Search PubMed⌕ Search

Biomedical subjects

D G Levitt

Publications and source records attributed to D G Levitt.

At least 19 recordsLinked to original sources
PubMed1995

The multisubunit active site of fumarase C from Escherichia coli.

The crystal structure of the tetrameric enzyme, fumarase C from Escherichia coli, has been determined to a resolution of 2.0 A. A tungstate derivative used in the X-ray analysis is a competitive inhibitor and places the active site of fumarase in a region which includes atoms from three of the four subunits. The polypeptide conformation is similar to that of delta-crystallin and is comprised of three domains. The central domain, D2, is a unique five-helix bundle. The association of the D2 domains results in a tetramer which has a core of 20 alpha-helices. The other two domains, D1 and D3, cap the helical bundle on opposite ends giving both the single subunit and the tetramer a dumbbell-like appearance. Fumarase C has sequence homology to the eukaryotic fumarases, aspartase, arginosuccinate lyase, adenylosuccinate lyase and delta-crystallin.

Adenylosuccinate Lyase↗
PubMed1992

Crystal structure of Escherichia coli malate dehydrogenase. A complex of the apoenzyme and citrate at 1.87 A resolution.

The crystal structure of malate dehydrogenase from Escherichia coli has been determined with a resulting R-factor of 0.187 for X-ray data from 8.0 to 1.87 A. Molecular replacement, using the partially refined structure of porcine mitochondrial malate dehydrogenase as a probe, provided initial phases. The structure of this prokaryotic enzyme is closely homologous with the mitochondrial enzyme but somewhat less similar to cytosolic malate dehydrogenase from eukaryotes. However, all three enzymes are dimeric and form the subunit-subunit interface through similar surface regions. A citrate ion, found in the active site, helps define the residues involved in substrate binding and catalysis. Two arginine residues, R81 and R153, interacting with the citrate are believed to confer substrate specificity. The hydroxyl of the citrate is hydrogen-bonded to a histidine, H177, and similar interactions could be assigned to a bound malate or oxaloacetate. Histidine 177 is also hydrogen-bonded to an aspartate, D150, to form a classic His.Asp pair. Studies of the active site cavity indicate that the bound citrate would occupy part of the site needed for the coenzyme. In a model building study, the cofactor, NAD, was placed into the coenzyme site which exists when the citrate was converted to malate and crystallographic water molecules removed. This hypothetical model of a ternary complex was energy minimized for comparison with the structure of the binary complex of porcine cytosolic malate dehydrogenase. Many residues involved in cofactor binding in the minimized E. coli malate dehydrogenase structure are homologous to coenzyme binding residues in cytosolic malate dehydrogenase. In the energy minimized structure of the ternary complex, the C-4 atom of NAD is in van der Waals' contact with the C-3 atom of the malate. A catalytic cycle involves hydride transfer between these two atoms.

Amino Acid Sequence↗
PubMed1992

Shaking of the intact rat and intestinal angulation diminish the jejunal unstirred layer.

A sizeable pre-epithelial diffusion barrier (unstirred layer) is present during perfusion of the rat jejunum. In the present study, three rapidly transported compounds, CO, [14C]warfarin, and glucose (5.5 mmol/L), were used as probes to assess the ability of manipulations to reduce the unstirred layer. This layer was 700-800 microns thick in a 30-cm jejunal segment perfused in conventional fashion on the abdominal wall. Placement of four sharp angulations in the segment or replacement in the abdominal cavity reduced the maximal unstirred layer to 200-400 microns. Increasingly rapid shaking of the anesthetized, intact rat on a platform shaker produced progressively thinner unstirred layers. At 250 revolutions per minute, the maximal layer ranged from 32 to 68 microns for the three probes and may have been appreciably less if the epithelium offered appreciable resistance. Shaking yields a > 15-fold reduction in unstirred layer resistance and provides a means for measuring this resistance and for obtaining more accurate assessment of the true in vivo transport Michaelis constant (Km) of any compound.

Animals↗
PubMed1992

POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids.

