Proton exclusion by an aquaglyceroprotein: a voltage clamp study

The energetic barrier to single-file water flow through narrow channels

Various nanoscopic channels of roughly equal diameter and length facilitate single-file diffusion at vastly different rates. The underlying variance of the energetic barriers to transport is poorly understood. First, water partitioning into channels so narrow that individual molecules cannot overtake each other incurs an energetic penalty. Corresponding estimates vary widely depending on how the sacrifice of two out of four hydrogen bonds is accounted for. Second, entropy differences between luminal and bulk water may arise: additional degrees of freedom caused by dangling OH-bonds increase entropy. At the same time, long-range dipolar water interactions decrease entropy. Here, we dissect different contributions to Gibbs free energy of activation, ΔG ^‡, for single-file water transport through narrow channels by analyzing experimental results from water permeability measurements on both bare lipid bilayers and biological water channels that (i) consider unstirred layer effects and (ii) adequately count the channels in reconstitution experiments. First, the functional relationship between water permeabilities and Arrhenius activation energies indicates negligible differences between the entropies of intraluminal water and bulk water. Second, we calculate ΔG ^‡ from unitary water channel permeabilities using transition state theory. Plotting ΔG ^‡ as a function of the number of H-bond donating or accepting pore-lining residues results in a 0.1 kcal/mol contribution per residue. The resulting upper limit for partial water dehydration amounts to 2 kcal/mol. In the framework of biomimicry, our analysis provides valuable insights for the design of synthetic water channels. It thus may aid in the urgent endeavor towards combating global water scarcity.

Biophysical Reviews' "Meet the Councilor Series"-a profile of Peter Pohl

It is my pleasure to write a few words to introduce myself to the readers of Biophysical Reviews as part of the "Meet the Councilor Series." Currently, I am serving the second period as IUPAB councilor after having been elected first in 2017. Initially, I studied Biophysics in Moscow (Russia) and later Medicine in Halle (Germany). My scientific carrier took me from the Medical School of the Martin Luther University of Halle-Wittenberg, via the Leibniz Institute for Molecular Pharmacology (Berlin) and the Institute for Biology at the Humboldt University (Berlin) to the Physics Department of the Johannes Kepler University in Linz (Austria). My key research interests lie in the molecular mechanisms of transport phenomena occurring at the lipid membrane, including (i) spontaneous and facilitated transport of water and other small molecules across membranes in reconstituted systems, (ii) proton migration along the membrane surface, (iii) protein translocation, and (iv) bilayer mechanics. Training of undergraduate, graduate, and postdoctoral researchers from diverse academic disciplines has been-and shall remain-a consistent part of my work.

Micropipette Aspiration-Based Assessment of Single Channel Water Permeability

Measurements of the unitary hydraulic conductivity of membrane channels, p_f , may be hampered by difficulties in producing sufficient quantities of purified and reconstituted proteins. Low yield expression, the purely empiric choice of detergents, as well as protein aggregation and misfolding during reconstitution may result in an average of less than one reconstituted channel per large unilamellar vesicle. This limits their applicability for p_f measurements, independent of whether light scattering or fluorescence quenching of encapsulated dyes is monitored. Here the micropipette aspiration technique is adopted because its superb sensitivity allows resolving p_f values for one order of magnitude smaller protein densities in sphingomyelin and cholesterol rich giant unilamellar vesicles (GUVs). Protein density is derived from intensity fluctuations that fluorescently labeled channels in the aspirated GUV induce by diffusing through the diffraction limited spot. A perfusion system minimizes unstirred layers in the immediate membrane vicinity as demonstrated by the distribution of both encapsulated and extravesicular aqueous dyes. p_f amounted to 2.4 ± 0.1 × 10^-13 cm³ s^-1 for aquaporin-1 that served as a test case. The new assay paves the way for directly monitoring the effect that interaction of aquaporins with other proteins or inhibitors may have on p_f on a single sample.

