PubMed Health⌕ Search

Biomedical subjects

G I Birnbaum

Publications and source records attributed to G I Birnbaum.

At least 19 recordsLinked to original sources
PubMed1996

Experiments in microgravity: a comparison of crystals of a carbohydrate-binding fab grown on the ground, on space shuttle Discovery and on space station Mir.

The Fab fragment of the hybridoma antibody (YsT9.1) specific to Brucella abortus has been crystallized on earth using both Linbro plates and ground-based models of the flight hardware, as well as in microgravity on board the space shuttle Discovery and the space station Mir. Large-scale experiments using Linbro plates gave two different crystal morphologies, pyramidal and rhomboid, depending on conditions. The pyramidal crystals proved to scatter X-rays to higher resolution, and conditions within the ground-based flight hardware for both Discovery and Mir were adjusted to produce crystals with this morphology. The experiment on Discovery produced large crystals in each of ten chambers. The experiment on Mir produced crystals in only one of the five assigned chambers, despite the fact that the simultaneous ground-based experiment produced large crystals in every corresponding chamber. Data collection was attempted for crystals from both space and ground-based experiments. Higher resolution data was obtained from crystals grown on Discovery than from either Mir or ground-based crystals, even though the crystals obtained from Discovery were smaller and forced to grow over a much shorter period of time because of the shorter length of the shuttle mission.

Journal Article↗
PubMed1994

1.70 A resolution structure of myoglobin from yellowfin tuna. An example of a myoglobin lacking the D helix.

The crystal structure of metmyoglobin from yellowfin tuna (Thunnus albacares) has been determined by molecular replacement methods and refined to a conventional R factor of 0.177 for all observed reflections in the range of 6.0-1.70 A resolution. Like other myoglobins for which a high-resolution structure is available, the polypeptide chain is organized into several helices that cooperate to form a hydrophobic pocket into which the heme prosthetic group is non-covalently bound; however, the D helix observed in other myoglobins is absent in myoglobin from yellowfin tuna and has been replaced with a random coil. As well, the A helix has a pronounced kink due to the presence of Pro16. The differences in structure between this and sperm whale myoglobin can be correlated with their reported dioxygen affinity and dissociation. The structure is in agreement with reported fluorescence data which show an increased Trp14.heme distance in yellowfin tuna compared to sperm whale myoglobin.

Journal Article↗
PubMed1991

Synthesis and anticancer activity of various 3'-deoxy pyrimidine nucleoside analogues and crystal structure of 1-(3-deoxy-beta-D-threo-pentofuranosyl)cytosine.

Various 3'-deoxy pyrimidine nucleoside analogues have been synthesized for evaluation as potential anticancer and antiviral agents. Among these compounds, 1-(3-deoxy-beta-D-threo-pentofuranosyl)cytosine (10, 3'-deoxy-ara-C) and 3'-deoxycytidine (22) had significant anticancer activity against CCRF-CEM, L1210, P388, and S-180 cancer cell lines in vitro, producing ED50 values of 2, 10, 5, and 34 microM, respectively, for 3'-deoxy-ara-C (10); and 25, 5, 2.5, and 15 microM, respectively, for 3'-deoxycytidine (22). Thus, 3'-deoxy-ara-C (10) was 12.5 times more active against CCRF-CEM cells than 3'-deoxycytidine (22). The 2'-O-acetyl, 5'-O-acetyl, and 2',5'-di-O-acetyl derivatives of 3'-deoxy-ara-C (10), compounds 34, 31, and 30, demonstrated anticancer activity in the same range as 3'-deoxy-ara-C (10) against CCRF-CEM, L1210, P388, and S-180 cells. The 5'-O-acetyl derivative (31) had significantly greater activity against CCRF-CEM with an ED50 value of 0.4, but this compound also showed similar activity, as did 3'-deoxy-ara-C, against L1210, P388, and S-180 with ED50 values of 3, 3, and 13 microM, respectively. 3'-Deoxy-ara-C was also evaluated in vitro against HSV-2, HCMV, and GPCMV viruses and was found to be not very active with respective IC50 values of 110, 220, and 1000 microM. The single-crystal structure of 3'-deoxy-ara-C (10) was determined by X-ray crystallography. There are two molecules of the nucleoside and one molecule of water in the asymmetric unit. The sugar moieties of the two nucleoside molecules adopt different conformations. In molecule A, the ring pucker is C3'-endo with P = 18.7 degrees and tau m = 37.3 degrees, while the CH2OH side chain is gauche+. In molecule B, the ring pucker is C2'-endo with P = 156.8 degrees and tau m = 37.8 degrees and the side chain is trans.

