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At least 1,171 records · Page 65Linked to original sources
PubMed2001

Fluorescence spectroscopy studies of vaccinia type IB DNA topoisomerase. Closing of the enzyme clamp is faster than DNA cleavage.

The prototypic type IB topoisomerase isolated from vaccinia virus cleaves the phosphodiester backbone of duplex DNA at the sequence 5'-(C/T)CCTT, forming a covalent 3'-phosphotyrosyl adduct. A precleavage conformational change in which the enzyme clamps circumferentially around the DNA has been implicated on the basis of structural and biochemical studies. However, no direct measurements to elucidate this key step have been obtained to date. To address this shortcoming we have developed two new fluorescence assays that allow detection of conformational changes in both the enzyme and substrate DNA, and allow determination of the thermodynamic and kinetic mechanism for noncovalent DNA binding and phosphodiester cleavage. The results indicate that clamp closing occurs in a rapid step (>25 s(-1)) that is at least 14-fold faster than the maximal rate of DNA cleavage. Opening of the clamp to release the noncovalently bound substrate is also 5-8-fold more rapid than DNA cleavage. We propose a model in which DNA cleavage and religation are connected through a single high energy transition state involving covalent bond breaking. Alternative models that involve a slow precleavage conformational step are not easily reconciled with the available data.

DNA↗
PubMed2002

On the specificity of interaction between the Saccharomyces cerevisiae clamp loader replication factor C and primed DNA templates during DNA replication.

Replication factor C (RFC) catalyzes assembly of circular proliferating cell nuclear antigen clamps around primed DNA, enabling processive synthesis by DNA polymerase during DNA replication and repair. In order to perform this function efficiently, RFC must rapidly recognize primed DNA as the substrate for clamp assembly, particularly during lagging strand synthesis. Earlier reports as well as quantitative DNA binding experiments from this study indicate, however, that RFC interacts with primer-template as well as single- and double-stranded DNA (ssDNA and dsDNA, respectively) with similar high affinity (apparent K(d) approximately 10 nm). How then can RFC distinguish primed DNA sites from excess ssDNA and dsDNA at the replication fork? Further analysis reveals that despite its high affinity for various DNA structures, RFC selects primer-template DNA even in the presence of a 50-fold excess of ssDNA and dsDNA. The interaction between ssDNA or dsDNA and RFC is far less stable than between primed DNA and RFC (k(off) > 0.2 s(-1) versus 0.025 s(-1), respectively). We propose that the ability to rapidly bind and release single- and double-stranded DNA coupled with selective, stable binding to primer-template DNA allows RFC to scan DNA efficiently for primed sites where it can pause to initiate clamp assembly.

Binding Sites↗
PubMed2003

Ordered ATP hydrolysis in the gamma complex clamp loader AAA+ machine.

The gamma complex couples ATP hydrolysis to the loading of beta sliding clamps onto DNA for processive replication. The gamma complex structure shows that the clamp loader subunits are arranged as a circular heteropentamer. The three gamma motor subunits bind ATP, the delta wrench opens the beta ring, and the delta' stator modulates the delta-beta interaction. Neither delta nor delta' bind ATP. This report demonstrates that the delta' stator contributes a catalytic arginine for hydrolysis of ATP bound to the adjacent gamma(1) subunit. Thus, the delta' stator contributes to the motor function of the gamma trimer. Mutation of arginine 169 of gamma, which removes the catalytic arginines from only the gamma(2) and gamma(3) ATP sites, abolishes ATPase activity even though ATP site 1 is intact and all three sites are filled. This result implies that hydrolysis of the three ATP molecules occurs in a particular order, the reverse of ATP binding, where ATP in site 1 is not hydrolyzed until ATP in sites 2 and/or 3 is hydrolyzed. Implications of these results to clamp loaders of other systems are discussed.