Single-file transport of water through membrane channels

Water at interfaces governs many processes on the molecular scale from electrochemical and enzymatic reactions to protein folding. Here we focus on water transport through proteinaceous pores that are so narrow that the water molecules cannot overtake each other in the pore. After a short introduction into the single-file transport theory, we analyze experiments in which the unitary water permeability, pf, of water channel proteins (aquaporins, AQPs), potassium channels (KcsA), and antibiotics (gramicidin-A derivatives) has been obtained. A short outline of the underlying methods (scanning electrochemical microscopy, fluorescence correlation spectroscopy, measurements of vesicle light scattering) is also provided. We conclude that pf increases exponentially with a decreasing number NH of hydrogen bond donating or accepting residues in the channel wall. The variance in NH is responsible for a more than hundredfold change in pf. The dehydration penalty at the channel mouth has a smaller effect on pf. The intricate link between pf and the Gibbs activation energy barrier, ΔG‡t, for water flow suggests that conformational transitions of water channels act as a third determinant of pf.

YidC and SecYEG form a heterotetrameric protein translocation channel

The heterotrimeric SecYEG complex cooperates with YidC to facilitate membrane protein insertion by an unknown mechanism. Here we show that YidC contacts the interior of the SecY channel resulting in a ligand-activated and voltage-dependent complex with distinct ion channel characteristics. The SecYEG pore diameter decreases from 8 Å to only 5 Å for the YidC-SecYEG pore, indicating a reduction in channel cross-section by YidC intercalation. In the presence of a substrate, YidC relocates to the rim of the pore as indicated by increased pore diameter and loss of YidC crosslinks to the channel interior. Changing the surface charge of the pore by incorporating YidC into the channel wall increases the anion selectivity, and the accompanying change in wall hydrophobicity is liable to alter the partition of helices from the pore into the membrane. This could explain how the exit of transmembrane domains from the SecY channel is facilitated by YidC.

Tuning membrane protein mobility by confinement into nanodomains

High-speed atomic force microscopy (HS-AFM) can be used to visualize function-related conformational changes of single soluble proteins. Similar studies of single membrane proteins are, however, hampered by a lack of suitable flat, non-interacting membrane supports and by high protein mobility. Here we show that streptavidin crystals grown on mica-supported lipid bilayers can be used as porous supports for membranes containing biotinylated lipids. Using SecYEG (protein translocation channel) and GlpF (aquaglyceroporin), we demonstrate that the platform can be used to tune the lateral mobility of transmembrane proteins to any value within the dynamic range accessible to HS-AFM imaging through glutaraldehyde-cross-linking of the streptavidin. This allows HS-AFM to study the conformation or docking of spatially confined proteins, which we illustrate by imaging GlpF at sub-molecular resolution and by observing the motor protein SecA binding to SecYEG.

Protons and Hydroxide Ions in Aqueous Systems

Understanding the structure and dynamics of water's constituent ions, proton and hydroxide, has been a subject of numerous experimental and theoretical studies over the last century. Besides their obvious importance in acid-base chemistry, these ions play an important role in numerous applications ranging from enzyme catalysis to environmental chemistry. Despite a long history of research, many fundamental issues regarding their properties continue to be an active area of research. Here, we provide a review of the experimental and theoretical advances made in the last several decades in understanding the structure, dynamics, and transport of the proton and hydroxide ions in different aqueous environments, ranging from water clusters to the bulk liquid and its interfaces with hydrophobic surfaces. The propensity of these ions to accumulate at hydrophobic surfaces has been a subject of intense debate, and we highlight the open issues and challenges in this area. Biological applications reviewed include proton transport along the hydration layer of various membranes and through channel proteins, problems that are at the core of cellular bioenergetics.