Animals↗
PubMed1991

Synthesis and anticancer and antiviral activities of various 2'- and 3'-methylidene-substituted nucleoside analogues and crystal structure of 2'-deoxy-2'-methylidenecytidine hydrochloride.

Various 2'- and 3'-methylidene-substituted nucleoside analogues have been synthesized and evaluated as potential anticancer and/or antiviral agents. Among these compounds, 2'-deoxy-2'-methylidene-5-fluorocytidine (22) and 2'-deoxy-2'-methylidenecytidine (23) not only demonstrated potent anticancer activity in culture against murine L1210 and P388 leukemias, Sarcoma 180, and human CCRF-CEM lymphoblastic leukemia, producing ED50 values of 1.2 and 0.3 microM, 0.6 and 0.4 microM, 1.5 and 1.5 microM, and 0.05 and 0.03 microM, respectively, but also were active in mice against murine L1210 leukemia. Of all the tested drug dosage levels (25, 50, and 75 mg/kg, respectively) compound 23 had no toxic deaths and compound 22 yielded only one toxic death at the highest dosage level. On the contrary, in the same study, 1-beta-D-arabinofuranosylcytosine (ara-C) resulted in 2/5, 5/5, and 5/5 toxic deaths, respectively. Both compounds 22 and 23 have shown better anticancer activity than ara-C, yielding higher T/C x 100 values and some long-term survivors (greater than 60 days). In addition, compounds 22 and 23 were found to have, respectively, approximately 130 and 40 times lower binding affinity for cytidine/deoxycytidine deaminase derived from human KB cells compared to ara-C, suggesting that the two 2'-methylidene-substituted analogues may be more resistant to deamination. Cytoplasmic deoxycytidine kinase (dCK) was required for compounds 22 and 23 action. Furthermore, compounds 14, 22, 23, and 24 also have antiherpes simplex virus type 1 (HSV-1) and type 2 (HSV-2) activity in cell culture. In addition, the crystal structure of 2'-deoxy-2'-methylidenecytidine hydrochloride (23-HCl) was determined by X-ray crystallography.

Animals↗
PubMed1990

Structure of oncomodulin refined at 1.85 A resolution. An example of extensive molecular aggregation via Ca2+.

The crystal structure of oncomodulin, a 12,000 Mr protein isolated from rat tumours, has been determined by molecular replacement using the carp parvalbumin structure as a starting model. Refinement was performed by cycles of molecular fitting and restrained least-squares, using area-detector intensity data to 1.85 A resolution. For the 5770 reflections in the range 6.0 to 1.85 A, which were used in the refinement, the crystallographic R-factor is 0.166. The refined model includes residues 2 to 108, three Ca2+ and 87 water molecules per oncomodulin molecule. The oncomodulin backbone is closely related to that of parvalbumin; however, some differences are found after a least-squares fit of the two backbones, with root-mean-square (r.m.s.) deviations of 1 to 2 A in residues 2 to 6, 59 to 61 of the CD loop, 87, 90 and 108. The overall r.m.s. deviation of the backbone residues 5 to 108 is 0.62 A. Each of the two Ca2+ atoms that are bound to the CD and EF loops is co-ordinated to seven oxygen atoms, including one water molecule. The third Ca2+ is also seven-co-ordinated, to five oxygen atoms belonging to three different oncomodulin molecules and to two water molecules which form hydrogen bonds to a fourth oncomodulin; thus, this intermolecular Ca2+ and its equivalents interlink the molecules into zigzag layers normal to the b axis with a spacing of b/2 or 32.14 A. No such extensive molecular aggregation has been reported for any of the related Ca-binding regulatory proteins of the troponin-C family studied thus far. The Ca-O distances in all three polyhedra are in the range 2.07 A to 2.64 A, indicating tightly bound Ca polyhedra.

