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At least 37 records · Page 2Linked to original sources
PubMed2001

Discontinuous single electrode voltage-clamp measurements: assessment of clamp accuracy in Vicia faba guard cells.

The use of a discontinuous single electrode voltage-clamp (dSEVC) offers an attractive alternative to the patch-clamp technique, since whole-cell measurements can be performed with a single sharp electrode. Comparison of current-voltage relations, however, revealed a weaker voltage dependence of channels measured with the dSEVC compared to patch clamp. The accuracy of the dSEVC was tested on Vicia faba guard cells impaled with double-barrelled electrodes. The actual clamp potential was measured independently of the dSEVC, at the second barrel. The weaker voltage dependence of ion channels appeared to be due to an overestimation of the clamp potential by the dSEVC. The deviation between the intended and actual clamp potential showed a linear relationship with the injected current; on average a 126 mV deviation was found for a clamp current of 1 nA. The deviation was probably caused by a slow settling capacity at the electrode, not compensated by the dSEVC amplifier. It is concluded that the dSEVC method in its current state is only suited for the study of small ion conductances in plant cells.

Cell Membrane↗
PubMed2005

Open clamp structure in the clamp-loading complex visualized by electron microscopic image analysis.

Ring-shaped sliding clamps and clamp loader ATPases are essential factors for rapid and accurate DNA replication. The clamp ring is opened and resealed at the primer-template junctions by the ATP-fueled clamp loader function. The processivity of the DNA polymerase is conferred by its attachment to the clamp loaded onto the DNA. In eukarya and archaea, the replication factor C (RFC) and the proliferating cell nuclear antigen (PCNA) play crucial roles as the clamp loader and the clamp, respectively. Here, we report the electron microscopic structure of an archaeal RFC-PCNA-DNA complex at 12-A resolution. This complex exhibits excellent fitting of each atomic structure of RFC, PCNA, and the primed DNA. The PCNA ring retains an open conformation by extensive interactions with RFC, with a distorted spring washer-like conformation. The complex appears to represent the intermediate, where the PCNA ring is kept open before ATP hydrolysis by RFC.

DNA Replication↗
PubMed1998

ATP binding to the Escherichia coli clamp loader powers opening of the ring-shaped clamp of DNA polymerase III holoenzyme.

The Escherichia coli gamma complex serves as a clamp loader, catalyzing ATP-dependent assembly of beta protein clamps onto primed DNA templates during DNA replication. These ring-shaped clamps tether DNA polymerase III holoenzyme to the template, facilitating rapid and processive DNA synthesis. This report focuses on the role of ATP binding and hydrolysis catalyzed by the gamma complex during clamp loading. We show that the energy from ATP binding to gamma complex powers several initial events in the clamp loading pathway. The gamma complex (gamma2 delta delta'chi psi) binds two ATP molecules (one per gamma subunit in the complex) with high affinity (Kd = 1-2. 5 x 10(-6) M) or two adenosine 5'-O-(3-thiotriphosphate)(ATPgammaS) molecules with slightly lower affinity (Kd = 5-6.5 x 10(-6) M). Experiments performed prior to the first ATP turnover (kcat = 4 x 10(-3) s-1 at 4 degreesC), or in the presence of ATPgammaS (kcat = 1 x 10(-4) s-1 at 37 degreesC), demonstrate that upon interaction with ATP the gamma complex undergoes a change in conformation. This ATP-bound gamma complex binds beta and opens the ring at the dimer interface. Still prior to ATP hydrolysis, the composite of gamma complex and the open beta ring binds with high affinity to primer-template DNA. Thus ATP binding powers all the steps in the clamp loading pathway leading up to the assembly of a gamma complex. open beta ring.DNA intermediate, setting the stage for ring closing and turnover of the clamp loader, steps that may be linked to subsequent hydrolysis of ATP.

Adenosine Triphosphate↗
PubMed2004

Molecular mechanism of DNA replication-coupled inactivation of the initiator protein in Escherichia coli: interaction of DnaA with the sliding clamp-loaded DNA and the sliding clamp-Hda complex.

