The conformation of polyriboadenylic acid at low temperature and neutral pH. A single-stranded rodlike structure.

The conformation of single-stranded polyrA in aqueous solution has been measured at temperatures down to ?12°C. The radius of gyration of low-molecular-weight polyrA varies very little with temperature in this range. By studying the dependence of radius of gyration on temperature for several polyrA fractions, we show that the dependence of the radius upon chain length is consistent with formation of a single-stranded rodlike structure at low temperature. The structure has an approximate length of 3.2 Å/nucleotide.     

Closed-state inactivation as a mechanism for decreased K current at low extracellular pH

Extracellular acidification regulates the biophysical properties of many voltage-gated potassium channels. Most often acidic pH reduces peak current and enhances current decay during depolarization. Here we review recent data from single channel and voltage clamp fluorimetry studies, which suggest that these two effects of protons are mediated by distinct kinetic processes. This new mechanistic insight directly demonstrates that the whilst the enhanced decay of current observed with acidic pH is due to an accelerated entry of open channels into P/C-type inactivation, the main mechanism for the reduction in peak channel conductance is a stabilization of resting channels in closed-inactivated states. Thus acidic pH acts to reduce the conductance of open channels, as well as to prevent other channels from opening at all, and in so doing, reveals that both open- and closed-state inactivation processes can co-exist in Kv channels.     

Response of two wetland plant species to Cd exposure at low and neutral pH

Emerged and submerged plants are used in treating various metal-containing wastewaters, such as stormwater (neutral pH) and acid mine drainage (low pH). The aim was to investigate the appearance of a set of possible mechanisms to detoxify Cd in plants and whether their appearance differ due to the surrounding pH and/or plant type. One emergent (Carex rostrata) and one submerged (Elodea canadensis) macrophyte were exposed to 0, 0.05, and 0.5 μM Cd for 3 d in hydroponic solutions at pH 3.5 and 6.9. We analysed cadmium accumulation, thiol-rich peptide concentrations and cell wall-bound Cd in plants, organic acid content and pH change in surrounding water cation exchange capacity (CEC) of plant tissue. Both plant species accumulated Cd in their tissues, and thus did not exclude it and C. rostrata decreased the relative Cd distribution to its shoots with increasing Cd addition. In both species, Cd was immobilized through cell wall binding, and thiol-rich peptides synthesized in the presence of Cd that may participate in Cd binding. In addition, E. canadensis increased its CEC by synthesizing new metal-binding sites in the cell walls. Organic acid composition in surrounding water did not change with Cd addition and had no effect on Cd detoxification. However, E. canadensis increased the surrounding pH from pH 3.5 in the presence of Cd; the surrounding pH did not, however, influence the detoxification mechanisms.     

Microbial sulphate reduction at a low pH

It is now well established that microbial sulphate-reduction can proceed in environments with a pH<5. This review summarizes existing reports on sulphate reduction at low pH and discusses possible pH effects on sulphate-reducing bacteria. Microbial sulphate reduction has been observed in acidic lakes, wetlands, mesocosms, acidic sulphate soils and bioreactors. Possible inhibitory factors include the metabolites H(2)S and organic acids, which can be toxic depending on pH. Metal sulphide precipitation and competition with other bacteria, namely iron-reducing bacteria, can inhibit sulphate reduction. Theoretical considerations show that normal sulphate reduction rates are too low to maintain a neutral micro niche in an acidic environment. The first acidotolerant sulphate-reducing bacteria have been isolated recently.     

Cellular expansion at low temperature as a cause of membrane lesions

Rates of solute leakage from excised discs of cucumber (Cucumis sativus L. cv Straight Eight) cotyledons were altered by temperature during plasmolysis in the manner of a simple diffusion phenomenon; the log of the leakage rate increased in proportion to the temperature. During deplasmolysis, however, leakage rates responded to temperature with a very different pattern: chilling conditions (below about 20°C) caused large increases in leakage rates, indicating disruption of membrane integrity in the tissues. The time course of restoration of normal leakage rates after deplasmolysis/chilling damage indicated a rapid repair of the lesions. A similar sensitivity to low temperatures was found during rehydration after leaf desiccation, with low temperatures again causing high leakage rates. It is suggested that low temperatures interfere with membrane expansion, possibly by lowering elasticity and hindering the incorporation of lipid material into the expanding membrane. The expansion of tissues at low temperatures may cause lesions in cellular membranes, contributing to chilling injury.     

