Is the kinetome conserved?

Computational biologists have labored for decades to produce kinetic models to mechanistically explain complex metabolic phenomena. The estimation of numerical values for the large number of kinetic parameters required for constructing large‐scale models has been a major challenge. This collection of kinetic constants has recently been termed the kinetome (Nilsson et al, 2017). In this Commentary, we discuss the recent advances in the field that suggest that the kinetome may be more conserved than expected. A conserved kinetome will accelerate the development of future kinetic models of integrated cellular functions and expand their scope and usability in many fields of biology and biomedicine.Subject Categories: Computational Biology, Metabolism

This Commentary highlights recent discoveries suggesting that the kinetome (a collection of kinetic parameters) can be conserved and discusses how a conserved kinetome will accelerate the development of future kinetic models.     

How does plasma membrane surface area accommodate alterations in guard cell volume during stomatal closing?

During stomatal movement, guard cells undergo considerable and repetitive variations in cell volume and consequently surface area over a period of minutes. Due to limited stretching capability of the plasma membrane, alterations in the surface area must accommodate the volume changes through membrane turnover. Using fluorescence imaging and electrophysiology techniques, extensive studies imply that endocytosis may be a critical mechanism for the plasma membrane turnover. In contrast to the conventional studies, using transmission electronic microscope in combination with laser confocal microscope so that the membrane turnover can be detected without a resolution limitation, our works, recently published in the Journal of Experimental Botany, has provided strong evidences that excretion and folding of plasma membrane are critical for the accommodation of the cell volume alterations in intact guard cells in Vicia faba L. These results have opened a new perspective on the mechanism for the membrane turnover during stomatal movement. In this addendum, we further discuss some key issues about the mechanisms for the accommodation of the cell volume alterations during stomatal movements.Key words: stomata, guard cell, plasma membrane, surface area, endocytosis, excretion, accommodationGuard cells control stomatal movement thereby regulating gas exchange in plants. During stomatal movement, guard cells undergo considerable and repetitive variations in cell volume and consequently surface area over a period of minutes. It was proposed that the alterations of the plasma membrane surface area could be up to 40%,¹ whereas the maximum possible stretching of membranes was limited to only about 2%.² Furthermore, due to the presence of a turgor pressure, it has been commonly thought that membrane infoldings should not occur in the guard cells.³ Therefore, it is reasonable to propose that alterations in the surface area must be accomplished by addition and removal of membrane material to and from the plasma membrane.⁴ While many studies imply that endocytosis most likely functions to accommodate the alterations in guard cell volume, many crucial questions about this mechanism deserve to be argued.     

Is the mammalian cell plasma membrane a barrier to oxygen transport?

Oxygen transport in the Chinese hamster ovary (CHO) plasma membrane has been studied by observing the collision of molecular oxygen with nitroxide radical spin labels placed in the lipid bilayer portion of the membrane at various distances from the membrane surface using the long-pulse saturation-recovery electron spin resonance (ESR) technique. The collision rate was estimated for 5-, 12-, and 16-doxylstearic acids from spin-lattice relaxation times (T1) measured in the presence and absence of molecular oxygen. Profiles of the local oxygen transport parameters across the membrane were obtained showing that the oxygen diffusion-concentration product is lower than in water for all locations at 37 degrees C. From oxygen transport parameter profiles, the membrane oxygen permeability coefficients were estimated according to the procedure developed earlier by Subczynski et al. (Subczynski, W. K., J. S. Hyde, and A. Kusumi. 1989. Proceedings of the National Academy of Sciences, USA. 86:4474-4478). At 37 degrees C, the oxygen permeability coefficient for the plasma membrane was found to be 42 cm/s, about two times lower than for a water layer of the same thickness as the membrane. The oxygen concentration difference across the CHO plasma membrane at physiological conditions is in the nanomolar range. It is concluded that oxygen permeation across the cell plasma membrane cannot be a rate-limiting step for cellular respiration. Correlations of the form PM = cKs between membrane permeabilities PM of small nonelectrolyte solutes of mol wt less than 50, including oxygen, and their partition coefficients K into hexadecane and olive oil are reported. Hexadecane: c = 26 cm/s, s = 0.95; olive oil: c = 23 cm/s, s = 1.56. These values of c and s differ from those reported in the literature for solutes of 50 less than mol wt less than 300 (Walter, A., and J. Gutknecht. 1986. Journal of Membrane Biology. 90:207-217). It is concluded that oxygen permeability through membranes can be reliably predicted from measurement of partition coefficients.     