Amino Acid Sequence↗
PubMed1988

Unusual structural features of 2',3'-dideoxycytidine, an inhibitor of the HIV (AIDS) virus.

The structure and conformation of 2',3'-dideoxycytidine, a potent inhibitor of the human immunodeficiency virus, was determined by X-ray crystallography. The nucleoside crystallizes in the tetragonal space group P4(1)2(1)2 with cell dimensions a = b = 8.698(4) and c = 26.155(9) A. Atomic parameters were refined by full-matrix least squares to a final value of R = 0.037 for 1926 observed reflections. The conformation of the furanose ring corresponds to the unusual C3'exo/C4'endo (3T4) pucker, similar to that found in one of the molecules of 3'-azidothymidine (AZT). The glycosidic torsion angle is also smaller than expected. The relevance of these unusual structural features to anti-AIDS activity is assessed.

Acquired Immunodeficiency Syndrome↗
PubMed1988

Crystal structure of T4-lysozyme generated from synthetic coding DNA expressed in Escherichia coli.

The polypeptide produced by expressing a chemically synthesized gene coding for the amino-acid sequence of T4-lysozyme has been crystallized and subjected to X-ray diffraction. The crystal structure has been refined to a standard R-factor of 0.191 for data between 8 and 2 A resolution. The refined model is essentially the same as the well-known structure of wild-type T4-lysozyme determined previously by Matthews et al. (1987). Some small changes in the C-terminal region, which is important in maintaining the folded structure, have been noted. In addition to confirming that the synthetic gene product is very close to the wild type, this structure provides a benchmark for protein engineering experiments on the folding and the catalytic activity of this molecule by the method of gene synthesis.

Chromatography, High Pressure Liquid↗
PubMed1987

Crystallization and preliminary X-ray diffraction study of a xylanase from Trichoderma harzianum.

A 20,000 Mr xylanase from Trichoderma harzianum has been purified and crystallized from 20% (w/v) saturated ammonium sulphate solutions. The unit cell is orthorhombic, space group P2(1)2(1)2(1), with unit cell lengths a = 44.2 A, b = 94.1 A, c = 51.6 A. Data from native crystals and several potential heavy-atom derivatives have been collected. An X-ray analysis to at least 2.8 A resolution appears to be feasible.

Crystallization↗
PubMed1984

8-Chloroguanosine: solid-state and solution conformations and their biological implications.

The three-dimensional structure of 8-chloroguanosine dihydrate was determined by X-ray crystallography. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), and the cell dimensions are a = 4.871 (1) A, b = 12.040 (1) A, and c = 24.506 (1) A. The structure was determined by direct methods, and least-squares refinement, which included all hydrogen atoms, converged at R = 0.031 for 1599 observed reflections. The conformation about the glycosidic bond is syn with chi CN = -131.1 degrees. The ribose ring has a C(2')-endo/C-(1')-exo (2T1) pucker, and the gauche+ conformation of the -CH2OH side chain is stabilized by an intramolecular O-(5')-H...N(3) hydrogen bond. Conformational analysis by means of 1H NMR spectroscopy showed that, in dimethyl sulfoxide, the sugar ring exhibits a marked preference for the C(2')-endo conformation (approximately 70%) and a conformation about the glycosidic bond predominantly syn (approximately 90%), hence similar to that in the solid state. However, the conformation of the exocyclic 5'-CH2OH group exhibits only a moderate preference for the gauche+ rotamer (approximately 40%), presumably due to the inability to form the intramolecular hydrogen bond to N(3) in a polar medium. The conformational features are examined in relation to the behavior of 8-substituted purine nucleosides in several enzymatic systems, with due account taken of the steric bulk and electronegativities of the 8-substituents.

Guanosine↗
PubMed1984

Tautomerism and conformation of the promutagenic analogue N6-methoxy-2',3',5'-tri-O-methyladenosine.

