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Biomedical subjects

S C Harvey

Publications and source records attributed to S C Harvey.

At least 73 records · Page 4Linked to original sources
PubMed1996

Determinants of competitive antagonist sensitivity on neuronal nicotinic receptor beta subunits.

We constructed a series of chimeric and mutant neuronal nicotinic acetylcholine receptor beta subunits to map amino acid residues that determine sensitivity to competitive antagonists. The beta 2 and beta 4 subunits form pharmacologically distinct receptors when expressed in combination with the alpha 3 subunit in Xenopus oocytes. At equipotent acetylcholine concentrations, alpha 3 beta 2 is 56-fold more sensitive to blockage by dihydro-beta-erythroidine than is alpha 3 beta 4. The alpha 3 beta 2 combination is also sensitive to long-term blockade by neuronal bungarotoxin, whereas alpha 3 beta 4 is not. Pharmacological analysis of receptors formed by chimeric beta subunits reveals that amino acid residues that determine both dihydro-beta-erythroidine and neuronal bungarotoxin sensitivity are located within several sequence segments. The major determinant of sensitivity to both competitive antagonists is located between residues 54 and 63. A minor determinant of sensitivity to both antagonists lies between residues 1 and 54, whereas a minor determinant of NBT sensitivity lies between residues 74 and 80. Within region 54-63 of beta 2, mutant beta 2 subunits were used to identify threonine 59 as a residue critical in determining competitive antagonist sensitivity. Changing threonine 59 to lysine, as occurs in beta 4, causes a 9-fold decrease in dihydro-beta-erythroidine sensitivity and a 71-fold decrease in neuronal bungarotoxin sensitivity. Changing polar threonine 59 to negatively charged aspartate causes a 2.5-fold increase in neuronal bungarotoxin sensitivity and has no effect on dihydro-beta-erythroidine sensitivity.

Animals↗
PubMed1996

Molecular modelling of (A4T4NN)n and (T4A4NN)n: sequence elements responsible for curvature.

The molecular modelling program JUMNA has been used to investigate the origins of the strikingly different curvature of the two sequences, (A4T4NN)n and (T4A4NN)n. Gel electrophoresis and cyclisation studies have shown that only the former of these two sequences is significantly curved. By developing novel superhelical symmetry constraints we were able to study the energetic and structural aspects of polymeric DNA having a controlled curvature. The results obtained (which do not take into account specific hydration effects) correlate well with the experimental data and offer a molecular level explanation of curvature. Although curvature is found to be initiated by specific dinucleotide junctions, deformations spread to surrounding dinucleotide steps and, moreover, sequence effects beyond the dinucleotide level are observed.

Base Sequence↗
PubMed1996

Molecular modeling of closed circular DNA thermodynamic ensembles.

Many modeling studies of supercoiled DNA are based on equilibrium structures from theoretical calculations or energy minimization. Since closed circular DNAs are flexible, it is possible that errors are introduced by calculating properties from a single minimum energy structure, rather than from a complete thermodynamic ensemble. We have investigated this question using molecular dynamics simulations on a low resolution molecular mechanics model in which each base pair is represented by three points (a plane). This allows the inclusion of sequence-dependent variations of tip, inclination, and twist. Three kinds of sequences were tested: (1) homogeneous DNA, in which all base pairs have the helicoidal parameters of an ideal, average B-DNA; (2) random sequence DNA; and (3) curved DNA. We examined the rate of convergence of various structural parameters. Convergence for most of these is slowest for homogeneous sequences, more rapid for random sequences, and most rapid for curved sequences. The most slowly converging parameter is the antipodes profile. In a plasmid with N base pairs (bp), the antipodes distance is the distance dij from base pair i to base pair j halfway around the plasmid, j = i + N/2. The antipodes profile at time tau is a plot of dij over the range i = 1, N/2. In a homogeneous plasmid, convergence requires that the antipodes profile averaged over time must be flat. Even in the small plasmids examined here, the average properties of the ensembles were found to differ from those of static equilibrium structures. These effects will be even more dramatic for larger plasmids. Further, average and dynamic properties are affected by both plasmid size and sequence.

Chemical Phenomena↗
PubMed1996

Molecular dynamics simulations of small DNA plasmids: effects of sequence and supercoiling on intramolecular motions.

