Role of Water in the Enzymatic Catalysis: Study of ATP plus AMP -> 2ADP Conversion by Adenylate Kinase

The catalytic conversion ATP + AMP -> 2ADP by the enzyme adenylate kinase (ADK) involves the binding of one ATP. molecule to the LID domain and one AMP molecule to the NMP domain. The latter is followed by a. phosphate transfer and then the release of two ADP molecules. We have computed a novel two-dimensional configurational free energy surface (2DCFES), with one reaction coordinate each for the LID and the NMP domain motions, while considering explicit water interactions. Our computed 2DCFES clearly reveals the existence of a stable half-open half-closed (HOHC) intermediate stale of the enzyme. Cycling of the enzyme through the HOHC state reduces the conformational free energy barrier for. the reaction by about 20 kJ/mol. We find that the stability of the HOHC state (missed in all earlier studies with implicit solvent model) is largely because of the increase of specific interactions of the polar amino acid side chains with water, particularly with the arginine and the histidine residues. Free energy surface of the LID domain is rather rugged, which can conveniently slow down LID's conformational motion, thus facilitating a new substrate capture after the product release in the catalytic cycle.

Observation of Water-Mediated Helix-Terminating Conformation in a Dehydrophenylalanine Peptide: Crystal and Solution Structure of the Octapeptide Ac-.DELTA.Phe-Val-.DELTA.Phe-Phe-Ala-Val-.DELTA.Phe-Gly-OMe

We have synthesised and determined the solution conformation and X-ray crystal structure of the octapeptide Ac-Delta Phe(1)-Val(2)-Delta Phe(3)-Phe(4)-Ala(5)-Val(6)-Delta Phe(7)-Gly(8)-OCH3 (Delta Phe = alpha,beta-dehydrophenylalanine) containing three Delta Phe residues as conformation constraining residues. In the solid state, the peptide folds into (i) an N-terminal (3)10(R)-helical pentapeptide segment, (ii) a middle non-helical segment, and (iii) a C-terminal incipient (3)10(L)-helical segment. The results of H-1 NMR data also suggest that a similar multiple-turn conformation for the peptide is largely maintained in solution. Though the C-terminal helix is incipient, the overall conformation of the octapeptide matches well with the conformation of the hairpins reported. Comparison of the pi-turn seen in the octapeptide molecule with those observed in proteins at the C-terminal end of helixes shows the structural similarity among them. A water molecule mediates the 5 --> 2 hydrogen bond in the pi-turn region. This is the first example of a water-inserted pi-turn in oligopeptides reported so far. Comparison between the present octapeptide and another (3)10(R)-helical dehydro nonapeptide Boc-Val-Delta Phe-Phe-Ala-Phe-Delta Phe-Val-Delta Phe-Gly-OCH3 solved by us recently, demonstrates the possible sequence-dependent conformational variations in alpha,beta-dehydrophenylalanine-containing oligopeptides.

Purification and partial characterization of acyl carrier proteins from developing oil seeds of pisa (Actinodaphne hookeri) and ground nut (Arachis hypogaea)

Acyl carrier proteins (ACP) were purified to homogeneity in the active form from developing seeds of pisa (Actinodaphne hookeri) which synthesizes exclusively trilaurin and from ground nut (Arachis hypogaea) which synthesizes triacylglycerols containing long chain fatty acids. Two major isoforms of ACPs were purified from developing pisa seeds using DEAE-cellulose, Superose-6 FPLC and C-4 reversed phase HPLC chromatographic methods. In contrast, only a single form of ACP was present in ground nut seeds which was purified by anion-exchange and activated thiol-Sepharose 4B affinity chromatography. The two isoforms of ACPs from pisa showed nearly the same specific activity of 6,706 and 7,175 pmol per min per mg protein while ground nut ACP showed a specific activity of 3,893 pmol per min per mg protein when assayed using E. coli acyl-ACP synthetase and [1-C-14]palmitic acid. When compared with E. coli ACP, the purified ACPs from both the seeds showed considerable difference in their mobility in native PAGE, but showed similar mobility in SDS-PAGE under reducing conditions. In the absence of reducing agents formation of dimers was quite prominent. The ACPs from both the seed sources were acid- and heat-stable. The major isoform of pisa seed ACP and the ground nut ACP contain 91 amino acids with M(r) 11,616 and 1,228 respectively. However, there is significant variation in their amino acid composition. A comparision of the amino acid sequence in the N-terminal region of pisa and ground nut seed ACPs showed considerable homology between themselves and with other plant ACPs but not with E. coli ACP.