N6-Methoxy-2',3',5'-tri-O-methyladenosine crystallizes in space group P2(1)2(1)2(1) with cell dimensions a = 4.693, b = 11.412, c = 31.741 A. Least-squares refinement of diffractometer data converged at R = 0.038. The location of a hydrogen atom at N1 and the observed bond lengths and bond angles indicate unequivocally the imino tautomer of the adenine moiety. The N6-methoxy group is oriented syn to N1 and the glycosidic torsion angle XCN is -3.6 degrees, i.e. in the anti range. The furanose ring has a C2'-exo/C3'- endo pucker (P = 0.9 degrees) and is unusually flattened (tau m = 30.0 degrees). The conformations of the O-methyl groups of the ribose ring are compared with those of monomethylated nucleosides, including the biologically important 2'-O-methyl nucleosides. Evidence is presented for the existence of C-H ... N intermolecular hydrogen bonds between adenine moieties. Bearing in mind that N6-methoxyadenosine is a promutagenic analogue, the results are compared with those for the corresponding promutagenic N4-methoxycytidine. They are also discussed in relation to the tautomerism, the conformation of the N6-methoxy group, and the associated base-pairing abilities in the absence and presence of polymerases.

Adenosine↗
PubMed1981

Comparison of solid state and solution conformations of R and S epimers of 8,5'-cycloadenosine and their relevance to some enzymatic reactions.

The C(5')-R epimer of 8,5'-cycloadenosine crystallizes in the monoclonic space group P2(1) (Z = 2) with unit cell dimensions a = 5.755 (1), b = 16.895 (1), and c = 5.511 (1) A and beta = 104.16 (1) degree. X-ray intensity data were measured on a diffractometer, and the crystal structure was determined by direct methods. Least-squares refinement converged at R = 0.037 for 1008 reflections. The conformation about the glycosyl bond is anti, as imposed by the 8,5' cyclization, with XCN = 29.8 degrees. The ribose ring adopts the unusual C(1')endo-O(4')exp (o1T) conformation with pseudo-rotation parameters P = 289.0 degrees and tau m = 490 degrees. The six-membered ring formed by the 8,5' linkage is approximately a half-chair with C(4') and O(4'), respectively, above and below a plane defined by the other four atoms. These results are compared with those previously reported for the corresponding S epimer [Haromy, T. P., Raleigh, J., & Sundaralingam, M. (1980) Biochemistry 19, 1718-1722]. The conformations of the sugar rings and the exocyclic groups of both epimers in the solid state are compared to the conformations in solution, as determined by analysis of the systems of proton-proton vicinal coupling constants from the 1H NMR spectra. The foregoing findings are employed to examine the role of the conformational parameters of adenosine and 5'-AMP in reactions catalyzed by the appropriate enzymes.

AMP Deaminase↗
PubMed1979

Solution of conformation and crystal structure of methyl 3,6-dideoxy-beta-D-ribohexopyranoside, an immunodominant sugar of O-antigens.

The crystal structure of methyl 3,6-dideoxy-beta-D-ribohexopyranoside monohydrate was determined by direct methods. Crystals are monoclinic, space group P2(1), with cell dimensions a=9.089(1), b=7.668(1), c=6.956(1) A, beta=101.12 degrees. The molecule adopts the 1C1 chair conformation. The same conformation was also found in both aqueous and chloroform solutions. The pyranose ring is only slightly distorted, and the consequences of this observation on antigen structure are discussed.

Antigens, Bacterial↗
PubMed1979

Conformation of exocyclic amino groups in purines and pyrimidines: crystal structure and conformation of 1-methyl-N4-hydroxycytosine hydrochloride.