How should the optical tweezers experiment be used to characterize the red blood cell membrane mechanics?

Stretching red blood cells using optical tweezers is a way to characterize the mechanical properties of their membrane by measuring the size of the cell in the direction of the stretching (axial diameter) and perpendicularly (transverse diameter). Recently, such data have been used in numerous publications to validate solvers dedicated to the computation of red blood cell dynamics under flow. In the present study, different mechanical models are used to simulate the stretching of red blood cells by optical tweezers. Results first show that the mechanical moduli of the membranes have to be adjusted as a function of the model used. In addition, by assessing the area dilation of the cells, the axial and transverse diameters measured in optical tweezers experiments are found to be insufficient to discriminate between models relevant to red blood cells or not. At last, it is shown that other quantities such as the height or the profile of the cell should be preferred for validation purposes since they are more sensitive to the membrane model.     

Is the membrane attack complex of complement an enzyme?

Summary Recent studies on the functional activities of the membrane attack complex of complement, C5b-9, are reviewed. A new speculative hypothesis has been advanced to account for the ability of complement to mediate lysis of various targets. This hypothesis has three major elements: 1) that the membrane attack complex is an enzyme; 2) that the substrate for this putative enzyme is a membrane constituent; 3) that the substrate specificity of the putative enzyme is dependent on the species source of individual complement components within the C5b-9 complex.Abbreviations E = sheep red cells - A = rabbit IgM anti-Forssman antibody - Hu or hu = human - GP or gp = guinea pig     

Is the flavin-deficient red blood cell common in Maremma, Italy, an important defense against malaria in this area?

There is a high prevalence of a familial flavin-deficient red blood cell in Ferrara province in the Po delta in northern Italy, believed to have been selected for by malaria which was endemic from the 12th century. In the present study, activities of FAD-dependent red-cell glutathione reductase (EGR) in the Grosseto area of Maremma on the west coast of Italy where malaria was endemic from 300 B.C. are compared both with activities in the Ferrara area and with activities where there was no history of endemic malaria--in the Florence area and in London in people of Anglo-Saxon origin. EGR activities were similar in Grosseto and Ferrara and were significantly lower than in Florence and London. As previously found in Ferrara, low EGR activity in Grosseto was shown to be unrelated to low dietary riboflavin intake. These findings in Grosseto, suggesting selection by malaria, are particularly interesting because, unlike the situation in Ferrara and most other malarial areas, the prevalence of thalassemia and glucose-6-phosphate dehydrogenase deficiency is very low, and they do not appear to have been selected for in Maremma. It is possible that a flavin-deficient red cell, known to inhibit growth of the malaria parasite, was an important protecting factor in the population of this area over the centuries.     

Why are polar residues within the membrane core evolutionary conserved?

Here, we present a study of polar residues within the membrane core of alpha-helical membrane proteins. As expected, polar residues are less frequent in the membrane than expected. Further, most of these residues are buried within the interior of the protein and are only rarely exposed to lipids. However, the polar groups often border internal water filled cavities, even if the rest of the sidechain is buried. A survey of their functional roles in known structures showed that the polar residues are often directly involved in binding of small compounds, especially in channels and transporters, but other functions including proton transfer, catalysis, and selectivity have also been attributed to these proteins. Among the polar residues histidines often interact with prosthetic groups in photosynthetic- and oxidoreductase-related proteins, whereas prolines often are required for conformational changes of the proteins. Indeed, the polar residues in the membrane core are more conserved than other residues in the core, as well as more conserved than polar residues outside the membrane. The reason is twofold; they are often (i) buried in the interior of the protein and (ii) directly involved in the function of the proteins. Finally, a method to identify which polar residues are present within the membrane core directly from protein sequences was developed. Applying the method to the set of all human membrane proteins the prediction indicates that polar residues were most frequent among active transporter proteins and GPCRs, whereas infrequent in families with few transmembrane regions, such as non-GPCR receptors.     