In Escherichia coli, the ATP-DnaA protein initiates chromosomal replication. After the DNA polymerase III holoenzyme is loaded on to DNA, DnaA-bound ATP is hydrolysed in a manner depending on Hda protein and the DNA-loaded form of the DNA polymerase III sliding clamp subunit, which yields ADP-DnaA, an inactivated form for initiation. This regulatory DnaA-inactivation represses extra initiation events. In this study, in vitro replication intermediates and structured DNA mimicking replicational intermediates were first used to identify structural prerequisites in the process of DnaA-ATP hydrolysis. Unlike duplex DNA loaded with sliding clamps, primer RNA-DNA heteroduplexes loaded with clamps were not associated with DnaA-ATP hydrolysis, and duplex DNA provided in trans did not rescue this defect. At least 40-bp duplex DNA is competent for the DnaA-ATP hydrolysis when a single clamp was loaded. The DnaA-ATP hydrolysis was inhibited when ATP-DnaA was tightly bound to a DnaA box-bearing oligonucleotide. These results imply that the DnaA-ATP hydrolysis involves the direct interaction of ATP-DnaA with duplex DNA flanking the sliding clamp. Furthermore, Hda protein formed a stable complex with the sliding clamp. Based on these, we suggest a mechanical basis in the DnaA-inactivation that ATP-DnaA interacts with the Hda-clamp complex with the aid of DNA binding.

Adenosine Triphosphatases↗
PubMed2003

Voltage-clamp-controlled current-clamp recordings from neurons: an electrophysiological technique enabling the detection of fast potential changes at preset holding potentials.

Investigations of the properties of fast, transient potential changes (e.g. receptor potentials or synaptic potentials) in excitable cells by means of current-clamp recording techniques require the exact adjustment and control of membrane potentials. Usually, the desired membrane potential values are set by current injection via the recording electrode and are controlled manually by regulating the current strength necessary to maintain a constant potential. However, this technique is associated with a number of disadvantages. A single-electrode current- and voltage-clamp amplifier was therefore modified to compensate for slow membrane potential changes without affecting faster voltage responses. Basically, low-pass filters with selectable time constants were incorporated into the voltage-clamp feedback circuit to control the amplifier's response speed. In addition, the amplifier's electronic circuits were altered to enable current pulse injection into the cells. Thus, while recording at preset and controlled membrane potentials, it was possible to monitor the cell's input resistance or current/voltage relationship. This new recording technique has been designated "voltage-clamp-controlled current clamp" (VCcCC) and its performance was tested by intracellular recordings from neocortical and neostriatal neurons in vitro using either conventional microelectrodes or patch-clamp electrodes.

Amplifiers, Electronic↗
PubMed2006

Overproduction and purification of RFC-related clamp loaders and PCNA-related clamps from Saccharomyces cerevisiae.

The replication clamp PCNA and its loader RFC (Replication Factor C) are central factors required for processive replication and coordinated DNA repair. Recently, several additional related clamp loaders have been identified. These alternative clamp loaders contain the small Rfc2-5 subunits of RFC, but replace the large Rfc1 subunit by a pathway-specific alternative large subunit, Rad24 for the DNA damage checkpoint, Ctf18 for the establishment of sister chromatid cohesion, and Elg1 for a general function in chromosome stability. In order to define biochemical functions for these loaders, the loaders were overproduced in yeast and purified at a milligram scale. To aid in purification, the large subunit of each clamp loader was fused to a GST-tag that, after purification could be easily removed by a rhinoviral protease. This methodology yielded all clamp loaders in high yield and with high enzymatic activity. The yeast 9-1-1 checkpoint clamp, consisting of Rad17, Mec3, and Ddc1, was overproduced and purified in a similar manner.

DNA Repair↗
PubMed2002

Clamp loaders and sliding clamps.

A coherent view of the structure and function of DNA polymerase processivity factors (sliding clamps and clamp loaders) is emerging from recent structural studies. Crystal structures of sliding clamps from the T4 and RB69 bacteriophages, and from an archaebacterium expand the gallery of ring-shaped processivity factors and clarify how the clamp interacts with the DNA polymerase. Crystallographic and electron microscopic views of clamp loaders from bacteria, archaebacteria and eukaryotes emphasize their common architecture and have produced models of how ATPbinding might be coupled to clamp opening/loading.

