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Biomedical subjects

C Ban

Publications and source records attributed to C Ban.

At least 19 recordsLinked to original sources
PubMed2002

Eclamptic encephalopathy: MRI, including diffusion-weighted images.

Eclampsia is a rare condition peculiar to pregnant and puerperal women. We analyse imaging features in five patients with eclampsia, and determine whether diffusion-weighted imaging (DWI) could differentiate cytotoxic and vasogenic oedema in four of them. All were imaged within 4 days of the onset of symptoms. We found lesions with a prolonged T2 in the brain of all five patients, in the basal ganglia in four, pons in three and posterior cerebral white matter in two. Isotropic DWI revealed variable intensity in these regions. The ADC was decreased in one, and increased in all the others. The lesion with reduced ADC progressed to infarction.

Adult↗
PubMed2001

[Incidence of ocular trauma in Clinical Hospital Oradea between 1997-1999].

The purpose of the study is to analyse the great number of ocular injuries which were diagnosed and treated in the out-patients clinic or in the hospital in 1997-1999. Ocular trauma seems to be related to the working place or the main activities of the patients, such as agriculture or housekeeping. Ocular injuries in children are significant as number and prognosis. Blunt trauma, ocular perforations, ocular foreign bodies and burns were studied separately for children, housekeepers, unemployed, working and retired people. Due to their number and complexity, ocular trauma represent a very important part in the activity of an ophthalmology department. The conclusion of the study is the number of ocular injuries decreased over the years because of the reduced industrial activity in our town. Similar ocular injuries in retired and working people suggest that retired people are still active. The prognosis of ocular trauma is better if the patients come early to be seen by the specialist, if the treatment is adequate and if the department has a proper equipment for advanced surgery techniques.

Ambulatory Care↗
PubMed2000

Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA.

DNA mismatch repair is critical for increasing replication fidelity in organisms ranging from bacteria to humans. MutS protein, a member of the ABC ATPase superfamily, recognizes mispaired and unpaired bases in duplex DNA and initiates mismatch repair. Mutations in human MutS genes cause a predisposition to hereditary nonpolyposis colorectal cancer as well as sporadic tumours. Here we report the crystal structures of a MutS protein and a complex of MutS with a heteroduplex DNA containing an unpaired base. The structures reveal the general architecture of members of the MutS family, an induced-fit mechanism of recognition between four domains of a MutS dimer and a heteroduplex kinked at the mismatch, a composite ATPase active site composed of residues from both MutS subunits, and a transmitter region connecting the mismatch-binding and ATPase domains. The crystal structures also provide a molecular framework for understanding hereditary nonpolyposis colorectal cancer mutations and for postulating testable roles of MutS.

Adenosine Triphosphatases↗
PubMed2000

[A myopia study of glaucoma patients following pilocarpine instillation].

AIM: Our research studies transitory myopia induced by Pilocarpine treatment in glaucoma patients. MATERIAL AND METHODS: 48 patients with open angle glaucoma were selected, visual acuity and refraction were measured before and after the instillation of Pilocarpine 2%, for two hours. Induced myopia was compared for different ages and it was established the influence of Timolol and Acetazolamide administered in the same time. RESULTS: Transitory myopia is important in young patients, reduced after 50 years and absent after 70 years. Acetazolamide increases myopia, Timolol has no effect on refraction. CONCLUSIONS: The study confirms the unpleasant effect of Pilocarpine and suggests not performing refractometry in the first two hours after the instillation of the drug.

Adult↗
PubMed1999

Oligomerization of a MutS mismatch repair protein from Thermus aquaticus.

The MutS DNA mismatch protein recognizes heteroduplex DNAs containing mispaired or unpaired bases. We have examined the oligomerization of a MutS protein from Thermus aquaticus that binds to heteroduplex DNAs at elevated temperatures. Analytical gel filtration, cross-linking of MutS protein with disuccinimidyl suberate, light scattering, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry establish that the Taq protein is largely a dimer in free solution. Analytical equilibrium sedimentation showed that the oligomerization of Taq MutS involves a dimer-tetramer equilibrium in which dimer predominates at concentrations below 10 microM. The DeltaG(0)(2-4) for the dimer to tetramer transition is approximately -6.9 +/- 0.1 kcal/mol of tetramer. Analytical gel filtration of native complexes and gel mobility shift assays of an maltose-binding protein-MutS fusion protein bound to a short, 37-base pair heteroduplex DNA reveal that the protein binds to DNA as a dimer with no change in oligomerization upon DNA binding.