The Sodium Glucose Cotransporter SGLT1 Is an Extremely Efficient Facilitator of Passive Water Transport

The small intestine is void of aquaporins adept at facilitating vectorial water transport, and yet it reabsorbs ∼8 liters of fluid daily. Implications of the sodium glucose cotransporter SGLT1 in either pumping water or passively channeling water contrast with its reported water transporting capacity, which lags behind that of aquaporin-1 by 3 orders of magnitude. Here we overexpressed SGLT1 in MDCK cell monolayers and reconstituted the purified transporter into proteoliposomes. We observed the rate of osmotic proteoliposome deflation by light scattering. Fluorescence correlation spectroscopy served to assess (i) SGLT1 abundance in both vesicles and plasma membranes and (ii) flow-mediated dilution of an aqueous dye adjacent to the cell monolayer. Calculation of the unitary water channel permeability, pf, yielded similar values for cell and proteoliposome experiments. Neither the absence of glucose or Na(+), nor the lack of membrane voltage in vesicles, nor the directionality of water flow grossly altered pf Such weak dependence on protein conformation indicates that a water-impermeable occluded state (glucose and Na(+) in their binding pockets) lasts for only a minor fraction of the transport cycle or, alternatively, that occlusion of the substrate does not render the transporter water-impermeable as was suggested by computational studies of the bacterial homologue vSGLT. Although the similarity between the pf values of SGLT1 and aquaporin-1 makes a transcellular pathway plausible, it renders water pumping physiologically negligible because the passive flux would be orders of magnitude larger.

The mobility of single-file water molecules is governed by the number of H-bonds they may form with channel-lining residues

Channel geometry governs the unitary osmotic water channel permeability, p_f, according to classical hydrodynamics. Yet, p_f varies by several orders of magnitude for membrane channels with a constriction zone that is one water molecule in width and four to eight molecules in length. We show that both the p_f of those channels and the diffusion coefficient of the single-file waters within them are determined by the number N_H of residues in the channel wall that may form a hydrogen bond with the single-file waters. The logarithmic dependence of water diffusivity on N_H is in line with the multiplicity of binding options at higher N_H densities. We obtained high-precision p_f values by (i) having measured the abundance of the reconstituted aquaporins in the vesicular membrane via fluorescence correlation spectroscopy and via high-speed atomic force microscopy, and (ii) having acquired the vesicular water efflux from scattered light intensities via our new adaptation of the Rayleigh-Gans-Debye equation.

High-speed AFM images of thermal motion provide stiffness map of interfacial membrane protein moieties

The flexibilities of extracellular loops determine ligand binding and activation of membrane receptors. Arising from fluctuations in inter- and intraproteinaceous interactions, flexibility manifests in thermal motion. Here we demonstrate that quantitative flexibility values can be extracted from directly imaging the thermal motion of membrane protein moieties using high-speed atomic force microscopy (HS-AFM). Stiffness maps of the main periplasmic loops of single reconstituted water channels (AqpZ, GlpF) revealed the spatial and temporal organization of loop-stabilizing intraproteinaceous H-bonds and salt bridges.

Ion conductivity of the bacterial translocation channel SecYEG engaged in translocation

While engaged in protein transport, the bacterial translocon SecYEG must maintain the membrane barrier to small ions. The preservation of the proton motif force was attributed to (i) cation exclusion, (ii) engulfment of the nascent chain by the hydrophobic pore ring, and (iii) a half-helix partly plugging the channel. In contrast, we show here that preservation of the proton motif force is due to a voltage-driven conformational change. Preprotein or signal peptide binding to the purified and reconstituted SecYEG results in large cation and anion conductivities only when the membrane potential is small. Physiological values of membrane potential close the activated channel. This voltage-dependent closure is not dependent on the presence of the plug domain and is not affected by mutation of 3 of the 6 constriction residues to glycines. Cellular ion homeostasis is not challenged by the small remaining leak conductance.

