Use of restrained molecular dynamics in water to determine three-dimensional protein structure: prediction of the three-dimensional structure of Ecballium elaterium trypsin inhibitor II

Refinement of distance geometry (DG) structures of EETI-II (Heitz et al.: Biochemistry 28:2392-2398, 1989), a member of the squash family trypsin inhibitor, have been carried out by restrained molecular dynamics (RMD) in water. The resulting models show better side chain apolar/polar surface ratio and estimated solvation free energy than structures refined "in vacuo." The consistent lower values of residual NMR constraint violations, apolar/polar surface ratio, and solvation free energy for one of these refined structures allowed prediction of the 3D folding and disulfide connectivity of EETI-II. Except for the few first residues for which no NMR constraints were available, this computer model fully agreed with X-ray structures of CMTI-I (Bode et al.: FEBS Lett. 242:285-292, 1989) and EETI-II complexed with trypsin that appeared after the RMD simulation was completed. Restrained molecular dynamics in water is thus proved to be highly valuable for refinement of DG structures. Also, the successful use of apolar/polar surface ratio and of solvation free energy reinforce the analysis of Novotny et al. (Proteins 4:19-30, 1988) and shows that these criteria are useful indicators of correct versus misfolded models.     

Interactions between anion exchange and other membrane proteins in rabbit kidney medullary collecting duct cells

Summary In separated outer medullary collecting duct (MCD) cells, the time course of binding of the fluorescent stilbene anion exchange inhibitor, DBDS (4,4-dibenzamido-2,2-stilbene disulfonate), to the MCD cell analog of band 3, the red blood cell (rbc) anion exchange protein, can be measured by the stopped-flow method and the reaction time constant, _DBDS, can be used to report on the conformational state of the band 3 analog. In order to validate the method we have now shown that the ID_50,DBDS,MCD (0.5±0.1 m) for the H₂-DIDS (4,4-diisothiocyano-2,2-dihydrostilbene disulfonate) inhibition of _DBDS is in agreement with the ID_50,Cl ^–,_MCD (0.94±0.07 m) for H₂-DIDS inhibition of MCD cell Cl^– flux, thus relating _DBDS directly to anion exchange. The specific cardiac glycoside cation transport inhibitor, ouabain, not only modulates DBDS binding kinetics, but also increases the time constant for Cl^– exchange by a factor of two, from _Cl=0.30±0.02 sec to 0.56±0.06 sec (30mm NaHCO₃). The ID_50,DBDS,MCD for the ouabain effect on DBDS binding kinetics is 0.003±0.001 m, so that binding is about an order of magnitude tighter than that for inhibition of rbc K⁺ flux (K _I,K ⁺,_rbc=0.017 m). These experiments indicate that the Na⁺,K^–-ATPase, required to maintain cation gradients across the MCD cell membrane, is close enough to the band 3 analog that conformational information can be exchanged. Cytochalasin E (CE), which binds to the spectrin/actin complex in rbc and other cells, modulates DBDS binding kinetics with a physiological ID_50,DBDS,MCD (0.076±0.005 m); 2 m CE also more than doubles the Cl^– exchange time constant from 0.20±0.04 sec to 0.50±0.08 sec (30mm NaHCO₃). These experiments indicate that conformational information can also be exchanged between the MCD cell band 3 analog and the MCD cell cytoskeleton.     

Growth responses of rice in ammonium-based nutrient solution with variable calcium supply

It is commonly known that calcium promotes NO₃ ^- uptake in many crop species. However, calcium enhancement of NH₄ ⁺ uptake by plants has received little attention. This study aimed to evaluate the effect of Ca supplements on NH₄ ⁺ uptake and plant growth in solution cultured rice. Supplemental Ca applied at vegetative and reproductive phases of plant ontogeny tended to stimulate NH₄ ⁺ absorption, and accordingly resulted in a better straw and grain yield. However, excessively supplied Ca (400 ppm) was detrimental to plant growth. Increases in straw and grain yield observed at Ca levels up to 300 ppm were linked to the Ca-enhanced activities of glutamine synthetase (GS), glutamate synthase (GOGAT), and ribulose 1, 5-bisphosphate carboxylase/oxygenase (Rubisco).     

