Crystal structures of Y41H and Y41F mutants of gene V protein from Ff phage suggest possible protein-protein interactions in the GVP-ssDNA complex

Gene V protein (GVP) encoded by the filamentous phage Ff (M13, fl, fd) is a homodimeric protein of 87 amino acids that binds to single-stranded DNA (ssDNA) nonspecifically and cooperatively. The structure (monoclinic C2 form) of the wild-type protein has been determined and refined at 1.8-A resolution [Skinner et al. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 2071-2075]. The monomer structure consists of a somewhat distorted five-stranded beta-barrel core with three prominent loops: a DNA-binding loop, a dyad loop, and a dimer contact loop. The amino acid residue at position 41 plays an important role in the dimer-dimer interactions of the protein-ssDNA complex. Two Y41 mutant structures have been studied by X-ray crystallography. The Y41F GVP structure has been refined to an R-factor of 0.180 at 2.2-A resolution and is very similar to the wild-type (wt) structure (rmsd of all C alpha atoms = 0.30 A). In contrast, Y41H GVP forms a new crystal lattice in the space group P2(1)2(1)2(1) with a = 77.18 A, b = 84.17 A, and c = 28.62 A. Its structure has been solved by the molecular replacement method and refined to an R-factor of 0.170 at 2.5-A resolution. The two monomers of Y41H are crystallographically independent, and their structures remain similar to wt-GVP but with significant differences, particularly in the DNA-binding hairpin region. In both crystals, the loop (residues 36-43) that contains the Y41 residue is involved in the crystal dimer packings but in a different manner. The dimer-dimer contacts found in the wt-GVP crystal may be important for GVP aggregation in the absence of DNA. In the presence of DNA, the dimer-dimer contacts may switch to the type found in the Y41H crystal, allowing the GVP-ssDNA complex to form cooperatively. A model of the complex, consistent with existing biochemical and biophysical data, has been constructed from those crystal packing data.

E. coli penicillin acylase isolation by selective release, aqueous two-phase partitioning and ultrafiltration

A procedure has been developed for the purification of penicillin acylase from E. coli fermentation broths. The method described is based primarily on selective release from biomass, charge-directed partitioning in an aqueous two-phase system, and the use of ultrafiltration membranes to recycle the modified polyethylene glycol required and to further purify the enzyme. Each step has been discussed and comparisons have been made with other approaches, where possible. Suggestions have been made for optimisation in process engineering. The approach developed may be applicable to other beta-lactam antibiotic acylases or more generally to some of the other E. coli periplasmic proteins.

Structure of the gene V protein of bacteriophage f1 determined by multiwavelength x-ray diffraction on the selenomethionyl protein

The crystal structure of the dimeric gene V protein of bacteriophage f1 was determined using multiwavelength anomalous diffraction on the selenomethionine-containing wild-type and isoleucine-47-->methionine mutant proteins with x-ray diffraction data phased to 2.5 A resolution. The structure of the wild-type protein has been refined to an R factor of 19.2% using native data to 1.8 A resolution. The structure of the gene V protein was used to obtain a model for the protein portion of the gene V protein-single-stranded DNA complex.

Vibrational analysis of nucleic acids. I. The phosphodiester group in dimethyl phosphate model compounds: (CH3O)2PO2-, (CD3O)2PO2-, and (13CH3O)2PO2-

Normal coordinate analyses and vibrational assignments are presented for the dimethyl phosphate anion [(CH3O)2PO2-] and its deuteriomethyl [(CD3O)2PO2-] and carbon-13 [(13CH3O)2PO2-] derivatives in the gauche-gauche conformation. The dimethyl phosphate anion, which is the simplest model for the nucleic acid phosphodiester moiety, exhibits many of the spectral complexities of DNA and RNA and has previously resisted a complete and consistent vibrational analysis. In the present study we make use of new experimental data on the dimethyl phosphate isotopomers, including Raman depolarization measurements, to develop a consistent valence force field for normal modes of the C--O--P--O--C phosphodiester network and its hydrogenic substituents, as well as for stretching and bending modes of the O--P--O network of the anionic phosphodioxy group (PO2-). The force field established for dimethyl phosphate incorporates one significant nonbonded force constant, introduced from ab initio calculations, to account for interaction between the two ester C--O bonds. This study resolves previous problematic assignments for conformation-sensitive symmetric (in-phase) and asymmetric (out-of-phase) skeletal stretching modes of the ester linkages and demonstrates substantial anharmonicity in the hydrogen-stretching vibrations of the methyl substituents. New assignments are proposed for Raman bands of the phosphodioxy group, which may serve as potential indicators of structure and interaction of the DNA phosphates.