Is the incidence of malaria decreasing in endemic area of Turkey?

Much international business and tourism travels occur, as well as the deployment of soldiers to other places. The aim of this study was both to determine incidence of malaria in the military hospital, Diyarbakir, southeast region of Turkey, and to point out the incidence of this disease. During the study period (1997-2004), 609 cases were found in a military hospital, which is in an endemic area for vivax malaria. This article review trends in current malaria status as well as possible factors for the decreasing prevalence throughout the study period.     

Is the nuclear envelope a ‘generator’ of membrane?

Summary Early diplotene oocytes from Necturus maculosus ranging from 0.2 to 0.5 mm in diameter were examined by electron microscopy. In the smallest oocytes of this range, the cytoplasm is largely devoid of membranes, but contains primarily ribosomes and mitochondria. In slightly larger oocytes, smooth-surfaced cytomembranes first appear in the perinuclear cytoplasm. At this time, the outer layer of the germinal vesicle nuclear envelope (GVNE) shows frequent connections with long membranous lamellae that extend for considerable, but variable distances into the juxtanuclear ooplasm. The number of smooth membranous lamellae increases tremendously as the oocytes increase in diameter. In such oocytes as well, frequent continuities are observed between the outer membrane of the GVNE and many of the cytoplasmic membranes. Eventually, as the ooplasm becomes populated with extensive numbers of membranous lamellae, instances of continuity between the membranous lamellae and nuclear envelope now become sparse and eventually non-existent. The frequent connections observed between membranous lamellae and the outer membrane of the GVNE during a circumscribed interval of diplotene strongly implicate the GVNE in the generation of extensive amounts of cytoplasmic membrane. The ooplasm of larger oocytes in the size range indicated contain numerous Golgi complexes and large quantities of annulate lamellae most of which are positioned in the peripheral or subcortical ooplasm, as well as extensive quantities of smooth membranes of the endoplasmic reticulum and lipid droplets.     

Initial steps of αand β-d-glucose binding to intact red cell membrane

Summary The kinetics of the initial phases of d-glucose binding to the glucose transport protein (GLUT1) of the human red cell can be followed by stopped-flow measurements of the time course of tryptophan (trp) fluorescence enhancement. A number of control experiments have shown that the trp fluorescence kinetics are the result of conformational changes in GLUT1. One shows that nontransportable l-glucose has no kinetic response, in contrast to d-glucose kinetics. Other controls show that d-glucose binding is inhibited by cytochalasin B and by extracellular d-maltose. A typical time course for a transportable sugar, such as d-glucose, consists of a zero-time displacement, too fast for us to measure, followed by three rapid reactions whose exponential time courses have rate constants of0.5–100 sec^+–1 at 20°C. It is suggested that the zero-time displacement represents the initial bimolecular ligand/GLUT1 association. Exponential 1 appears to be located at, or near, the external membrane face where it is involved in discriminating among the sugars. Exponential 3 is apparently controlled by events at the cytosolic face. Trp kinetics distinguish the K _d of the epimer, d-galactose, from the K _dfor d-glucose, with results in agreement with determinations by other methods. Trp kinetics distinguish between the binding of the - and -d-glucose anomers. The exponential 1 activation energy of the -anomer, 13.6 ± 1.4 kcal mol^+–1, is less than that of -d-glucose, 18.4 ± 0.8 kcal mol^+–1, and the two Arrhenius lines cross at 23.5°C. The temperature dependence of the kinetic response following -d-glucose binding illustrates the interplay among the exponentials and the increasing dominance of exponential 2 as the temperature increases from 22.3 to 36.6°C. The existence of these interrelations means that previously acceptable approximations in simplified reaction schemes for sugar transport will now have to be justified on a point-to-point basis.We should like to express our thanks to Michael R. Toon for his important contributions. This work was supported in part by a grant-in-aid from the American Heart Association, by the Squibb Institute for Medical Research and by The Council for Tobacco Research.     