Control of photosynthesis in leaves as revealed by rapid gas exchange and measurements of the assimilatory force FA

The rapid transients of CO₂ gas exchange have been measured in leaves ofHelianthus annuus L. In parallel experiments the assimilatory force F_A, which is the product of the phosphorylation potential and the redox ratio NADPH/NADP, has been calculated from measured ratios of dihydroxyacetone phosphate to phosphoglycerate in the chloroplast stroma and in leaves. The following results were obtained: (i) When the light-dependent stroma alkalization was measured under steady-state conditions for photosynthesis in air containing 2000 μl · l^-1 CO₂, alkalization increased with photosynthesis as the quantum flux density (irradiance) was increased. This contrasts to the light-dependent stroma alkalisation measured in dark-adapted leaves during the dark-light transient (Laisk et al. 1989, Planta177, 350–358) which reached a maximum at a quantum flux density far below that necessary to saturate photosynthesis. This maximum was about three times higher than the maximum stroma alkalization at light- and CO₂-saturated photosynthesis. (ii) Accurate calculations of the assimilatory force F_A require a consideration of the stromal pH. However, under many conditions, changes in the stromal pH resulting from changes in photosynthetic flux can be neglected because they are small. (iii) Stromal ratios of dihydroxyacetone phosphate to phosphoglycerate are generally lower than ratios measured in leaf extracts. The value of F_A calculated from stromal metabolites was about 30% lower than F_A calculated from cellular metabolites. Still, it appears sufficient for many purposes to calculate F_A from metabolite measurements in leaf extracts. (iv) In the light, the catalytic capacity of the photosynthetic apparatus is adjusted to the level of irradiance. The response of carbon assimilation to large increases in irradiance is slow because it requires enzyme activation. Deactivation of the Calvin cycle induced by decreases in irradiance is slower than activation. (v) Changes in catalytic capacity and in the availability or level of substrates such as CO₂ alter the flux resistance of the Calvin cycle. A decrease in flux resistance explains why F_A often does not increase by much and may actually decrease when carbon flux is increased. Adjustments of flux resistances in the Calvin cycle and of photosystem-II activity in the electron-transport chain permit varying rates of photosynthesis at low levels of ATP and NADPH. As NADP remains available, the danger of over-reduction which leads to photoinactivation of electron transport is minimized. K.R. und U.H. were guests of the Estonian Academy of Sciences. Support by the Estonian Academy of Sciences, the Sonderforschungsbereich 251 of the University of Würzburg and the Fonds der Chemischen Industrie is gratefully acknowledged.     

Stomatal response to humidity in sugarcane and soybean: effect of vapour pressure difference on the kinetics of the blue light response

Abstract. The effect of atmospheric humidity on the kinetics of stomatal responses was quantified in gas exchange experiments using sugarcane ( Saccharum spp. hybrid) and soybean ( Glycine max ). Pulses of blue light were used to elicit pulses of stomatal conductance that were mediated by the specific blue light response of guard cells. Kinetic parameters of the conductance response were more closely related to leaf-air vapour pressure difference (VPD) than to relative humidity or transpiration. Increasing VPD significantly accelerated stomatal opening in both sugarcane and soybean, despite an approximately five-fold faster response in sugarcane. In contrast, the kinetics of stomatal recovery (closure) following the pulse were similar in the two species. Acceleration of opening by high VPD was observed even under conditions where soybean exhibited a feedforward response of decreasing transpiration (E) with increasing evaporative demand (VPD). This result suggests that epidermal, rather than bulk leaf, water status mediates the VPD effect on stomatal kinetics. The data are consistent with the hypothesis that increased cpidermal water loss at high VPD decreases the backpressure exerted by neighbouring cells on guard cells. allowing more rapid stomatal opening per unit of guard cell metabolic response to blue light.     

豆科根瘤内气体交换和气体扩散模型研究

近年来的研究表明根瘤皮层内存在着可调节的气体扩散屏障,它是由根瘤皮层内的一层细胞及填充在胞间隙的水层构成的,而根瘤是通过改变填充该层胞间隙的水层厚度来调节对气体扩散的阻力。本文概述了关于模拟豆科根瘤内气体交换和气体扩散的数学模型研究,阐明调节根瘤内含类菌体细胞维持低氧分压的有关问题。模型研究使我们获得了对共生固氮根瘤内极为复杂的微生态环境的初步认识,有待于通过改进试验和借助其他理论进一步探索根瘤气体交换和气体扩散的本质。     

Evidence for Involvement of a Zymogen Granule Na+/H+ Exchanger in Enzyme Secretion from Rat Pancreatic Acinar Cells