Photolysis of nitrosamines and nitrosamides at neutral pH: a spin-trap study

A model system has been used to study the types of radicals formed on denitrosation of N-nitroso compounds. Free radicals were formed at room temperature (22 degrees-23 degrees C) and neutral pH by photolytic cleavage of N-nitroso bonds and were partially characterized following their addition to the spin traps 5,5-dimethyl-1-pyrroline-N-oxide (DMPO) and N-tert-butyl-alpha-phenyl-nitrone (PBN). Carbon-centered radical adducts were obtained during nitrosamine photolysis and nitrogen-centered radical adducts during nitrosamide photolysis. Since both the nitrosamines and nitrosamides initially form nitrogen-centered radicals on photolysis, a secondary reaction or rearrangement must occur after initial N-nitroso bond cleavage in the nitrosamines. Mechanisms are proposed to account for these results.     

Formation of tannin-albumin nano-particles at neutral pH as measured by light scattering techniques

Aggregation phenomena of tannin with bovine serum albumin were investigated by light scattering techniques including photon correlation spectroscopy and Rayleigh scattering. Tannin and albumin formed particles with diameters less than 1 microm at neutral pH. As revealed by this study, light scattering methods are useful in investigating aggregation phenomena of biomolecules and in directly quantifying tannin content.     

Improved low pH bicelle system for orienting macromolecules over a wide temperature range

We have prepared and characterized a novel bicelle system composed of 1,2-di-O-dodecyl-sn-glycero-3-phos- phocholine (DIODPC) and 3-(chloramidopropyl)dimethylammonio-2-hydroxyl-1-propane sulfonate (CHAPSO). At the optimal DIODPC/CHAPSO molar ratio of 4.3:1, this medium becomes magnetically oriented from pH 6.5 down to pH 1.0. Unlike previously reported bicelle preparations, these bicelles are chemically stable at low pH and are capable of inducing protein alignment, as illustrated by the large residual dipolar couplings measured for rusticyanin from Thiobacillus ferrooxidans at pH 2.1. The DIODPC/CHAPSO system is particularly useful for measuring residual dipolar couplings of macromolecules that require very acidic conditions.     

Stability of trimeric DENV envelope protein at low and neutral pH: An insight from MD study

Change in pH plays a crucial role in the stability and function of the dengue envelope (DENV) protein during conformational transition from dimeric (pre-fusion state) to trimeric form (post-fusion state). In the present study we have performed various molecular dynamics (MD) simulations of the trimeric DENV protein at different pH and ionic concentrations. We have used total binding energy to justify the stability of the complex using the MMPBSA method. We found a remarkable increase in the stability of the complex at neutral pH (pH ~ 7) due to the increment of sodium ions. However, at very low pH (pH ~ 4), the total energy of the complex becomes high enough to destabilize the complex. At a specific pH, almost at a range of 6, the stability of the complex is significantly better than the stability of the trimer at neutral pH, which connotes that the trimer is most stable at this pH (pH ~ 6).     

Directed evolution of Thermotoga neapolitana xylose isomerase: high activity on glucose at low temperature and low pH

The Thermotoga neapolitana xylose isomerase (TNXI) is extremely thermostable and optimally active at 95 degrees C. Its derivative, TNXI Val185Thr (V185T), is the most active type II xylose isomerase reported, with a catalytic efficiency of 25.1 s(-1) mM(-1) toward glucose at 80 degrees C (pH 7.0). To further optimize TNXI's potential industrial utility, two rounds of random mutagenesis and low temperature/low pH activity screening were performed using the TNXI V185T-encoding gene as the template. Two highly active mutants were obtained, 3A2 (V185T/L282P) and 1F1 (V185T/L282P/F186S). 1F1 was more active than 3A2, which in turn was more active than TNXI V185T at all temperatures and pH values tested. 3A2 and 1F1's high activities at low temperatures were due to significantly lower activation energies (57 and 44 kJ/mol, respectively) than that of TNXI and V185T (87 kJ/mol). Mutation L282P introduced a kink in helix alpha7 of 3A2's (alpha/beta)8 barrel. Surprisingly, this mutation kinetically destabilized 3A2 only at pH 5.5. 1F1 displayed kinetic stability slightly above that of TNXI V185T. In 1F1, mutation F186S creates a cavity that disrupts a four-residue network of aromatic interactions. How the conformation of the neighboring residues is affected by this cavity and how these conformational changes increase 1F1's stability still remain unclear.     