Real-time monitoring of membrane-protein reconstitution by isothermal titration calorimetry

Phase diagrams offer a wealth of thermodynamic information on aqueous mixtures of bilayer-forming lipids and micelle-forming detergents, providing a straightforward means of monitoring and adjusting the supramolecular state of such systems. However, equilibrium phase diagrams are of very limited use for the reconstitution of membrane proteins because of the occurrence of irreversible, unproductive processes such as aggregation and precipitation that compete with productive reconstitution. Here, we exemplify this by dissecting the effects of the K⁺ channel KcsA on the process of bilayer self-assembly in a mixture of Escherichia coli polar lipid extract and the nonionic detergent octyl-β-d-glucopyranoside. Even at starting concentrations in the low micromolar range, KcsA has a tremendous impact on the supramolecular organization of the system, shifting the critical lipid/detergent ratios at the onset and completion of vesicle formation by more than 2-fold. Thus, equilibrium phase diagrams obtained for protein-free lipid/detergent mixtures would be misleading when used to guide the reconstitution process. To address this issue, we demonstrate that, even under such nonequilibrium conditions, high-sensitivity isothermal titration calorimetry can be exploited to monitor the progress of membrane-protein reconstitution in real time, in a noninvasive manner, and at high resolution to yield functional proteoliposomes with a narrow size distribution for further downstream applications.

Glycerol modulates water permeation through Escherichia coli aquaglyceroporin GlpF

Among aquaglyceroporins that transport both water and glycerol across the cell membrane, Escherichia coli glycerol uptake facilitator (GlpF) is the most thoroughly studied. However, one question remains: Does glycerol modulate water permeation? This study answers this fundamental question by determining the three-dimensional potential of mean force of glycerol along the permeation path through GlpF's conducting pore. There is a deep well near the Asn-Pro-Ala (NPA) motifs (6.5kcal/mol below the bulk level) and a barrier near the selectivity filter (10.1kcal/mol above the well bottom). This profile owes its existence to GlpF's perfect steric arrangement: The glycerol-protein van der Waals interactions are attractive near the NPA but repulsive elsewhere in the conducting pore. In light of the single-file nature of waters and glycerols lining up in GlpF's amphipathic pore, it leads to the following conclusion: Glycerol modulates water permeation in the μM range. At mM concentrations, GlpF is glycerol-saturated and a glycerol residing in the well occludes the conducting pore. Therefore, water permeation is fully correlated to glycerol dissociation that has an Arrhenius activation barrier of 6.5kcal/mol. Validation of this theory is based on the existent in vitro data, some of which have not been given the proper attention they deserved: The Arrhenius activation barriers were found to be 7kcal/mol for water permeation and 9.6kcal/mol for glycerol permeation; The presence of up to 100mM glycerol did not affect the kinetics of water transport with very low permeability, in apparent contradiction with the existent theories that predicted high permeability (0M glycerol).

Molecular dynamics study of the archaeal aquaporin AqpM

Background

Aquaporins are a large family of transmembrane channel proteins that are present throughout all domains of life and are implicated in human disorders. These channels, allow the passive but selective movement of water and other small neutral solutes across cell membranes. Aquaporins have been classified into two sub-families: i) strict aquaporins that only allow the passage of water and ii) the less selective aquaglyceroporins that transport water and other neutral solutes, such as glycerol, CO₂ or urea. Recently, the identification and characterization of a number of archaeal and bacterial aquaporins suggested the existence of a third sub-family; one that is neither a strict aquaporin nor an aquaglyceroporin. The function and phylogeny of this third family is still a matter of debate.

Results

Twenty nanosecond molecular dynamics (MD) simulation of a fully hydrated tetramer of AqpM embedded in a lipid bilayer permitted predictions to be made of key biophysical parameters including: single channel osmotic permeability constant (p_f), single channel diffusive permeability constant (p_d), channel radius, potential water occupancy of the channel and water orientation inside the pore. These properties were compared with those of well characterized representatives of the two main aquaporin sub-families. Results show that changes in the amino acid composition of the aromatic/arginine region affect the size and polarity of the selectivity filter (SF) and could help explain the difference in water permeability between aquaporins. In addition, MD simulation results suggest that AqpM combines characteristics of strict aquaporins, such as the narrow SF and channel radius, with those of aquaglyceroporins, such as a more hydrophobic and less polar SF.

Conclusions

MD simulations of AqpM extend previous evidence that this archaeal aquaporin exhibits hybrid features intermediate between the two known aquaporin sub-families, supporting the idea that it may constitute a member of a novel class of aquaporins.