Molecular structure of cyclic diguanylic acid at 1 A resolution of two crystal forms: self-association, interactions with metal ion/planar dyes and modeling studies

Cyclic ribodiguanylic acid, c-(GpGp), is the endogenous effector regulator of cellulose synthase. Its three dimensional structure from two different crystal forms (tetragonal and trigonal) has been determined by x-ray diffraction analysis at 1 A resolution. Both structures were solved by direct methods and refined by block-matrix least squares refinement to R-factors of 0.112 (tetragonal) and 0.119 (trigonal). In both crystal forms, two independent c-(GpGp) molecules associate with each other to form a self-intercalated dimer. All four c-(GpGp) molecules have very similar backbone conformation. The riboses are in the C3'-endo pucker with pseudorotation angles ranging from -7.2 degrees to 16.5 degrees and the bases have anti glycosyl chi angles (-175.5 degrees to 179.7 degrees). In the tetragonal form, a hydrated cobalt ion is found to coordinate to two N7 atoms of adjacent guanines, forcing these two guanines to destack with a large dihedral angle (33 degrees). This metal coordination mechanism has been noted previously in other Pt- or Co-GMP complexes and may be relevant to the binding of the anticancer drug cisplatin to a GpG sequence in DNA. A model of the adduct between cisplatin and a d(CAATGGATTG) duplex has been constructed in which the induced bending of the DNA helix at the Pt crosslinking site is 33 degrees, consistent with earlier electrophoretic analyses. Moreover, c-(GpGp) exhibits unusual spectral properties not seen in other cyclic dinucleotides. It interacts with planar organic intercalator molecules in ways similar to double helical DNA. We propose a cage-like model consisting of a tetrameric c-(GpGp) aggregate in which a large cavity (host molecule) is generated to afford a binding site for certain planar intercalators (guests molecules). The aggregate likely uses a hydrogen bonding scheme the same as that found in the G-quartet molecules, e.g., telomere DNA. The conformation of c-(GpGp) also suggests that certain nearest-neighbor intercalators may be synthesized on the basis of its unique molecular framework. Modeling studies have been carried out to test this hypothesis.

Protective effects of silybin and tetrandrine on the outcome of spontaneously hypertensive rats subjected to acute coronary artery occlusion

The effects of silybin and tetrandrine on the survival of spontaneously hypertensive rats subjected to acute coronary artery occlusion were investigated. The mortality after acute coronary occlusion in spontaneously hypertensive rats (66.7%) was higher than that of control Wistar-Kyoto rats (20%, P < 0.05). Oral administration of silybin (300 mg/kg daily) for 8-12 days reduced mortality in spontaneously hypertensive rats (0, P < 0.01 in comparison with untreated spontaneously hypertensive rats). Administration of tetrandrine 40 mg/kg daily for 8-12 days reduced the mortality to some extent (22.2%, P = 0.051, as compared with control rats). Silybin reduced blood pressure and the incidence of post-occlusion arrhythmias in spontaneously hypertensive rats to the same extent as tetrandrine. Both silybin and tetrandrine decreased the severity of ventricular hypertrophy. Although there were significant decreases in risk zone and infarct zone in silybin- and tetrandrine-treated rats, the ratio of infarct to risk zone was not changed. The results implies that silybin may be beneficial when used in hypertensive patients who develop acute myocardial infarction.

[A study on the relationship between Helicobacter pylori and chronic gastritis and peptic ulcer by the case-control method and sequential analysis]

The association between Helicobacter pylori and the chronic gastritis and peptic ulcer was investigated by the case-control method, 1:1 matched study and sequential analysis. The results of three methods showed that the degree of association between Helicobacter pylori and the chronic gastritis and peptic ulcer was significant (chi 2 = 22.70, P < 0.001, OR = 15.63, 95% CI of OR was 5.05, 48.43), especially that between Helicobacter pylori and active chronic gastritis (OR = 20.92). The results indicate that Helicobacter pylori might be an etiological factor for patients with chronic gastritis and peptic ulcer.

Molecular and crystal structures of ecteinascidins: potent antitumor compounds from the Caribbean tunicate Ecteinascidia turbinata

Some members of marine alkaloid ecteinascidins (Et's), isolated from the Caribbean tunicate Ecteinascidia turbinata, exhibit potent anticancer activity. The three dimensional structures of the N12-formyl derivative of Et729 1a and the natural N12-oxide of Et743 2 have been determined by x-ray crystallography at 0.9 A resolution. Compounds 1a and 2 crystallize in the space groups P2(1)2(1)2(1) (a = 23.214(9) A, b = 28.541(10) A and c = 13.303(9) A) and P2(1) (a = 11.720(5) A, b = 13.230(4) A, c = 28.557(5) A, beta = 90.22(2) degrees), respectively. Their crystal structures have been solved by the Patterson search method, which located the sulfur atoms permitting the phase extension. The final crystallographic R-factors are 0.059 and 0.069 for 1a and 2, respectively. There are two independent molecules, associated as a dimer, in the asymmetric unit of crystals of both 1a and 2. The structure determination allows an unequivocal assignment of the relative configuration of all the chiral centers. Assuming that ecteinascidins and safracin C (whose absolute configuration is known) have the same absolute configuration at C1 position, then the absolute configurations of various chiral positions in Ets are C1(R), N2(R), C3(R), C4(R), C11(R), C13(S), C21(S) and C22(R), respectively. The four independent Et molecules adopt two conformations in which the position of ring C relative to rings A & B is different. The molecules have a compact shape and they are conformationally strained due to a severe van der Waals clash between the sulfur atom and the aromatic ring A. By analogy to the related saframycin, the potent biological activity of Et's may be associated with their ability to form a covalent adduct to DNA using the reactive carbinolamine group. The covalent binding interaction between the Et and the N2 of guanine in the minor groove of the DNA double helix has been studied by computer modelling which suggests that rings A and B "stack" against the DNA backbone. While the bulky drug molecule makes numerous contacts with DNA, it does not significantly distort the conformation of the DNA double helix.

