How does carbon dioxide permeate cell membranes? A discussion of concepts, results and methods

Measuring cerebral enzymatic activity, brain pH and extracranial muscle metabolism with hyperpolarized 13C-pyruvate

Hyperpolarized carbon-13 (13C) magnetic resonance imaging (MRI) has shown promise for non-invasive assessment of the cerebral metabolism of [1-13C]pyruvate in both healthy volunteers and patients. The exchange of pyruvate to lactate catalysed by lactate dehydrogenase (LDH) and that of pyruvate flux to bicarbonate through pyruvate dehydrogenase (PDH) are the most widely studied reactions in vivo. Here we show the potential of the technique to probe additional enzymatic activity within the brain. Approximately 50 s after intravenous injection of hyperpolarized pyruvate, high-flip-angle pulses were used to detect cerebral 13C-labelled carbon dioxide (13CO2), in addition to the 13C-bicarbonate (H13CO3 -) subsequently formed by carbonic anhydrase (CA). Brain pH measurements, which were weighted towards the extracellular compartment, were calculated from the ratio of H13CO3 - to 13CO2 in seven volunteers using the Henderson-Hasselbalch equation, demonstrating an average pH ± SD of 7.40 ± 0.02, with inter-observer reproducibility of 0.04. In addition, hyperpolarized [1-13C]aspartate was also detected, demonstrating irreversible pyruvate carboxylation to oxaloacetate by pyruvate carboxylase (PC) and subsequent transamination by aspartate aminotransferase (AST), with the average flux being on average 11% ± 3% of that through PDH. A hyperpolarized [1-13C]alanine signal was also detected, but this was localized to extracranial muscle tissue in keeping with skeletal alanine aminotransferase (ALT) activity. The results demonstrate the potential of hyperpolarized 13C-MRI to assess cerebral and extracerebral [1-13C]pyruvate metabolism in addition to LDH and PDH activity. Non-invasive measurements of brain pH could be particularly important in assessing cerebral pathology given the wide range of disease processes that alter acid-base balance.

Cholesterol inhibits oxygen permeation through biological membranes: mechanism against double-bond peroxidation

The presence of oxygen molecules (O2) in biological membranes promotes lipid peroxidation of phospholipids with unsaturated acyl chains. On the other hand, cholesterol is considered to be an antioxidant molecule as it has a significant barrier effect on the permeation of O2 across membranes. However, a comprehensive explanation of how cholesterol affects the distribution and diffusion of O2 within lipid bilayers is yet to be established. In this study, we investigated the interaction of oxygen molecules with polyunsaturated lipid bilayers using molecular dynamics (MD) simulations. The degree of lipid unsaturation and the concentration of cholesterol were varied to study the permeation of O2. The free energy profile of O2 diffusing from the water phase to the lipid bilayer was calculated using biased umbrella MD simulations. The results show that O2 passively translocates into the membrane without changing the physical properties of the bilayer. Interestingly, in the unsaturated lipid bilayers the presence of cholesterol led to a significantly decreased permeation of O2 and an increase in the lipid chain order. Our results indicate that the hydroxyl groups of cholesterol strongly interact with the O2 molecules effectively inhibiting interactions between the oxygens and the double bonds in unsaturated lipid tails. In addition, a linear relationship between permeation and the ratio of membrane thickness and area per lipid was found. These insights can help our understanding of how the degree of unsaturation in a lipid tail and cholesterol affect lipid peroxidation at the molecular level.

Microbially Induced Calcium Carbonate Precipitation by Sporosarcina pasteurii: a Case Study in Optimizing Biological CaCO3 Precipitation

Current production of traditional concrete requires enormous energy investment that accounts for approximately 5 to 8% of the world's annual CO2 production. Biocement is a building material that is already in industrial use and has the potential to rival traditional concrete as a more convenient and more environmentally friendly alternative. Biocement relies on biological structures (enzymes, cells, and/or cellular superstructures) to mineralize and bind particles in aggregate materials (e.g., sand and soil particles). Sporosarcina pasteurii is a workhorse organism for biocementation, but most research to date has focused on S. pasteurii as a building material rather than a biological system. In this review, we synthesize available materials science, microbiology, biochemistry, and cell biology evidence regarding biological CaCO3 precipitation and the role of microbes in microbially induced calcium carbonate precipitation (MICP) with a focus on S. pasteurii. Based on the available information, we provide a model that describes the molecular and cellular processes involved in converting feedstock material (urea and Ca2+) into cement. The model provides a foundational framework that we use to highlight particular targets for researchers as they proceed into optimizing the biology of MICP for biocement production.

Aquaporins and CO2 diffusion across biological membrane

Despite the physiological significance of effective CO₂ diffusion across biological membranes, the underlying mechanism behind this process is not yet resolved. Particularly debatable is the existence of CO₂-permeable aquaporins. The lipophilic characteristic of CO₂ should, according to Overton's rule, result in a rapid flux across lipid bilayers. However, experimental evidence of limited membrane permeability poses a challenge to this idea of free diffusion. In this review, we summarized recent progress with regard to CO₂ diffusion, and discussed the physiological effects of altered aquaporin expression, the molecular mechanisms of CO₂ transport via aquaporins, and the function of sterols and other membrane proteins in CO₂ permeability. In addition, we highlight the existing limits in measuring CO₂ permeability and end up with perspectives on resolving such argument either by determining the atomic resolution structure of CO₂ permeable aquaporins or by developing new methods for measuring permeability.

A Hitchhiker's Guide to Supplying Enzymatic Reducing Power into Synthetic Cells

The construction from scratch of synthetic cells by assembling molecular building blocks is unquestionably an ambitious goal from a scientific and technological point of view. To realize functional life-like systems, minimal enzymatic modules are required to sustain the processes underlying the out-of-equilibrium thermodynamic status hallmarking life, including the essential supply of energy in the form of electrons. The nicotinamide cofactors NAD(H) and NADP(H) are the main electron carriers fueling reductive redox reactions of the metabolic network of living cells. One way to ensure the continuous availability of reduced nicotinamide cofactors in a synthetic cell is to build a minimal enzymatic module that can oxidize an external electron donor and reduce NAD(P)+. In the diverse world of metabolism there is a plethora of potential electron donors and enzymes known from living organisms to provide reducing power to NAD(P)+ coenzymes. This perspective proposes guidelines to enable the reduction of nicotinamide cofactors enclosed in phospholipid vesicles, while avoiding high burdens of or cross-talk with other encapsulated metabolic modules. By determining key requirements, such as the feasibility of the reaction and transport of the electron donor into the cell-like compartment, we select a shortlist of potentially suitable electron donors. We review the most convenient proteins for the use of these reducing agents, highlighting their main biochemical and structural features. Noting that specificity toward either NAD(H) or NADP(H) imposes a limitation common to most of the analyzed enzymes, we discuss the need for specific enzymes─transhydrogenases─to overcome this potential bottleneck.