Major intrinsic proteins in biomimetic membranes

Biological membranes define the structural and functional boundaries in living cells and their organelles. The integrity of the cell depends on its ability to separate inside from outside and yet at the same time allow massive transport of matter in and out the cell. Nature has elegantly met this challenge by developing membranes in the form of lipid bilayers in which specialized transport proteins are incorporated. This raises the question: is it possible to mimic biological membranes and create a membrane based sensor and/or separation device? In the development of a biomimetic sensor/separation technology, a unique class of membrane transport proteins is especially interesting-the major intrinsic proteins (MIPs). Generally, MIPs conduct water molecules and selected solutes in and out of the cell while preventing the passage of other solutes, a property critical for the conservation of the cells internal pH and salt concentration. Also known as water channels or aquaporins they are highly efficient membrane pore proteins some of which are capable of transporting water at very high rates up to 10(9) molecules per second. Some MIPs transport other small, uncharged solutes, such as glycerol and other permeants such as carbon dioxide, nitric oxide, ammonia, hydrogen peroxide and the metalloids antimonite, arsenite, silicic and boric acid depending on the effective restriction mechanism of the protein. The flux properties of MIPs thus lead to the question ifMIPs can be used in separation devices or as sensor devices based on, e.g., the selective permeation of metalloids. In principle a MIP based membrane sensor/separation device requires the supporting biomimetic matrix to be virtually impermeable to anything but water or the solute in question. In practice, however, a biomimetic support matrix will generally have finite permeabilities to both electrolytes and non-electrolytes. The feasibility of a biomimetic MIP device thus depends on the relative transport contribution from both protein and biomimetic support matrix. Also the biomimetic matrix must be encapsulated in order to protect it and make it sufficiently stable in a final application. Here, I specifically discuss the feasibility of developing osmotic biomimetic MIP membranes, but the technical issues are of general concern in the design ofbiomimetic membranes capable of supporting selective transmembrane fluxes.

Membrane solubilisation and reconstitution by octylglucoside: comparison of synthetic lipid and natural lipid extract by isothermal titration calorimetry

We have studied the solubilisation and reconstitution of lipid membranes composed of either synthetic phosphatidylcholine or Escherichia. coli polar lipid extract by the non-ionic detergent octylglucoside. For both lipid systems, composition-dependent transformations of unilamellar vesicles into micelles or vice versa were followed by high-sensitivity isothermal titration calorimetry. Data obtained over a range of detergent and lipid concentrations could be rationalised in terms of a three-stage phase separation model involving bilayer, bilayer/micelle coexistence, and micellar ranges, yielding the detergent/lipid phase diagrams and the bilayer-to-micelle partition coefficients of both detergent and lipid. The most notable difference between the lipids investigated was a substantial widening of the bilayer/micelle coexistence range for E. coli lipid, which was due to an increased preference of the detergent and a decreased affinity of the lipid for the micellar phase as compared with the bilayer phase. These effects on the bilayer-to-micelle partition coefficients could be explained by the high proportion in E. coli membranes of lipids possessing negative spontaneous curvature, which hampers both their transfer into strongly curved micellar structures as well as the insertion of detergent into condensed bilayers.