Additional antitumor ecteinascidins from a Caribbean tunicate: crystal structures and activities in vivo

Ecteinascidins (Ets), isolated from the Caribbean tunicate Ecteinascidia turbinata, protect mice in vivo against P388 lymphoma, B16 melanoma, M5076 ovarian sarcoma, Lewis lung carcinoma, and the LX-1 human lung and MX-1 human mammary carcinoma xenografts. Crystal structures of two tris(tetrahydroisoquinoline) Ets were investigated with single crystals of the 21-O-methyl-N12-formyl derivative of Et 729 and the natural N12-oxide of Et 743. Representatives of an additional class of Ets, Et 722 and Et 736, isolated from the same organism, were assigned tetrahydro-beta-carboline-substituted bis(tetrahydroisoquinoline) structures by NMR and fast atom bombardment MS spectra.

Location-dependent variations in the material properties of the anterior cruciate ligament

Our recent anterior drawer studies in human cadaveric knees [Guan and Butler, Adv. Bioengng 17, 5 (1990); Guan et al., Trans. orthop. Res. Soc. 16, 589 (1991)] have suggested that anterior bundles of the anterior cruciate ligament (ACL) develop higher load-related material properties than posterior bundles. This was confirmed when we reevaluated the axial failure data for these bundle-bone specimens from an earlier study [Butler et al., J. Biomechanics 19, 425-432 (1986)]. The purpose of this study was to determine, in a larger data set, if anteromedial and anterolateral bundles of the anterior cruciate ligament exhibit significantly larger load-related material properties than the posterior ligament bundles. Seven ACL-bone units from seven donors (the three tissues from the original study plus four new ones) were subdivided into three subunits, preserving the bone insertions. The subunits were failed in tension at a constant strain rate (100% s-1) and four material properties were compared within and between donors. The anterior bundles developed significantly larger moduli, maximum stresses, and strain energy densities to maximum stress than the posterior subunits. Moduli for the anterior vs posterior subunits averaged 284 MPa vs 155 MPa, maximum stresses averaged 38 MPa vs 15 MPa, and strain energy densities averaged 2.7 N m cc-1 vs 1.1 N m cc-1, respectively. No significant differences were found, however, among strains to maximum stress or between any of the other properties for the two anterior subunits. These results are important to the design of ligament replacements and suggest new experiments designed to distinguish in vivo force levels in these ACL bands, a possible reason for the material differences.

Membrane affinity chromatography used for the separation of trypsin inhibitor

Polysulphone (PS) was chemically modified by acrylation-amination and by chloromethylation-amination, respectively. An ultrafiltration membrane of chemically modified polysulphone (CMPS) was prepared by the phase inversion method. Trypsin was then covalently bonded onto the CMPS membrane by diazotization. The activity of immobilized trypsin reaches up to 10200 U/g; 15 mg trypsin was immobilized on 1 g CMPS membrane. Separation of soybean trypsin inhibitor was carried out on the affinity membrane, yielding 6.5 mg pure trypsin inhibitor in one run. The enzyme membrane has good activity and stability.

[Reaction between monoclonal antibodies to porcine zona pellucida and human and porcine ovary in vitro]

Reaction between monoclonal antibodies to porcine zona pellucida (LPD8, LPC4) and human and porcine ovaries was studied by ABC immunohistochemistry technique in vitro. When slices of human and porcine ovaries were stained with ABC, not only the zona pellucida but also the ovum cytoplasm was stained. Other regions of the ovary, such as granulosa cell, theca cell and connective tissue, could not be stained. These results suggest that the monoclonal antibodies to porcine zona pellucida probably have no direct effect on the endocrine function of ovary, but they may combine with ovum cytoplasm and inhibit follicular growth, so that the number of follicles reduces and endocrine function of the ovary decreases. We do not think that the prospects of continual study on LPD8, LPC4 are good.

[Clinical analysis of surgical repair in 21 cases of transverse facial cleft]

The paper introduced 6 surgical procedures for repairing the transverse facial cleft. To assess the advantages and disadvantages of these procedures, the observation and comparison about the postoperative long-term results were made. A new method called lower lip triangular flap method which was designed by the author was introduced in details. The selection of these surgical procedures and the essential parts of the operation were also discussed.