Observations on Levitt's “New Theory of Transport”

Levitt (1974) (Biochim. Biophys. Acta 373, 115–131) has recently developed a “New Theory of Transport for Cell Membrane Pores” based on the supposition that equivalent pores in the red cell membrane are so small that water and small solute molecules such as urea can not pass each other. Levitt's concept is based on the implicit assumption that urea and water are spherical molecules. We have shown, using a scale model, that Levitt's supposition is not in agreement with the actual molecular shapes. Levitt has further asserted that there is a serious methodological error in measurements reported fifteen years ago by Goldstein and Solomon (1960) (J. Gen. Physiol. 44, 1–17). We have shown that the supposed “methodological error” lies in the fact that Levitt made his mathematical analysis of the appropriate equations under conditions significantly different from those employed by Goldstein and Solomon. A computer solution of the equations under the actual conditions used shows that Levitt's assertion is not justified.     

Boundary conditions for- single-ion diffusion.

We have constructed a theory for diffusion through the pore of a single-ion channel by taking a limit of a random walk around a cycle of states. Similar to Levitt's theory of single-ion diffusion, one obtains boundary conditions for the Nernst-Planck equation that guarantee that the pore is occupied by at most one ion. Two of the terms in the boundary conditions are identical to those given by Levitt. However, the construction gives rise to a third term not found in Levitt's theory. With this term, the channel spends exponentially distributed intervals in the empty state. Ion sample paths have been simulated to help visualize trajectories near the channel entrances, with and without the new term. We use the modified Levitt theory to fit several potential profiles to the conductance data of Russell et al. In particular, we have analyzed the profile for Na+ in gramicidin calculated by Roux and Karplus. The peak-to-peak amplitude of their result must be reduced to at most 35% of its original value to fit the data. But with this reduction, excellent fits are obtained.     

Reflection coefficients of permeant nonelectrolytes for dog and beef red cell membranes.

The reflection coefficient, sigma, for several small permeant nonelectrolytes was determined for dog and beef red blood cell membranes. Our sigma values were considerably higher than those previously reported for dog cells; e.g., out sigma urea was 87% higher than the sigma urea of Rich, Sha'afi, Barton and Solomon (J. Gen. Physiol. 50: 2391, 1967). Our sigma values for urea were only slightly greater in beef cells than previously reported by Farmer and Macey (Biochim. Biophys. Acta 290: 290, 1972). We found that a trend exists when (1 - sigma) is plotted against the log of the permeability coefficient, omega. This observation is also consistent with our previously reported sigma data for human red cell membranes (Owen & Eyring, J. Gen. Physiol. 66: 241, 1972). This trend suggests that small hydrophilic molecules interact highly with cell membrane water. The exceptions to this trend were lipophilic molecules, indicating they do not interact with water while penetrating the red cell membrane.     

Permeability and Reflection Coefficients of Urea and Small Amides in the Human Red Cell

Measurement of the transport parameters that govern the passage of urea and amides across the red cell membrane leads to important questions about transport of water. It had initially been thought that small protein channels, permeable to water and small solutes, traversed the membrane (see Solomon, 1987). Recently, however, very strong evidence has been presented that the 28 kDa protein, CHIP28, found in the red cell membrane, is the locus of the water channel (see Agre et al., 1993). CHIP28 transports water very rapidly but does not transport small nonelectrolytes such as urea. The irreversible thermodynamic parameter, σ _i , the reflection coefficient, is a measure of the relationship between the permeability of the solute and that of water. If a solute permeates by dissolution in the membrane, σ _i = 1.0; if it permeates by passage through an aqueous channel, σ _i < 1.0. For urea, Goldstein and Solomon (1960) found that σ_urea= 0.62 ± 0.03 which meant that urea crosses the red cell membrane in a water-filled channel. This result and many subsequent observations that showed that σ_urea < 1.0 are at variance with the observation that CHIP28 is impermeable to urea. In view of this problem, we have made a new series of measurements of σ _i for urea and other small solutes by a different method, which obviates many of the criticisms Macey and Karan (1993) have made of our earlier method. The new method (Chen et al., 1988), which relies upon fluorescence of the intracellular dye, fluorescein sulfonate, leads to the corrected value, σ_urea,corr= 0.64 ± 0.03 for ghosts, in good agreement with earlier data for red cells. Thus, the conclusion on irreversible thermodynamic and other grounds that urea and water share a common channel is in disagreement with the view that CHIP28 provides the sole channel for water entrance into the cell. Received: 6 February 1996/Revised: 20 May 1996     

Ion flow in the bath and flux interactions between channels.