Adenosine Triphosphatases↗
PubMedDate not supplied

Influence of clamping-induced ischemia and reperfusion on the response of a mouse melanoma to radiation and hyperthermia.

PURPOSE: To study the response of a mouse melanoma to radiation and hyperthermia under acute hypoxia and reperfusion. MATERIALS AND METHODS: B16F1 melanoma of 100+/-10 mm3, in C57BL mouse, were locally exposed to 10Gy gamma radiation (RT), 43 degrees C for 30 min (HT) in a water bath, or RT followed immediately by HT, under clamping (acute hypoxia) or 1 h after reperfusion. Tumour regression, volume doubling time (VDT), growth delay (GD), apoptosis and microvascular density (MVD) were studied. RESULTS: Under clamping, HT increased the VDT and GD to > 20 days above control and resulted in > 50% regression (PR) in all the tumours, whilst RT + HT synergistically enhanced VDT and GD. Under reperfusion, HT produced 25% PR against 16% by RT, with no increase in VDT and GD compared to RT. RT + HT significantly enhanced VDT and GD above that of RT or HT, but did not further increase PR of reperfused tumours. HT under clamping caused > 50% increase in apoptic cells over control and decreased MVD to 1/3rd of control. RT + HT further enhanced apoptotic cells to > 70% and reduced MVD to 1/6th of control. CONCLUSIONS: These results suggest that combination of radiotherapy with hyperthermia could benefit treatment of tumours with ischemia-induced acute hypoxia.

Animals↗
PubMed2001

Increased FiO2 improves intrathecal oxygenation during thoracic aortic cross-clamping in pigs.

OBJECTIVES: To investigate the effect of 100% oxygen ventilation on cerebrospinal fluid (CSF) oxygenation in 11 pigs during thoracic aortic cross-clamping. DESIGN: An aorto-aortic shunt was used for control of central hemodynamics and study of hypoperfusion by exsanguination. CSF PO2, PCO2 and pH were continuously monitored before and during clamping. The changes in hemodynamic parameters and intrathecal gas tensions in response to variations in proximal mean aortic pressure and fraction of inspired oxygen (FiO2) were recorded. RESULTS: Baseline CSF PO2 decreased from 4.8 +/- 1.9 to 2.6 +/- 2.2 kPa following aortic occlusion. Increasing FiO2 to 1.0 resulted in a significant increase in CSF PO2 to 4.1 +/- 3.0 with a return to 2.7 +/- 2.1 kPa after reducing FiO2 to 0.4 again. The same variations in FiO2 did not induce any significant changes in CSF PO2 during hypotension. CONCLUSION: Increased FiO2 during experimental thoracic aortic cross-clamping with stable proximal arterial pressure helps to maintain CSF PO2, whereas severe hypotension could not be compensated for by hyperoxemia.

Animals↗
PubMedDate not supplied

The synthesis of 2'-O-methyl G-clamp containing oligonucleotides and their inhibition of the HIV-1 Tat-TAR interaction.

We have synthesised a 2'-O-methyl riboside phosphoramidite derivative of the cytosine analogue 9-(2-aminoethoxy)-phenoxazine ('G-clamp') and successfully incorporated it into a series of small steric blocking 2'-O-methyl oligonucleotides targeting the stem-loop region of HIV-1 TAR RNA. The 'G-clamp' containing oligonucleotides show significant increases in binding to a model TAR RNA system when the 'G-clamp' is positioned opposite the loop region. The oligonucleotides also display dose-dependent inhibition of Tat-dependent transcription of an HIV DNA template in HeLa cell nuclear cell extract.

Amides↗
PubMed1969

The ventral photoreceptor cells of Limulus. 3. A voltage-clamp study.

