HMG1 domains: the victims of circumstance

The method of circular dichroism (CD) was used to compare DNA behavior during its interaction with linker histone H1 and with non-histone chromosomal protein HMG1 at different ionic strength and at different protein content in the system. The role of negatively charged C-terminal fragment of HMG1 was analyzed using recombinant protein HMG1-(A + B), which lacks the C terminal amino acid sequence. The psi-type CD spectra were common for DNA interaction with histone H1, but no spectra of this type were observed in HMG1-DNA systems even at high ionic strength. The CD spectrum of the truncated recombinant protein at high salt concentration somewhat resembled the psi-type spectrum. Two very intense positive bands were located near 215 nm and near 273 nm, and the whole CD spectrum was positive. The role of C-terminal tail of HMG1 in formation of the ordered DNA-protein complexes is discussed.     

Organization of Methanobacterium thermoautotrophicum bacteriophage psi M1 DNA

Summary M1 is a virulent bacteriophage of Methanobacterium thermoautotrophicum strain Marburg. Restriction enzyme analysis of the linear, 30.4 kb phage DNA led to a circular map of the 27.1 kb M1 genome. M1 is thus circularly permuted and exhibits terminal redundancy of approximately 3 kb. Packaging of M1 DNA from a concatemeric precursor initiates at the pac site which was identified at coordinate 4.6 kb on the circular genome map. It proceeds clockwise for at least five packaging rounds. Headful packaging was also shown for M2, a phage variant with a 0.7 kb deletion at coordinate 23.25 on the map.     

Chloroplast volume: cell water potential relationships and acclimation of photosynthesis to leaf water deficits

Studies were undertaken to determine if there is an association between nonstomatally-mediated acclimation of photosynthesis to low water potential (w) and the maintenance of chloroplast volume during water stress. Spinach plants either kept well watered throughout their growth (non-acclimated), or subjected to water stress such that leaf w dropped to -1.5 megapascals (MPa) and then were rewatered (acclimated) were subjected to drought episodes. During these stress periods, photosynthesis was maintained to a greater extent in acclimated plants as compared to non-acclimated plants at w below -1 MPa.Estimates of internal leaf [CO₂] suggested that photosynthetic acclimation to low w was not primarily due to altered stomatal response. As w dropped from initial values, a decline in steady state levels of ribulose 1,5-bisphosphate (RuBP) occurred in both non-acclimated and acclimated plants. RuBP decline was less severe in acclimated plants.Low w effects on chloroplast volume in non-acclimated and acclimated plants were estimated by measuring the volume of intact chloroplasts isolated from plants in solutions which were made isotonic to declining leaf osmotic potential during the drought episodes. Chloroplast volume was maintained to a greater extent at low w in acclimated, as compared with non-acclimated plants. Although substantial osmotic adjustment occurred in both non-acclimated and acclimated plants, the extent of osmotic adjustment was the same. These data were interpreted as supporting the hypothesis that cellular-level acclimation to low w is associated with chloroplast volume maintenance, and this physiological acclimation is correlated with enhanced photosynthetic capacity of the leaf at low w.Abbreviations [CO₂]_i internal leaf CO₂ concentration - s osmotic potential - RWC relative water content - RuBP ribulose 1,5-bisphosphate - w water potential     

Preparations of Ψ-peptide bond and peptide-aldehyde inhibitors of atrial granule serine proteinase, a candidate processing enzyme of pro-atrial natriuretic factor