We present an exact solution to the linearized Nernst-Planck-Poisson equation for spherically symmetric current flow. This solution differs from Levitt's solution (Levitt, D. G. 1992. Biophys. J., Eq. A5) by its dependence on an additional parameter, which is equal to the net ion flux for monovalent ion-selective channels. For ion-selective channels, this solution may provide better boundary conditions to modelling the flow in the channel pore itself, although only at low salt concentrations. We use the solution to estimate the effects of flux interaction between closely packed channels.     

Dynamics of oligomer formation by denatured carbonic anhydrase II

Aggregation and subsequent development of protein deposition diseases originate from conformational changes in corresponding amyloidogenic proteins. Many proteins unrelated to amyloidoses also fibrillate at the appropriate conditions. These proteins serve as a model for studying the processes of protein misfolding, oligomerization and fibril formation. The accumulated data support the model where protein fibrillogenesis proceeds via the formation of a relatively unfolded amyloidogenic conformation. The urea-induced unfolding of bovine carbonic anhydrase II, BCA II, is characterized by a combination of high-resolution NMR, circular dichroism spectroscopy and small angle X-ray scattering. It is shown that the formation of associates of protein molecules in complex with solvent (water and urea), APS, takes place in the presence of 4-6 M urea. The subsequent increase in urea concentration to 8 M is accompanied by a disruption of APS and leads to a complete unfolding of a protein molecule. Analysis of BCA II self-association in the presence of 4.2 M urea revealed that APS are relatively large mostly beta-structural blocks with the averaged molecular mass of 190-220 kDa. This work also demonstrates some novel NMR-based methodological approaches that provide useful information on protein self-association.     

Modeling of hydration of incorrect nucleic acid base pairs by the Monte Carlo method

The hydration of water bridged base pairs of nucleic acids have been simulated via the Monte Carlo method. The simulation have shown that water molecules forming H-bonds with both bases preserve this H-bonding with large probability in the water surrounding. This fact supports the supposition about the important role of water molecules in wrong base pair formation and about the role of these base pairs in the structure and functioning of nucleic acids.     

Modulation of water and urea transport in human red cells: Effects of pH and phloretin

Summary It has previously been shown by Macey and Farmer (Biochim. Biophys. Acta 211:104–106, 1970) that phloretin inhibits urea transport across the human red cell membrane yet has no effect on water transport. Jennings and Solomon (J. Gen. Physiol. 67:381–397, 1976) have shown that there are separate lipid and protein binding sites for phloretin on the red cell membrane. We have now found that urea transport is inhibited by phloretin binding to the lipids with aK ₁ of 25±8 m in reason-able agreement with theK _D of 54±5 m for lipid binding. These experiments show that lipid/protein interactions can alter the conformational state of the urea transport protein. Phloretin binding to the protein site also modulates red cell urea transport, but the modulation is opposed by the specific stilbene anion transport inhibitor, DIDS (4,4-diisothiocyano-2,2-stilbene disulfonate), suggesting a linkage between the urea transport protein and band 3. Neither the lipid nor the protein phloretin binding site has any significant effect on water transport. Water transport is, however, inhibited by up to 30% in a pH-dependent manner by DIDS binding, which suggests that the DIDS/band 3 complex can modulate water transport.     

Utilization of urea by leaves of bromeliad <Emphasis Type="Italic">Vriesea gigantea</Emphasis> under water deficit: much more than a nitrogen source

Vriesea gigantea Gaudichaud is an epiphytic bromeliad with a high capacity to take up urea. In plants, urea is hydrolyzed by urease into ammonium and CO₂, providing nitrogen to the plant. Most studies of urea nutrition have focused only on nitrogen metabolism, whereas scarce attention has been given to CO₂ assimilation. Therefore, this study attempted to investigate whether urea could play an important role as a carbon source, which could be of a significant importance under water deficit conditions because of the limitation in atmospheric CO₂ influx into the leaves due to stomatal closure. In this study, detached leaves of V. gigantea were exposed to water deficit and supplied with urea. The most photosynthetic parts of the leaf (mainly the apical leaf portion) showed higher urease activities and CO₂ buildup near chloroplasts, particularly during the nighttime under water deficit conditions when compared to urea application without the water deficit. Moreover, part of the CO₂ generated from urea hydrolysis was fixed into malate, probably via phosphoenolpyruvate carboxylase. Therefore, urea may contribute to the carbon balance of plants under water deficit conditions. Our data suggest that, besides being a source of nitrogen, urea might also be an important carbon source during CO₂-limited conditions in leaves of epiphytic bromeliads.     