Aquaporins Display a Diversity in their Substrates

Aquaporins constitute a family of transmembrane proteins that function to transport water and other small solutes across the cell membrane. Aquaporins family members are found in diverse life forms. Aquaporins share the common structural fold consisting of six transmembrane alpha helices with a central water-transporting channel. Four such monomers assemble together to form tetramers as their biological unit. Initially, aquaporins were discovered as water-transporting channels, but several studies supported their involvement in mediating the facilitated diffusion of different solutes. The so-called water channel is able to transport a variety of substrates ranging from a neutral molecule to a charged molecule or a small molecule to a bulky molecule or even a gas molecule. This article gives an overview of a diverse range of substrates conducted by aquaporin family members. Prime focus is on human aquaporins where aquaporins show a wide tissue distribution and substrate specificity leading to various physiological functions. This review also highlights the structural mechanisms leading to the transport of water and glycerol. More research is needed to understand how one common fold enables the aquaporins to transport an array of solutes.

Carbon dioxide equivalent emissions from corn silage fermentation

The European Climate Law recently codified the goal for European climate neutrality by 2050, highlighting the need for sustainable farming practices within a robust and transparent carbon dioxide equivalent (CO₂e) accounting system. In the present study, a series of equations were proposed for the estimation of CO₂e emissions from corn silage fermentation. Systematic review of previous meta-analyses of corn silage fermentation identified the mean and standard deviation statistics for key model inputs of acetic acid, ethanol, lactic acid, ammonia, and volatile-corrected dry matter loss. Estimates of CO₂e emissions were determined for a mock dataset comprising 1,000 iterations of randomly-generated values for each metric in accordance with mean and variance statistics of the source data. Estimates for CO₂e emissions of corn silage based on meta-analysis review of laboratory experiments were 1.9 ± 5.6% (GWP₂₀) and 0.2 ± 5.5% (GWP₁₀₀) of silage dry matter. Furthermore, model results demonstrated a precedent for CO₂ recycling by silage microorganisms, which was supported by genome annotation of strains belonging to common silage species. Linear model equations for GWP₂₀ and GWP₁₀₀ with inputs and outputs in mg kg^-1 silage dry matter were developed, where inputs are acetic acid (A), ethanol (E), lactic acid (L), and volatile corrected dry matter loss (D_V). Linear equations are (for GWP₂₀; Eq. 11): GWP 20 = - 3626.1 - 0.04343 A + 0.8011 E - 0.03173 L + 1.46573 D V and for GWP₁₀₀; Eq. 12: GWP 100 = - 8526.10 - 0.22403 A - 0.11963 E - 0.03173 L + 1.46573 D V . .

Effect of CO2 Content in Air on the Activity of Carbonic Anhydrases in Cytoplasm, Chloroplasts, and Mitochondria and the Expression Level of Carbonic Anhydrase Genes of the α- and β-Families in Arabidopsis thaliana Leaves

The carbonic anhydrase (CA) activities of the preparations of cytoplasm, mitochondria, chloroplast stroma, and chloroplast thylakoids, as well as the expression levels of genes encoding αCA1, αCA2, αCA4, βCA1, βCA2, βCA3, βCA4, βCA5, and βCA6, were measured in the leaves of Arabidopsis thaliana plants, acclimated to different CO₂ content in the air: low (150 ppm, lCO₂), normal (450 ppm, nCO₂), and high (1200 ppm, hCO₂). To evaluate the photosynthetic apparatus operation, the carbon assimilation and chlorophyll a fluorescence were measured under the same conditions. It was found that the CA activities of the preparations of cytoplasm, chloroplast stroma, and chloroplast thylakoids measured after two weeks of acclimation were higher, the lower CO₂ concentration in the air. That was preceded by an increase in the expression levels of genes encoding the cytoplasmic form of βCA1, and other cytoplasmic CAs, βCA2, βCA3, and βCA4, as well as of the chloroplast CAs, βCA5, and the stromal forms of βCA1 in a short-term range 1–2 days after the beginning of the acclimation. The dependence on the CO₂ content in the air was most noticeable for the CA activity of the preparations of the stroma; it was two orders higher in lCO₂ plants than in hCO₂ plants. The CA activity of thylakoid membranes from lCO₂ plants was higher than that in nCO₂ and hCO₂ plants; however, in these plants, a significant increase in the expression levels of the genes encoding αCA2 and αCA4 located in thylakoid membranes was not observed. The CA activity of mitochondria and the expression level of the mitochondrial βCA6 gene did not depend on the content of carbon dioxide. Taken together, the data implied that in the higher plants, the supply of inorganic carbon to carboxylation sites is carried out with the cooperative functioning of CAs located in the cytoplasm and CAs located in the chloroplasts.

Mesophyll conductance is unaffected by expression of Arabidopsis PIP1 aquaporins in the plasmalemma of Nicotiana

In plants with C3 photosynthesis, increasing the diffusion conductance for CO2 from the substomatal cavity to chloroplast stroma (mesophyll conductance) can improve the efficiencies of both CO2 assimilation and photosynthetic water use. In the diffusion pathway from substomatal cavity to chloroplast stroma, the plasmalemma and chloroplast envelope membranes impose a considerable barrier to CO2 diffusion, limiting photosynthetic efficiency. In an attempt to improve membrane permeability to CO2, and increase photosynthesis in tobacco, we generated transgenic lines in Nicotiana tabacum L. cv Petite Havana carrying either the Arabidopsis PIP1;2 (AtPIP1;2) or PIP1;4 (AtPIP1;4) gene driven by the constitutive dual 2x35S CMV promoter. From a collection of independent T0 transgenics, two T2 lines from each gene were characterized, with western blots confirming increased total aquaporin protein abundance in the AtPIP1;2 tobacco lines. Transient expression of AtPIP1;2-mGFP6 and AtPIP1;4-mGFP6 fusions in Nicotiana benthamiana identified that both AtPIP1;2 and AtPIP1;4 localize to the plasmalemma. Despite achieving ectopic production and correct localization, gas exchange measurements combined with carbon isotope discrimination measurements detected no increase in mesophyll conductance or CO2 assimilation rate in the tobacco lines expressing AtPIP. We discuss the complexities associated with trying to enhance gm through modified aquaporin activity.