Adenosine Triphosphatases↗
PubMed1999

Transformation of MutL by ATP binding and hydrolysis: a switch in DNA mismatch repair.

The MutL DNA mismatch repair protein has recently been shown to be an ATPase and to belong to an emerging ATPase superfamily that includes DNA topoisomerase II and Hsp90. We report here the crystal structures of a 40 kDa ATPase fragment of E. coli MutL (LN40) complexed with a substrate analog, ADPnP, and with product ADP. More than 60 residues that are disordered in the apoprotein structure become ordered and contribute to both ADPnP binding and dimerization of LN40. Hydrolysis of ATP, signified by subsequent release of the gamma-phosphate, releases two key loops and leads to dissociation of the LN40 dimer. Dimerization of the LN40 region is required for and is the rate-limiting step in ATP hydrolysis by MutL. The ATPase activity of MutL is stimulated by DNA and likely acts as a switch to coordinate DNA mismatch repair.

Adenosine Triphosphatases↗
PubMed1998

Crystal structure and ATPase activity of MutL: implications for DNA repair and mutagenesis.

MutL and its homologs are essential for DNA mismatch repair. Mutations in genes encoding human homologs of MutL cause multiorgan cancer susceptibility. We have determined the crystal structure of a 40 kDa N-terminal fragment of E. coli MutL that retains all of the conserved residues in the MutL family. The structure of MutL is homologous to that of an ATPase-containing fragment of DNA gyrase. We have demonstrated that MutL binds and hydrolyzes ATP to ADP and Pi. Mutations in the MutL family that cause deficiencies in DNA mismatch repair and a predisposition to cancer mainly occur in the putative ATP-binding site. We provide evidence that the flexible, yet conserved, loops surrounding this ATP-binding site undergo conformational changes upon ATP hydrolysis thereby modulating interactions between MutL and other components of the repair machinery.

Adenosine Diphosphate↗
PubMed1998

Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases.

MutS, MutL and MutH are the three essential proteins for initiation of methyl-directed DNA mismatch repair to correct mistakes made during DNA replication in Escherichia coli. MutH cleaves a newly synthesized and unmethylated daughter strand 5' to the sequence d(GATC) in a hemi-methylated duplex. Activation of MutH requires the recognition of a DNA mismatch by MutS and MutL. We have crystallized MutH in two space groups and solved the structures at 1.7 and 2.3 A resolution, respectively. The active site of MutH is located at an interface between two subdomains that pivot relative to one another, as revealed by comparison of the crystal structures, and this presumably regulates the nuclease activity. The relative motion of the two subdomains in MutH correlates with the position of a protruding C-terminal helix. This helix appears to act as a molecular lever through which MutS and MutL may communicate the detection of a DNA mismatch and activate MutH. With sequence homology to Sau3AI and structural similarity to PvuII endonuclease, MutH is clearly related to these enzymes by divergent evolution, and this suggests that type II restriction endonucleases evolved from a common ancestor.

Amino Acid Sequence↗
PubMed1998

[Pseudophacos explant: the causes and the functional results].

We've studied a number of 20 cases of pseudophakic explantation performed in the Eye Center Timişoara between 1991-1997 from 2605 pseudophakic implantations. The interval between implantation and the moment of explantation was between 4 days and 7 years. The causes which indicated pseudophakic explantation were: pseudophakic bullous keratopathy, IOL decentration and dislocation, uveitis, persistent secondary glaucoma. The study refers to the established treatment for avoiding the explantation and also to the functional results obtained after pseudophakic explantation. Most of the explanted artificial lens cases were anterior chamber lens--13, all of them ALCON type, also we've explanted 4 pupillary implants Fedorov type. The visual acuities obtained after explantation were between hand movement perception and 10/10. Before surgery, visual acuity was between light perception and 10/10. The best functional results were obtained in pseudophakic decentration and dislocation cases and the worst in pseudophakic bullous keratopathy, uveitis and secondary glaucoma cases.