Pentavalent methylated arsenicals are substrates of human AQP9

Liver aquaglyceroporin AQP9 facilitates movement of trivalent inorganic arsenite (As(III)) and organic monomethylarsonous acid (MAs(III)). However, the transport pathway for the two major pentavalent arsenic cellular metabolites, MAs(V) and DMAs(V), remains unknown in mammals. These products of arsenic metabolism, in particular DMAs(V), are the major arsenicals excreted in the urine of mammals. In this study, we examined the uptake of the two pentavalent organic arsenicals by human AQP9 in Xenopus laevis oocytes. Xenopus laevis oocytes microinjected with AQP9 cRNA exhibited uptake of both MAs(V) and DMAs(V) in a pH-dependent manner. The rate of transport was much higher at acidic pH (pH5.5) than at neutral pH. Hg(II), an aquaporin inhibitor, inhibited transport of As(III), MAs(III), MAs(V) and DMAs(V) via AQP9. However, phloretin, which inhibits water and glycerol permeation via AQP9, can only inhibit transport of pentavalent MAs(V) and DMAs(V) but not trivalent As(III) and MAs(III), indicating the translocation mechanisms of these arsenic species are not exactly the same. Reagents such as FCCP, valinomycin and nigericin that dissipate transmembrane proton potential or change the transmemebrane pH gradient did not significantly inhibit all arsenic transport via AQP9, suggesting the transport of pentavalent arsenic is not proton coupled. The results suggest that in addition to the initial uptake of trivalent inorganic As(III) inside cells, AQP9 plays a dual role in the detoxification of arsenic metabolites by facilitating efflux from cells.

Plant aquaporin selectivity: where transport assays, computer simulations and physiology meet

Plants contain a large number of aquaporins with different selectivity. These channels generally conduct water, but some additionally conduct NH(3), CO(2) and/or H(2)O(2). The experimental evidence and molecular basis for the transport of a given solute, the validation with molecular dynamics simulations and the physiological impact of the selectivity are reviewed here. The aromatic/arginine (ar/R) constriction is most important for solute selection, but the exact pore requirements for efficient conduction of small solutes remain difficult to predict. Yeast growth assays are valuable for screening substrate selectivity and are explicitly shown for hydrogen peroxide and methylamine, a transport analog of ammonia. Independent assays need to address the relevance of different substrates for each channel in its physiological context. This is emphasized by the fact that several plant NIP channels, which conduct several solutes, are specifically involved in the transport of metalloids, such as silicic acid, arsenite, or boric acid in planta.

Molecular recognition in biomolecules studied by statistical-mechanical integral-equation theory of liquids

Recent progress in the theory of molecular recognition in biomolecules is reviewed, which has been made based on the statistical mechanics of liquids or the RISM/3D-RISM theory during the last five years in the authors' group. The method requires just the structure of protein and the potential energy parameters for the biomolecules and solutions as inputs. The calculation is carried out in two steps. The first step is to obtain the pair correlation functions for solutions consisting of water and ligands based on the RISM theory. Then, given the pair correlation functions prepared in the first step, we calculate the 3D-distribution functions of water and ligands around and inside protein based on the 3D-RISM theory. The molecular recognition of a ligand by the protein is realized by the 3D-distribution functions: if one finds some conspicuous peaks in the distribution of a ligand inside protein, then the ligand is regarded as "recognized" by the protein. Some biochemical processes are investigated, which are intimately related to the molecular recognition of small ligands including water, noble gases, and ions by a protein.

Determinants of water permeability through nanoscopic hydrophilic channels

Naturally occurring pores show a variety of polarities and sizes that are presumably directly linked to their biological function. Many biological channels are selective toward permeants similar or smaller in size than water molecules, and therefore their pores operate in the regime of single-file water pores. Intrinsic factors affecting water permeability through such pores include the channel-membrane match, the structural stability of the channel, the channel geometry and channel-water affinity. We present an extensive molecular dynamics study on the role of the channel geometry and polarity on the water osmotic and diffusive permeability coefficients. We show that the polarity of the naturally occurring peptidic channels is close to optimal for water permeation, and that the water mobility for a wide range of channel polarities is essentially length independent. By systematically varying the geometry and polarity of model hydrophilic pores, based on the fold of gramicidin A, the water density, occupancy, and permeability are studied. Our focus is on the characterization of the transition between different permeation regimes in terms of the structure of water in the pores, the average pore occupancy and the dynamics of the permeating water molecules. We show that a general relationship between osmotic and diffusive water permeability coefficients in the single-file regime accounts for the time averaged pore occupancy, and that the dynamics of the permeating water molecules through narrow non single file channels effectively behaves like independent single-file columns.