The HVCN1 voltage-gated proton channel contributes to pH regulation in canine ventricular myocytes

KEY POINTS

Intracellular pH (pH_i ) regulation is crucial for cardiac function, as acidification depresses contractility and causes arrhythmias. H⁺ ions are generated in cardiomyocytes from metabolic processes and particularly from CO₂ hydration, which has been shown to facilitate CO₂ -venting from mitochondria. Currently, the NHE1 Na⁺ /H⁺ exchanger is viewed as the dominant H⁺ -extrusion mechanism in cardiac muscle. We show that the HVCN1 voltage-gated proton channel is present and functional in canine ventricular myocytes, and that HVCN1 and NHE1 both contribute to pH_i regulation. HVCN1 provides an energetically-efficient mechanism of H⁺ -extrusion that would not cause Na⁺ -loading, which can cause pathology, and that could contribute to transport-mediated CO₂ disposal. These results provide a major advance in our understanding of pH_i regulation in cardiac muscle.

ABSTRACT

Regulation of intracellular pH (pH_i ) in cardiomyocytes is crucial for cardiac function; however, currently known mechanisms for direct or indirect extrusion of acid from cardiomyocytes seem insufficient for energetically-efficient extrusion of the massive H⁺ loads generated under in vivo conditions. In cardiomyocytes, voltage-sensitive H⁺ channel activity mediated by the HVCN1 proton channel would be a highly efficient means of disposing of H⁺ , while avoiding Na⁺ -loading, as occurs during direct acid extrusion via Na⁺ /H⁺ exchange or indirect acid extrusion via Na⁺ -HCO₃ ^- cotransport. PCR and immunoblotting demonstrated expression of HVCN1 mRNA and protein in canine heart. Patch clamp analysis of canine ventricular myocytes revealed a voltage-gated H⁺ current that was highly H⁺ -selective. The current was blocked by external Zn²⁺ and the HVCN1 blocker 5-chloro-2-guanidinobenzimidazole (ClGBI). Both the gating and Zn²⁺ blockade of the current were strongly influenced by the pH gradient across the membrane. All characteristics of the observed current were consistent with the known hallmarks of HVCN1-mediated H⁺ current. Inhibition of HVCN1 and the NHE1 Na⁺ /H⁺ exchanger, singly and in combination, showed that either mechanism is largely sufficient to maintain pH_i in beating cardiomyocytes, but that inhibition of both activities causes rapid acidification. These results show that HVCN1 is expressed in canine ventricular myocytes and provides a major H⁺ -extrusion activity, with a capacity similar to that of NHE1. In the beating heart in vivo, this activity would allow Na⁺ -independent extrusion of H⁺ during each action potential and, when functionally coupled with anion transport mechanisms, could facilitate transport-mediated CO₂ disposal. Abstract figure legend The HVCN1 proton channel is expressed in canine ventricular myocytes and contributes to H⁺ extrusion. This article is protected by copyright. All rights reserved.

CO2 permeability of the rat erythrocyte membrane and its inhibition

We have studied the CO₂ permeability of the erythrocyte membrane of the rat using a mass spectrometric method that employs ¹⁸O-labelled CO₂. The method yields, in addition, the intraerythrocytic carbonic anhydrase activity and the membrane HCO₃^- permeability. For normal rat erythrocytes, we find at 37 °C a CO₂ permeability of 0.078 ± 0.015 cm/s, an intracellular carbonic anhydrase activity of 64,100, and a bicarbonate permeability of 2.1 × 10^-3cm/s. We studied whether the rat erythrocyte membrane possesses protein CO₂ channels similar to the human red cell membrane by applying the potential CO₂ channel inhibitors pCMBS, Dibac, phloretin, and DIDS. Phloretin and DIDS were able to reduce the CO₂ permeability by up to 50%. Since these effects cannot be attributed to the lipid part of the membrane, we conclude that the rat erythrocyte membrane is equipped with protein CO₂ channels that are responsible for at least 50% of its CO₂ permeability.

Hypercapnia-induces IRE1α-driven Endoplasmic Reticulum-associated Degradation of the Na,K-ATPase β-subunit

Acute respiratory distress syndrome (ARDS) is often associated with elevated levels of CO2 (hypercapnia) and impaired alveolar fluid clearance. Misfolding of the Na,K-ATPase (NKA), a key molecule involved in both alveolar epithelial barrier tightness and in resolution of alveolar edema, in the endoplasmic reticulum (ER) may decrease plasma membrane (PM) abundance of the transporter. Here, we investigated how hypercapnia affects the NKA β-subunit (NKA-β) in the ER. Exposing murine precision-cut lung slices (PCLS) and human alveolar epithelial A549 cells to elevated CO2 levels led to a rapid decrease of NKA-β abundance in the ER and at the cell surface. Knockdown of ER alpha-mannosidase I (MAN1B1) and ER degradation enhancing alpha-mannosidase like protein 1 by siRNA or treatment with the MAN1B1 inhibitor, kifunensine rescued loss of NKA-β in the ER, suggesting ER-associated degradation (ERAD) of the enzyme. Furthermore, hypercapnia activated the unfolded protein response (UPR) by promoting phosphorylation of inositol-requiring enzyme 1α (IRE1α) and treatment with a siRNA against IRE1α prevented the decrease of NKA-β in the ER. Of note, the hypercapnia-induced phosphorylation of IRE1α was triggered by a Ca2+-dependent mechanism. Additionally, inhibition of the inositol trisphosphate receptor decreased phosphorylation levels of IRE1α in PCLS and A549 cells, suggesting that Ca2+ efflux from the ER might be responsible for IRE1α activation and ERAD of NKA-β. In conclusion, here we provide evidence that hypercapnia attenuates maturation of the regulatory subunit of NKA by activating IRE1α and promoting ERAD, which may contribute to impaired alveolar epithelial integrity in patients with ARDS and hypercapnia.

Role of cAMP in Double Switch of Glucagon Secretion

Glucose metabolism plays a crucial role in modulating glucagon secretion in pancreatic alpha cells. However, the downstream effects of glucose metabolism and the activated signaling pathways influencing glucagon granule exocytosis are still obscure. We developed a computational alpha cell model, implementing metabolic pathways of glucose and free fatty acids (FFA) catabolism and an intrinsically activated cAMP signaling pathway. According to the model predictions, increased catabolic activity is able to suppress the cAMP signaling pathway, reducing exocytosis in a Ca²⁺-dependent and Ca²⁺ independent manner. The effect is synergistic to the pathway involving ATP-dependent closure of K_ATP channels and consequent reduction of Ca²⁺. We analyze the contribution of each pathway to glucagon secretion and show that both play decisive roles, providing a kind of "secure double switch". The cAMP-driven signaling switch plays a dominant role, while the ATP-driven metabolic switch is less favored. The ratio is approximately 60:40, according to the most recent experimental evidence.