A new interactive graphics program is described that provides a quick and simple procedure for identifying, displaying, and manipulating the indentations, cavities, or holes in a known protein structure. These regions are defined as, e.g., the xo, yo, zo values at which a test sphere of radius r can be placed without touching the centers of any protein atoms, subject to the condition that there is some x < xo and some x > xo where the sphere does touch the protein atoms. The surfaces of these pockets are modeled using a modification of the marching cubes algorithm. This modification provides identification of each closed surface so that by "clicking" on any line of the surface, the entire surface can be selected. The surface can be displayed either as a line grid or as a solid surface. After the desired "pocket" has been selected, the amino acid residues and atoms that surround this pocket can be selected and displayed. The protein database that is input can have more than one protein "segment," allowing identification of the pockets at the interface between proteins. The use of the program is illustrated with several specific examples. The program is written in C and requires Silicon Graphics graphics routines.

Algorithms↗
PubMed1992

Human jejunal unstirred layer: evidence for extremely efficient luminal stirring.

Previous studies employing the osmotic transient technique have suggested that the human jejunal lumen is poorly stirred with a resultant unstirred layer thickness of approximately 600 microns. However, assuming negligible epithelial resistance to glucose absorption, we recently estimated that the unstirred layer thickness seemingly could not exceed 48 microns in the human jejunum. Because disaccharidases are located on the brush border, the rate of disaccharide hydrolysis can be used to determine unstirred layer thickness, independent of epithelial transport. In the present report, we utilized published hydrolysis data for sucrose and maltose to calculate the unstirred layer thickness in the normal human jejunum. This calculation indicated that the unstirred layer thickness was only approximately 35 microns, less than one-fifteenth of previously reported 600-microns values obtained with the osmotic transient technique. Diffusion through a 600-microns unstirred layer would be the rate-limiting step in absorption of all rapidly transported compounds. In contrast, with a 35-microns unstirred layer, variations in epithelial function or luminal stirring could readily influence the absorption.

Diffusion↗
PubMed1991

Purification and crystallization of recombinant Escherichia coli malate dehydrogenase.

Malate dehydrogenase from Escherichia coli has been crystallized with polyethylene glycol and citrate buffer at pH 5.7. The enzyme was obtained from an E. coli strain in which the chromosomal malate dehydrogenase gene was contained on a pBR322 vector. Two types of crystals have been observed; a monoclinic C2 form and an orthorhombic C222(1) form, which is found infrequently. Monoclinic crystals were used as seeds in several rounds of crystallization until large crystals suitable for diffraction analysis were available. A complete X-ray data set to 2.0 A has been collected.

Chromatography, Ion Exchange↗
PubMed1991

General continuum theory for multiion channel. I. Theory.

It is assumed that the channel is completely characterized by three factors: (a) its geometric shape, (b) the potential energy interaction between an ion and the channel wall, and (c) the potential energy interaction between two ions at arbitrary positions in the channel. The total potential energy of an ion in a multiion channel can be described by a summation over factors b and c. The ion-water interaction is described by a continuum diffusion coefficient which is determined by the channel geometry (c). Given this physical description, a theory is described that predicts the flux of all the ion species that are present, with no additional assumptions about, e.g., the maximum number of ions allowed in the channel, location of binding sites or shape of energy barriers. The solution is based on a combination of the Nernst-Planck and Poisson equation. The Poisson potential is corrected for the ion's self potential. A hard sphere ion-ion interaction is included that prevents ions from piling up on top of each other in regions where the channel wall has a high charge density. An exact analytical solution is derived for the region in the bulk solution, far from the channel mouth and this solution is used as a boundary condition for the numerical solution. The numerical solution is obtained by an interactive procedure that is surprisingly efficient. Application of the theory to the acetylcholine receptor channel is described in the companion paper (Levitt, D. G. 1990. Biophys. J. 59:278-288).

Ion Channels↗
PubMed1991

General continuum theory for multiion channel. II. Application to acetylcholine channel.