The structural basis of water permeation and proton exclusion in aquaporins

Aquaporins (AQPs) represent a ubiquitous class of integral membrane proteins that play critical roles in cellular osmoregulations in microbes, plants and mammals. AQPs primarily function as water-conducting channels, whereas members of a sub-class of AQPs, termed aquaglyceroporins, are permeable to small neutral solutes such as glycerol. While AQPs facilitate transmembrane permeation of water and/or small neutral solutes, they preclude the conduction of protons. Consequently, openings of AQP channels allow rapid water diffusion down an osmotic gradient without dissipating electrochemical potentials. Molecular structures of AQPs portray unique features that define the two central functions of AQP channels: effective water permeation and strict proton exclusion. This review describes AQP structures known to date and discusses the mechanisms underlying water permeation, proton exclusion and water permeability regulation.

Water transport in aquaporins: osmotic permeability matrix analysis of molecular dynamics simulations

Single-channel osmotic water permeability (p(f)) is a key quantity for investigating the transport capability of the water channel protein, aquaporin. However, the direct connection between the single scalar quantity p(f) and the channel structure remains unclear. In this study, based on molecular dynamics simulations, we propose a p(f)-matrix method, in which p(f) is decomposed into contributions from each local region of the channel. Diagonal elements of the p(f) matrix are equivalent to the local permeability at each region of the channel, and off-diagonal elements represent correlated motions of water molecules in different regions. Averaging both diagonal and off-diagonal elements of the p(f) matrix recovers p(f) for the entire channel; this implies that correlated motions between distantly-separated water molecules, as well as adjacent water molecules, influence the osmotic permeability. The p(f) matrices from molecular dynamics simulations of five aquaporins (AQP0, AQP1, AQP4, AqpZ, and GlpF) indicated that the reduction in the water correlation across the Asn-Pro-Ala region, and the small local permeability around the ar/R region, characterize the transport efficiency of water. These structural determinants in water permeation were confirmed in molecular dynamics simulations of three mutants of AqpZ, which mimic AQP1.

Molecular mechanisms of conduction and selectivity in aquaporin water channels

Aquaporins (AQP) are a family of membrane channels primarily responsible for conducting water across cellular membranes. The availability of a large body of high resolution structural data along with numerous atomic-scale simulation studies have resulted in an unprecedented level of understanding of the mechanism of function and selectivity in AQP. In this article, after summarizing major highlights of structure-functional studies of AQP, we will report on some of our recent large-scale molecular dynamics simulations investigating the mechanisms of permeation of various substances through pure lipid bilayers and through multiple pathways provided by tetrameric structures of different AQP. Comparison of the results obtained for structurally highly homologous, but functionally distinct, AQP allowed us to identify novel mechanisms of gating and selectivity of these channels and to design mutants with experimentally verified, altered properties. When applicable, special attention will be given to specific aromatic amino acids and their involvement in various functional aspects of AQP.

Exploring gas permeability of cellular membranes and membrane channels with molecular dynamics

Aquaporins are a family of membrane proteins specialized in rapid water conduction across biological membranes. Whether these channels also conduct gas molecules and the physiological significance of this potential function have not been well understood. Here we report 140 ns of molecular dynamics simulations of membrane-embedded AQP1 and of a pure POPE bilayer addressing these questions. The permeability of AQP1 to two types of gas molecules, O2 and CO2, was investigated using two complementary methods, namely, explicit gas diffusion simulation and implicit ligand sampling. The simulations show that the central (tetrameric) pore of AQP1 can be readily used by either gas molecule to permeate the channel. The two approaches produced similar free energy profiles associated with gas permeation through the central pore: a -0.4 to -1.7 kcal/mol energy well in the middle, and a 3.6-4.6 kcal/mol energy barrier in the periplasmic vestibule. The barrier appears to be mainly due to a dense cluster of water molecules anchored in the periplasmic mouth of the central pore by four aspartate residues. Water pores show a very low permeability to O2, but may contribute to the overall permeation of CO2 due to its more hydrophilic nature. Although the central pore of AQP1 is found to be gas permeable, the pure POPE bilayer provides a much larger cross-sectional area, thus exhibiting a much lower free energy barrier for CO2 and O2 permeation. As such, gas conduction through AQP1 may only be physiologically relevant either in membranes of low gas permeability, or in cells where a major fraction of the cellular membrane is occupied by AQPs.