Adenosine Triphosphate↗
PubMed2004

Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex.

Sliding clamps are ring-shaped proteins that encircle DNA and confer high processivity on DNA polymerases. Here we report the crystal structure of the five-protein clamp loader complex (replication factor-C, RFC) of the yeast Saccharomyces cerevisiae, bound to the sliding clamp (proliferating cell nuclear antigen, PCNA). Tight interfacial coordination of the ATP analogue ATP-gammaS by RFC results in a spiral arrangement of the ATPase domains of the clamp loader above the PCNA ring. Placement of a model for primed DNA within the central hole of PCNA reveals a striking correspondence between the RFC spiral and the grooves of the DNA double helix. This model, in which the clamp loader complex locks onto primed DNA in a screw-cap-like arrangement, provides a simple explanation for the process by which the engagement of primer-template junctions by the RFC:PCNA complex results in ATP hydrolysis and release of the sliding clamp on DNA.

Adenosine Triphosphate↗
PubMed2002

Aortic clamping during elective operations for infrarenal disease: The influence of clamping time on renal function.

OBJECTIVE: Aortic clamping proximal to the renal arteries is sometimes necessitated during infrarenal and juxtarenal aortic surgery and may be associated with an increased risk of renal ischemia and its consequences. The aim of the study was to estimate this risk and possibly identify a "safe" duration of renal ischemia. METHODS: Medical records were retrospectively reviewed for 60 consecutive patients (from 1987 to 1994) with abdominal aortic aneurysm (n = 43) and occlusive disease (n = 17) confined to the infrarenal or juxtarenal aorta who underwent infrarenal aortic reconstruction with temporary suprarenal clamping. The data obtained included risk factors, preoperative and postoperative serum creatinine level, blood urea nitrogen (BUN) value, proteinuria before surgery, and suprarenal clamping times. RESULTS: The mean age of the patients was 64.4 years (+/- 11.4 years), and 74% were men. Concomitant cardiac disease was present in 41% of the patients, and 9% had diabetes. The preoperative creatinine level was 1.21 mg/dL (+/- 0.54 mg/dL), and the BUN value was 16.6 mg/dL (+/- 7.8 mg/dL). During surgery, blood flow to the renal arteries was interrupted for 32.0 minutes (+/- 17 minutes). None of the surviving patients needed dialysis or had signs of acute renal failure after the operations, but transient azotemia (rise in creatinine level) occurred in 23% of the patients. Risk factors for this condition were high preoperative creatinine values and hypotension during surgery, but the main determinant was total renal ischemia time. Odds ratios for such transient renal dysfunction showed as much as a 10-fold risk when suprarenal aortic clamping was greater than 50 minutes as compared with 30 minutes or less. CONCLUSION: Postoperative renal function impairment is rare in this group of patients. If suprarenal clamp duration (renal ischemia time) is brief, patients with normal preoperative creatinine levels exhibit no increase or a marginal increase in BUN or creatinine levels after surgery. Accordingly, suprarenal aortic clamping less than 50 minutes in this patient group appears safe and well tolerated.

Adult↗
PubMed2001

Interplay of clamp loader subunits in opening the beta sliding clamp of Escherichia coli DNA polymerase III holoenzyme.

The Escherichia coli beta dimer is a ring-shaped protein that encircles DNA and acts as a sliding clamp to tether the replicase, DNA polymerase III holoenzyme, to DNA. The gamma complex (gammadeltadelta'chipsi) clamp loader couples ATP to the opening and closing of beta in assembly of the ring onto DNA. These proteins are functionally and structurally conserved in all cells. The eukaryotic equivalents are the replication factor C (RFC) clamp loader and the proliferating cell nuclear antigen (PCNA) clamp. The delta subunit of the E. coli gamma complex clamp loader is known to bind beta and open it by parting one of the dimer interfaces. This study demonstrates that other subunits of gamma complex also bind beta, although weaker than delta. The gamma subunit like delta, affects the opening of beta, but with a lower efficiency than delta. The delta' subunit regulates both gamma and delta ring opening activities in a fashion that is modulated by ATP interaction with gamma. The implications of these actions for the workings of the E. coli clamp loading machinery and for eukaryotic RFC and PCNA are discussed.