Advances in understanding the physiological role and locations of carbonic anhydrases in C3 plant cells

The review describes the structures of plant carbonic anhydrases (CAs), enzymes catalyzing the interconversion of inorganic carbon forms and belonging to different families, as well as the interaction of inhibitors and activators of CA activity with the active sites of CAs in representatives of these families. We outline the data that shed light on the location of CAs in green cells of C3 plants, algae and angiosperms, with the emphasis on the recently obtained data. The proven and proposed functions of CAs in these organisms are listed. The possibility of the involvement of several chloroplast CAs in acceleration of the conversion of bicarbonate to CO₂ and in supply of CO₂ for fixation by Rubisco is particularly considered. Special attention is paid to CAs in various parts of thylakoids and to discussion about current knowledge of their possible physiological roles. The review states that, despite the significant progress in application of the mutants with suppressed CAs synthesis, the approach based on the use of the inhibitors of CA activity in some cases remains quite effective. Combination of these two approaches, namely determining the effect of CA activity inhibitors in plants with certain knocked-out CA genes, turns out to be very useful for understanding the functions of other CAs.

O2 permeability of lipid bilayers is low, but increases with membrane cholesterol

Oxygen on its transport route from lung to tissue mitochondria has to cross several cell membranes. The permeability value of membranes for O₂ (P_O2), although of fundamental importance, is controversial. Previous studies by mostly indirect methods diverge between 0.6 and 125 cm/s. Here, we use a most direct approach by observing transmembrane O₂ fluxes out of 100 nm liposomes at defined transmembrane O₂ gradients in a stopped-flow system. Due to the small size of the liposomes intra- as well as extraliposomal diffusion processes do not affect the overall kinetics of the O₂ release process. We find, for cholesterol-free liposomes, the unexpectedly low P_O2 value of 0.03 cm/s at 35 °C. This P_O2 would present a serious obstacle to O₂ entering or leaving the erythrocyte. Cholesterol turns out to be a novel major modifier of P_O2, able to increase P_O2 by an order of magnitude. With a membrane cholesterol of 45 mol% as it occurs in erythrocytes, P_O2 rises to 0.2 cm/s at 35 °C. This P_O2 is just sufficient to ensure complete O₂ loading during passage of erythrocytes through the lung's capillary bed under the conditions of rest as well as maximal exercise.

Influence of Temperature and CO2 On Plasma-membrane Permeability to CO2 and HCO3- in the Marine Haptophytes Emiliania huxleyi and Calcidiscus leptoporus (Prymnesiophyceae)

Membrane permeabilities to CO₂ and HCO₃^- constrain the function of CO₂ concentrating mechanisms that algae use to supply inorganic carbon for photosynthesis. In diatoms and green algae, plasma membranes are moderately to highly permeable to CO₂ but effectively impermeable to HCO₃^- . Here, CO₂ and HCO₃^- membrane permeabilities were measured using an ¹⁸ O-exchange technique on two species of haptophyte algae, Emiliania huxleyi and Calcidiscus leptoporus, which showed that the plasma membranes of these species are also highly permeable to CO₂ (0.006-0.02 cm · s^-1 ) but minimally permeable to HCO₃^- . Increased temperature and CO₂ generally increased CO₂ membrane permeabilities in both species, possibly due to changes in lipid composition or CO₂ channel proteins. Changes in CO₂ membrane permeabilities showed no association with the density of calcium carbonate coccoliths surrounding the cell, which could potentially impede passage of compounds. Haptophyte plasma-membrane permeabilities to CO₂ were somewhat lower than those of diatoms but generally higher than membrane permeabilities of green algae. One caveat of these measurements is that the model used to interpret ¹⁸ O-exchange data assumes that carbonic anhydrase, which catalyzes ¹⁸ O-exchange, is homogeneously distributed in the cell. The implications of this assumption were tested using a two-compartment model with an inhomogeneous distribution of carbonic anhydrase to simulate ¹⁸ O-exchange data and then inferring plasma-membrane CO₂ permeabilities from the simulated data. This analysis showed that the inferred plasma-membrane CO₂ permeabilities are minimal estimates but should be quite accurate under most conditions.

Chemogenic Subqualities of Mouthfeel

Mouthfeel refers to the physical or textural sensations in the mouth caused by foods and beverages that are essential to the acceptability of many edible products. The sensory subqualities contributing to mouthfeel are often chemogenic in nature and include heat, burning, cooling, tingling, and numbing. These "chemesthetic" sensations are a result of the chemical activation of receptors that are associated with nerve fibers mediating pain and mechanotransduction. Each of these chemesthetic sensations in the oral cavity are transduced in the nervous system by a combination of different molecular channels/receptors expressed on trigeminal nerve fibers that innervate the mouth and tongue. The molecular profile of these channels and receptors involved in mouthfeel include many transient receptor potential channels, proton-sensitive ion channels, and potassium channels to name a few. During the last several years, studies using molecular and physiological approaches have significantly expanded and enhanced our understanding of the neurobiological basis for these chemesthetic sensations. The purpose of the current review is to integrate older and newer studies to present a comprehensive picture of the channels and receptors involved in mouthfeel. We highlight that there still continue to be important gaps in our overall knowledge on flavor integration and perception involving chemesthetic sensations, and these gaps will continue to drive future research direction and future investigation.

Rumen CO2 species equilibrium might influence performance and be a factor in the pathogenesis of subacute ruminal acidosis

This experiment was conducted to explore rumen carbon dioxide (CO₂) species equilibrium. Three lactating, fistulated cattle were consecutively exposed to three dietary treatments tailored to produce low rumen pH and increase the risk of subacute ruminal acidosis (SARA) by reducing physically effective neutral detergent fiber (Low _peNDF), increasing rumen degradable starch (High RDS) or both (Combined). Under these conditions, high and varied rumen concentrations of the CO₂ associated to water or dissolved CO₂ (dCO₂) were found. The results suggest that the activity of dCO₂ and bicarbonate (HCO₃⁻) represents an important component of the rumen environment. Rumen CO₂ holdup was associated with high dCO₂ and HCO₃⁻ activity as well as changes in the viscosity and surface tension of the rumen fluid. All dietary treatments produced low rumen pH, <5.5 for >3 h/d, a condition associated with SARA, but clinical SARA was observed only during CO₂ holdup. This pilot study highlights the possible role of CO₂ holdup and rumen CO₂ species in cattle performance and nutritional diseases. In the future, better estimations of CO₂ species might help clarify these findings.