Analysis of the red cell membrane in a family with hereditary elliptocytosis — total or partial of protein 4.1

Summary In a 12-year-old boy carrying a clinically silent elliptocytosis, we observed a total lack of red cell membrane band 4.1. Band 4.1 was partially absent in the father who also displayed a clinically silent elliptocytosis and, remarkably, in the mother although she presented normal discocytes. Band (2 and 2.1) phosphorylation was sharply reduced in the three persons examined. In the propositus and his mother, but not in his father, a clearly phosphorylated band appeared at the level of band 4.2. We suggest that the father and the mother carry two distinct alleles affecting differently the interactions, within the spectrin-actin protein 4.1 complex. The father's allele is elliptocytogenic in the heterozygous state and, among other molecular alterations, prevents the attachment of protein 4.1. The mother's allele is morphologically silent in the heterozygous state, yet it also affects the binding of protein 4.1, possibly because the latter is shortened. The propositus, being doubly heterozygous, has the same morphological phenotype as his father, but his protein 4.1 electrophoretic phenotype is the addition of both parental phenotypes. The distinct phosphorylation patterns in the region of bands 4.1 and 4.2 are also consistent with the two-allele hypothesis.     

Concanavalin A-agglutinability of membrane-skeleton-free vesicles and aged cellular remnants derived from human erythrocytes. Is the membrane skeleton required for agglutination?

Vesicles and cell remnants have been obtained by aging of erythrocytes in vitro. The vesicles lacking the membrane skeletal proteins and the remnants known to possess a rigid skeleton have been used to assess the role of membrane skeletal proteins in the process of Con A (concanavalin A)-mediated agglutination of erythrocytes. Both the vesicles and the remnants were found to bind Con A at the same density as did intact cells. The vesicles, isolated from normal as well as from the Con A-agglutinable trypsin- and Pronase-treated cells, failed to agglutinate with Con A. They were, however, well agglutinated by WGA (wheat-germ agglutinin) and RCA [Ricinus communis (castor bean) agglutinin], indicating that the vesicles are not defective in agglutination. Large, cytoskeleton-free, vesicles prepared by another procedure also gave the same results. The aged remnants from trypsin- and Pronase-treated erythrocytes showed significantly decreased agglutination with Con A, but were agglutinated as well as the fresh cells by WGA and RCA. The agglutination with Con A is thus abolished when the membrane skeleton is absent, and reduced when it is rigid, suggesting that the skeleton may play an important role in the agglutination of erythrocytes by Con A.     

How many pathways for invasion of the red blood cell by the malaria parasite?

Merozoites of the malaria parasite Plasmodium falciparum use several receptors for cellular engagement when they invade human red blood cells. Recently, a merozoite erythrocyte-binding protein, EBA-140, has been identified that specifically binds to glycophorin C on red blood cells. Up to 50% of Melanesians have a deletion in this gene, and the resultant Gerbich-negative red blood cells are relatively resistant to invasion. While discovery of multiple pathways for invasion could confound the search for suitable vaccine targets, they could also be considered in the design of therapeutic interventions that prevent malaria parasites entering red blood cells.     

Growth differentiation factor 11 locally controls anterior–posterior patterning of the axial skeleton

Growth and differentiation factor 11 (GDF11) is a transforming growth factor β family member that has been identified as the central player of anterior–posterior (A–P) axial skeletal patterning. Mice homozygous for Gdf11 deletion exhibit severe anterior homeotic transformations of the vertebrae and craniofacial defects. During early embryogenesis, Gdf11 is expressed predominantly in the primitive streak and tail bud regions, where new mesodermal cells arise. On the basis of this expression pattern of Gdf11 and the phenotype of Gdf11 mutant mice, it has been suggested that GDF11 acts to specify positional identity along the A–P axis either by local changes in levels of signaling as development proceeds or by acting as a morphogen. To further investigate the mechanism of action of GDF11 in the vertebral specification, we used a Cdx2-Cre transgene to generate mosaic mice in which Gdf11 expression is removed in posterior regions including the tail bud, but not in anterior regions. The skeletal analysis revealed that these mosaic mice display patterning defects limited to posterior regions where Gdf11 expression is deficient, whereas displaying normal skeletal phenotype in anterior regions where Gdf11 is normally expressed. Specifically, the mosaic mice exhibited seven true ribs, a pattern observed in wild-type (wt) mice (vs. 10 true ribs in Gdf11^−/− mice), in the anterior axis and nine lumbar vertebrae, a pattern observed in Gdf11 null mice (vs. six lumbar vertebrae in wt mice), in the posterior axis. Our findings suggest that GDF11, rather than globally acting as a morphogen secreted from the tail bud, locally regulates axial vertebral patterning.     

