminal junction, whereas His736 assists the second cleavage by Asn cyclization at the C-terminal junction. Mutations in these regions did not appear to destroy the endonuclease activity of VDE.

[Virological studies on HTLV-1 carrier pregnant women].

Vertical transmission of HTLV-1 (human T-cell leukemia virus type 1) from HTLV-1 carrier mothers to their newborns has been reported with transmission rates, ranging from 6% to 78%. This study was undertaken to identify the high risk group of vertical transmission by detecting viral antigen in cultured lymphocytes and provirus obtained from carrier mothers. Subjects of this study were 70 HTLV-1 carrier mothers who attended the department of obstetrics and gynecology of hospital located in the Kanto area (ATL non endemic area). HTLV-1 antigen was detected in 40 out of 55 (72.7%) in peripheral blood lymphocytes of carrier mothers. HTLV-1 antigen was detected in 2 out of 40 (5.0%) in cord blood lymphocytes of infants born of carrier mothers. These two infants were born from carrier mothers with positive antigen detection study. It seems that carrier mothers whose peripheral lymphocytes are positive for antigen expression by culture are a high risk group for vertical transmission.

Crystal structures of nucleic acid complexes of ribonuclease U2.

Crystal structures of adenine-specific Ustilago sphaerogena ribonuclease U2 complexed with the substrate analogues, d(ApG), d(ApGpG), and d(ApGpC), with the intermediate analogue, 2',3'-O-isopropylidene-adenosine, and with the product, 3'-AMP, have been determined. In each structure, the adenine base is recognized by the enzyme with four hydrogen-bonds. In the substrate analogue structures, the second base of guanine is sandwiched between His 101 and Tyr 107 side-chains, and forms two hydrogen-bonds with Tyr 107 O and Asp 108 O delta 1 atoms. The third base of the trinucleotides is in van der Waals interaction with the Tyr 78 side-chain. The phosphate group between the second and third nucleosides forms two hydrogen-bonds with the side chains of Asp 37 and Tyr 78. Oxygen atoms of the scissile phosphate group are involved in interactions with catalytic residues of Tyr 39, His 41, Glu 62, Arg 85, and His 101. These interactions indicate that either His 41 or Glu 62 acts as a general base and His 101 acts as a general acid in the first step of RNA hydrolysis.

No alteration in DNA topoisomerase I gene related to CPT-11 resistance in human lung cancer.

Mutations and reduced expression of DNA topoisomerase I (topo I) gene have been shown to be important in the acquisition of resistance to camptothecin and its analogues in vitro, but their significance has not been verified in vivo. We investigated possible topo I gene mutations and topo I mRNA expression levels in 127 samples obtained from 56 patients with lung tumors, including patients who had developed clinical resistance to topo I inhibitors. No mutations were detected in any of the samples examined and expression levels did not differ significantly between clinically resistant cases and others. However, the topo I mRNA expression level was significantly higher in small cell lung carcinomas than in non-small cell lung carcinomas (P < 0.05). These results suggest that topo I mRNA levels may affect CPT-11 sensitivity in human lung cancer. However, topo I gene mutations and reduced topo I mRNA expression may not be the main mechanism of clinically acquired resistance to camptothecin analogues in vivo.

Folding-dependent in vitro protein splicing of the Saccharomyces cerevisiae VMA1 protozyme.

VMA1 translational product undergoes excision of a 50-kDa intervening segment (VDE: VMA1-derived endonuclease) and religation of the flanking regions to create a 69-kDa catalytic subunit of vacuolar membrane H+-ATPase. VDEs conjugated with polypeptides at both N- and C-terminal ends were expressed in Escherichia coli and examined for their ability to catalyze self-splicing. Processed VDE was found in soluble pools, while unspliced precursors accumulated in insoluble pools, forming inclusion bodies. We demonstrate in vitro protein splicing by refolding of the denatured precursor molecules. The processing reaction efficiently occurs with the purified precursor peptide. VDE bracketed by only 6 proximal and 4 distal amino acids is autocatalytically processed.

Decreased L-selectin expression in CD34-positive cells from patients with chronic myelocytic leukaemia.

Abnormal adhesive interaction between bone marrow stroma and progenitors, one of the causes of unregulated proliferation in chronic myelocytic leukaemia (CML), may be caused by some alterations in adhesion molecules on CML progenitors. We investigated the expression of adhesion molecules (CD44, VLA-5, VLA-4, LFA-1, ICAM-1, L-selectin and c-kit) on bone marrow CD34++ cells from 16 CML patients by three-colour flow cytometry. The mean percentage of cells expressing L-selectin in the CD34++CD38+(or)++ fraction from untreated CML patients was significantly lower, and that in the CD34++CD38- fraction tended to be lower than that from normal controls. Among 11 CML patients treated with interferon-alpha (IFN-alpha), the mean percentage of the cells expressing L-selectin in the CD34++CD38- fraction from three patients with a low percentage of Ph1(+) cells in bone marrow was significantly higher than that from five patients with a high percentage of Ph1(+) cells. In addition, L-selectin expression rate was inversely correlated to the percentage of Ph1(+) cells. There was no significant difference between the untreated patients and normal controls with regard to the expression rates of the other adhesion molecules in each CD34++ fraction except LFA-1. These data suggest that decreased L-selectin expression in CML CD34++ cells reflects one of the features of malignant CML progenitors.

Influence of paternal (252) Cf neutron exposure on abnormal sperm, embryonal lethality, and liver tumorigenesis in the F(1) offspring of mice.

Experiments were conducted to determine whether neutron-induced genetic damage in parental germline cells can lead to development of cancer in the offspring. Seven-week-old C3H male mice were irradiated with (252) Cf neutrons at a dose of 0, 50, 100, or 200 cGy. Two weeks or three months after irradiation, the male mice were mated with virgin 9-week-old C57BL females. Two weeks after irradiation, the irradiated male mice showed an increased incidence of sperm abnormalities, which led to embryo lethalities in a dose-dependent manner when they were mated with unirradiated female mice. Furthermore, liver tumors in male offspring of male mice in the 50 cGy group were significantly increased in 19 of 44 (43.2%) animals, in clear contrast to the unirradiated group (1 of 31; 3.2%) (P < 0.01). In the 100 cGy group, 6 of 39 (15%) mice had lesions. At 3 months after irradiation abnormal sperm and embryonal lethality were not significantly increased. The incidences of liver tumors in male offspring from the 50 cGy, 100 and 200 cGy groups were 6 of 20 (30%), 5 of 22 (23%) and 1 of 19 (5%), respectively, which are not significantly increased compared with the control. It is concluded that increased hepatic tumor risk in the F(1) generation may be caused by genetic transmission of hepatoma-associated trait(s) induced by (252) Cf neutron irradiation.