Small (600 base pair) DNA plasmids were modeled with a simplified representation (3DNA) and the intramolecular motions were studied using molecular mechanics and molecular dynamics techniques. The model is detailed enough to incorporate sequence effects. At the same time, it is simple enough to allow long molecular dynamics simulations. The simulations revealed that large-scale slithering occurs in a homogeneous sequence. In a heterogeneous sequence, containing numerous small intrinsic curves, the centers of the curves are preferentially positioned at the tips of loops. With more curves than loop tips (two in unbranched supercoiled DNA), the heterogeneous sequence plasmid slithers short distances to reposition other curves into the loop tips. However, the DNA is immobilized most of the time, with the loop tips positioned over a few favored curve centers. Branching or looping also appears in the heterogeneous sequence as a new method of repositioning the loop tips. Instead of a smooth progression of increasing writhing with increasing linking difference, theoretical studies have predicted that there is a threshold between unwrithed and writhed DNA at a linking difference between one and two. This has previously been observed in simulations of static structures and is demonstrated here for dynamic homogeneous closed DNA. Such an abrupt transition is not found in the heterogeneous sequence in both the static and dynamic cases.

DNA, Superhelical↗
PubMed1996

Action at a distance in supercoiled DNA: effects of sequence on slither, branching, and intramolecular concentration.

We report a computer modeling study of DNA supercoiling in model plasmids over the size range of 140-1260 bp. We used a computer model with basepair resolution. Molecular dynamics was used to produce ensembles at 300 K and to investigate intramolecular motions. The plasmid models varied by their sequence. The sequence types employed for comparison included a curve-bearing plasmid, a heterogenous sequence plasmid, and a homogenous sequence. Within the three sequence types tested at the 1260-bp plasmid size, we observed several sequence-dependent phenomena. Writhe, radius of gyration, slither motion, and branching probability were seen to be sequence dependent. Branching probability was the least in the homogenous plasmid and the greatest in the curve-bearing plasmid. The curve imposed a symmetry on the plasmid that was absent in the heterogenous sequence. Significant localizations and enhancements of intramolecular concentration were seen to a persistence length. Molecular dynamics allowed us to observe the mechanism of branch formation and reabsorption. We observed a size-dependent change in the types of motion observed in plasmids. Slither motion predominated in plasmids up to 600 bp in size, whereas global rearrangements were more important in the 1260 mer.

Base Sequence↗
PubMed1996

Multiple determinants of dihydro-beta-erythroidine sensitivity on rat neuronal nicotinic receptor alpha subunits.

Neuronal nicotinic acetylcholine receptors are differentially sensitive to blockade by the competitive antagonist dihydro-beta-erythroidine. Both alpha and beta subunits participate in determining sensitivity to this antagonist. The alpha subunit contribution to dihydro-beta-erythroidine sensitivity is illustrated by comparing the alpha 4 beta 4 receptor and the alpha 3 beta 4 receptor, which differ in sensitivity to dihydro-beta-erythroidine by approximately 120-fold. IC50 values for blocking alpha 4 beta 4 and alpha 3 beta 4, responding to EC20 concentrations of acetylcholine, were 0.19 +/- 0.06 and 23.1 +/- 10.2 microM, respectively. To map the sequence segments responsible for this difference, we constructed a series of chimeric alpha subunits containing portions of the alpha 4 and alpha 3 subunits. These chimeras were coexpressed with beta 4, allowing pharmacological characterization. We found determinants of dihydro-beta-erythroidine sensitivity to be distributed throughout the N-terminal extracellular domain of the alpha subunit. These determinants were localized to sequence segments 1-94, 94-152, and 195-215. Loss of determinants within segment 1-94 had the largest effect, decreasing dihydro-beta-erythroidine sensitivity by 4.3-fold.

Acetylcholine↗
PubMed1996

DNA topological context affects access to eukaryotic DNA topoisomerase I.