Is the K permeability of the resting membrane controlled by the excitable K channel?

To test whether or not the potassium permeability of the resting membrane is controlled by the excitable K channels (delayed rectifier), we examined changes in the Na and K permeability ratio, PNa/PK, of the squid axon before and after the excitable K channels were blocked. The blockage of the K channels was accomplished by three independent methods: internal application of tetraethylammonium, internal application of 4-aminopyridine plus Cs, and prolong internal perfusion of NaF solution. The permeability ratio was determined using two different methods: the conventional electrophysiological method and a new method based on the measurements of the hyperpolarizing effect of Na removal. We found that blocking the K channels did not cause a proportional decrease in the K permeability of the resting membrane, suggesting that the semipermeable property of the resting membrane is not determined by the excitable K channels.     

Does the energy state of mitochondria influence the surface potential of the inner mitochondrial membrane? A critical appraisal

Binding of 8-anilino-1-naphthalene sulphonate (ANS) to rat liver mitochondria and submitochondrial inside-out particles was measured under energized and de-energized conditions. In mitochondria, energization/de-energization changed the binding capacity for ANS extrapolated for its infinitely high concentration, whereas the apparent Kd value remained unchanged. In submitochondrial particles apparent Kd was changed but the extrapolated maximum binding was not altered. These results are compatible with theoretical considerations assuming a free permeability of mitochondrial membranes to ANS and its distribution according to the transmembrane potential. The spin-labelled cationic amphiphile, 4-(dodecyl dimethyl ammonium)-1-oxyl-2,2,6,6-tetramethyl piperidine bromide (CAT12), was trapped by de-energized mitochondria in such a way that about half of the bound probe became inaccessible to reduction by externally added ascorbate. This inaccessible fraction was increased by energization. This indicates that this cationic probe can penetrate through the inner mitochondrial membrane. De-energization produced a parallel shift of the Lineweaver-Burk plots for the oxidation of external ferrocytochrome c by mitoplasts and of succinate by submitochondrial particles. A similar shift was obtained by a partial inhibition of succinate oxidation by antimycin A. Thus, the observed changes of the kinetics of the two membrane-bound enzyme systems on de-energization can be interpreted as reflecting changes of the control points of mitochondrial respiration rather than changes of the surface potential. It is concluded that neither the fluorescent probe ANS, the spin-labelled amphiphilic cation CAT12, nor the kinetics of some respiratory enzyme systems provide a sufficient proof for changes of the surface potential of the inner mitochondrial membrane upon energization.     

Why does the mammalian red blood cell have aquaporins?

Aquaporins are now known to mediate the rapid exchange of water across the plasma membranes of diverse cell types. This exchange has been studied and kinetically characterized in red blood cells (erythrocytes; RBC) from many animal species. In recent years, a favoured method has been one based on NMR spectroscopy. Despite knowledge of their molecular structure the physiological raison d' etre of aquaporins in RBCs is still only speculated upon. Here, we present two hypotheses that account for the fact that the exchange of water is so fast in RBCs. The first is denoted the "oscillating sieve" hypothesis and it posits that known membrane undulations at frequencies up to 30 Hz with displacements up to 0.3 microm are energetically favoured by the high water permeability of the membrane. The second denoted the "water displacement" hypothesis is based on the known rapid exchange across the RBC membrane of ions such as Cl- and HCO3- and solutes such as glucose, all of whose molecular volumes are significantly greater than that of water. The ideas are generalizable to other cell types and organelles.