Adenosine Triphosphate↗
PubMed1997

Structural analyses of gp45 sliding clamp interactions during assembly of the bacteriophage T4 DNA polymerase holoenzyme. I. Conformational changes within the gp44/62-gp45-ATP complex during clamp loading.

A multisubunit ring-shaped protein complex is used to tether the polymerase to the DNA at the primer-template junction in most DNA replication systems. This "sliding clamp" interacts with the polymerase, completely encircles the DNA duplex, and is assembled onto the DNA by a specific clamp loading complex in an ATP-driven process. Site-specific mutagenesis has been used to introduce single cysteine residues as reactive sites for adduct formation within each of the three subunits of the bacteriophage T4-coded sliding clamp complex (gp45). Two such mutants, gp45S19C and gp45K81C, are reacted with the cysteine-specific photoactivable cross-linker TFPAM-3 and used to track the changes in the relative positioning of the gp45 subunits with one another and with the other components of the clamp loading complex (gp44/62) in the various stages of the loading process. Cross-linking interactions performed in the presence of nucleotide cofactors show that ATP binding and hydrolysis, interaction with primer-template DNA, and release of ADP all result in significant conformational changes within the clamp loading cycle. A structural model is presented to account for the observed rearrangements of intersubunit contacts within the complex during the loading process.

Adenosine Triphosphate↗
PubMed2004

Occluding clamp technique during coronary artery bypass grafting: single or double-clamp technique?

BACKGROUND: External manipulation of the diseased aorta during cardiac surgery is the most important mechanism leading to the detachment of atherosclerotic debris due, especially, to the use of aortic clamping. The aim of the present study was to determine the best occluding clamp technique to minimize the risk of postoperative cerebrovascular accidents in patients who undergo isolated coronary artery bypass grafting (CABG): single-clamp technique (SCT) or double-clamp technique (DCT)? METHODS: Two hundred and eighty-one consecutive patients undergoing isolated CABG in our center between January 2001 and December 2003 were enrolled. SCT was used in 145 cases and DCT was used in 136 cases. Postoperative adverse events were retrospectively compared between these two groups. RESULTS: The aortic cross-clamp times were longer for patients in the SCT group, whereas the mean cardiopulmonary bypass time was shorter in the DCT group. There were no differences between the two groups in terms of postoperative stroke (0.6% SCT vs 0.7% DCT, p = NS) and hospital mortality (1.3% SCT vs 1.4% DCT, p = NS). CONCLUSIONS: The results of this study suggest that, among patients who undergo CABG, there are no differences in neurologic outcome between those in whom DCT was used and those in whom SCT was employed.

Aged↗
PubMed2004

The interpretation of current-clamp recordings in the cell-attached patch-clamp configuration.

In these experiments we have investigated the feasibility and accuracy of recording steady-state and dynamic changes in transmembrane potential noninvasively across an intact cell-attached patch using the current-clamp mode of a conventional patch-clamp amplifier. Using an equivalent circuit mimicking simultaneous whole-cell voltage-clamp and cell-attached current-clamp recordings we have defined both mathematically and experimentally the relationship between the membrane patch resistance, the seal resistance, and the fraction of the whole-cell potential recorded across an intact membrane patch. This analysis revealed a steep increase in the accuracy of recording of steady-state membrane potential as the seal/membrane ratio increases from 0. The recording accuracy approaches 100% as the seal/membrane ratio approaches infinity. Membrane potential measurements across intact cell-attached patches in rat basophilic leukemia cells and rat megakaryocytes revealed a surprisingly high degree of accuracy and demonstrated the ability of this noninvasive technique to follow dynamic changes in potential in nonexcitable cells.

Adenosine Diphosphate↗
PubMed2004

The PCNA-RFC families of DNA clamps and clamp loaders.

