The 6.9-A structure of GlpF: a basis for homology modeling of the glycerol channel from Escherichia coli

The three-dimensional structure of GlpF, the glycerol facilitator of Escherichia coli, was determined by cryo-electron microscopy. The 6.9-A density map calculated from images of two-dimensional crystals shows the GlpF helices to be similar to those of AQP1, the erythrocyte water channel. While the helix arrangement of GlpF does not reflect the larger pore diameter as seen in the projection map, additional peripheral densities observed in GlpF are compatible with the 31 additional residues in loops C and E, which accordingly do not interfere with the inner channel construction. Therefore, the atomic structure of AQP1 was used as a basis for homology modeling of the GlpF channel, which is predicted to be free of bends, wider, and more vertically oriented than the AQP1 channel. Furthermore, the residues facing the GlpF channel exhibit an amphiphilic nature, being hydrophobic on one side and hydrophilic on the other side. This property may partially explain the contradiction of glycerol diffusion but limited water permeation capacity.     

Glycerol inhibits water permeation through Plasmodium Falciparum aquaglyceroporin

Plasmodium falciparum aquaglyceroporin (PfAQP) is a multifunctional membrane protein in the plasma membrane of P. falciparum, the parasite that causes the most severe form of malaria. The current literature has established the science of PfAQP’s structure, functions, and hydrogen-bonding interactions but left unanswered the following fundamental question: does glycerol modulate water permeation through aquaglyceroporin that conducts both glycerol and water? This paper provides an affirmative answer to this question of essential importance to the protein’s functions. On the basis of the chemical-potential profile of glycerol from the extracellular bulk region, throughout PfAQP’s conducting channel, to the cytoplasmic bulk region, this study shows the existence of a bound state of glycerol inside aquaglyceroporin’s permeation pore, from which the dissociation constant is approximately 14 μM. A glycerol molecule occupying the bound state occludes the conducting pore through which permeating molecules line up in single file by hydrogen-bonding with one another and with the luminal residues of aquaglyceroporin. In this way, glycerol inhibits permeation of water and other permeants through aquaglyceroporin. The biological implications of this theory are discussed and shown to agree with the existent in vitro data. It turns out that the structure of aquaglyceroporin is perfect for the van der Waals interactions between the protein and glycerol to cause the existence of the bound state deep inside the conducting pore and, thus to play an unexpected but significant role in aquaglyceroporin’s functions.     

Stopped-flow spectrophotometric assay of glycerol permeation in Escherichia coli: applicability and limitations.

The passive permeation and facilitated diffusion of glycerol in various strains of Escherichia coli have been studied by stopped-flow spectrophotometry. Contrary to the prediction for glycerol entry by simple diffusion, the reciprocal relaxation time (1/tau, s-1) for the passive permeation of glycerol in cells grown in the presence of glucose was not constant but decreased as the glycerol concentration increased above 100 mM. This anomaly was not due to refractive index differences or to the presence of residual levels of the glycerol facilitator protein in non-induced cells. Although reciprocal relaxation times for glycerol-induced E. coli exhibited the expected elevation relative to non-induced cells, a similar anomalous decrease 1/tar (s-1) with increasing glycerol concentration was observed. In addition, at early times after suspension in dilute buffer, the 1/tau (s-1) values obtained for induced or non-induced E. coli swelling in glycerol were considerably greater than for organisms incubated in dilute buffer for longer times. We concluded that either this spectrophotometric technique was not monitoring solely the permeation of glycerol into E. coli, or concentrations of glycerol above 100 mM significantly perturbed the structure of the E. coli cell envelope.     

Free-energy landscape of glycerol permeation through aquaglyceroporin GlpF determined from steered molecular dynamics simulations

The free-energy landscape of glycerol permeation through the aquaglyceroporin GlpF has been estimated in the literature by the nonequilibrium method of steered molecular dynamics (SMD) simulations and by the equilibrium method of adaptive biasing force (ABF) simulations. However, the ABF results qualitatively disagree with the SMD results that were based on the Jarzynski equality (JE) relating the equilibrium free-energy difference to the nonequilibrium work of the irreversible pulling experiments. In this paper, I present a new SMD study of the glycerol permeation through GlpF to explore the free-energy profile of glycerol along the permeation channel. Instead of the JE in terms of thermodynamic work, I use the fluctuation-dissipation theorem (FDT) of Brownian dynamics (BD), in terms of mechanical work, for extracting the free-energy difference from the nonequilibrium work of irreversible pulling experiments. The results of this new SMD-BD-FDT study are in agreement with the experimental data and with the ABF results.     