The general theory (Levitt, D. G. 1990. Biophys. J. 59:271-277) is applied to a model channel that resembles the acetylcholine receptor channel (ACH). The model incorporates the known features of the ACH geometry and fixed charge locations. The channel has a wide mouth facing the outer solution, tapering to a narrow region facing the interior of the cell. Rings of fixed negative charge are placed at the two surfaces where the bilayer begins, corresponding to the known charges at the ends of the M2 segment. It is assumed that the forces acting on the ion are electrostatic: ion-channel wall, ion-ion, Born image and applied voltage. Analytical expressions for these forces are derived that take account of the low dielectric lipid region. In addition, there is a local hard sphere repulsive force that prevents ions from piling up on each other in regions of the channel with a high fixed charge density. A classical continuum theory is used to obtain an expression for the diffusion coefficient in the channel. The model can mimic the major qualitative and, in many cases, quantitative experimental features of the ACH channel: current-voltage relation, conductance versus concentration and interaction between monovalent and divalent ions. The model calculations were also compared with the site directed mutagenesis experiments of Imoto, K., C. Busch, B. Sakmann, M. Mishina, T. Konno, J. Nakai, H. Bujo, Y. Mori, K. Fukuda, and S. Numa. (1988. Nature (Lond.). 335:645-648) in which the charge at the ends of the channel was systematically varied.

Animals↗
PubMed1990

Diffusion and kinetic approaches to describe permeation in ionic channels.

Diffusion and reaction rate theories provide convenient approaches for describing permeation in ionic channels. Both approaches have strengths and weaknesses. Diffusion theories realistically approximate the physical process of ion movement within an aqueous pore, but those theories do not handle ionic interactions easily. Reaction rate theories are easy to use, and they provide a mathematical summarization of the data that is valuable for communicating experimental results. During ion permeation, however, the basic assumptions of reaction rate theory are not met. Therefore, rate theories do not provide true physical descriptions of ion permeation.

Animals↗
PubMed1990

An experimental model for measuring middle ear antimicrobial drug penetration in otitis media.

Bacteria are an important cause of acute otitis media and successful treatment depends on achieving inhibitory or bacteriacidal antimicrobial drug concentrations in the middle ear. To evaluate further otitis media treatment success and failure, we developed a chinchilla model to study antimicrobial drug penetration through the middle ear mucosa. Using quantitative histomorphometry, we measured the middle ear space in 10 chinchillas and found a mean +/- SD volume of 2.09 +/- 0.08 ml and a mean +/- SD surface area of 14.41 +/- 1.48 cm2. To measure the apparent rate constant (Kc) of antibiotic elimination from the middle ear, through the middle ear mucosa, an antibiotic solution was inoculated into the middle ear cavity, and samples were aspirated between 1 and 8 hr later. In normal ears, the mean Kc +/- SD for amoxicillin was 0.118 +/- 0.013 hr-1, that for a trimethoprim 0.461 +/- 0.090 hr-1, and that for sulfamethoxazole 0.265 +/- 0.062 hr-1. In ears inoculated with type 7F Streptococcus pneumoniae to induce acute otitis media, the Kc +/- SD increased for all three drugs (P less than 0.05): amoxicilin to 0.286 +/- 0.089 hr-1, trimethoprim to 0.662 +/- 0.118 hr-1, and sulfamethoxazole to 0.411 +/- 0.056 hr-1. These values demonstrate that amoxicillin had the lowest apparent penetration rate constant of the three antibiotics but the greatest increase from normal to infected mucosa (142%). Trimethoprim had the highest apparent penetration rate constant of the three antibiotics but the smallest increase from normal to infected mucosa (44%), while the sulfamethoxazone apparent penetration rate constant increased from normal to infected mucosa by 55%.(ABSTRACT TRUNCATED AT 250 WORDS)

Amoxicillin↗
PubMed1990

Physiological measurements of luminal stirring in the dog and human small bowel.