Pseudo-peptide bond inhibitors (-bond inhibitors) and peptide-aldehyde inhibitors of atrial granule serine proteinase, the candidate processing enzyme of pro-atrial natrieuretic factor, are prepared in high yield and purity by novel synthetic routes. The -bond compounds retain essential residues for enzyme binding, but place the enzyme inhibition site in the midst of the peptide sequence. Thus, Bz-APR--LR and Bz-APR--SLRR can be considered readthrough inhibitors of atrial granule serine proteinase. The most potent -peptide, Bz-APR--SLRR (IC₅₀=250 M), is about fivefold less potent than the best peptide-aldehyde inhibitor (EACA-APR-CHO), and both the -bond and peptide-aldehyde compounds are competitive, reversible inhibitors of the enzyme. The -bond peptides containing two C-terminal Arg residues are three-to tenfold more potent than the analogous compounds containing only one C-terminal Arg residue, confirming the importance of both Arg residues in the enzyme processing recognition site. As expected, because of their moderate potencies, the -peptides are not useful affinity ligands for purification of atrial granule serine proteinase, but both peptide aldehydes are effective affinity ligands [Damodaran and Harris (1995),J. Protein Chem., this issue].Abbreviations AGSP atrial granule serine proteinase - ANF atrial natriuretic factor - Bz benzoyl - DIEA diisopropylethylamine - DIPCDI diisopropylcarbodiimide - DMF dimethylformamide - DMSO dimethylsulfoxide - EACA 6(e)-aminocaproic acid - EtOAc ethyl acetate - HEPES N-2-hydroxyethylpiperazine-N-propanesulfonic acid - HOBt N-hydroxybenzotriazole - HPLC high-performance liquid chrornatography - NMR nuclear magnetic resonance - PEG polyethylene glycol-3350 - PyBOP benzotriazole-1-yl-oxy-trispyrrolidino-phosphonium-hexafluorophospate - TEA triethylamine - TFA trifluoroacetic acid - THF tetrahydrofuran - TLC thin-layer chromatography - UV ultraviolet - pseudo-peptide bond -CH₂-NH-. Single-letter abbreviations are used to denote amino acids     

A use of Ramachandran potentials in protein solution structure determinations

A strategy is developed to use database-derived - constraints during simulated annealing procedures for protein solution structure determination in order to improve the Ramachandran plot statistics, while maintaining the agreement with the experimental constraints as the sole criterion for the selection of the family. The procedure, fully automated, consists of two consecutive simulated annealing runs. In the first run, the database-derived - constraints are enforced for all aminoacids (but prolines and glycines). A family of structures is then selected on the ground of the lowest violations of the experimental constraints only, and the - values for each residue are examined. In the second and final run, the database-derived - constraints are enforced only for those residues which in the first run have ended in one and the same favored - region. For residues which are either spread over different favored regions or concentrated in disallowed regions, the constraints are not enforced. The final family is then selected, after the second run, again only based on the agreement with the experimental constraints. This automated approach was implemented in DYANA and was tested on as many as 12 proteins, including some containing paramagnetic metals, whose structures had been previously solved in our laboratory. The quality of the structures, and of Ramachandran plot statistics in particular, was notably improved while preserving the agreement with the experimental constraints.     

The effect of pinealectomy on entrainment of the locomotor activity rhythm in sparrows maintained on various short days

Summary Pinealectomy of house sparrows on 3L:21D (3 h light per 24 h) resulted in a significant increase in the time between the onset of perch-hopping activity and lights on (on) as well as the time between the offset of activity and lights of (off). The daily variance in on and off was also increased following the removal of the pineal gland. On longer light cycles (i.e., 5L:19D; 7L:17D), neither on or off, nor the variance of on or off was different between sham-pinealectomized and pinealectomized sparrows. Upon returning the birds to an ultrashort light cycle, 1L:23D, off, as well as the variance in on and off were again found to be significantly larger in the pinealectomized birds when compared to sham-operated controls. These results indicate that the effects of pinealectomy on the entrained rhythm of locomotor activity are most pronounced when birds are exposed to a weak entraining agent, such as an ultrashort light: dark cycle. In view of the observation that pinealectomy can alter the phase relationship between activity onset and offset, it is suggested that the pineal gland may be involved in the coupling of the oscillators that regulate activity onset and offset.     