Electrostatic tuning of permeation and selectivity in aquaporin water channels

Water permeation and electrostatic interactions between water and channel are investigated in the Escherichia coli glycerol uptake facilitator GlpF, a member of the aquaporin water channel family, by molecular dynamics simulations. A tetrameric model of the channel embedded in a 16:0/18:1c9-palmitoyloleylphosphatidylethanolamine membrane was used for the simulations. During the simulations, water molecules pass through the channel in single file. The movement of the single file water molecules through the channel is concerted, and we show that it can be described by a continuous-time random-walk model. The integrity of the single file remains intact during the permeation, indicating that a disrupted water chain is unlikely to be the mechanism of proton exclusion in aquaporins. Specific hydrogen bonds between permeating water and protein at the channel center (at two conserved Asp-Pro-Ala "NPA" motifs), together with the protein electrostatic fields enforce a bipolar water configuration inside the channel with dipole inversion at the NPA motifs. At the NPA motifs water-protein electrostatic interactions facilitate this inversion. Furthermore, water-water electrostatic interactions are in all regions inside the channel stronger than water-protein interactions, except near a conserved, positively charged Arg residue. We find that variations of the protein electrostatic field through the channel, owing to preserved structural features, completely explain the bipolar orientation of water. This orientation persists despite water translocation in single file and blocks proton transport. Furthermore, we find that for permeation of a cation, ion-protein electrostatic interactions are more unfavorable at the conserved NPA motifs than at the conserved Arg, suggesting that the major barrier against proton transport in aquaporins is faced at the NPA motifs.     

Glycerol conductance and physical asymmetry of the Escherichia coli glycerol facilitator GlpF

The aquaglyceroporin GlpF is a transmembrane channel of Escherichia coli that facilitates the uptake of glycerol by the cell. Its high glycerol uptake rate is crucial for the cell to survive in very low glycerol concentrations. Although GlpF allows both influx and outflux of glycerol, its structure, similar to the structure of maltoporin, exhibits a significant degree of asymmetry. The potential of mean force characterizing glycerol in the channel shows a corresponding asymmetry with an attractive vestibule only at the periplasmic side. In this study, we analyze the potential of mean force, showing that a simplified six-step model captures the kinetics and yields a glycerol conduction rate that agrees well with observation. The vestibule improves the conduction rate by 40% and 75% at 10- micro M and 10-mM periplasmic glycerol concentrations, respectively. In addition, neither the conduction rate nor the conduction probability for a single glycerol (efficiency) depends on the orientation of GlpF. GlpF appears to conduct equally well in both directions under physiological conditions.     

Survival of frozen-thawed human red cells as a function of the permeation of glycerol and sucrose

Previous studies have demonstrated that glycerol does not have to permeate bovine red cells to protect them against subsequent freezing and thawing. The present study is concerned with the relation between solute permeation and freezing injury of human red cells. Cells were held in 2 m glycerol for 30 sec to 10 min at 0 °C and then frozen to ?196 °C at 60 °C/min. Cells cooled at this rate have a very low probability of undergoing intracellular freezing. Percent survivals (≡percent unhemolyzed) increased by 21% (from 66 to 80%) over the first 3-min period. Extrapolation to zero time (and zero glycerol permeation) yields a survival of 57%. Between 30 sec and 3 min the calculated osmolal ratio of intracellular glycerol to other solutes increased 240% (from 2.5 to 5.7). The human red cell is impermeable to sucrose at 0 °C. Cells suspended in 1.40 m sucrose (equiosmolal to 2.0 m glycerol) for 0.5 to 10 min prior to freezing yielded as high survivals after thawing as did cells in glycerol.These data indicate that prior permeation of additive is not a prerequisite for the survival of red cells subjected to subsequent freezing and thawing. Although sucrose and glycerol protect equally well to this point, differences appear when attempts are made to remove the additive. Over 90% of the cells survive the removal of glycerol. Only some 30% survive the removal of sucrose. Cells frozen in an equisomolal solution of sodium chloride do not even survive the initial freezing and thawing.The findings indicate that slow freezing injury cannot be accounted for in terms of the attainment of a critical minimum volume, nor can it be considered to be equivalent to posthypertonic hemolysis.     

