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Biomedical subjects

H M Berman

Publications and source records attributed to H M Berman.

At least 73 records · Page 4Linked to original sources
PubMed1988

A systematic study of patterns of hydration in nucleic acids:(I) guanine and cytosine.

The hydration sites of guanine and cytosine are defined by examination of the crystal structures of bases, nucleosides, nucleotides, and three dinucleoside phosphate salts. The patterns of hydration for two guanine and cytosine containing oligonucleotides are then predicted. The relationship between these structural motifs and thermodynamic parameters is discussed.

Crystallography↗
PubMed1986

Crystallization and preliminary X-ray study of AMP nucleosidase.

Adenosine-5'-monophosphate nucleosidase from Escherichia coli has been crystallized in the presence of its strong competitive inhibitor formycin 5'-monophosphate and its allosteric activator adenosine 5'-triphosphate. Crystals are tetragonal bipyramids which grow to 1.2 mm in the longest dimension, are resistant to radiation damage, and diffract to a resolution of 3.5 A. The space group is P4(1)2(1)2 or P4(3)2(1)2, and the unit cell dimensions are a = 120.1 A and c = 243.7 A. The asymmetric unit is estimated to contain four subunits of 52,000 daltons. The crystals appear suitable for single crystal x-ray structure investigation.

Crystallization↗
PubMed1986

Hydration of nucleic acid crystals.

Can we make any generalizations from examination of the crystal structures in hand? The results of study of the very well-determined high-resolution structures indicate that the counterions have a very strong effect on organizing the water structure and that these counterions are bonded in a sequence-specific manner. Hence, the sodium ion bonds in the minor groove of ApU and only to the phosphate backbone in GpC. Not surprisingly then, the water network in ApU is predominantly in its minor groove. Similarly, the negative sulfate counterion in the major groove of the 3:2 complex between proflavine and CpG has a significant influence on the water structure in that crystal. The crystallization of two positive proflavine molecules with two negative nucleic acid chains obviates the need for inorganic ions and may provide additional insight about nucleic acid water structure. The presence of the charged aromatic hydrocarbon appears to provide the correct mixture of hydrophilicity and hydrophobicity that allows for both the gathering and ordering of water molecules around the nucleic acid molecule, not unlike what was previously observed in the semiclathrate structures. This same type of hydrophobic aggregation might pertain along the major groove side of structures containing the appropriate arrangement of methyl-containing thymine bases. Although it is very tempting at this point to make further rules and predictions, experience has shown that, especially in the case of nucleic acids, such prognostications would be premature. What is clearly needed are some more high-quality crystal structures of a variety of sequences under different and controlled conditions. Analyses of these may then put us in a position to successfully predict both the structure of water and its effects on nucleic acid conformation.

Computer Simulation↗
PubMed1984

Crystallization and preliminary X-ray study of a complex between d(ATGCAT) and actinomycin D.

Crystals of a 2:1 complex between the self-complementary DNA hexamer d(ATGCAT) and the antitumor drug actinomycin D have been grown from solutions of polyethylene glycol 400. The crystals are orthorhombic with space group P2(1)2(1)2(1) and a = 95.6, b = 42.7, and c = 40.8 A. A Patterson map calculated from preliminary diffractometer data as well as packing considerations suggest a model in which the actinomycin D is intercalated into a double-stranded DNA hexamer. There are four such complexes in the asymmetric unit.

Crystallization↗
PubMed1983

Monte Carlo studies on water in the dCpG/proflavin crystal hydrate.

The extensive water network identified in the crystallographic studies of the dCpG/Proflavin hydrate by Neidle, Berman and Shieh (Nature 288, 129, 1980) forms an ideal test case for a) assessing the accuracy of theoretical calculations on nucleic acid--water systems based on statistical thermodynamic computer simulation, and b) the possible use of computer simulation in predicting the water positions in crystal hydrates for use in the further refinement and interpretation of diffraction data. Monte Carlo studies have been carried out on water molecules in the unit cell of dCpG/proflavin, with the nucleic acid complex fixed and the condensed phase environment of the system treated by means of periodic boundary conditions. Intermolecular interactions are described by potential functions representative of quantum mechanical calculations developed by Clementi and coworkers, and widely used in recent studies of the aqueous hydration of various forms of DNA fragments. The results are analyzed in terms of hydrogen bond topology, hydrogen bond distances and energies, mean water positions, and water crystal probability density maps. Detailed comparison of calculated and experimentally observed results are given, and the sensitivity of results to choice of potential is determined by comparison with simulation results based on a set of empirical potentials.

Acridines↗
PubMed1981

An improved basal medium for Y-1 mouse adrenal cortex tumor cells in culture. 2. Stability of steroidogenic pathway and chromosome number.