Humans↗
PubMed1997

Crystal structure of an alternating octamer r(GUAUGUA)dC with adjacent G x U wobble pairs.

The crystal structure of the RNA duplex, r(GUAUGUA)dC, with a 3'-terminal deoxy C residue, has been determined at 1.38 A resolution. The r(GUAUGU) hexameric consensus sequence is present at the exon-intron junction in pre-mRNAs of yeast and higher eukaryotic organisms. The crystal belongs to the rhombohedral space group R3. The hexagonal unit cell dimensions are a = b = 39.71 A, c = 68.15 A and gamma = 120 degrees with one duplex in the asymmetric unit. The structure was solved using the molecular replacement method. The final model contains 332 atoms of the duplex and 67 solvent molecules. The R-factor is 17.6% (Rfree of 23.1%) for 4035 reflections with F > or = 1.5sigma(F) in the resolution range 10.0 to 1.38 A. The duplex is of the A-type with a pseudodyad relating the two strands. The RNA helix is slightly distorted, in spite of the presence of two adjacent G x U wobble base-pairs located at the center of the helix. The twist angle between the wobble pairs, 38.1 degrees, is above the average value and those between the wobble base-pairs and the flanking Watson-Crick base-pairs, 26.7 degrees and 26.3 degrees, respectively, are lower than the average values. The twist between the junction base-pairs are about 24 degrees. The G x U wobble pairs are bridged by water molecules and solvated in the grooves. G x U base-pairs are as stable as the Watson-Crick A x U pairs and only slightly less stable than the G x C pairs accounting for their frequent occurrence in RNA.

Crystallography, X-Ray↗
PubMed1997

Crystal structure of d(GCGCGCG) with 5'-overhang G residues.

The crystal structure of the DNA heptamer d(GCGCGCG) has been solved at 1.65 A resolution by the molecular replacement method and refined to an R-value of 0.184 for 3598 reflections. The heptamer forms a Z-DNA d(CGCGCG)2 with 5'-overhang G residues instead of an A-DNA d(GCGCGC)2 with 3'-overhang G residues. The overhang G residues from parallel strands of two adjacent duplexes form a trans reverse Hoogsteen G x G basepair that stacks on the six Z-DNA basepairs to produce a pseudocontinuous helix. The reverse Hoogsteen G x G basepair is unusual in that the displacement of one G base relative to the other allows them to participate in a bifurcated (G1)N2 . . . N7(G8) and an enhanced (G8)C8-H . . . O6(G1) hydrogen bond, in addition to the two usual hydrogen bonds. The 5'-overhang G residues are anti and C2'-endo while the 3'-terminal G residues are syn and C2'-endo. The conformations of both G residues are different from the syn/C3'-endo for the guanosine in a standard Z-DNA. The two cobalt hexammine ions bind to the phosphate groups in both GpC and CpG steps in Z(I) and Z(II) conformations. The water structure motif is similar to the other Z-DNA structures.

Base Composition↗
PubMed1996

Structure of the purine-pyrimidine alternating RNA double helix, r(GUAUAUA)d(C), with a 3'-terminal deoxy residue.

The crystal structure of the purine-pyrimidine alternating octameric RNA helix, r(GUAUAUA)d(C), carrying a 3'-terminal deoxycytidine residue, has been determined at 2.2 A resolution. The molecule crystallizes in the rhombohedral space group R3 (hexagonal cell constants: a = b = 43.07,c = 59.36 A;alpha = beta = 90,gamma = 120 degrees )with one duplex in an asymmetric unit. The structure was solved by molecular replacement and refined with 83 and 2/3 solvent molecules and 2/3 sodium ions to a final R factor of 15.6% using 1775 reflections (86%). The duplexes are approximately linear, their global helix axes are inclined by 10 degrees with respect to the 3(2)-screw axes, and they are stacked on top of each other in a head-to-tail fashion. The twist between the junction base pairs of the stacked duplexes is negligible resulting in a discontinuity of the helix backbones and grooves. The sodium ions on the threefold axis play a significant role in the organization of the packing network. The helical parameters, particularly the twist and the roll, of this alternating sequence are in accord with Calladine's rules. Almost all the 2'-hydroxyl groups are involved in specific hydrogen-bonding interactions, either directly to the sugar ring oxygens O4' on the 3' side, or, through water bridges, to the sugars, phosphates, or bases. This hydrogen bonding of the 2'-hydroxyl groups restrains the conformation of the sugar-phosphate backbone and the glycosidic torsion angles of this RNA fragment. The lack of intermolecular packing contacts in the grooves provides a clear picture of the groove solvation.