Permeability of the 17-day fetal rat pancreas to glycerol and dimethylsulfoxide

Experimentally induced diabetes in rats can be reversed by the transplantation of several fresh or frozen-thawed fetal pancreases. An important question to both the mechanistic and practical aspects of cryobiology is the role played by the permeation of protective additives during freezing, thawing, and subsequent dilution. Answers require knowledge of the kinetics of permeation of the specific additive into the cell or tissue. In this paper, we report isotopic measurements of the rate of permeation of 2 M glycerol and 1 and 2 M dimethylsulfoxide (Me₂SO) into 17-day fetal pancreases at 0 and 22 °C. In Me₂SO, equilibrium was achieved in about 10–15 min at 0 °C and in less than 10 min at 22 °C. In glycerol, equilibrium was attained in about 60 min at 22 °C; but at 0 °C permeation was only 65% complete after 180 min. In general, Me₂SO permeated 10–30 times more rapidly than glycerol at 0 °C, and glycerol permeated about 10 times more rapidly at 22 than at 0 °C.The kinetics of permeation were more characteristic of a two-compartment than a single-compartment system. In all probability, the two compartments are the intercellular space and the intracellular space. The permeability data suggest that each compartment occupies about half the total volume.     

Glycerol facilitator GlpF and the associated aquaporin family of channels

The aqua (glycero) porins conduct water (and glycerol) across cell membranes. The structure of these channels reveals a tripathic channel that supports a hydrophobic surface and, opposite to this, a line of eight hydrogen-bond acceptors and four hydrogen-bond donors. The eight carbonyls act as acceptors for water (or glycerol OH) molecules. The central water molecule in the channel is oriented to polarize hydrogen atoms outward from the center. This arrangement suggests how the structure prevents the potentially lethal conduction of protons across the membrane. The structure also suggests the mechanism behind the selectivity of aquaglyceroporins for glycerol, the basis for enantioselectivity among alditols, and the basis for the prevention of any leakage of the electrochemical gradient.     

The mechanism of glycerol conduction in aquaglyceroporins.

BACKGROUND: The E. coli glycerol facilitator, GlpF, selectively conducts glycerol and water, excluding ions and charged solutes. The detailed mechanism of the glycerol conduction and its relationship to the characteristic secondary structure of aquaporins and to the NPA motifs in the center of the channel are unknown. RESULTS: Molecular dynamics simulations of GlpF reveal spontaneous glycerol and water conduction driven, on a nanosecond timescale, by thermal fluctuations. The bidirectional conduction, guided and facilitated by the secondary structure, is characterized by breakage and formation of hydrogen bonds for which water and glycerol compete. The conduction involves only very minor changes in the protein structure, and cooperativity between the GlpF monomers is not evident. The two conserved NPA motifs are strictly linked together by several stable hydrogen bonds and their asparagine side chains form hydrogen bonds with the substrates passing the channel in single file. CONCLUSIONS: A complete conduction of glycerol through the GlpF was deduced from molecular dynamics simulations, and key residues facilitating the conduction were identified. The nonhelical parts of the two half-membrane-spanning segments expose carbonyl groups towards the channel interior, establishing a curve-linear pathway. The conformational stability of the NPA motifs is important in the conduction and critical for selectivity. Water and glycerol compete in a random manner for hydrogen bonding sites in the protein, and their translocations in single file are correlated. The suggested conduction mechanism should apply to the whole family.     