Secondary structural effects on protein NMR chemical shifts

For an amino acid in protein, its chemical shift, (, )_s, is expressed as a function of its backbone torsion angles ( and ) and secondary state (s): (, )_{s=, )_coil+(, )_s}, where (, )_coil represents its chemical shift at coil state (s=coil); (, )_s (s=sheet or helix) is herein defined as secondary structural effect correction factor, which are quantitatively determined from Residue-specific Secondary Structure Shielding Surface (RSS) for ¹³CO, ¹³C, ¹³C,¹H, ¹⁵N, and ¹HN nuclei. The secondary structural effect correction factors defined in this study differ from those in earlier investigations by separating out the backbone conformational effects. As a consequence, their magnitudes are significantly smaller than those earlier reported. The present (, )_sheet and (, )_helix were found varying little with backbone conformation and the 20 amino acids, specifically for ¹³CO, ¹³C, and ¹H nuclei. This study also carries out some useful investigations on other chemical shift prediction approaches – the traditional shielding surfaces, SHIFTS, SHIFTX, PROSHIFT, and identifies some unexpected shortcomings with these methods. It provides some useful insights into understanding protein chemical shifts and suggests a new route to improving chemical shifts prediction. The RSS surfaces were incorporated into the program PRSI [Wang and Jardetzky, J. Biomol. NMR, 28: 327–340 (2004)], which is available for academic users at http://www.pronmr.com or by sending email to the author (yunjunwang@yahoo.com).     

Phlorizin binding to isolated enterocytes: Membrane potential and sodium dependence

Summary Phlorizin binding is studied in isolated intestinal epithelial cells of the chick. Cells are ATP depleted to allow extensive manipulation of ionic gradients and membrane potential (). Phlorizin binding is assayed at steady state. Carrier specific phlorizin binding is defined asd-glucose (90 mM) inhibitable binding. Specific binding displays simple Michaelian kinetics as a function of phlorizin. indicating the presence of a single homogeneous binding site. Sodium concentrations and modify the apparent binding affinity but not the maximum number of binding sites. In contrast, the activation curve as a function of sodium concentrations is sigmoid and the apparent maximum number of binding sites at saturating sodium is phlorizin dependent. The rate of phlorizin association is both and sodium-concentration dependent. Dissociation is sodium-concentration dependent but not dependent. Theoretical analysis indicates binding order of substrates is random. In addition, data suggests that the phlorizin/sodium stoichiometry is 2:1. The dependence can be explained by two models: either translocation is the -dependent step and the free carrier is anionic, or sodium binding is the -dependent step.     

The mitochondrial membrane potential (deltapsi(m)) in apoptosis; an update

Mitochondrial dysfunction has been shown to participate in the induction of apoptosis and has even been suggested to be central to the apoptotic pathway. Indeed, opening of the mitochondrial permeability transition pore has been demonstrated to induce depolarization of the transmembrane potential (_m), release of apoptogenic factors and loss of oxidative phosphorylation. In some apoptotic systems, loss of _m may be an early event in the apoptotic process. However, there are emerging data suggesting that, depending on the model of apoptosis, the loss of _m may not be an early requirement for apoptosis, but on the contrary may be a consequence of the apoptotic-signaling pathway. Furthermore, to add to these conflicting data, loss of _m has been demonstrated to not be required for cytochrome c release, whereas release of apoptosis inducing factor AIF is dependent upon disruption of _m early in the apoptotic pathway. Together, the existing literature suggests that depending on the cell system under investigation and the apoptotic stimuli used, dissipation of _m may or may not be an early event in the apoptotic pathway. Discrepancies in this area of apoptosis research may be attributed to the fluorochromes used to detect _m. Differential degrees of sensitivity of these fluorochromes exist, and there are also important factors that contribute to their ability to accurately discriminate changes in _m.     

Effects of water stress on the gas exchange,the activities of some enzymes of carbon and nitrogen metabolism,and on the pool sizes of some organic acids in maize leaves

Water-stressed maize (Zea mays L.) leaves showed a large decrease in leaf conductance during photosynthesis. Net CO₂ uptake and evaporation declined fast at mild stress (=–0.6 to –1.0 MPa) and slower at more severe stress (=–1.0 to -1.2 MPa), whereas the CO₂ concentration in the intercellular spaces (C_i) did not drop to the CO₂ compensation point. The activities of the enzymes of photosynthetic carbon metabolism tested in this study dropped by approx. 30% at =-1.2 MPa. Glutamine synthetase activity was unaffected by water stress, whereas the activity of nitrate reductase was almost completely inhibited. The decline of enzyme activities in relation to was correlated with a concomitant decrease in the content of total soluble protein of the stressed leaves. The total leaf pools of malate, pyruvate and oxaloacetate decreased almost linearly in relation to , thus obviously contradicting the almost constant C_i. In comparison to the controls (=0.6 MPa) the content of citrate and isocitrate increaed markedly at =-0.9 MPa and decreased again at =-1.2 MPa.Abbreviations PCR photosynthetic carbon reduction cycle - PCO photosynthetic carbon oxidation cycle - PEP phosphoenolypyruvate - RuBP ribulose-1,5-bisphosphate     