The proliferating cell nuclear antigen PCNA functions at multiple levels in directing DNA metabolic pathways. Unbound to DNA, PCNA promotes localization of replication factors with a consensus PCNA-binding domain to replication factories. When bound to DNA, PCNA organizes various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modeling. Its modification by ubiquitin directs the cellular response to DNA damage. The ring-like PCNA homotrimer encircles double-stranded DNA and slides spontaneously across it. Loading of PCNA onto DNA at template-primer junctions is performed in an ATP-dependent process by replication factor C (RFC), a heteropentameric AAA+ protein complex consisting of the Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Loading of yeast PCNA (POL30) is mechanistically distinct from analogous processes in E. coli (beta subunit by the gamma complex) and bacteriophage T4 (gp45 by gp44/62). Multiple stepwise ATP-binding events to RFC are required to load PCNA onto primed DNA. This stepwise mechanism should permit editing of this process at individual steps and allow for divergence of the default process into more specialized modes. Indeed, alternative RFC complexes consisting of the small RFC subunits together with an alternative Rfc1-like subunit have been identified. A complex required for the DNA damage checkpoint contains the Rad24 subunit, a complex required for sister chromatid cohesion contains the Ctf18 subunit, and a complex that aids in genome stability contains the Elg1 subunit. Only the RFC-Rad24 complex has a known associated clamp, a heterotrimeric complex consisting of Rad17, Mec3, and Ddc1. The other putative clamp loaders could either act on clamps yet to be identified or act on the two known clamps.

DNA↗
PubMed1987

Beta cell response to the hyperglycaemic clamp in three patients with insulinoma: a study using a hyperglycaemic glucose clamp.

To determine the mechanism responsible for deficient carbohydrate metabolism in patients with insulinoma, we studied three affected patients and seven normal controls using the hyperglycaemic clamp method (8.4 mmol/l) with the BIOSTATOR (GCIIS). In insulinoma patients, the amount of glucose necessary to reach the hyperglycaemic clamp was less than that required in normal controls (6.19 +/- 1.19 mg/min/kg vs. 9.95 +/- 0.53 mg/min/kg) (p less than 0.05). There was no significant difference in metabolized glucose (M) in the stable phase of the hyperglycaemic clamp; however, the M/IRI in this phase was less in those with insulinoma (7.9 +/- 0.50) than in controls (22.26 +/- 4.14) (p less than 0.05). There was no difference in beta cell secretory response to hyperglycaemic stimulus (defined as the increase in the concentration of C-peptide from the basal state to the stable phase of the hyperglycaemic clamp) between the two groups. Hepatic insulin extraction was significantly lower in patients with insulinoma than in normal controls (+0.72 +/- 0.07 vs. +0.85 +/- 0.01). Finally, the ratios of fractional turnover of glucose (K/IRI); glucose clearance/IRI and total rate of elimination of glucose from the extracellular pool/IRI were also all lower in patients with insulinoma than in controls (p less than 0.05). These data support the conclusion that deficient glucose metabolism seen in these patients is not related to a lack of response to glucose on the part of normal or neoplastic islet tissue.(ABSTRACT TRUNCATED AT 250 WORDS)

Adenoma, Islet Cell↗
PubMed2003

Mechanism of loading the Escherichia coli DNA polymerase III beta sliding clamp on DNA. Bona fide primer/templates preferentially trigger the gamma complex to hydrolyze ATP and load the clamp.

The Escherichia coli DNA polymerase III gamma complex clamp loader assembles the ring-shaped beta sliding clamp onto DNA. The core polymerase is tethered to the template by beta, enabling processive replication of the genome. Here we investigate the DNA substrate specificity of the clamp-loading reaction by measuring the pre-steady-state kinetics of DNA binding and ATP hydrolysis using elongation-proficient and deficient primer/template DNA. The ATP-bound clamp loader binds both elongation-proficient and deficient DNA substrates either in the presence or absence of beta. However, elongation-proficient DNA preferentially triggers gamma complex to release beta onto DNA with concomitant hydrolysis of ATP. Binding to elongation-proficient DNA converts the gamma complex from a high affinity ATP-bound state to an ADP-bound state having a 10(5)-fold lower affinity for DNA. Steady-state binding assays are misleading, suggesting that gamma complex binds much more avidly to non-extendable primer/template DNA because recycling to the high affinity binding state is rate-limiting. Pre-steady-state rotational anisotropy data reveal a dynamic association-dissociation of gamma complex with extendable primer/templates leading to the diametrically opposite conclusion. The strongly favored dynamic recognition of extendable DNA does not require the presence of beta. Thus, the gamma complex uses ATP binding and hydrolysis as a mechanism for modulating its interaction with DNA in which the ATP-bound form binds with high affinity to DNA but elongation-proficient DNA substrates preferentially trigger hydrolysis of ATP and conversion to a low affinity state.