Fast and selective ammonia transport by aquaporin-8

The transport of ammonia/ammonium is fundamental to nitrogen metabolism in all forms of life. So far, no clear picture has emerged as to whether a protein channel is capable of transporting exclusively neutral NH(3) while excluding H(+) and NH(4)(+). Our research is the first stoichiometric study to show the selective transport of NH(3) by a membrane channel. The purified water channel protein aquaporin-8 was reconstituted into planar bilayers, and the exclusion of NH(4)(+) or H(+) was established by ensuring a lack of current under voltage clamp conditions. The single channel water permeability coefficient of 1.2 x 10(-14) cm(3)/subunit/s was established by imposing an osmotic gradient across reconstituted planar bilayers, and resulting minute changes in ionic concentration close to the membrane surface were detected. It is more than 2-fold smaller than the single channel ammonia permeability (2.7 x 10(-14) cm(3)/subunit/s) that was derived by establishing a transmembrane ammonium concentration gradient and measuring the resulting concentration increases adjacent to the membrane. This permeability ratio suggests that electrically silent ammonia transport may be the main function of AQP8.

Mechanism of gating and ion conductivity of a possible tetrameric pore in aquaporin-1

While substrate permeation through monomeric pores of aquaporins is well characterized, little is known about the possible tetrameric pore. AQP1 has been suggested to function as an ion channel upon cGMP activation, although this idea has been controversial. Taking a theoretical and experimental approach, we demonstrate that the current might arise through the tetrameric pore and propose a plausible mechanism for conduction and gating. In response to simulated ion permeation, immediate hydration of the putative central pore was facilitated by moderate conformational changes of pore-lining residues. cGMP is found to interact with an unusually arginine-rich, cytoplasmic loop (loop D) facilitating its outward motion, which is hypothesized to trigger the opening of a cytoplasmic gate. Physiological analyses of wild-type AQP1 and a designed mutant in which two arginines of the gating loop are replaced by alanine provide experimental support for identifying a key component of the proposed mechanism.

Mobility of a one-dimensional confined file of water molecules as a function of file length

Confinement of water by pore geometry to a one-dimensional file of molecules interacting with the pore alters the diffusion coefficient D(W). Here we report an exponential dependence of D(W) on the number of water positions in the pore. The result is based on measurements of single channel water permeabilities of structurally similar peptidic nanopores of different length. The inconsistency with predictions from continuum or kinetic models indicates that pore occupancy is reduced in single file transport. In longer pores (e.g., in aquaporins) the presence of charged residues increases D(W).

Single-channel water permeabilities of Escherichia coli aquaporins AqpZ and GlpF

From equilibrium molecular dynamics simulations we have determined single-channel water permeabilities for Escherichia coli aquaporin Z (AqpZ) and aquaglyceroporin GlpF with the channels embedded in lipid bilayers. GlpF's osmotic water permeability constant pf exceeds by 2-3 times that of AqpZ and the diffusive permeability constant (pd) of GlpF is found to exceed that of AqpZ 2-9-fold. Achieving complete water selectivity in AqpZ consequently implies lower transport rates overall relative to the less selective, wider channel of GlpF. For AqpZ, the ratio pf/pd congruent with 12 is close to the average number of water molecules in the channel lumen, whereas for GlpF, pf/pd congruent with 4. This implies that single-file structure of the luminal water is more pronounced for AqpZ, the narrower channel of the two. Electrostatics profiles across the pore lumens reveal that AqpZ significantly reinforces water-channel interactions, and weaker water-water interactions in turn suppress water-water correlations relative to GlpF. Consequently, suppressed water-water correlations across the narrow selectivity filter become a key structural determinant for water permeation causing luminal water to permeate slower across AqpZ.