Significance of temperature and preincubation temperature on survival of Listeriamonocytogenes at pH 4·8

Listeria monocytogenes is a food-borne pathogenic bacterium that can be found in softcheese. At the beginning of cheese ripening, the pH is about 4·85–4·90. The aimof this work was to study the influence of temperature, preincubation temperature (temperature atwhich the inoculum was cultivated) and initial bacterial concentration on the survival of L.monocytogenes (strain Scott A) at pH 4·8. It was demonstrated in an earlier study thatthese factors did influence growth kinetics. Survival studies of L. monocytogenes weredone in a laboratory broth simulating cheese composition. Four test temperatures (2, 6, 10 and14°C) and two preincubation temperatures were studied (30°C or the test temperature). Listeria monocytogenes (strain Scott A) was unable to grow at pH 4·8 under allconditions tested. The time for 10% survival was about 11 and 2 d, at 2°C with preincubationat 2°C and 30°C, respectively; 9 d at 6°C with preincubation at 6°C; 4 d at 6°Cwith preincubation at 30°C; and 1 d at 14°C with preincubation at 14°C or at 30°C.The results show that survival of L. monocytogenes (strain Scott A) at pH 4·8 is notdependent on initial bacterial concentration but on both the test and preincubation temperatures.     

The surface conformation of Sindbis virus glycoproteins E1 and E2 at neutral and low pH, as determined by mass spectrometry-based mapping

Sindbis virus contains two membrane glycoproteins, E1 and E2, which are organized into 80 trimers of heterodimers (spikes). These trimers form a precise T=4 icosahedral protein lattice on the surface of the virus. Very little is known about the organization of the E1 and E2 glycoproteins within the spike trimer. To gain a better understanding of how the proteins E1 and E2 are arranged in the virus membrane, we have used the techniques of limited proteolysis and amino acid chemical modification in combination with mass spectrometry. We have determined that at neutral pH the E1 protein regions that are accessible to proteases include domains 1-21 (region encompassing amino acids 1 to 21), 161-176, and 212-220, while the E2 regions that are accessible include domains 31-84, 134-148, 158-186, 231-260, 299-314, and 324-337. When Sindbis virus is exposed to low pH, E2 amino acid domains 99-102 and 262-309 became exposed while other domains became inaccessible. Many new E1 regions became accessible after exposure to low pH, including region 86-91, which is in the putative fusion domain of E1 of Semliki Forest virus (SFV) (M. C. Kielian et al., J. Cell Biol. 134:863-872, 1996). E1 273-287 and region 145-158 were also exposed at low pH. These data support a model for the structure of the alphavirus spike in which the E1 glycoproteins are centrally located as trimers which are surrounded and protected by the E2 glycoprotein. These data improve our understanding of the structure of the virus membrane and have implications for understanding the protein conformational changes which accompany the process of virus-cell membrane fusion.     

Peptidylglycine alpha-amidating reaction: evidence for a two-step mechanism involving a stable intermediate at neutral pH

In our previous study of the rat brain alpha-amidating activity, we suggested that a protein of 41 kdal (41K protein) that shows no alpha-amidating activity is required for the reaction at neutral pH in addition to an alpha-amidating enzyme of 36 kdal (36K enzyme). Here we report on the purification of both proteins to near homogeneity and provide evidence that alpha-amidation proceeds via a two-step mechanism involving a stable intermediate at neutral pH, which is initially formed by the 36K enzyme and then readily converted into an amide product by the 41K protein.