We have characterized a Na⁺/H⁺ exchanger in the membrane of isolated zymogen granules (ZG) from rat exocrine pancreas and investigated its role in secretagogue-induced enzyme secretion. ZG Na⁺/H⁺ exchanger activity was estimated by measuring Na⁺ or Li⁺ influx and consequent osmotic swelling and lysis of ZG incubated in Na- or Li-acetate. Alternatively, intragranule pH was investigated by measuring absorbance changes in ZG which had been preloaded with the weak base acridine orange. Na⁺- or Li⁺-dependent ZG lysis was enhanced by increasing inward to outward directed H⁺ gradients. Na⁺-dependent ZG lysis was not prevented by an inside-positive K⁺ diffusion potential generated by valinomycin which argues against parallel operation of separate electrogenic Na⁺ and H⁺ permeabilities and for coupled Na⁺/H⁺ exchange through an electroneutral carrier. Na⁺- and Li⁺-dependent ZG lysis was inhibited by EIPA (EC₅₀∼25 μm) and benzamil (EC₅₀∼100 μm), but only weakly by amiloride. Similarly, absorbance changes due to release of acridine orange from acidic granules into the medium were obtained with Na⁺ and Li⁺ salts only, and were inhibited by EIPA, suggesting the presence of a Na⁺/H⁺ exchanger in the membrane. Na⁺ dependent lysis of ZG was inhibited by 0.5 mm MgATP and MgATP-γ-S by about 60% and 35%, respectively. Inhibition by MgATP was prevented by incubation of ZG with alkaline phosphatase (100 U/ml), or by the calmodulin antagonists calmidazolium (0.75 μm), trifluoperazine (100 μm) and W-7 (500 μm), suggesting that the ZG Na⁺/H⁺ exchanger is regulated by a ZG membrane-bound calmodulin-dependent protein kinase. Na⁺ dependence of secretagogue (CCK-OP)-stimulated amylase secretion was investigated in digitonin permeabilized rat pancreatic acini and was higher in acini incubated in Na⁺ containing buffer (30 mm NaCl/105 mm KCl buffer; 6.4 ± 0.4% of total amylase above basal) compared to buffer without Na⁺ (0 mm NaCl/135 mm KCl buffer; 4.7 ± 0.4% of total amylase above basal, P < 0.03). EIPA (50 μm) reduced CCK-OP-induced amylase secretion in Na⁺ containing buffer from 7.5 ± 0.6% to 4.1 ± 0.8% (P < 0.02). In the absence of Na⁺ in the buffer, CCK-OP-stimulated amylase release was not inhibited by 50 μm EIPA. The data suggest that an amiloride insensitive, EIPA inhibitable Na⁺/H⁺ exchanger is present in ZG membranes, which is stimulated by calmodulin antagonists and could be involved in secretagogue-induced enzyme secretion from rat pancreatic acini. Received: 7 December 1995/Revised: 2 April 1996     

Divalent cations modify adsorption of 5′-AMP onto precipitated calcium phosphate: A model for cation modulation of adsorptive processes in primitive aqueous environments

The adsorption of 5′-AMP onto precipitated calcium phosphate (CaPi) requires the presence of soluble calcium and this dependence exhibits a Michaelian-like behavior. This result suggests that the formation of a complex between 5′-AMP and free Ca²⁺ (CaAMP) is a prelude to the adsorption of the nucleotide in the solid matrix. At concentrations one order of magnitude higher, Mn²⁺ and Mg²⁺ can substitute for soluble Ca²⁺ in the adsorption of 5′-AMP onto solid CaPi. However, when added simultaneously with 5′-AMP to a heterogeneous mixture that contains CaPi and soluble Ca²⁺, Mn²⁺ and Mg²⁺ inhibit the adsorption of 5′-AMP in a concentration-dependent manner. This suggests the formation of complexes that are much less effective for 5′-AMP adsorption than the CaAMP complex. On the other hand, Mn²⁺ and Mg²⁺ cannot promote desorption of the nucleotide attached to the precipitate in the presence of soluble Ca²⁺ if they are added after adsorption has attained equilibrium. Although desorption of 5′-AMP can be obtained by a sequential dilution of the soluble phase with buffer and no nucleotide in a process that obeys a Langmuir equation, the lack of effect of Mn²⁺ or Mg²⁺ when adsorption has attained its maximal value suggests strong interactions between the CaAMP complex and the solid matrix when adsorption equilibrium is reached. The divalent cations present in the matrix also participate with different selectivity in the attachment of the CaAMP complex, indicating that a cation-exchange mechanism could have acted in the modulation of adsorptive/desorptive processes involving biomonomers and phosphate surfaces in primitive aqueous environments. Received: 11 December 1995 / Accepted: 5 April 1996