Adenosine Triphosphate↗
PubMed2000

Structure-based predictions of Rad1, Rad9, Hus1 and Rad17 participation in sliding clamp and clamp-loading complexes.

The repair of damaged DNA is coupled to the completion of DNA replication by several cell cycle checkpoint proteins, including, for example, in fission yeast Rad1(Sp), Hus1(Sp), Rad9(Sp) and Rad17(Sp). We have found that these four proteins are conserved with protein sequences throughout eukaryotic evolution. Using computational techniques, including fold recognition, comparative modeling and generalized sequence profiles, we have made high confidence structure predictions for the each of the Rad1, Hus1 and Rad9 protein families (Rad17(Sc), Mec3(Sc) and Ddc1(Sc) in budding yeast, respectively). Each of these families was found to share a common protein fold with that of PCNA, the sliding clamp protein that tethers DNA polymerase to its template. We used previously reported genetic and biochemical data for these proteins from yeast and human cells to predict a heterotrimeric PCNA-like ring structure for the functional Rad1/Rad9/Hus1 complex and to determine their exact order within it. In addition, for each individual protein family, contact regions with neighbors within the PCNA-like ring were identified. Based on a molecular model for Rad17(Sp), we concluded that members of this family, similar to the subunits of the RFC clamp-loading complex, are capable of coupling ATP binding with conformational changes required to load a sliding clamp onto DNA. This model substantiates previous findings regarding the behavior of Rad17 family proteins upon DNA damage and within the RFC complex of clamp-loading proteins.

Adenosine Triphosphate↗
PubMed2003

Laparoscopic partial nephrectomy for renal tumor: single center experience comparing clamping and no clamping techniques of the renal vasculature.

PURPOSE: We performed a nonrandomized retrospective comparison of 2 techniques for laparoscopic partial nephrectomy, that is without and with clamping the renal vessels. MATERIALS AND METHODS: Between December 1997 and February 2002, 28 consecutive patients underwent transperitoneal laparoscopic partial nephrectomy for renal tumor. In group 1 (12 patients) partial nephrectomy was performed with ultrasonic shears and bipolar cautery without clamping the renal vessels, while in group 2 (16 patients) the renal pedicle was clamped before tumor excision. In group 2 patients intracorporeal kidney cooling was achieved by a ureteral catheter connected to 4C solution. Intracorporeal freehand suturing techniques were used to close the collecting system when opened and approximate the renal parenchyma. RESULTS: All procedures were successfully completed laparoscopically. Mean renal ischemia time +/- SD was 27.3 +/- 7 minutes (range 15 to 47) in group 2 patients. Mean laparoscopic operating time was 179.1 +/- 86 minutes (range 90 to 390) in group 1 compared with 121.5 +/- 37 minutes (range 60 to 210) in group 2 (p = 0.004). Mean intraoperative blood loss was significantly higher in group 1 than in group 2 (708.3 +/- 569 versus 270.3 +/- 281 ml., p = 0.014). Three patients in group 1 and 2 in group 2 required blood transfusions. Immediately postoperatively mean creatinine was 1.26 +/- 0.36 and 1.45 +/- 0.61 mg./dl. in groups 1 and 2, respectively (p = 0.075). Surgical margins were negative in all specimens. Pathological examination revealed renal cell cancer in 18 cases (stages pT1 in 17 and pT3a in 1), oncocytoma in 4, angiomyolipoma in 5 and renal adenoma in 1. CONCLUSIONS: Laparoscopic partial nephrectomy represents a feasible option for patients with small renal masses. Clamping the renal vessels during tumor resection and suturing the kidney mimics the open technique and seems to be associated with less blood loss and shorter laparoscopic operative time.

Aged↗