The effects of a 9-year nitrogen and water addition on soil aggregate phosphorus and sulfur availability in a semi-arid grassland

Previous studies have demonstrated that higher nitrogen (N) and water availability affect both above- and below-ground communities, soil carbon and N pools, and microbial activity in semi-arid grasslands of Inner Mongolia. However, how soil phosphorus (P) and sulfur (S) pools, and related soil enzyme activities (as indicators of P and S cycles) respond to long-term N and water addition has still remained unclear. Since 2005, a field experiment with urea and water amendments has been conducted to examine their effects on total and available P and S concentrations and alkaline phosphomonoesterase (PME) and aryl-sulfatase (ArS) activities in three soil aggregate fractions: large macroaggregates (>2 mm), small macroaggregates (0.25–2 mm), and microaggregates (<0.25 mm) in an Inner Mongolia semi-arid grassland. Normalized to aggregate mass, microaggregates retained the highest total P and S concentrations. Both N and water additions increased the available P (by up to 84.5%) and the available S (by up to 150%) in the soil aggregate fractions. Soil acidification, as a result of the N addition, decreased both alkaline PME and ArS activities by up to 62.9% and 39.6%, respectively, while the water addition increased their activities. Our observations revealed that soil acidification (under the N addition) and elevated enzyme activity (under the water addition) played important roles in the levels of soil available P and S. The depression of P- and S-acquiring enzymes with soil acidification may decrease P and S availability, potentially impacting ecosystem processes and limiting the restoration of these grassland systems. The water addition was shown to be a more effective practice than the urea amendment for improving soil structure, supplying available P and S, and maintaining the sustainability of this semi-arid grassland.     

Mechanisms of hyperosmotic acclimation in Xenopus laevis (salt,urea or mannitol)

The acclimation of the clawed toad Xenopus laevis to hyperosmotic solutions of NaCl (balanced solution of sea salt), urea or mannitol was studied. The animals could not be acclimated to salt solutions more concentrated centrated than 400 mosm·l^-1. Urea was tolerated till 500 mmol·l^-1. Plasma osmolality was always hyperosmotic to the environmental solution, but with diminished osmotic gradient at the highest tolerated solutions. Plasma urea concentration approached 90 mmol·l^-1, similar in the three solutions of acclimation. Urine volume was very small under all conditions. Serum aldosterone and corticosterone did not differ significantly, although there was a slight tendency towards lower aldosterone in the NaCl solution. In vivo water uptake in tap water acclimated animals was very small, and was higher in the other groups. Only the salt- and urea-acclimated, but not the tap water and mannitol-acclimated groups responded with a clear increase following injection of oxytocin or theophylline. In vitro urea fluxes were similar and invariable in both directions under all conditions. No significant effect of theophylline was observed. Sodium transport measured by the short-circuit technique in vitro was lower in salt- and mannitol-acclimation conditions, and was stimulated significantly under all conditions in response to serosal oxytocin or theopylline. It is concluded that Xenopus laevis can osmoregulate at a limited range of external solutions. It is limited in the increase of its plasma urea concentration; the transport properties of the skin do not change very much upon acclimation, except for the hydroosmotic response to oxytocin.Abbreviations I _sc short circuit current - PD potential difference - SW balanced sea water - TW tap water     

Indigenous Ecological Knowledge as Situated Practices: Understanding Fishers' Knowledge in the Western Solomon Islands

ABSTRACT   In this article, we draw on research among fisherfolk of Roviana Lagoon, Solomon Islands, to examine certain epistemological assumptions of the "indigenous knowledge" concept. We describe how approaches to knowledge in Roviana differ from prevailing models of knowledge that distinguish between cognitive aspects and other modalities of knowing. For many Roviana fishers, ecological knowledge is not analytically separated from the changing contexts of everyday activities such as navigating and fishing. Inspired by Roviana epistemologies, we argue that a practice-oriented approach provides a more sympathetic and informative theoretical framework for understanding knowledge and its role in contemporary marine-resource conservation efforts. The theoretical and methodological implications of the perspective are illustrated with examples from an ongoing marine conservation project in the western Solomon Islands that integrates indigenous knowledge, remote-sensing techniques, and Geographic Information System (GIS) technologies.     

Plant plasma membrane water permeability and slow freezing injury

Abstract Evaluation of existing experimental evidence supports the hypothesis that, under natural or slow rates of freezing, plasma membrane permeability does not significantly limit water efflux from plant cells. Water efflux at slow freezing rates is controlled largely by the rate of heat removal from the plant cells. These conclusions are in direct contrast to the recent views of Levitt (1978).     

Confirmation of the predicted source of a slow folding reaction: proline 8 of bovine pancreatic trypsin inhibitor

A major question in protein structural analysis concerns the applicability of results from model systems to other proteins. Theoretical approaches seem the best manner of transferring information from one system to another, but their accuracy in the model systems must first be tested with results from experiment. Since bovine pancreatic trypsin inhibitor (BPTI) is a model system for the evaluation of energy minimization and molecular dynamics routines, we can use folding and stability measurements to examine the reliability of these methods. All two-disulfide mutants of BPTI investigated thus far have two very slow folding reactions which have characteristics of proline isomerization. These reactions may occur because the non-native cis form of two of the four prolines in BPTI significantly destabilizes the folded state of the protein. Previous energy minimization studies of wild-type BPTI suggested that the cis form of Pro8 was the most destabilizing of the four prolines [Levitt,M. (1981) J. Mol. Biol., 145, 251-263]. In this paper, we show that mutation of Pro8----Gln in the two-disulfide bond mutant Val30/Ala51 results in a loss of the slowest folding reaction, consistent with Levitt's prediction.     