Water transport by the bacterial channel alpha-hemolysin

This study is an investigation of the ability of the bacterial channel alpha-hemolysin to facilitate water permeation across biological membranes. alpha-Hemolysin channels were incorporated into rabbit erythrocyte ghosts at varying concentrations, and water permeation was induced by mixing the ghosts with hypertonic sucrose solutions. The resulting volume decrease of the ghosts was followed by time-resolved optical absorption at pH 5, 6, and 7. The average single-channel permeability coefficient of alpha-hemolysin for water ranged between 1.3x10-12 cm/s and 1.5x10-12 cm/s, depending on pH. The slightly increased single-channel permeability coefficient at lower pH-values was attributed to an increase in the effective pore size. The activation energy of water transport through the channel was low (Ea=5.4 kcal/mol), suggesting that the properties of water inside the alpha-hemolysin channel resemble those of bulk water. This conclusion was supported by calculations based on macroscopic hydrodynamic laws of laminar water flow. Using the known three-dimensional structure of the channel, the calculations accurately predicted the rate of water flow through the channel. The latter finding also indicated that water permeation data can provide a good estimate of the pore size for large channels.     

On the definition, nomenclature and classification of water channel proteins (aquaporins and relatives)

A water channel protein (WCP) or a water channel can be defined as a transmembrane protein that has a specific three-dimensional structure with a pore that provides a pathway for water permeation across biological membranes. The pore is formed by two highly conserved regions in the amino acid sequence, called NPA boxes (or motifs) with three amino acid residues (asparagine-proline-alanine, NPA) and several surrounding amino acids. The NPA boxes have been called the "signature" sequence of WCPs. WCPs are a family of proteins belonging to the Membrane Intrinsic Proteins (MIPs) superfamily. In addition, in the MIP superfamily (with more than 1000 members) there are also proteins with no channel activity. The WCP family include three subfamilies: aquaporins, aquaglyceroporins and S-aquaporins. (1) The aquaporins (AQPs) are water selective or specific water channels, also named by various authors as "orthodox", "ordinary", "conventional", "classical", "pure", "normal", or "sensu strictu" aquaporins); (2) The aquaglyceroporins are permeable to water, but also to other small uncharged molecules, in particular glycerol; this family includes the glycerol facilitators, abbreviated as GlpFs, from glycerol permease facilitators. The "signature" sequence for aquaglyceroporins is the aspartic acid residue (D) in the second NPA box. (3) The third subfamily of WCPs have little conserved amino acid sequences around the NPA boxes, unclassifiable to the first two subfamilies. I recommend to use always for this subfamily the name S-aquaporins. They are also named "superaquaporins", "aquaporins with unusual (or deviated) NPA boxes", "subcellular aquaporins", or "sip-like aquaporins". I also recommend to use always the spelling aquaporin (not aquaporine), and, for various AQPs, the abbreviation AQP followed immediately by the number, (e.g. AQP1), with no space or - which might create confusions with "minus".     

Conformational dynamics of a membrane transport protein probed by H/D exchange and covalent labeling: the glycerol facilitator

Glycerol facilitator (GF) is a tetrameric membrane protein responsible for the selective permeation of glycerol and water. Each of the four GF subunits forms a transmembrane channel. Every subunit consists of six helices that completely span the lipid bilayer, as well as two half-helices (TM7 and TM3). X-ray crystallography has revealed that the selectivity of GF is due to its unique amphipathic channel interior. To explore the structural dynamics of GF, we employ hydrogen/deuterium exchange (HDX) and oxidative labeling with mass spectrometry (MS). HDX-MS reveals that transmembrane helices are generally more protected than extramembrane segments, consistent with data previously obtained for other membrane proteins. Interestingly, TM7 does not follow this trend. Instead, this half-helix undergoes rapid deuteration, indicative of a highly dynamic local structure. The oxidative labeling behavior of most GF residues is consistent with the static crystal structure. However, the side chains of C134 and M237 undergo labeling although they should be inaccessible according to the X-ray structure. In agreement with our HDX-MS data, this observation attests to the fact that TM7 is only marginally stable. We propose that the highly mobile nature of TM7 aids in the efficient diffusion of guest molecules through the channel ("molecular lubrication"). In the absence of such dynamics, host-guest molecular recognition would favor semipermanent binding of molecules inside the channel, thereby impeding transport. The current work highlights the complementary nature of HDX, covalent labeling, and X-ray crystallography for the characterization of membrane proteins.     