Environmental and Endogenous Acids Can Trigger Allergic-Type Airway Reactions

Inflammatory allergic and nonallergic respiratory disorders are spreading worldwide and often coexist. The root cause is not clear. This review demonstrates that, from a biochemical point of view, it is ascribable to protons (H+) released into cells by exogenous and endogenous acids. The hypothesis of acids as the common cause stems from two considerations: (a) it has long been known that exogenous acids present in air pollutants can induce the irritation of epithelial surfaces, particularly the airways, inflammation, and bronchospasm; (b) according to recent articles, endogenous acids, generated in cells by phospholipases, play a key role in the biochemical mechanisms of initiation and progression of allergic-type reactions. Therefore, the intracellular acidification and consequent Ca2+ increase, induced by protons generated by either acid pollutants or endogenous phospholipases, may constitute the basic mechanism of the multimorbidity of these disorders, and environmental acidity may contribute to their spread.

Single-cell O2 exchange imaging shows that cytoplasmic diffusion is a dominant barrier to efficient gas transport in red blood cells

Blood is routinely tested for gas-carrying capacity (total hemoglobin), but this cannot determine the speed at which red blood cells (RBCs) exchange gases. Such information is critical for evaluating the physiological fitness of RBCs, which have very limited capillary transit times (<1 s) for turning over substantial volumes of gas. We developed a method to quantify gas exchange in individual RBCs and used it to show that restricted diffusion, imposed by hemoglobin crowding, is a major barrier to gas flows. Consequently, hematological disorders manifesting a change in cell shape or hemoglobin concentration have uncharted implications on gas exchange, which we illustrate using inherited anemias. With its single-cell resolution, the method can identify physiologically inferior subpopulations, providing a clinically useful appraisal of blood quality.

Disorders of oxygen transport are commonly attributed to inadequate carrying capacity (anemia) but may also relate to inefficient gas exchange by red blood cells (RBCs), a process that is poorly characterized yet assumed to be rapid. Without direct measurements of gas exchange at the single-cell level, the barriers to O₂ transport and their relationship with hematological disorders remain ill defined. We developed a method to track the flow of O₂ in individual RBCs by combining ultrarapid solution switching (to manipulate gas tension) with single-cell O₂ saturation fluorescence microscopy. O₂ unloading from RBCs was considerably slower than previously estimated in acellular hemoglobin solutions, indicating the presence of diffusional barriers in intact cells. Rate-limiting diffusion across cytoplasm was demonstrated by osmotically induced changes to hemoglobin concentration (i.e., diffusive tortuosity) and cell size (i.e., diffusion pathlength) and by comparing wild-type cells with hemoglobin H (HbH) thalassemia (shorter pathlength and reduced tortuosity) and hereditary spherocytosis (HS; expanded pathlength). Analysis of the distribution of O₂ unloading rates in HS RBCs identified a subpopulation of spherocytes with greatly impaired gas exchange. Tortuosity imposed by hemoglobin was verified by demonstrating restricted diffusivity of CO₂, an acidic gas, from the dissipative spread of photolytically uncaged H⁺ ions across cytoplasm. Our findings indicate that cytoplasmic diffusion, determined by pathlength and tortuosity, is a major barrier to efficient gas handling by RBCs. Consequently, changes in RBC shape and hemoglobin concentration, which are common manifestations of hematological disorders, can have hitherto unrecognized and clinically significant implications on gas exchange.

Ocean Acidification and Coastal Marine Invertebrates: Tracking CO2 Effects from Seawater to the Cell

In the last few decades, numerous studies have investigated the impacts of simulated ocean acidification on marine species and communities, particularly those inhabiting dynamic coastal systems. Despite these research efforts, there are many gaps in our understanding, particularly with respect to physiological mechanisms that lead to pathologies. In this review, we trace how carbonate system disturbances propagate from the coastal environment into marine invertebrates and highlight mechanistic links between these disturbances and organism function. We also point toward several processes related to basic invertebrate biology that are severely understudied and prevent an accurate understanding of how carbonate system dynamics influence organismic homeostasis and fitness-related traits. We recommend that significant research effort be directed to studying cellular phenotypes of invertebrates acclimated or adapted to elevated seawater pCO₂ using biochemical and physiological methods.

Photosynthetic efficiency and mesophyll conductance are unaffected in Arabidopsis thaliana aquaporin knock-out lines

Improving photosynthetic efficiency is widely regarded as a major route to achieving much-needed yield gains in crop plants. In plants with C3 photosynthesis, increasing the diffusion conductance for CO2 transfer from substomatal cavity to chloroplast stroma (gm) could help to improve the efficiencies of CO2 assimilation and photosynthetic water use in parallel. The diffusion pathway from substomatal cavity to chloroplast traverses cell wall, plasma membrane, cytosol, chloroplast envelope membranes, and chloroplast stroma. Specific membrane intrinsic proteins of the aquaporin family can facilitate CO2 diffusion across membranes. Some of these aquaporins, such as PIP1;2 in Arabidopsis thaliana, have been suggested to exert control over gm and the magnitude of the CO2 assimilation flux, but the evidence for a direct physiological role of aquaporins in determining gm is limited. Here, we estimated gm with four different methods under a range of light intensities and CO2 concentrations in two previously characterized pip1;2 knock-out lines as well as pip1;3 and pip2;6 knock-out lines, which have not been previously evaluated for a role in gm. This study presents the most in-depth analysis of gm in Arabidopsis aquaporin knock-out mutants to date. Surprisingly, all methods failed to show any significant differences between the pip1;2, pip1;3, or pip2;6 mutants and the Col-0 control.

The human central nervous system discharges carbon dioxide and lactic acid into the cerebrospinal fluid

BACKGROUND

The central nervous system was previously thought to draw oxygen and nutrition from the arteries and discharge carbon dioxide and other metabolic wastes into the venous system. At present, the functional role of cerebrospinal fluid in brain metabolism is not fully known.

METHODS

In this prospective observational study, we performed gas analysis on venous blood and cerebrospinal fluid simultaneously acquired from 16 consecutive preoperative patients without any known neurological disorders.