Journal Article↗
PubMed1996

RNA - synthesis, purification and crystallization.

Protocols for the routine chemical synthesis and purification of milligram quantities of RNA and DNA-RNA chimeras meeting the demands of X-ray crystallography are described. An efficient screening protocol to test the crystallizability of the molecules and the optimization of the crystallization conditions are presented, so as to allow reproduction by others. Essentially the same crystallization conditions as for DNA oligomers can be employed for RNA crystallization. Specific examples involving alternating octamers, G/C-rich decamers, sequences with overhangs, and drug complexes of chimeras are discussed. Success of the methods is attested by the crystals obtained which diffract to high resolution.

Journal Article↗
PubMed1996

Crystal structure of the self-complementary 5'-purine start decamer d(GCGCGCGCGC) in the Z-DNA conformation. I.

Alternating self-complementary oligonucleotides starting with a 5'-pyrimidine usually form left-handed Z-DNA; however, with a 5'-purine start sequence they form the right-handed A-DNA. Here we report the crystal structure of the decamer d(GCGCGCGCGC) with a 5'-purine start in the Z-DNA form. The decamer crystallizes in the hexagonal space group P6(5)22, unit cell dimensions a = b = 18.08 and c = 43.10 A, with one of the following four dinucleotide diphosphates in the asymmetric unit: d(pGpC)/d(GpCp)/d(pCpG)/d(CpGp). The molecular replacement method, starting with d(pGpC) of the isomorphous Z-DNA hexamer d(araC-dG)3 without the 2'-OH group of arabinose, was used in the structure analysis. The method gave the solution only after the sugar-phosphate conformation of the GpC step was manipulated. The refinement converged to a final R value of 18.6% for 340 unique reflections in the resolution range 8.0-1.9 A. A result of the sequence alternation is the alternation in the nucleotide conformation; guanosine is C3'-endo, syn, and cytidine is C2'-endo, anti. The CpG step phosphodiester conformation is the same as ZI or ZII, whereas that of the GpC step phosphodiester is "intermediate" in the sense that zeta (O3'-P bond) is the same as ZII but alpha (P-O5' bond) is the same as ZI. The duplexes generated from the dinucleotide asymmetric unit are stacked one on top of the other in the crystal to form an infinite pseudocontinuous helix. This renders it a quasi-polymerlike structure that has assumed the Z-DNA conformation further strengthened by the long inner Z-forming stretch d(CG)4. An interesting feature of the structure is the presence of water strings in both the major and the minor grooves. In the minor groove the cytosine carbonyl oxygen atoms of the GpC and CpG steps are cross-bridged by water molecules that are not themselves hydrogen bonded but are enclosed by the water rings in the mouth of the minor groove. In the major groove three independent water molecules form a zigzagging continuous water string that runs throughout the duplex.

Base Sequence↗
PubMed1996

Crystal structure of the self-complementary 5'-purine start decamer d(GCACGCGTGC) in the A-DNA conformation. II.

The crystal structure of the alternating 5'-purine start decamer d(GCGCGCGCGC) was found to be in the left-handed Z-DNA conformation. Inasmuch as the A.T base pair is known to resist Z-DNA formation, we substituted A.T base pairs in the dyad-related positions of the decamer duplex. The alternating self-complementary decamer d(GCACGCGTGC) crystallizes in a different hexagonal space group, P6(1)22, with very different unit cell dimensions a = b = 38.97 and c = 77.34 A compared with the all-G.C alternating decamer. The A.T-containing decamer has one strand in the asymmetric unit, and because it is isomorphous to some other A-DNA decamers it was considered also to be right-handed. The structure was refined, starting with the atomic coordinates of the A-DNA decamer d(GCGGGCCCGC), by use of 2491 unique reflections out to 1.9-A resolution. The refinement converged to an R value of 18.6% for a total of 202 nucleotide atoms and 32 water molecules. This research further demonstrates that A.T base pairs not only resist the formation of Z-DNA but can also assist the formation of A-DNA by switching the helix handedness when the oligomer starts with a 5'-purine; also, the length of the inner Z-DNA stretch (d(CG)n) is reduced from an octamer to a tetramer. It may be noted that these oligonucleotide properties are in crystals and not necessarily in solutions.