In the dark, the ventral photoreceptor of Limulus exhibits time-variant currents under voltage-clamp conditions; that is, if the membrane potential of the cell is clamped to a depolarized value there is an initial large outward current which slowly declines to a steady level. The current-voltage relation of the cell in the dark is nonlinear. The only ion tested which has any effect on the current-voltage relation is potassium; high potassium shifts the reversal potential towards zero and introduces a negative slope-conductance region. When the cell is illuminated under voltage-clamp conditions, an additional current, the light-induced current, flows across the cell membrane. The time course of this current mimics the time course of the light response (receptor potential) in the unclamped cell; namely, an initial transient phase is followed by a steady-state phase. The amplitude of the peak transient current can be as large as 60 times the amplitude of the steady-state current, while in the unclamped cell the amplitude of the peak transient voltage never exceeds 4 times the amplitude of the steady-state voltage. The current-voltage relations of the additional light-induced current obtained for different instants of time are also nonlinear, but differ from the current-voltage relations of the dark current. The ions tested which have the greatest effect on the light-induced current are sodium and calcium; low sodium decreases the current, while low calcium increases the current. The data strongly support the hypothesis that two systems of electric current exist in the membrane. Thus the total ionic current which flows in the membrane is accounted for as the sum of a dark current and a light-induced current.

Animals↗
PubMed1969

Differences between pacemaker and nonpacemaker neurons of Aplysia on voltage clamping.

The responses of pacemaker and nonpacemaker Aplysia neurons to voltage clamp commands of less than 200 msec duration are essentially identical. For moderate depolarizing commands there is an early inward transient current followed by a late outward current and an outward tail current when the membrane is clamped back to resting potential. On long (1-2 sec) commands in pacemakers there is a marked sag in the late current and an inward tail current. E(tail), the potential of the membrane at which there is no net current flow under the conditions prevailing at the end of the clamp, shifts from about -9.0 mv on short commands to +5.0 mv on long commands. In contrast there is no marked sag of the late current or inward tail current on long commands in nonpacemakers, and E(tail) is near -9.0 mv for both short and long commands. The current sag and shift in E(tail) can be ascribed to a decreased conductance (presumably to K(+)) at the end of the long as compared to the short command in half of the pacemaker neurons. In the remaining cells the essential difference from nonpacemakers appears to be either a greater restricted extracellular space or a more active potential-dependent electrogenic Na(+) pump in pacemakers.

Animals↗
PubMed1972

Sodium flux in Necturus proximal tubule under voltage clamp.

Na transport and electrical properties of Necturus renal proximal tubules were analyzed, in vivo, by a voltage clamp method which utilizes an axial electrode in the tubule lumen for passage of current and simultaneous determination of net fluid (or Na) flux by the split droplet method. When the average spontaneous transepithelial potential difference of -8 mv (lumen negative) was reduced to zero by current passage, net Na flux doubled from a mean of 107 to 227 pmoles/cm(2) per sec. The relationship between flux and potential over the range -25 to +10 mv was nonlinear, with flux equilibrium at -15 mv and droplet expansion at more negative values. Calculated Na permeability at flux equilibrium was 7.0 x 10(-6) cm/sec. Voltage transients, similar to those caused by intraepithelial unstirred layers, were observed at the end of clamping periods. Tubular electrical resistance measured by brief square or triangle wave pulses (<100 msec) averaged 43 ohm cm(2). The epithelial current-voltage relationship was linear over the range -100 to +100 mv, but displayed marked hysteresis during low frequency (<0.04 Hz) triangle wave clamps. The low transepithelial resistance and large opposing unidirectional ion fluxes suggest that passive ionic movements occur across extracellular shunt pathways, while the voltage transients and current-voltage hysteresis are consistent with the development of a local osmotic gradient within epithelium.

Animals↗
PubMed1978

Properties of internally perfused, voltage-clamped, isolated nerve cell bodies.