The resistance to absorption resulting from poor stirring of luminal contents (RLum) is considered to be equivalent to an unstirred layer of greater than 600 microns in the human small intestine. We measured RLum in the jejunum of conscious dogs by assessing the absorption rate of two rapidly absorbed probes, glucose, and [14C]warfarin. When RLum was expressed as an unstirred layer, the maximal thickness of the unstirred layer (assuming negligible epithelial cell resistance) was only approximately 35 and 50 microns for perfusion rates of 26 and 5 ml/min, respectively. Maximal unstirred layer thickness for the human jejunum, calculated from previous studies of glucose absorption, yielded a mean value of only 40 microns (range: 23 to 65 microns). Since epithelial resistance appears to be negligible during absorption of low concentrations of glucose, the maximal unstirred layer of 40 microns should be close to the true value for glucose in the human small intestine. We conclude that the unstirred layer for rapidly absorbed compounds in dogs and man are less than one-tenth of previously reported values, but this layer still may remain the rate limiting step in absorption of rapidly transported compounds.

Animals↗
PubMed1989

Continuum model of voltage-dependent gating. Macroscopic conductance, gating current, and single-channel behavior.

It is assumed that the conformational change of the voltage-gated channel is continuous, characterized by movement along a generalized one-dimensional reaction coordinate, x, varying from 0 to 1. This large conformational change is coupled to the movement of most of the gating charge. Superimposed on this large movement is a smaller, very fast conformational change that opens or closes the channel. The large conformational change perturbs the channel so that opening is favored near x = 1 and closing is favored near x = 0. The movement along the x axis is described by a generalized Nernst-Planck equation, whereas the open-close transition is modeled as a discrete reaction-rate process. The macroscopic conductance, gating current, and single-channel behavior of a simple, linearized version of the model is described. Although the model has only seven adjustable constants (about the same as would be required for a conventional three-state model), it can mimic the behavior of the delayed rectified K+ channel with 12 or more closed states. The single-channel behavior of the model can have bursts of rapid openings and closings, separated by long closed times. If the conformational change is assumed to correspond to the rotation and translation of charged helices, then this model can be used to estimate the effective rotational diffusion coefficient of the helix. Such calculations for the delayed rectifier K+ channel indicate that the motion must be very restricted.

Electric Conductivity↗
PubMed1988

Use of weak acids to determine the bulk diffusion limitation of H+ ion conductance through the gramicidin channel.

The addition of 2 M formic acid at pH 3.75 increased the single channel H+ ion conductance of gramicidin channels 12-fold at 200 mV. Other weak acids (acetic, lactic, oxalic) produce a similar, but smaller increase. Formic acid (and other weak acids) also blocks the K+ conductance at pH 3.75, but not at pH 6.0 when the anion form predominates. This increased H+ conductance and K+ block can be explained by formic acid (HF) binding to the mouth of the gramicidin channel (Km = 1 M) and providing a source of H+ ions. A kinetic model is derived, based on the equilibrium binding of formic acid to the channel mouth, that quantitatively predicts the conductance for different mixtures of H+, K+, and formic acid. The binding of the neutral formic acid to the mouth of the gramicidin channel is directly supported by the observation that a neutral molecule with a similar structure, formamide (and malonamide and acrylamide), blocks the K+ conductance at pH 6.0. The H+ conductance in the presence of formic acid provides a lower bound for the intrinsic conductance of the gramicidin channel when there is no diffusion limitation at the channel mouth. The 12-fold increase in conductance produced by formic acid suggests that greater than 90% of the total resistance to H+ results from diffusion limitation in the bulk solution.

Amides↗
PubMed1988

Electrostatic radius of the gramicidin channel determined from voltage dependence of H+ ion conductance.

The results of Decker and Levitt (1987) suggest that the conductance of H+ ion through the gramicidin channel is limited primarily by diffusion in the bulk solution at the channel mouth. It is assumed in this paper that the H+ conductance is 100% diffusion limited. This means that all the factors that influence the H+ flux are external to the channel and are presumed to be known. In particular, the diffusion coefficient of H+ in this region is assumed to be equal to the bulk solution value and the only force acting on the ion is that due to the applied voltage. A model of the H+ flux is derived, based on the Nernst-Planck equation. It has three adjustable parameters: the electrostatic radius, the capture distance, and the radius of the H+ ion. The acceptable range of the parameters was determined by comparing the predictions of the model with the experimental measurements of the H+ conductance at pH 3.75. The best fit was obtained for an electrostatic radius in the range 2.3-2.7 A. This is in good agreement with earlier predictions (2.5 A) based on the assumption that the dielectric constant of the channel water is equal to that of bulk water. The addition of 1 M choline Cl- (an impermeant) increases the H+ current at low voltage and decreases it at high voltage. The increase can be explained by the small surface charge that results from the separation of charge produced by exclusion of the large choline cation (relative to Cl-) from the membrane surface. The decrease at high voltages can be accounted for by the change in the profile of the applied potential produced by the increase in ionic strength.