We have analyzed the reactivity of a 217 base pair segment of the intrinsically curved Crithidia fasciculata kinetoplast DNA towards eukaryotic DNA topoisomerase I. The substrates were open [linear fragment and nicked circle] and closed minidomains [closed relaxed circle and circles with linking differences of -1 and -2]. We interpreted the results with the aid of a model that was used to predict the structures of the topoisomers. The modelling shows that the delta Lk(-1) form is unusually compact because of the curvature in the DNA. To determine the role of sequence-directed curvature in both the experimental and modeling studies, controls were examined in which the curved Crithidia sequence was replaced by an uncurved sequence obtained from the plasmid pBR322. Reactivity of the Crithidia DNA [as analyzed both by the cleavage and topoisomerization reactions] markedly varied among the DNA forms: (i) the hierarchy of overall reactivity observed is: linear fragment > nicked circular, closed circular [delta Lk(0)], interwound [delta Lk(-2)] > bent interwound [delta Lk(-1)]; (ii) the intensity of several cleavage positions differs among DNA forms. The results show that eukaryotic DNA topoisomerase I is very sensitive to the conformation of the substrates and that its reactivity is modulated by the variation of the compactness of the DNA molecule. The C. fasciculata sequence contains a highly curved segment that determines the conformation of the closed circle in a complex way.

Animals↗
PubMed1996

The effect of bupivacaine skull block on the hemodynamic response to craniotomy.

The placement of pointed cranial pins into the periosteum is a recognized acute noxious stimulation during intracranial surgery which can result in sudden increases in blood pressure and heart rate, causing increases in intracranial pressure. A skull block (blockade of the nerves that innervate the scalp, including the greater and lesser occipital nerves, the supraorbital and supratrochlear nerves, the auriculotemporal nerves, and the greater auricular nerves) may be effective in reducing hypertension and tachycardia. Twenty-one patients were allocated in a prospective, double-blind fashion to a control group or a bupivacaine group. After a standardized induction and 5 min prior to head pinning, a skull block was performed. Patients in the control group received a skull block of normal saline, while the bupivacaine group received a skull block with 0.5% bupivacaine. Systolic (SAP), diastolic (DAP), mean arterial pressure (MAP), heart rate (HR), and end-tidal isoflurane were recorded at the following times: 5 min after the induction of anesthesia, during performance of the skull block, during head pinning, and 5 min after head pinning. Significant increases in SAP of 40 +/- 6 mm Hg, DAP of 30 +/- 5 mm Hg, MAP of 32 +/- 6 mm Hg, and HR of 22 +/- 5 bpm occurred during head pinning in the control group, while remaining unchanged in the bupivacaine group. These results demonstrate that a skull block using 0.5% bupivacaine successfully blunts the hemodynamic response to head pinning.

Adolescent↗
PubMed1996

Management of cancer pain.

Pain is often the first symptom of cancer. Pain and fear of pain are concerns of most cancer patients and their families. The therapeutic options available to control pain are numerous, allowing practitioners to better individualize treatment. We present an overview of the pathophysiology of cancer pain, the current theories of pharmacologic opioid management, advantages of adjuvant drugs, and the range of invasive and noninvasive procedures that practitioners can offer their patients who have cancer-related pain.

Drug Tolerance↗
PubMed1995

An oligodeoxyribonucleotide that supports catalytic activity in the hammerhead ribozyme domain.

A study of the activity of deoxyribonucleotide-substituted analogs of the hammerhead domain of RNA catalysis has led to the design of a 14mer oligomer composed entirely of deoxyribonucleotides that promotes the cleavage of an RNA substrate. Characterization of this reaction with sequence variants and mixed DNA/RNA oligomers shows that, although the all-deoxyribonucleotide oligomer is less efficient in catalysis, the DNA/substrate complex shares many of the properties of the all-RNA hammerhead domain such as multiple turnover kinetics and dependence on Mg2+ concentration. On the other hand, the values of kinetic parameters distinguish the DNA oligomer from the all-RNA oligomer. In addition, an analog of the oligomer having a single ribonucleotide in a strongly conserved position of the hammerhead domain is associated with more efficient catalysis than the all-RNA oligomer.

Base Sequence↗
PubMed1995

Dehydrating agents sharply reduce curvature in DNAs containing A tracts.