RESULTS

The carbon dioxide partial pressure (pCO₂) (p < 0.0001) and lactic acid level (p < 0.001) in the cerebrospinal fluid were significantly higher than those in the peripheral venous blood, suggesting that a considerable proportion of metabolic carbon dioxide and lactic acid is discharged from the central nervous system into the cerebrospinal fluid. The oxygen partial pressure (pO₂) was much higher in the cerebrospinal fluid than in the venous blood, corroborating the conventional theory of cerebrospinal fluid circulatory dynamics. The pCO₂ of the cerebrospinal fluid showed a strong negative correlation with age (R = - 0.65, p = 0.0065), but the other studied variables did not show significant correlation with age.

CONCLUSION

Carbon dioxide and lactic acid are discharged into the circulating cerebrospinal fluid, as well as into the venules. The level of carbon dioxide in the cerebrospinal fluid significantly decreased with age.

Learning RuBisCO's birth and subsequent environmental adaptation

It is believed that organisms that first appeared after the formation of the earth lived in a very limited environment, making full use of the limited number of genes. From these early organisms' genes, more were created by replication, mutation, recombination, translocation, and transmission of other organisms' DNA; thus, it became possible for ancient organisms to grow in various environments. The photosynthetic CO₂-fixing enzyme RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) began to function in primitive methanogenic archaea and has been evolved as a central CO₂-fixing enzyme in response to the large changes in CO₂ and O₂ concentrations that occurred in the subsequent 4 billion years. In this review, the processes of its adaptation to be specialized for CO₂ fixation will be presented from the viewpoint of functions and structures of RuBisCO.

Proton Transport Chains in Glucose Metabolism: Mind the Proton

The Embden-Meyerhof-Parnas (EMP) pathway comprises eleven cytosolic enzymes interacting to metabolize glucose to lactic acid [CH3CH(OH)COOH]. Glycolysis is largely considered as the conversion of glucose to pyruvate (CH3COCOO-). We consider glycolysis to be a cellular process and as such, transporters mediating glucose uptake and lactic acid release and enable the flow of metabolites through the cell, must be considered as part of the EMP pathway. In this review, we consider the flow of metabolites to be coupled to a flow of energy that is irreversible and sufficient to form ordered structures. This latter principle is highlighted by discussing that lactate dehydrogenase (LDH) complexes irreversibly reduce pyruvate/H+ to lactate [CH3CH(OH)COO-], or irreversibly catalyze the opposite reaction, oxidation of lactate to pyruvate/H+. However, both LDH complexes are considered to be driven by postulated proton transport chains. Metabolism of glucose to two lactic acids is introduced as a unidirectional, continuously flowing pathway. In an organism, cell membrane-located proton-linked monocarboxylate transporters catalyze the final step of glycolysis, the release of lactic acid. Consequently, both pyruvate and lactate are discussed as intermediate products of glycolysis and substrates of regulated crosscuts of the glycolytic flow.

Cholesterol is the main regulator of the carbon dioxide permeability of biological membranes

We present here a compilation of membrane CO₂ permeabilities (Pco₂) for various cell types from the literature. Pco₂ values vary over more than two orders of magnitude. Relating Pco₂ to the cholesterol content of the membranes shows that, with the exception of red blood cells, it is essentially membrane cholesterol that determines the value of Pco₂. Thus, the observed strong modulation of Pco₂ in the majority of membranes is caused by cholesterol rather than gas channels.

CO₂ Permeability of Biological Membranes and Role of CO₂ Channels

We summarize here, mainly for mammalian systems, the present knowledge of (a) the membrane CO₂ permeabilities in various tissues; (b) the physiological significance of the value of the CO₂ permeability;

CO2 permeability and carbonic anhydrase activity of rat cardiomyocytes

AIM

To determine the CO₂ permeability (P_CO2 ) of plasma membranes of cardiomyocytes. These cells were chosen because heart possesses the highest rate of O₂ consumption/CO₂ production in the body.

METHODS

Cardiomyocytes were isolated from rat hearts using the Langendorff technique. Cardiomyocyte suspensions exhibited a vitality of 2-14% and were studied by the previously described mass spectrometric ¹⁸ O-exchange technique deriving P_CO2 . We showed by mass spectrometry and by carbonic anhydrase (CA) staining that non-vital cardiomyocytes are free of CA and thus do not contribute to the mass spectrometric signal, which is determined exclusively by the fully functional vital cardiomyocytes.

RESULTS

Lysed cardiomyocytes yielded an intracellular CA activity for vital cells of 5070; that is, the rate of CO₂ hydration inside the cell is accelerated 5071-fold. Using this number, analyses of the mass spectrometric recordings from cardiomyocyte suspensions yield a P_CO2 of 0.10 cm s^-1 (SD ± 0.06, n = 15) at 37 °C.

CONCLUSION

In comparison with the P_CO2 of other cells, this value is quite high and about identical to that of the human red cell membrane. As no major protein CO₂ channels such as aquaporins 1 and 4 are present in rat cardiac sarcolemma, the high P_CO2 of this membrane is likely due to its low cholesterol content of about 0.2 (mol cholesterol)·(mol total membrane lipids)^-1 . Previous work predicted a P_CO2 of ≥0.1 cm s^-1 from this level of cholesterol. We conclude that the low cholesterol establishes a P_CO2 high enough to render the membrane resistance to CO₂ diffusion almost negligible, even under conditions of maximal O₂ consumption of the heart.

Reconstructing coral calcification fluid dissolved inorganic carbon chemistry from skeletal boron: An exploration of potential controls on coral aragonite B/Ca

The boron geochemistry of coral skeletons reflects the dissolved inorganic carbon (DIC) chemistry of the calcification fluid from which the skeletons precipitates and may be a valuable tool to investigate the effects of climate change on coral calcification. In this paper I calculate the predicted B/Ca of aragonite precipitating from seawater based fluids as a function of pH, [DIC] and [Ca²⁺]. I consider how different co-precipitating DIC species affect aragonite B/Ca and also estimate the impact of variations in the B(OH)₄^-/co-precipitating DIC aragonite partition coefficient (K_D), which may be associated with changes in the DIC and Ca²⁺ chemistry of the calcification fluid. The coral skeletal B/Ca versus calcification fluid pH relationships reported previously can be reproduced by estimating B(OH)₄^- and co-precipitating DIC speciation as a function of pH_CF and assuming that K_D are constant i.e. unaffected by calcification fluid saturation state. Assuming that B(OH)₄^- co-precipitates with CO₃^2-, then observed patterns can be reproduced by a fluid with approximately constant [DIC] i.e. increasing pH_CF concentrates CO₃^2-, as a function of DIC speciation. Assuming that B(OH)₄^- co-precipitates with HCO₃^- only or CO₃^2- + HCO₃^- then the observed patterns can be reproduced if [DIC]_CF and pH_CF are positively related i.e. if DIC is increasingly concentrated in the calcification fluid at higher pH_CF probably by CO₂ diffusion into the calcification site.