Base Sequence↗
PubMed1994

Crystal structure of the highly distorted chimeric decamer r(C)d(CGGCGCCG)r(G).spermine complex--spermine binding to phosphate only and minor groove tertiary base-pairing.

The crystal structure of the self-complementary chimeric decamer duplex r(C)d(CGGCGCCG)r(G), with RNA base pairs at both termini, has been solved at 1.9 A resolution by the molecular replacement method and refined to an R value of 0.145 for 2,314 reflections. The C3'-endo sugar puckers of the terminal riboses apparently drive the entire chimeric duplex into an A-DNA conformation, in contrast to the B-DNA conformation adopted by the all-deoxy decamer of the same sequence. Five symmetry related duplexes encapsulate a spermine molecule which interacts with ten phosphate groups, both directly and through water molecules to form multiple ionic and hydrogen bonding interactions. The spermine interaction severely bends the duplexes by 31 degrees into the major groove at the fourth base pair G(4).C(17), jolts it and slides the 'base plate' into the minor groove. This base pair, together with the adjacent base pair in the top half and the corresponding pseudo two-fold related base pairs in the bottom half, form four minor groove base-paired multiples with the terminal base pairs of two neighboring duplexes.

Base Composition↗
PubMed1994

A single 2'-hydroxyl group converts B-DNA to A-DNA. Crystal structure of the DNA-RNA chimeric decamer duplex d(CCGGC)r(G)d(CCGG) with a novel intermolecular G-C base-paired quadruplet.

We have found that the introduction of a single 2'-hydroxyl group on the sugar-phosphate backbone of the B-DNA decamer d(CCGGCGCCGG) transforms it to A-DNA. Thus, for the first time the X-ray structures of the same sequence have been observed in both the A and B-DNA conformations, permitting a comparison. Crystals of the DNA-RNA chimeric decamer d(CCGGC)r(G)d(CCGG) belong to the orthorhombic space group P2(1)2(1)2(1) with unit cell dimensions a = 25.63 A, b = 45.24 A and c = 47.99 A, and one decamer duplex in the asymmetric unit. The structure was solved by a rigid body search using the coordinates of the isomorphous structure d(CCCGGCCGGG) and refined to an R value of 0.136 using 2753 unique reflections at 1.9 A resolution. The final model contains 406 nucleotide atoms and 61 water molecules. The chimeric duplex exhibits typical A-DNA geometry, with all the sugars in the C(3')-endo puckering and the base-pairs inclined and displaced from the helix axis. The 2'-hydroxyl groups on rG6 and rG16 protrude into the minor groove surface and form different types of hydrogen bonds; that on strand 1 forms an intermolecular hydrogen bond with the furanose ring O(4') of a symmetry-related C1 residue, while that on strand 2 is involved in two water bridges. Crystal packing forces the G4-G17 base-pair in the top half of the duplex to slide significantly into the minor groove compared to the corresponding G7-G14 base-pair in the bottom half, resulting in these base-pairs exhibiting different base stacking and intermolecular interactions. The base G4 of the G4-G17 base-pair forms an unorthodox base "triple", G4*(G10-C11), hydrogen-bonding through its minor groove sites N(2) and N(3) to the minor groove atoms N(2) and O(2) of both bases of the G10-C11 base-pair of a symmetry-related molecule. The base G10 of this triple in turn forms a second similar unorthodox base triple, G10*(G3*C18), with the adjacent base-pair G3-C18 of the duplex, thus G10 is involved in a double triple. On the other hand, in the bottom half of the duplex, the C7-G14 base-pair is involved only in a single similar unorthodox base triple with G20, (C7-G14)*G20, while the adjacent base-pair rG6-C15 is involved in a novel quadruple with C1-G20, (rG6-C15) *(C1-G20), where the latter base-pairs are hydrogen-bonded to each other via the minor groove sites G(N(2))...C(O(2)).(ABSTRACT TRUNCATED AT 400 WORDS)

Base Composition↗