The effect of gentamicin on the biophysical properties of phosphatidic acid liposomes is influenced by the O-C = O group of the lipid

We previously reported that gentamicin binds to liposomes composed of anionic phospholipids and depresses glycerol permeability and raises the activation energy for glycerol permeation in these liposomes. We postulated that these changes in the glycerol permeability and in the activation energy (Ea) for glycerol permeation were due to hydrogen bonding between O-C = O groups in the hydrogen belt and one or more amino groups of gentamicin. To test this hypothesis, we examined the effects of gentamicin on the membrane surface potential, the glycerol permeability coefficient (p), the Ea for glycerol permeation, and the aggregation of liposomes composed of 1:1 phosphatidylcholine (PC) and phosphatidic acid with the acyl chains of phosphatidic acid in either an ester (PA) or an ether (PA*) linkage. Gentamicin depressed the membrane surface electrostatic potential, measured by the partitioning of methylene blue between the bulk solution and the liposomal membrane, to an equivalent degree in PC-PA and PC-PA* liposomes, which indicates that substitution of the ether for the ester linkage did not interfere with the electrostatic interaction between the cationic drug and the negatively charged phosphate head group. Gentamicin caused a temperature-dependent decrease of p and raised Ea for glycerol permeation from 17.7 +/- 0.3 to 21.6 +/- 0.4 kcal/mol in PC-PA liposomes but had little or no effect on these parameters in PC-PA* liposomes. In contrast, gentamicin induced a significantly greater degree of aggregation of PC-PA* liposomes compared to that of PC-PA liposomes.(ABSTRACT TRUNCATED AT 250 WORDS)     

Transport of water and glycerol in aquaporin 3 is gated by H(+).

Aquaporins (AQPs) were expressed in Xenopus laevis oocytes in order to study the effects of external pH and solute structure on permeabilities. For AQP3 the osmotic water permeability, L(p), was abolished at acid pH values with a pK of 6.4 and a Hill coefficient of 3. The L(p) values of AQP0, AQP1, AQP2, AQP4, and AQP5 were independent of pH. For AQP3 the glycerol permeability P(Gl), obtained from [(14)C]glycerol uptake, was abolished at acid pH values with a pK of 6.1 and a Hill coefficient of 6. Consequently, AQP3 acts as a glycerol and water channel at physiological pH, but predominantly as a glycerol channel at pH values around 6.1. The pH effects were reversible. The interactions between fluxes of water and straight chain polyols were inferred from reflection coefficients (sigma). For AQP3, water and glycerol interacted by competing for titratable site(s): sigma(Gl) was 0.15 at neutral pH but doubled at pH 6.4. The sigma values were smaller for polyols in which the -OH groups were free to form hydrogen bonds. The activation energy for the transport processes was around 5 kcal mol(-1). We suggest that water and polyols permeate AQP3 by forming successive hydrogen bonds with titratable sites.     

Molecular dynamics simulations of the gramicidin A-dimyristoylphosphatidylcholine system with an ion in the channel pore region

To investigate the process of ion permeation in an ion channel systematically, we performed molecular dynamics (MD) simulations on a gramicidin A (GA)-phospholipid model system with an ion in the channel pore region. Each of the three types of ions (Ca2+, Na+ Cl-) was placed at five different positions along the channel axis by replacing a water molecule. MD simulations were performed on each system at constant pressure and constant temperature. The MD trajectories showed that the Ca2+ and Na+ ions could stably fluctuate in the pore region, but the Cl- ion was pushed out because of the unfavorable interaction with the channel. This result is consistent with experimental data. It was also found that the conformation of the GA channel underwent a significant change due to the presence of the ion, and the two ends of the GA monomer were more flexible than its middle region. In particular, the dramatic change of local pore radius near the ion indicated this kind of deformation. The strong interaction between the ion and carbonyl oxygen atoms of GA was the major contributor to this change. Furthermore, it was found that the ethanolamine group of the GA molecule was the most flexible group in the GA channel and often observed to block the entrance of GA. These results imply that the deformation of channel structure plays a very important factor in ion permeation, and the ethanolamine group may play a key role in regulating ion entry into the pore. In conclusion, our results indicate that the ion has a dominant influence on the structure of the GA channel and that the flexibility of the ion channel is a crucial factor in the ion permeation process.     