Temperature and moisture effects on C and N mineralization from surface applied clover residue

A better understanding of the effect of temperature (T) and moisture on soil microbial activity should improve our ability to predict N mineralization from soil organic matter and crop residues. The objective of this study was to evaluate the effects of water potential () and T on C and N mineralization from unamended Cecil loamy sand soil (clayey, kaolinitic, thermic Typic Kanhapludult) and from crimson clover (Trifolium incarnatum L.) residues applied on the soil surface. Cecil soil was packed into acrylic plastic cylinders, adjusted to -5.0, -1.5, -0.03, or -0.003 MPa, treated with clover residues on the surface or left unamended, and incubated at 10, 20, 28, or 35°C for 21 d. Headspace gas samples for CO2 and N2O determinations were taken periodically and NH3 evolved was trapped. Inorganic N in soil and residue extracts was analyzed after 21 d. When increased from -5.0 to -0.003 MPa, total CO2 evolved from unamended soil increased linearly with ln(-), whereas total CO2 evolved from clover residue increased exponentially with . In both cases the effect of was enhanced as T increased. Two-dimensional (T, ) equations were developed to describe these effects. Apparent net mineralized N from the clover residue increased with until it reached a maximum between -0.5 and -0.03 Mpa.     

Kinetics of Δψ-Dependent Sucrose Transport in Plasma Membrane Vesicles from Higher Plant Cells

The inside-out vesicles of plasma membranes were isolated from pumpkin stem cells, and the kinetics of sucrose efflux induced by the K⁺-diffusion potential (_D) was studied by measuring light transmission. Two phases differing in their rates and duration were identified in _D-dependent changes of light transmission. The increase in _Delevated the rate and magnitude of the fast phase in light transmission changes but did not markedly affect the rate of the slow phase. These two phases also differed in their sensitivity to inhibitors and to changes in sucrose concentration in the external medium. Measurements of _Dduring sucrose transport by means of the fluorescence probe dis-C₃-(5) revealed differences in the magnitude of _Dand its stability in vesicles loaded with sucrose and mannitol, as well as under the action of inhibitors. The two-phase dependence of sucrose efflux from vesicles on the applied diffusion potential is discussed in the context of modern concepts on the functioning of sucrose carriers in the membranes.     

Water potential of standing-dead shoots of an intertidal grass

Summary Dead stems and leaves of smooth cordgrass (Spartina alterniflora Loisel.) undergo substantial fungal decay in the standing position. We conducted a series of experiments to determine the probable range of water availabilities that cordgrass-fungal decomposers experience; we determined the effects of duration of wetting and drying, site on shoots, leaching of osmotica, and stage of decomposition on water potential () of cordgrass shoots. Dried pieces of cordgrass shoots took up water rapidly when submerged, rising from values which were probably less than –150 megapascals (MPa) water potential to about –3.5 (soaked in seawater) or –1.5 (soaked in tapwater) within 5 min. Air-drying resulted in a return to low (<–7.5 MPa) within an hour. Literature reports show that most litter and wood-decomposing fungi which have been tested cannot grow at more negative than –6 MPa. The more lignified stems showed a more negative matric than leaves at water contents greater than 25% fresh weight. As leaves decomposed in the marsh, their increased (from –1.7 to –0.5 MPa, under standard conditions of 30 min freshwater soaking and 30 min air-drying), similar to what other investigators have found for wheat and forest litter. The water content at which cordgrass leaves reached –6 MPa was about 23% fresh weight, within the range (15–32%) found for wheat straw and forest litter.     