The hydrochloride salt of 1-methyl-N4-hydroxycytosine crystallizes in the triclinic space group P1 with cell dimensions: a = 8.232(1), b = 9.293(1), c = 5.416(1) A (1 A = 0.1 nm); alpha = 91.95(1), beta = 91.72(2), gamma = 71.56(1) degrees (SE in parentheses). The structure was solved by direct methods and refined to R = 3.7% for 1514 reflections. Despite the absence of an intramolecular hydrogen bond in the solid state, the N4-hydroxy substituent is syn to the ring N(3). This conformation, which probably prevails also in the neutral form, is of relevance to the mechanism of attack of cytosine by hydroxylamine, known to involve predominantly the cytosine cation, as well as to the mechanism of hydroxylamine mutagenesis. Such conformational aspects are also relevant to other phenomena, including translation and restriction.

Crystallization↗
PubMed1978

A purine nucleoside unequivocally constrained in the syn form. Crystal structure and conformation of 8-(alpha-hydroxyisopropyl)-adenosine.

Crystals of 8-(alpha-hydroxyisopropyl)-adenosine dihydrate, C13H19N5O5.2H2O, belong to the monoclinic space group P21. Cell dimensions are a = 8.259 (1), b = 11.117 (2), c = 9.663 (1) A, beta = 109.65 (2) degrees. Intensity data were collected on a four-circle diffractometer and the structure was solved by direct methods. Block diagonal least-squares refinement led to R = 0.031 for 1467 reflections. The glycosyl torsion angle chiCN is 241.4 degrees, corresponding to a syn conformation. The conformation of the exocyclic C(4')-C(5') bond is gauche-gauche and the sugar pucker is C(2') endo. It is considered that the bulky, tetrahedral, neutral 8-substituent, with an effective van der Waals radius of 3.5--4.0 A, provides an adenosine analogue which should exhibit the syn conformation about the glycosidic bond in solution as well as in solid state, irrespective of the nature of the sugar pucker. It should therefore be suitable for studies of interactions with enzyme systems requiring the anti conformation of the nucleoside or nucleotide.

Adenosine↗
PubMed1977

alpha-Nucleosides in biological systems. Crystal structure and conformation of alpha-cytidine.

The structure of alpha-cytidine, C9H13N3O5, monoclinic with space group C2 and cell parameters a = 20.064 (3) A, b = 7.100 (1) A, c = 7.860 (2) A, beta = 104.60 (2) degrees, Z = 4, was determined by X-ray diffraction using a combination of direct methods, Patterson and difference Fourier techniques and refined by block-diagonal least-squares to a final R of 0.033 for 1002 reflections measured on a diffractometer. The glycosidic torsional angle, chiCN = -28.4 degrees, is in the anti region; the sugar pucker is C(2')exo-C(3')endo in a nearly pure 32H twist; and the conformation of C(4')-C(5') is gauche-gauche. The molecules are bound by hydrogen bonds in the lattice with little likelihood of base-stacking interactions. The molecular features of the compound are compared and contrasted with those of its naturally occurring beta-anomer, and some biological implications of this structure, and alpha-nucleosides in general, are discussed.

Cytidine↗
PubMed1976

Mechanism of hydroxylamine mutagenesis. Crystal structure and conformation of 1,5-dimethyl-N4-hydroxycytosine.

The crystal structure of the title compound, which is a formal analogue of 5-methyl-N4-hydroxycytosine nucleosides, has been determined by X-ray diffraction. The space group is P2(1)/c with a = 7.368 (2), b = 12.096 (3), c = 9.192 (4) A, beta = 113.94 (3) degrees. Three-dimensional intensity data were collected with a four-circle diffractometer, and the structure was refined by block-diagonal least-squares to R = 0.053. The compound is in the imino form, and the exocyclic N4-OH is located essentially in the plane of the pyrimidine ring, and syn to the ring (N(3). There is an intramolecular hydrogen bond involving the N(3)-H as donor and O(4) as acceptor, viz. N(3)-H(31)----O(4)-H. With this conformation, which probably prevails also in solution, the compound would be unable to participate in normal Watson-Crick base pairing. It is shown that a similar situation may prevail for N4-hydroxycytosine nucleosides. The implications with regard to the molecular mechanism of hydroxylamine mutagenesis, with particular reference to the T-even bacteriophages, are discussed. Analogous considerations are applied to an examination of the possible behaviour of hydroxylamine-modified adenine nucleosides.

Cytosine↗