The structural properties of magainin in water, TFE/water, and aqueous urea solutions: molecular dynamics simulations

Here, the MD simulations and comparative structural analysis of Magainin in water, TFE/water, and 2M, 4M, and BM urea solutions is reported. For MAG-TFE/water and MAG-2M urea the largely alpha helical conformation of the peptide is maintained throughout the 9-ns simulation. While in water, 4M urea, and 8M urea, the helix length decreases and at the same time helix radius increases. This suggests a more destabilized magainin secondary structure. Our simulation data reveals that the stabilizing effect of TFE is induced by preferential accumulation of TFE molecules around the alpha helical peptide. These results indicate that an aqueous urea solution solvates the surface of polypeptide chain more favorably than pure water. Urea molecules interact more favorably with nonpolar groups of the peptide in comparison with water, and the presence of urea improves the interactions of water molecules with the hydrophilic groups of the peptide. At 8M urea, there are more direct interactions between the urea and solute, and the helix is destabilized. At 2M urea, the interaction of urea molecules and nonpolar residues are weak, therefore, the presence of urea molecules decreases the interactions of water molecules with hydrophilic groups. Urea could not deteriorate the peptide secondary structure with time from an initial helix structure.     

Structural details of urea binding to barnase: a molecular dynamics analysis.

BACKGROUND: The molecular mechanism of urea-induced protein unfolding has not been established. It is generally thought that denaturation results from the stabilizing interactions of urea with portions of the protein that are buried in the native state and become exposed upon unfolding of the protein. RESULTS: We have performed molecular dynamics simulations of barnase (a 110 amino acid RNase from Bacillus amyloliquefaciens) with explicit water and urea molecules at 300 K and 360 K. The native conformation was unaffected in the 300 K simulations at neutral and low pH. Two of the three runs at 360 K and low pH showed some denaturation, with partial unfolding of the hydrophobic core 2. The first solvation shell has a much higher density of urea molecules (water/urea ratio ranging from 2.07 to 2.73) than the bulk (water/urea ratio of 4.56). About one half of the first-shell urea molecules are involved in hydrogen bonds with polar or charged groups on the barnase surface, and between 15% and 18% of the first-shell urea molecules participate in multiple hydrogen bonds with barnase. The more stably bound urea molecules tend to be in crevices or pockets on the barnase surface. CONCLUSIONS: The simulation results indicate that an aqueous urea solution solvates the surface of a polypeptide chain more favorably than pure water. Urea molecules interact more favorably with nonpolar groups of the protein than water does, and the presence of urea improves the interactions of water molecules with the hydrophilic groups of the protein. The results suggest that urea denaturation involves effects on both nonpolar and polar groups of proteins.     

Can one measure the free energy of binding of the histone octamer to different DNA sequences by salt-dependent reconstitution?

I explain why many recently reported measurements for the "free energy" of positioning of the histone octamer on different DNA sequences are likely to be in error: i.e. because histone octamers do not equilibrate between different DNA molecules at low salt, but only at high salt. Thus, the reported "free energies" refer to an equilibrium at high salt, under nearly dissociating conditions between protein and DNA, and they are likely to be much too small on an absolute scale. There are many other lines of evidence to suggest that the preferences of the histone octamer for different DNA sequences are rather strong and of importance in biological systems.     

Theoretical analysis of systematic errors introduced by a pedicel-girdling technique used to estimate separately the xylem and phloem flows.

The water budget of fruits was analysed by means of a biophysical model of fruit growth, built and calibrated recently for peaches [Prunus persica (L.) Batsch]. This analysis was applied to the evaluation of systematic errors introduced by a pedicel-girdling method (with the observations being treated by means of a subtractive technique) used to separate the contributions of xylem and phloem flow to the total water inflow to the fruit. The flows were considered as solution transport through composite membranes and were calculated by means of equations drawn from non-equilibrium thermodynamics. The total inflow of water was simulated as dependent on the water status in the tree. The hourly time step was used for the simulation. The flows obtained by simulation of the pedicel-girdled fruit were compared with those found by simulation of the intact-pedicel fruit. The error introduced by the pedicel-girdling technique was evaluated theoretically and was shown to vary during the day, ranging from very small (relative error of 3-7%) at the period when the rate of fruit growth is maximal to 100% when the fruit volume does not change. The vascular flows obtained from the "girdling experiments" are discussed in relation to the possible theoretically estimated errors.