Diffusion↗
PubMed1988

Physiological measurement of luminal stirring in perfused rat jejunum.

Poor stirring of intestinal contents yields a preepithelial diffusion barrier that is thought to be the rate-limiting step in absorption of many compounds. In many previous studies, the resistance of this barrier is equal to an unstirred water layer of 300-800 micron. Using three probes, CO, glucose, and [14C]warfarin, we measured the preepithelial resistance in a 30-cm segment in rats that were 1) conscious, 2) anesthetized with pentobarbital sodium, or 3) anesthetized and laparotomized. Measurements with each of the probes showed that the maximal preepithelial resistance in conscious rats was equivalent to an unstirred layer of only approximately 100 micron. Anesthesia roughly doubled this resistance, and anesthesia and laparotomy caused a sixfold increase (unstirred layer of approximately 600 micron). We conclude that the luminal stirring is much more efficient than previously has been appreciated. The very thick jejunal unstirred layers reported previously (300-800 micron) reflect the results of studies performed under nonphysiological conditions or studies employing inappropriate techniques to measure luminal stirring.

Anesthesia↗
PubMed1988

Use of laminar flow and unstirred layer models to predict intestinal absorption in the rat.

Carbon monoxide (CO) and [14C]warfarin were used to measure the preepithelial diffusion resistance resulting from poor luminal stirring (RL) in the constantly perfused rat jejunum at varying degrees of distension (0.05, 0.1, and 0.2 ml/cm). RL was much greater than epithelial cell resistance, indicating that poor stirring was the limiting factor in absorption and that an appropriate model of stirring should accurately predict absorption. A laminar flow model accurately predicted the absorption rate of both probes at all levels of gut distension, as well as the absorption of glucose when RL was the rate-limiting factor in absorption. In contrast, an unstirred layer model would not have predicted that gut distension would have little influence on absorption, and would have underestimated [14C]warfarin absorption relative to CO. We concluded that in the perfused rat jejunum, laminar flow accurately models luminal stirring and an unstirred layer should be considered to be a unit of resistance in laminar flow, rather than a model of luminal stirring.

Animals↗
PubMed1987

Potassium-selective ion channels in a transformed insulin-secreting cell line.

K+ channels in inside-out patches from hamster insulin tumor (HIT) cells were studied using the patch-clamp technique. HIT cells provide a convenient system for the study of ion channels and insulin secretion. They are easy to culture, form gigaohm seals readily and secrete insulin in response to glucose. The properties of the cells changed with the passage number. For cell passage numbers 48 to 56, five different K+-selective channels ranging from 15 to 211 pS in symmetrical 140 mM KCl solutions were distinguished. The channels were characterized by the following features: a channel with a conductance (in symmetrical 140 mM KCl solutions) of 210 pS that was activated by noncyclic purine nucleotides and closed by H+ ions (pH = 6.8); a 211 pS channel that was Ca2+-activated and voltage dependent; a 185 pS channel that was blocked by TEA but was insensitive to quinine or nucleotides; a 130 pS channel that was activated by membrane hyperpolarization; and a small conductance (15 pS) channel that was not obviously affected by any manipulation. As determined by radioimmunoassay, cells from passage number 56 secreted 917 +/- 128 ng/mg cell protein/48 hr of insulin. In contrast, cells from passage number 77 revealed either no channel activity or an occasional nonselective channel, and secreted only 29.4 +/- 8.5 ng/mg cell protein/48 hr of insulin. The nonselective channel found in the passage 77 cells had a conductance of 25 pS in symmetrical 140 mM KCl solutions. Thus, there appears to be a correlation between the presence of functional K+ channels and insulin secretion.

Adenoma, Islet Cell↗