Carbon dioxide and water transport through plant aquaporins

Aquaporins are channel proteins that function to increase the permeability of biological membranes. In plants, aquaporins are encoded by multigene families that have undergone substantial diversification in land plants. The plasma membrane intrinsic proteins (PIPs) subfamily of aquaporins is of particular interest given their potential to improve plant water relations and photosynthesis. Flowering plants have between 7 and 28 PIP genes. Their expression varies with tissue and cell type, through development and in response to a variety of factors, contributing to the dynamic and tissue specific control of permeability. There are a growing number of PIPs shown to act as water channels, but those altering membrane permeability to CO₂ are more limited. The structural basis for selective substrate specificities has not yet been resolved, although a few key amino acid positions have been identified. Several regions important for dimerization, gating and trafficking are also known. PIP aquaporins assemble as tetramers and their properties depend on the monomeric composition. PIPs control water flux into and out of veins and stomatal guard cells and also increase membrane permeability to CO₂ in mesophyll and stomatal guard cells. The latter increases the effectiveness of Rubisco and can potentially influence transpiration efficiency.

Association between water and carbon dioxide transport in leaf plasma membranes: assessing the role of aquaporins

The role of some aquaporins as CO2 permeable channels has been controversial. Low CO2 permeability of plant membranes has been criticized because of unstirred layers and other limitations. Here we measured both water and CO2 permeability (Pos , PCO2 ) using stopped flow on plasma membrane vesicles (pmv) isolated from Pisum sativum (pea) and Arabidopsis thaliana leaves. We excluded the chemical limitation of carbonic anhydrase (CA) in the vesicle acidification technique for PCO2 using different temperatures and CA concentrations. Unstirred layers were excluded based on small vesicle size and the positive correlation between vesicle diameter and PCO2 . We observed high aquaporin activity (Pos 0.06 to 0.22 cm s-1 ) for pea pmv based on all the criteria for their function using inhibitors and temperature dependence. Inhibitors of Pos did not alter PCO2 . PCO2 ranged from 0.001 to 0.012 cm s-1 (mean 0.0079 + 0.0007 cm s-1 ) with activation energy of 30.2 kJ mol-1 . Intrinsic variation between pmv batches from normally grown or stressed plants revealed a weak (R2  = 0.27) positive linear correlation between Pos and PCO2 . Despite the low PCO2 , aquaporins may facilitate CO2 transport across plasma membranes, but probably via a different pathway than for water.

Measuring CO2 and HCO3- permeabilities of isolated chloroplasts using a MIMS-18O approach

To support photosynthetic CO2 fixation by Rubisco, the chloroplast must be fed with inorganic carbon in the form of CO2 or bicarbonate. However, the mechanisms allowing the rapid passage of this gas and this charged molecule through the bounding membranes of the chloroplast envelope are not yet completely elucidated. We describe here a method allowing us to measure the permeability of these two molecules through the chloroplast envelope using a membrane inlet mass spectrometer and 18O-labelled inorganic carbon. We established that the internal stromal carbonic anhydrase activity is not limiting for this technique, and precisely measured the chloroplast surface area and permeability values for CO2 and bicarbonate. This was performed on chloroplasts from several plant species, with values ranging from 2.3 × 10-4 m s-1 to 8 × 10-4 m s-1 permeability for CO2 and 1 × 10-8 m s-1 for bicarbonate. We were able to apply our method to chloroplasts from an Arabidopsis aquaporin mutant, and this showed that CO2 permeability was reduced 50% in the mutant compared with the wild-type reference.

Rectification of oxygen transfer through the rat colonic epithelium

AIM

To assess whether higher sensitivity of colonic epithelium to hypoxia at the serosal side is associated with oxygen transfer asymmetry.

METHODS

Rats were fed either with normal chow or a low-sodium diet. Tissues were mounted as flat sheets in a modified, airtight Ussing chamber with oxygen meters in each hemichamber. Mucosal samples from normal diet animals were studied under control conditions, in low-chloride solution and after adding chloride secretion inhibitors and chloride secretagogues. Samples from sodium-deprived rats were studied before and after ouabain addition. In separate experiments, the correlation between short-circuit current and oxygen consumption was analyzed. Finally, hypoxia was induced in one hemichamber to assess the relationship between its oxygen content and the oxygen pressure difference between both hemichambers.

RESULTS

In all studied conditions, oxygen consumption was larger in the serosal hemichamber than in the mucosal one (P = 0.0025 to P < 0.0001). Short-circuit current showed significant correlation with both total oxygen consumption (r = 0.765; P = 0.009) in normoxia and oxygen consumption in the serosal hemichamber (r = 0.754; P = 0.011) during mucosal hypoxia, but not with oxygen consumption in the mucosal hemichamber. When hypoxia was induced in the mucosal hemichamber, an oxygen pressure difference of 13 kPa with the serosal hemichamber was enough to keep its oxygen content constant. However, when hypoxia was induced in the serosal hemichamber, the oxygen pressure difference with the mucosal hemichamber necessary to keep its oxygen content constant was 40 kPa (P < 0.0001).

CONCLUSION

Serosal oxygen supply is more readily available to support short-circuit current. This may be partly due to a rectifying behavior of transepithelial oxygen transfer.

The water channel aquaporin-1a1 facilitates movement of CO₂ and ammonia in zebrafish (Danio rerio) larvae

The present study tested the hypothesis that zebrafish (Danio rerio) aquaporin-1a1 (AQP1a1) serves as a multi-functional channel for the transfer of the small gaseous molecules, CO2 and ammonia, as well as water, across biological membranes. Zebrafish embryos were microinjected with a translation-blocking morpholino oligonucleotide targeted to AQP1a1. Knockdown of AQP1a1 significantly reduced rates of CO2 and ammonia excretion, as well as water fluxes, in larvae at 4 days post fertilization (dpf). Because AQP1a1 is expressed both in ionocytes present on the body surface and in red blood cells, the haemolytic agent phenylhydrazine was used to distinguish between the contributions of AQP1a1 to gas transfer in these two locations. Phenylhydrazine treatment had no effect on AQP1a1-linked excretion of CO2 or ammonia, providing evidence that AQP1a1 localized to the yolk sac epithelium, rather than red blood cell AQP1a1, is the major site of CO2 and ammonia movements. The possibility that AQP1a1 and the rhesus glycoprotein Rhcg1, which also serves as a dual CO2 and ammonia channel, act in concert to facilitate CO2 and ammonia excretion was explored. Although knockdown of each protein did not affect the abundance of mRNA and protein of the other protein under control conditions, impairment of ammonia excretion by chronic exposure to high external ammonia triggered a significant increase in the abundance of AQP1a1 mRNA and protein in 4 dpf larvae experiencing Rhcg1 knockdown. Collectively, these results suggest that AQP1a1 in zebrafish larvae facilitates the movement of CO2 and ammonia, as well as water, in a physiologically relevant fashion.