The membrane properties of isolated neurons from Helix aspersa were examined by using a new suction pipette method. The method combines internal perfusion with voltage clamp of nerve cell bodies separated from their axons. Pretreatment with enzymes such as trypsin that alter membrane function is not required. A platinized platinum wire which ruptures the soma membrane allows low resistance access directly to the cell's interior improving the time resolution under voltage clamp by two orders of magnitude. The shunt resistance of the suction pipette was 10-50 times the neuronal membrane resistance, and the series resistance of the system, which was largely due to the tip diameter, was about 10(5) omega. However, the peak clamp currents were only about 20 nA for a 60-mV voltage step so that measurements of membrane voltage were accurate to within at least 3%. Spatial control of voltage was achieved only after somal separation, and nerve cell bodies isolated in this way do not generate all-or-none action potentials. Measurements of membrane potential, membrane resistance, and membrane time constant are equivalent to those obtained using intracellular micropipettes, the customary method. With the axon attached, comparable all-or-none action potentials were also measured by either method. Complete exchange of Cs+ for K+ was accomplished by internal perfusion and allowed K+ currents to be blocked. Na+ currents could then be blocked by TTX or suppressed by Tris-substituted snail Ringer solution. Ca2+ currents could be blocked using Ni2+ and other divalent cations as well as organic Ca2+ blockers. The most favorable intracellular anion was aspartate-, and the sequence of favorability was inverted from that found in squid axon.

Animals↗
PubMed2003

Structural basis for recruitment of translesion DNA polymerase Pol IV/DinB to the beta-clamp.

Y-family DNA polymerases can extend primer strands across template strand lesions that stall replicative polymerases. The poor processivity and fidelity of these enzymes, key to their biological role, requires that their access to the primer-template junction is both facilitated and regulated in order to minimize mutations. These features are believed to be provided by interaction with processivity factors, beta-clamp or proliferating cell nuclear antigen (PCNA), which are also essential for the function of replicative DNA polymerases. The basis for this interaction is revealed by the crystal structure of the complex between the 'little finger' domain of the Y-family DNA polymerase Pol IV and the beta-clamp processivity factor, both from Escherichia coli. The main interaction involves a C-terminal peptide of Pol IV, and is similar to interactions seen between isolated peptides and other processivity factors. However, this first structure of an entire domain of a binding partner with an assembled clamp reveals a substantial secondary interface, which maintains the polymerase in an inactive orientation, and may regulate the switch between replicative and Y-family DNA polymerases in response to a template strand lesion.

Bacterial Proteins↗
PubMed2000

PSI-BLAST searches using hidden markov models of structural repeats: prediction of an unusual sliding DNA clamp and of beta-propellers in UV-damaged DNA-binding protein.

We have designed hidden Markov models (HMMs) of structurally conserved repeats that, based on pairwise comparisons, are unconserved at the sequence level. To model secondary structure features these HMMs assign higher probabilities of transition to insert or delete states within sequence regions predicted to form loops. HMMs were optimized using a sampling procedure based on the degree of statistical uncertainty associated with parameter estimates. A PSI-BLAST search initialized using a checkpoint-recovered profile derived from simulated sequences emitted by such a HMM can reveal distant structural relationships with, in certain instances, substantially greater sensitivity than a normal PSI-BLAST search. This is illustrated using two examples involving DNA- and RNA-associated proteins with structurally conserved repeats. In the first example a putative sliding DNA clamp protein was detected in the thermophilic bacterium Thermotoga maritima. This protein appears to have arisen by way of a duplicated beta-clamp gene that then acquired features of a PCNA-like clamp, perhaps to perform a PCNA-related function in association with one or more of the many archaeal-like proteins present in this organism. In the second example, beta-propeller domains were predicted in the large subunit of UV-damaged DNA-binding protein and in related proteins, including the large subunit of cleavage-polyadenylation specificity factor, the yeast Rse1p and human SAP130 pre-mRNA splicing factors and the fission yeast Rik1p gene silencing protein.

Animals↗
PubMed2005

Detection of subunit interfacial modifications by tracing the evolution of clamp-loader complex.