The structural basis of DNA curvature remains elusive, because models for curvature based on crystallographic structures of molecules containing A tracts do not agree with any of the models for sequence-directed curvature based on solution studies. Here we demonstrate that the difference is probably due to MPD (2-methyl-2,4-pentanediol), the dehydrating agent commonly used in crystallography. One characteristic signature of curved DNA molecules is that they run anomalously slowly on polyacrylamide gels, appearing to be larger than they actually are. The gel anomalies of three curved DNAs from trypanosome kinetoplast minicircles drop monotonically with increasing MPD concentration, indicating that MPD straightens molecules that are curved in aqueous solution. This is not due to some non-specific effect of MPD on poly(dA) or polypurine tracts, because control molecules containing dA70 and dG43 run normally over the full range of MPD concentrations. Circular dichroism spectra are not affected by MPD, ruling out a conformational change to a structure outside the B-DNA family. The effect is not due to MPD-induced changes in phasing of the curved sequences, because MPD has virtually no effect on the linking numbers of relaxed plasmids containing either curved sequences or dA70. At the concentrations of MPD used in X-ray crystallography, the curvature of DNAs containing A tracts is substantially lower than in solution, which probably explains the ongoing discrepancies between the crystallographic results and models based on solution studies.

Animals↗
PubMed1995

Active transport of ions across membranes: energetic role of electrostatics and binding site asymmetry.

The active transport of ions across a membrane by an ATP-driven electrogenic ion pump is often described by an 'alternate access' model. The position of the binding site is assumed to be unchanged as the binding cavity opens alternatively to the uptake and discharge sides of the membrane. The ion binding affinity is higher on the uptake side of the membrane than on the discharge side. This difference in affinities is related to the maximum transport rate and to the efficiency with which ATP hydrolysis is coupled to active transport. Here we examine the electrostatic contribution to binding affinities, using a simple geometry for a model membrane-protein system, a continuum dielectric approximation, and a numerical method to calculate binding energy as a function of the binding site location. If the binding site is located asymmetrically, being further from the uptake side of the membrane than from the discharge side, there is a significant difference in binding free energy between the uptake and discharge states. This asymmetry can produce differences in affinities that are consistent with those measured for biological active transport systems. These results may account for the observed asymmetric location of the calcium binding site in the calcium ATPases from sarcoplasmic reticulum and from the plasma membrane. Electrostatic energy differences associated with binding site asymmetry may be a general feature of electrogenic transmembrane ion pumps.

Adenosine Triphosphatases↗
PubMed1995

What is the basis of sequence-directed curvature in DNAs containing A tracts?

A variety of solution and gel experiments show that DNAs containing tracts of 4-8 A's repeated in phase with the helix repeat are curved. Several independent analyses of these experiments argue that curvature resides in the A tracts themselves. In x-ray crystallographic studies of several DNAs containing A tracts, however, the A tracts are uncurved, leading to models in which curvature resides in the non-A tracts. This "curved general sequence model" has several problems, in our view. We review those, and we describe recent experiments that show that the dehydrating agents commonly used in x-ray crystallography markedly reduce curvature in gels and in solution, calling into question the ability of crystallography to determine the structural basis of DNA curvature. Finally, we discuss the critical role of hydration in curved DNAs and suggest new experiments that we hope could finally determine exactly which sequences are responsible for curvature.

Adenine↗
PubMed1994

Orientations of transfer RNA in the ribosomal A and P sites.

In protein synthesis, peptide bond formation requires that the tRNA carrying the amino acid (A site tRNA) contact the tRNA carrying the growing peptide chain (P site tRNA) at their 3' termini. Two models have been proposed for the orientations of two tRNAs as they would be bound to the mRNA in the ribosome. Viewing the tRNA as an upside down L, anticodon loop pointing down, acceptor stem pointing right, and calling this the front view, the R (Rich) model would have the back of the P site tRNA facing the front of the A site tRNA. In the S (Sundaralingam) model the front of the P site tRNA faces the back of the A site tRNA. Models of two tRNAs bound to mRNA as they would be positioned in the ribosomal A and P sites have been created using MC-SYM, a constraint satisfaction search program designed to build nucleic acid structures. The models incorporate information from fluorescence energy transfer experiments and chemical crosslinks. The models that best answer the constraints are of the S variety, with no R conformations produced consistent with the constraints.

Computer Simulation↗