Peptide building blocks from bacteriorhodopsin: Isolation and physicochemical characterization of two individual transmembrane segments

For protein engineering purposes, transmembrane segments of the structurally stable protein bacteriorhodopsin have been isolated and chemically characterized. Bacteriorhodopsin was cleaved by protease V8 fromStaphylococcus aureus to two fragments, V-1 and V-2. The V-2 fragment was separated by gel filtration in organic solvents and purified by reversed-phase FPLC. The fragment has been identified as the C-terminal, partially truncated double-loop of bacteriorhodopsin, including amino acids Val-167-Glu-232/4. Cleavage of V-2 by cyanogen bromide at the single Met-209 yielded two subfragments, which were purified to homogeneity by FPLC procedures. The N-terminal subfragment , consisted of a single transmembrane segment (helix F) of bacteriorhodopsin (Val-167-Met(Hse)-209). The C-terminal amphipathic subfragment , (Val-210-Glu-232/4) was identified as part of the C-terminal seventh helix of bacteriorhodopsin. Secondary structures of V-2, , and were investigated in organic solvents and micellar solutions. Native helical structures were partially retained in the solvent systems mentioned.     

The tRNATyr multigene family of Nicotiana rustica: genome organization,sequence analyses and expression in vitro

Tobacco tRNA^Tyr genes are mainly organized as a dispersed multigene family as shown by hybridization with a tRNA^Tyr-specific probe to Southern blots of Eco RI-digested DNA. A Nicotiana genomic library was prepared by Eco RI digestion of nuclear DNA, ligation of the fragments into the vector gtWES·B and in vitro packaging. The phage library was screened with a 5-labelled synthetic oligonucleotide complementary to nucleotides 18 to 37 of cytoplasmic tobacco tRNA^Tyr. Eleven hybridizing Eco RI fragments ranging in size from 1.7 to 7.5 kb were isolated from recombinant lambda phage and subcloned into pUC19 plasmid. Four of the sequenced tRNA^Tyr genes code for the known tobacco tRNA₁ ^Tyr (GA) and seven code for tRNA₂ ^Tyr (GA). The two tRNA species differ in one nucleotide pair at the basis of the TC stem. Only one tRNA^Tyr gene (pNtY5) contains a point mutation (T54A54). Comparison of the intervening sequences reveals that they differ considerably in length and sequence. Maturation of intron-containing pre-tRNAs was studied in HeLa and wheat germ extracts. All pre-tRNAs^Tyr-with one exception-are processed and spliced in both extracts. The tRNA^Tyr gene encoded by pNtY5 is transcribed efficiently in HeLa extract but processing of the pre-tRNA is impaired.     

Leaf water potential,component potentials and relative water content in a xeric grass,Agropyron dasystachyum (Hook.) Scribn.

Summary Leaf water potential ( _l ), osmotic potential ( _s ), pressure potential ( _p , turgor pressure), relative water content (R) and their interrelationships were determined for a xeric grass (Agropyron dasystachyum) found in the grasslands of Canada. Thermocouple psychrometers were used to measure _l and _s ; _p was obtained by subtraction. _l dropped from near 0 bars to about-28 bars as R went from 90% to 75%. R greater than 90% was not observed, perhaps because of a systematic error in determination of turgid water content. R remained relatively high in A. dasystachyum, even at low _l . The slope of the _l -R relationship was similar to other species which are generally considered to be drought tolerant. _p as high as 14 bars was observed. Most of the decrease in _l was accounted for by a decline in _p . The ability of A. dasystachyum to adjust to fluctuating water stress over the growing season is probably as much related to changes in tissue structure and turgor relationships as to simple changes in osmotic potential.     

Permeability change in transformed mouse fibroblasts caused by ionophores,and its relationship to membrane permeabilization by exogenous ATP

Summary Electrogenic ionophores have been found to induce membrane permeabilization in Swiss mouse 3T3 cells that had undergone spontaneous transformation (3T6 cells). Cells attached to plastic dishes were loaded with [³H] uridine, and then the medium was replaced by buffered salt solution at pH 7.8. The enhancement of membrane permeability was assayed by following the efflux of uridine nucleotides, normally impermeant substances. Titration with electrogenic ionophores, such as carbonylcyanidem-chlorophenylhydrazone (CCCP), SF-6847 and gramicidin D, markedly increased the membrane permeability within a very narrow range of ionophore concentration. Nonelectrogenic ionophores, such as monensin and nigericin, did not affect membrane permeability. Measurements of the distribution of the lipophilic cation tetraphenylphosphonium (TPP⁺) between the cells and their environment implied that the remarkable increase in permeability took place within a narrow range of membrane potential (). The data could be explaine by a threshold value, under which aqueous channels are opened in the plasma membrane. The effects exerted by electrogenic ionophores on the plasma membrane were found to be similar to those induced by exogenous ATP. In both cases rapid efflux of K⁺, influx of Na⁺ and reduction of preceded membrane permeabilization to low molecular weight, charged molecules, such as nucleotides. It is suggested that dissipation of induces conformational alterations in membranal components, and/or topological changes, such as aggregation of protein molecules, to form membranal aqueous channels. Electrogenic ionophores permeabilize both normal (3T3) and transformed (3T6) mouse fibroblasts, whereas ATP effects are specific for transformed cells. Thus, it is postulated that ATP actsvia specific sites on the surface of transformed cells.     