The archaeal and eukaryal clamp-loader and clamp proteins were investigated with the evolutionary trace method. The molecular phylogeny of the proteins suggested that the hetero-pentameric complex of the archaeal clamp-loader with two subunits (RFCL and RFCS) was not a preserved ancestral type, but a degenerated version of the eukaryal complex of five subunits (RFC1-5). The evolutionary trace of amino acid replacements during the course of subunit differentiation revealed that the replacements had accumulated preferentially at the subunit interface regions. Some of the interfacial modifications that might be responsible for the specific interaction between the subunits were conserved in the current complex.

Archaeal Proteins↗
PubMed1996

Trimethaphan versus sodium nitroprusside for the control of proximal hypertension during thoracic aortic cross-clamping: the effects on spinal cord ischemia.

Sodium nitroprusside (SNP) has been used to control the proximal hypertension associated with thoracic aortic cross-clamping (TACC) during thoracic aortic surgery. It worsens neurologic outcome, presumably by further decreasing distal arterial pressure and increasing cerebrospinal fluid (CSF) pressure, thereby worsening the spinal cord perfusion pressure (SCPP). Trimethaphan does not increase CSF pressure. Therefore, the present study investigates the effect of trimethaphan versus SNP to control proximal hypertension during TACC on neurologic outcome. Two groups, each with eight mongrel dogs, were studied. All animals underwent descending TACC for 45 min. The mean proximal aortic blood pressure was maintained at 95-100 mm Hg by the use of SNP or trimethaphan. Distal aortic pressure was allowed to vary. The dogs were neurologically evaluated 24 and 48 h later by a blinded observer. During cross-clamping, there was no difference in mean proximal aortic pressure between groups. After 10 min of cross-clamping, distal aortic pressure was higher (P < 0.01), CSF pressure was lower (P < 0.01), and SCPP was higher (P < 0.005) in the trimethaphan group as compared with the SNP group (group effect). Neurologic outcome as assessed by Tarlov's score was better at 24 and 48 h in the trimethaphan group (P < 0.05). Histopathologic injury trended with worsened neurologic outcome. We conclude that 1) trimethaphan produced higher SCPP than SNP, and 2) neurologic outcome was better in the trimethaphan group.

Animals↗
PubMed2001

Inhibition of phosphodiesterase type III before aortic cross-clamping preserves intramyocardial cyclic adenosine monophosphate during cardiopulmonary bypass.

UNLABELLED: Inotropes are often used to treat myocardial dysfunction shortly after cardiopulmonary bypass (CPB). beta-Adrenergic agonists improve contractility, in part by increasing cyclic adenosine monophosphate (cAMP) production, whereas phosphodiesterase type III inhibitors prevent its breakdown. CPB is associated with abnormalities at the beta-receptor level and diminished adenyl cyclase activity, both of which tend to decrease cAMP. These effects may be increased in the presence of preexisting myocardial dysfunction. We tested the hypothesis that inhibition of phosphodiesterase type III before global myocardial ischemia and pharmacologic arrest results in the preservation of intramyocardial cAMP concentration during CPB. Twenty adult patients undergoing coronary artery bypass grafting with CPB were studied. After CPB was instituted, a myocardial biopsy was obtained from the apex of the left ventricle. Patients were randomized to receive either placebo or milrinone (50 micro/kg) through the bypass pump 10 min before aortic cross-clamping. Another myocardial biopsy was performed adjacent to the left ventricular apex just before weaning from CPB. Myocardial cAMP concentration was determined by radioimmunoassay. Myocyte protein content was determined by the Bradford method by using a commercial kit. There were no significant demographic differences between the groups; however, patients in the Milrinone group had a lower left ventricular ejection fraction than placebo (41% +/- 13% vs 53% +/- 7%; P < 0.05). Patients who received milrinone had larger cAMP concentrations at the end of CPB compared with placebo (21 +/- 12.5 pmol/mg protein versus 12.8 +/- 2.2 pmol/mg protein; P < 0.05). The administration of milrinone before aortic cross-clamping is associated with increased intramyocardial cAMP concentration at the end of CPB. IMPLICATIONS: The administration of a single dose of milrinone before aortic cross-clamping resulted in significantly larger intramyocardial cyclic adenosine monophosphate concentration in myocardial biopsy specimens compared with controls.