Y-1 cells were passaged weekly for 6 wk in MACT IV medium without a period of adaptation to this basal medium that requires 1% dialyzed fetal bovine serum as a supplement. The steroid pathway and chromosome number, reported earlier for this cell line under culture conditions that used much higher concentrations of nondialyzed sera, remained stable despite dialysis and reduction of the fetal bovine serum to 1%.

Adrenal Cortex Hormones↗
PubMed1980

Highly structured water network in crystals of a deoxydinucleoside---drug complex.

X-ray diffraction analysis of crystals of the intercalative complex between the deoxyribonucleoside phosphate d(CpG) and the mutagen proflavine shows a highly structured arrangement of water molecules linked together by newtworks of hydrogen bonds to form four edge-linked pentagons per asymmetric unit. These pentagons have a general role in maximizing hydrogen bonding at 3.4-A intervals. The conformation of the deoxyribose sugar ring at the 3' end of one strand can depend on its local aqueous environment.

Acridines↗
PubMed1980

The structure of drug-deoxydinucleoside phosphate complex; generalized conformational behavior of intercalation complexes with RNA and DNA fragments.

A 2:2 complex of proflavine and deoxycytidylyl-3', 5'-guanosine has been crystallized and its structure determined by x-ray crystallography. The two dinucleoside phosphate strands form self complementary duplexes with Watson Crick hydrogen bonds. One proflavin is asymmetrically intercalated between the base pairs and the other is stacked above them. The conformations of the nucleotides are unusual in that one strand has C3',C2'endomixed sugar puckering and the other has C3',C3' endo deoxyribose sugars. These results show that the conformation of the 3'sugar is of secondary importance to the intercalated geometry.

Acridines↗
PubMed1979

Netropsin, a DNA-binding oligopeptide structural and binding studies.

The crystal structure of netropsin, an oligopeptide which binds to DNA, has been determined. The molecule is bowed with the amide groups on the concave side, and the carbonyl and methyl groups on the convex side. The amide groups participate in extensive hydrogen bonding with water molecules; the charged amino end groups interact with the sulfate anions. Binding of netropsin to poly(dA) . poly(dT) under conditions of different ionic strength was also studied. Utilizing the crystallographic as well as the binding data, it is possible to build a model which explains the specificity of this antibiotic.

Circular Dichroism↗
PubMed1978

Drug-nucleic acid interactions: conformational flexibility at the intercalation site.

The conformational features of the intercalation site in polynucleotides were examined. We found that, for all the crystal structures of drug-dinucleoside complexes studied thus far, two torsion angles differ from those found in A RNA (phi and chi) and that alternate sugar puckering is not a prerequisite for intercalation. This intercalation geometry, which is the basis of helix axis displacement in a polymer, would necessitate conformational changes in the adjacent nucleotides. The base-turn angle is less sensitive to the conformation of the backbone than it is to small alterations in the base-pairing geometry. We postulate that this angle is dependent on the nature of the intercalating drug.

Models, Chemical↗
PubMed1978

Modified bases in tRNA: the structures of 5-carbamoylmethyl- and 5-carboxymethyl uridine.

The crystal structures of two nucleosides, 5-carbamoylmethyluridine (1) and 5-carboxymethyluridine (2), were determined from three-dimensional x-ray diffraction data, and refined to R = 0.036 and R = 0.047, respectively. Compound 1 is in the C3'-endo conformation with chi +5.2 degrees (anti), psiinfinity = +63.4 degrees and psialpha = +180.0 degrees (tt); 2 is in the C2'endo conformation with chi +49.4 degrees (anti), psiinfinity -60.5 degrees and psialpha +60.0 degrees (gg). For each derivative, the plane of the side chain substituent is skewed with respect to the plane of the nucleobase; for 1, the carboxamide group is on the same side of the uracil plane vis a vis the ribose ring; for 2, the carboxyl group is on the opposite side of this plane. No base pairing is observed for either structure. Incorporation of structure 1 into a 3'-stacked tRNA anticodon appears to place 08 within hydrogen bonding distance of the 02' hydroxyl of ribose 33, which may limit the ability of such a molecule of tRNA to "wobble".

Anticodon↗
PubMed1977

Structure of a dinucleoside phosphate--drug complex as model for nucleic acid--drug interaction.

The crystal structure of a 3:2 complex of the frameshift mutagen proflavine with the dinucleoside phosphate cytidylyl-3'5'-guanosine has been determined. The complex has one drug molecule intercalated between Watson--Crick base pairs of the nucleotide duplex. The other two proflavine molecules are bound to the exterior of the miniature double helix. The orientation of the base pairs in this miniature double helix has aspects similar to that found in RNA 11.

Acridines↗