The activity of nitrate reductase and the pool sizes of some amino acids and some sugars in water-stressed maize leaves

The activity of nitrate reductase and the pool sizes of some amino acids and some sugars were measured in relation to the leaf water potential () of maize leaves. The activity of nitrate reductase was severely inhibited in water-stressed maize leaves. This was not due to substrate shortage or the presence of an inhibitor at reduced leaf water potential. While the typical proteinogenic amino acids valine, tyrosine, leucine and isoleucine were almost undetectable in the leaves of the control plants, their concentrations markedly increased with declining , thus indicating protein degradation. The concentrations of serine, glycine and glutamate increased upon water stress, their total amount in severely stressed leaves ranging 5- to 6-fold higher than the total amount of valine, tyrosine, leucine and isoleucine at this stage of water deficit. The pool sizes of glucose, fructose and sucrose decreased in relation to decreasing . The total amount of organic solutes remained almost constant at least up to a of approx.—1.0 MPa and then dropped to about 50% when reached –1.25 MPa.Abbreviations PCR photosynthetic carbon reduction cycle - PCO photosynthetic carbon oxidation cycle - PAR photosynthetically active radiation     

Synthesis and application of methyleneoxy pseudodipeptide building blocks in biologically active peptides

Summary. Pseudodipeptides H-Phe[CH₂O]Phe-OH, H-Tyr[CH₂O] Asp-OH and H-Pro[CH₂O]-D-Thr-OH were synthesized using the intramolecular Williamson reaction via substituted morpholin-3-one ring with the nitrogen atom protected with bulky Boc group. This protection and the substituent at C₅ position induced the stereospecific alkylation at the C₂ position introducing the side chain of the C-terminal amino acid mimetic. In the first pseudodipeptide a quenching of the enolate with benzaldehyde was followed by dehydration and corresponding double bond was hydrogenated with high stereospecific purity. In the other pseudodipeptides, this alkylation was carried out directly by tert-butyl 2-bromoacetate or acetaldehyde. However, in the latter reaction an R configuration of C₃ substituent in conjugated lactame ring was determined using a NOE NMR. Consequently, after opening this ring by acidic hydrolysis, the C-terminal part of corresponding pseudodipeptide possessed the side-chain of D-Thr mimetic, contrary to former one. Synthesized pseudodipeptides were introduced into HIV protease inhibitors and into peptides with oostatic activity.     

Leaf osmotic potentials of 104 plant species in relation to habitats and plant functional types in Hunshandak Sandland,Inner Mongolia,China

Leaf osmotic potentials ( _s) of 104 plant species from different habitats, i.e., fixed sand dunes, lowland and wetlands in Hunshandak Sandland, Inner Mongolia, China, were investigated. The values of _s were strongly species-specific, and varied from –6.54 MPa ( Caragana microphylla), to –0.44 MPa ( Digitaria ischaemum); 75% of plants investigated had _s from –1.01 to –3.0 MPa. Shrubs were found to have the lowest _s, with an average value of –3.19 MPa, while grasses showed the highest _s. The order of plant _s is shrubs<trees<grasses. The result may relate to anatomical features of shrubs. C₄ photosynthetic pathway plants showed lower _s values. The _s values of 104 species were negatively correlated with their rooting depths ( r ²=0.42; P <0.001). High hydraulic pressure resulting from the deep roots may well explain this trend. The value of _s increased as the environment became wetter, ranging from –0.79 MPa in wetlands to –2.09 MPa in fixed sand dunes. Although soil salt content was higher in wetlands, we did not find any effect on _s.An erratum to this article can be found at