3',5'-Cyclic-AMP Phosphodiesterases↗
PubMed1986

Cross-clamping of the thoracic aorta. Influence of aortic shunts, laminectomy, papaverine, calcium channel blocker, allopurinol, and superoxide dismutase on spinal cord blood flow and paraplegia in baboons.

There is a high incidence of paraplegia associated with thoracic aortic cross-clamping, even when cardiopulmonary bypass or shunts are used. In 56 adult baboons, spinal cord blood flow (SCBF), vascular anatomy, and paraplegia rates were evaluated. Tissue blood flow was measured by radioactive microspheres. Various procedures were used to increase SCBF and to prevent ischemia-reperfusion injury. It was found that the rate of paraplegia was inversely correlated with neural tissue ischemia (SCBF) and directly correlated with reperfusion hyperemia. Two methods completely prevented paraplegia. These two methods were a thoracic shunt with occlusion of the infrarenal aorta or cerebrospinal fluid drainage plus intrathecal papaverine injection, both of which were associated with an increased SCBF. Furthermore, papaverine dilated the anterior spinal artery (ASA) (p = 0.007) and increased the blood flow through the lower ASA. Whereas procedures utilizing a calcium channel blocker (flunarizine), allopurinol, superoxide dismutase (SOD), laminectomy alone, and a thoracoabdominal shunt not perfusing the arteria radicularis magna (ARM) all failed to prevent paraplegia, allopurinol (p = 0.026) and SOD (p = 0.004) did prevent gastric stress lesions, indicating that their failure to prevent paraplegia was not due to a lack of activity. Of great clinical interest is that, if a shunt is used and the ARM is perfused, infrarenal aortic cross-clamping increases SCBF, thus preventing paraplegia. Intrathecal application of papaverine proved to be even more effective in increasing SCBF and also completely prevented paraplegia. As this is a safer procedure than the insertion of shunts, this is the method of choice for the prevention of paraplegia associated with thoracic aortic cross-clamping. The preliminary trial using intrathecal papaverine in human beings has thus far shown no adverse side effects from the drug, and no paraplegia has occurred.

Allopurinol↗
PubMed1985

A new upper blepharoplasty clamp.

New right and left blepharoplasty clamps have been devised which conform to the three-dimensional curves of the adult upper eyelids. These are suggested for use in older patients who require excision of a large amount of skin and are an adjunct in upper blepharoplasty. We have used the new clamps successfully in 20 upper blepharoplasties. The clamps provide for a rapid, bloodless removal of large amounts of skin.

Equipment Design↗
PubMed2003

Pelvic C-clamp in a pediatric patient.

The pelvic C-clamp was designed to provide posterior stability temporarily to pelvic ring injuries associated with massive venous hemorrhage in adult patients. Pediatric pelvic ring injuries are uncommon, but when unstable injuries occur they may be coupled with visceral injuries and lethal hemorrhage. 1, 2 Anterior external frame fixators have been described in the treatment of these injuries in pediatric patients with few adverse outcomes and good long-term results. Although they provide adequate fixation, anterior frame application is complicated, time-consuming, and cumbersome as an emergency application. The pelvic C-clamp eliminated these problems, while providing fixation points that do not violate areas of cartilage or physeal growth. We present a case demonstrating that the pelvic C-clamp is a safe form of temporary fixation in a skeletally immature patient with a posterior pelvic ring injury associated with massive hemorrhage.

Child↗