Diffusive shunting of gases and other molecules in the renal vasculature: physiological and evolutionary significance

Countercurrent systems have evolved in a variety of biological systems that allow transfer of heat, gases, and solutes. For example, in the renal medulla, the countercurrent arrangement of vascular and tubular elements facilitates the trapping of urea and other solutes in the inner medulla, which in turn enables the formation of concentrated urine. Arteries and veins in the cortex are also arranged in a countercurrent fashion, as are descending and ascending vasa recta in the medulla. For countercurrent diffusion to occur, barriers to diffusion must be small. This appears to be characteristic of larger vessels in the renal cortex. There must also be gradients in the concentration of molecules between afferent and efferent vessels, with the transport of molecules possible in either direction. Such gradients exist for oxygen in both the cortex and medulla, but there is little evidence that large gradients exist for other molecules such as carbon dioxide, nitric oxide, superoxide, hydrogen sulfide, and ammonia. There is some experimental evidence for arterial-to-venous (AV) oxygen shunting. Mathematical models also provide evidence for oxygen shunting in both the cortex and medulla. However, the quantitative significance of AV oxygen shunting remains a matter of controversy. Thus, whereas the countercurrent arrangement of vasa recta in the medulla appears to have evolved as a consequence of the evolution of Henle’s loop, the evolutionary significance of the intimate countercurrent arrangement of blood vessels in the renal cortex remains an enigma.

Cardiac Morphology and Function, and Blood Gas Transport in Aquaporin-1 Knockout Mice

We have studied cardiac and respiratory functions of aquaporin-1-deficient mice by the Pressure-Volume-loop technique and by blood gas analysis. In addition, the morphological properties of the animals' hearts were analyzed. In anesthesia under maximal dobutamine stimulation, the mice exhibit a moderately elevated heart rate of < 600 min⁻¹ and an O₂ consumption of ~0.6 ml/min/g, which is about twice the basal rate. In this state, which is similar to the resting state of the conscious animal, all cardiac functions including stroke volume and cardiac output exhibited resting values and were identical between deficient and wildtype animals. Likewise, pulmonary and peripheral exchange of O₂ and CO₂ were normal. In contrast, several morphological parameters of the heart tissue of deficient mice were altered: (1) left ventricular wall thickness was reduced by 12%, (2) left ventricular mass, normalized to tibia length, was reduced by 10–20%, (3) cardiac muscle fiber cross sectional area was decreased by 17%, and (4) capillary density was diminished by 10%. As the P-V-loop technique yielded normal end-diastolic and end-systolic left ventricular volumes, the deficient hearts are characterized by thin ventricular walls in combination with normal intraventricular volumes. The aquaporin-1-deficient heart thus seems to be at a disadvantage compared to the wild-type heart by a reduced left-ventricular wall thickness and an increased diffusion distance between blood capillaries and muscle mitochondria. While under the present quasi-resting conditions these morphological alterations have no consequences for cardiac function, we expect that the deficient hearts will show a reduced maximal cardiac output.

The ins and outs of CO2

It is difficult to distinguish influx and efflux of inorganic C in photosynthesizing tissues; this article examines what is known and where there are gaps in knowledge. Irreversible decarboxylases produce CO2, and CO2 is the substrate/product of enzymes that act as carboxylases and decarboxylases. Some irreversible carboxylases use CO2; others use HCO3(-). The relative role of permeation through the lipid bilayer versus movement through CO2-selective membrane proteins in the downhill, non-energized, movement of CO2 is not clear. Passive permeation explains most CO2 entry, including terrestrial and aquatic organisms with C3 physiology and biochemistry, terrestrial C4 plants and all crassulacean acid metabolism (CAM) plants, as well as being part of some mechanisms of HCO3(-) use in CO2 concentrating mechanism (CCM) function, although further work is needed to test the mechanism in some cases. However, there is some evidence of active CO2 influx at the plasmalemma of algae. HCO3(-) active influx at the plasmalemma underlies all cyanobacterial and some algal CCMs. HCO3(-) can also enter some algal chloroplasts, probably as part of a CCM. The high intracellular CO2 and HCO3(-) pools consequent upon CCMs result in leakage involving CO2, and occasionally HCO3(-). Leakage from cyanobacterial and microalgal CCMs involves up to half, but sometimes more, of the gross inorganic C entering in the CCM; leakage from terrestrial C4 plants is lower in most environments. Little is known of leakage from other organisms with CCMs, though given the leakage better-examined organisms, leakage occurs and increases the energetic cost of net carbon assimilation.

Computing membrane-AQP5-phosphatidylserine binding affinities with hybrid steered molecular dynamics approach

In order to elucidate how phosphatidylserine (PS6) interacts with AQP5 in a cell membrane, we developed a hybrid steered molecular dynamics (hSMD) method that involved: (1) Simultaneously steering two centers of mass of two selected segments of the ligand, and (2) equilibrating the ligand-protein complex with and without biasing the system. Validating hSMD, we first studied vascular endothelial growth factor receptor 1 (VEGFR1) in complex with N-(4-Chlorophenyl)-2-((pyridin-4-ylmethyl)amino)benzamide (8ST), for which the binding energy is known from in vitro experiments. In this study, our computed binding energy well agreed with the experimental value. Knowing the accuracy of this hSMD method, we applied it to the AQP5-lipid-bilayer system to answer an outstanding question relevant to AQP5's physiological function: Will the PS6, a lipid having a single long hydrocarbon tail that was found in the central pore of the AQP5 tetramer crystal, actually bind to and inhibit AQP5's central pore under near-physiological conditions, namely, when AQP5 tetramer is embedded in a lipid bilayer? We found, in silico, using the CHARMM 36 force field, that binding PS6 to AQP5 was a factor of 3 million weaker than "binding" it in the lipid bilayer. This suggests that AQP5's central pore will not be inhibited by PS6 or a similar lipid in a physiological environment.