Permeation of volatile compounds through starch films

The aim of this study was to gain insight into the factors that affect the permeation of volatiles through starch films. These films were obtained by casting gelatinized starch/water/glycerol mixtures. The films were dried and conditioned under different conditions (temperature and relative humidity) resulting in films that vary in the degree of starch crystallinity and glycerol and water content. The permeation of two model volatiles (carvone and diacetyl) at 20 degrees C and at 30, 60, or 90% relative humidity (RH) was analyzed gravimetrically. Further, the solubility of the two model compounds (under conditions where the permeation experiments were carried out) was determined. From the obtained permeation and solubility data, the diffusion coefficients of these compounds in the different starch films were calculated. The crystallinity in the starch films increased with increasing water content of the films during preparation. The water content of the resulting films in turn increased with increasing glycerol and when the films were exposed to a higher RH during drying or conditioning. For films with the same composition, the flux for diacetyl was greater than for carvone. The solubilities of diacetyl and carvone were slightly dependent on the properties of the films. It was found that with increasing starch crystallinity the diffusion coefficient for both compounds decreases, which is probably due to the impermeability of starch crystallites. Interestingly, in films with about the same extent of crystallinity, the diffusion can be described with the free volume model, with water and glycerol determining the amount of free volume.     

Side-chain dynamics are critical for water permeation through aquaporin-1

Molecular dynamics simulations of aquaporin-1 embedded in a solvated lipid bilayer were carried out to investigate the mechanism of water permeation. The 2.2 Å resolution crystal structure of the bovine protein was used for five independent trajectories. During the equilibration and preparatory steps in which the protein was held fixed, water molecules inside the water channel adopted the same positions as observed in the crystal structure but they did not pass through the channel, suggesting that the dynamic motion of the protein is critical for water permeation. When the protein atoms were allowed to move, the side chains of the two asparagines in the two conserved Asn-Pro-Ala motifs near the center of the channel formed hydrogen bonds with water and helped water molecules move through the channel by actively aligning them for transport. The main-chain oxygen atoms, which were exposed to the pore surface in the crystal structure, also contributed to water transfer. Besides the constriction region observed in the crystal structure (Arg¹⁹⁷, Phe⁵⁸, His¹⁸², and Cys¹⁹¹), we found that His⁷⁶ and Val¹⁵⁵ act as a valve by dynamically blocking water permeation and helping control flow.     

Simulation study of a gramicidin/lipid bilayer system in excess water and lipid. II. Rates and mechanisms of water transport

A gramicidin channel in a fluid phase DMPC bilayer with excess lipid and water has been simulated. By use of the formal correspondence between diffusion and random walk, a permeability for water through the channel was calculated, and was found to agree closely with the experimental results of Rosenberg and Finkelstein (Rosenberg, P.A., and A. Finkelstein. 1978. J. Gen. Physiol. 72:327-340; 341-350) for permeation of water through gramicidin in a phospholipid membrane. By using fluctuation analysis, components of resistance to permeation were computed for movement through the channel interior, for the transition step at the channel mouth where the water molecule solvation environment changes, and for the process of diffusion up to the channel mouth. The majority of the resistance to permeation appears to occur in the transition step at the channel mouth. A significant amount is also due to structurally based free energy barriers within the channel. Only small amounts are due to local friction within the channel or to diffusive resistance for approaching the channel mouth.     

Role of equilibration before rapid freezing of mouse embryos

The time requirements for permeation by glycerol and dehydration by sucrose before rapid freezing of Day-3 mouse embryos by direct transfer to -180 degrees C were studied. When the embryos were equilibrated in 2.0, 3.0, or 4.0 M-glycerol + 0.25 M-sucrose for 2.5 to 40 min, the post-thaw viability increased (P less than 0.001) with the length of equilibration period at 4 degrees C. At 20 degrees C the volume of embryos increased with the duration of equilibration up to 20 min (P less than 0.001), but the post-thaw viability was not affected. The effect of equilibration in glycerol-sucrose was determined at 20 degrees C for embryos which were previously permeated by glycerol, dehydrated by sucrose or left in PBS + 5% FCS. The survival of previously permeated embryos was not affected by equilibration for 1-16 min in glycerol-sucrose. The maximum survival rate was attained after shorter equilibration in glycerol-sucrose for embryos without pretreatment (4 min) than for those previously dehydrated (8 min). It is concluded that increases in the intracellular glycerol level are beneficial for the viability of rapidly frozen mouse embryos and previous or concomitant exposure to sucrose unfavourably affects glycerol permeation.