Geochemistry of water and ground water in the Nhecolandia, Pantanal of Mato Grosso, Brazil: Variability and associated processes

A distinctive feature of the Nhecolandia, a sub-region of the Pantanal wetland in Brazil, is the presence of both saline and freshwater lakes. Saline lakes used to be attributed to a past and phase during the Pleistocene. However, recent studies have shown that saline and fresh water lakes are linked by a continuous water table, indicating that saline water could come from a contemporary concentration process. This concentration process could also be responsible for the large chemical variability of the waters observed in the area. A regional water sampling has been conducted in surface and sub-surface water and the water table, and the results of the geochemical and statistical analysis are presented. Based on sodium contents, the concentration shows a 1: 4443 ratio. All the samples belong to the same chemical family and evolve in a sodic alkaline manner. Calcite or magnesian calcite precipitates very early in the process of concentration, probably followed by the precipitation of magnesian silicates. The most concentrated solutions remain under-saturated with respect to the sodium carbonate salt, even if this equilibrium is likely reached around the saline lakes. Apparently, significant amounts of sulfate and chloride are lost simultaneously from the solutions, and this cannot be explained solely by evaporative concentration. This could be attributed to the sorption on reduced minerals in a green sub-surface horizon in the "cordilhieira" areas. In the saline lakes, low potassium, phosphate, magnesium, and sulfate are attributed to algal blooms. Under the influence of evaporation, the concentration of solutions and associated chemical precipitations are identified as the main factors responsible for the geochemical variability in this environment (about 92 % of the variance). Therefore, the saline lakes of Nhecolandia have to be managed as landscape units in equilibrium with the present water flows and not inherited from a past and phase. In order to elaborate hydrochemical tracers for a quantitative estimation of water flows, three points have to be investigated more precisely: (1) the quantification of magnesium involved in the Mg-calcite precipitation; (2) the identification of the precise stoichiometry of the Mg-silicate; and (3) the verification of the loss of chloride and sulfate by sorption onto labile iron minerals.

Optimal crop planning and conjunctive use of water resources in a coastal river basin

Due to increasing trend of intensive rice cultivation in a coastal river basin, crop planning and groundwater management are imperative for the sustainable agriculture. For effective management, two models have been developed viz. groundwater balance model and optimum cropping and groundwater management model to determine optimum cropping pattern and groundwater allocation from private and government tubewells according to different soil types (saline and non-saline), type of agriculture (rainfed and irrigated) and seasons (monsoon and winter). A groundwater balance model has been developed considering mass balance approach. The components of the groundwater balance considered are recharge from rainfall, irrigated rice and non-rice fields, base flow from rivers and seepage flow from surface drains. In the second phase, a linear programming optimization model is developed for optimal cropping and groundwater management for maximizing the economic returns. The models developed were applied to a portion of coastal river basin in Orissa State, India and optimal cropping pattern for various scenarios of river flow and groundwater availability was obtained.

Removal of As(V) by adsorption onto mixed rare earth oxides

Arsenic pollution of water is a major problem faced worldwide. Arsenic is a suspected carcinogen in human beings and is harmful to other living beings. In the present study, a novel adsorbent was used to remove arsenate [As(V)] from synthetic solutions. The adsorbent, which is a mixture of rare earth oxides, was found to adsorb As(V) rapidly and effectively. The effect of various parameters such as contact time, initial concentration, pH, and adsorbent dose on adsorption efficiency was investigated. More than 90% of the adsorption occurred within the first 10 min and the kinetic rate constant was found to be about 3.5 mg min(-1). Adsorption efficiency was found to be dependent on the initial As(V) concentration, and the adsorption behavior followed the Langmuir adsorption model. The optimum pH was found to be 6.5. The presence of other ions such as nitrate, phosphate, sulphate, and silicate decreased the adsorption of As(V) by about 20-30%. The adsorbed As(V) could be desorbed easily by washing the adsorbent with pH 12 solution. This study demonstrates the applicability of naturally occurring rare earth oxides as selective adsorbents for As(V) from solutions.

Slow orientational dynamics of water molecules at a micellar surface

The dynamics of water molecules near an aqueous micellar interface is studied in an atomistic molecular dynamics simulation of cesium pentadecafluorooctanoate (CsPFO) in water. The dipolar orientational time correlation function (tcf) and the translational diffusion of the water molecules are investigated. Results show that both the reorientational and the translational motion of water molecules near the micelle are restricted. In particular, the orientational tcf exhibits a very slow component in the long time which is slower than its bulk value by 2 orders of magnitude. This slow decay seems to be related to the slow decay often observed in experiments. The origin of the slow decay is analyzed.

Scalable weak aligning medium for enantiodiscrimination of water soluble chiral molecules

The study reports the first indication of a lyotropic liquid crystalline phase of an aqueous solution of polysaccharide xanthan gum, as a physical parameter dependent scalable and reversible weak alignment medium, for enantiodiscrimination of water soluble chiral molecules.

Biochemistry of water-logged soils. Part IV. Carbon and nitrogen transformations

1. During the fermentation of water-logged soil containing added substances with different carbon-nitrogen ratios, the reaction first turns slightly acid, but soon returns to the original hydrogen-ion concentration (pH 7·6). 2. The quantities of ammonia present in the medium increase up to a point, after which there is steady decrease. 3. There is nitrification only in the case of substances with narrow C/N ratios. The production of nitrate generally commences only after about a month, when the vigour of the initial fermentation has subsided and fairly large quantities of ammonia have accumulated in the medium. 4. The extent of mineralisation of nitrogen is determined chiefly by the C/N ratio, though in the cases of substances like mahua and lantana the presence of other constituents may also influence the processes. The quantities of mineralised nitrogen present in the soil system generally tend to decrease after about two months.

Dynamics of water at the interface of a small protein, enterotoxin

Fully atomistic molecular dynamics simulations have been carried out to investigate the correlation of biological activity with dynamics of water molecules in an aqueous protein solution of the toxic domain of enterotoxin (PDB ID: 1ETN). This is a small protein of 13 amino acid residues. Our study of this water soluble protein clearly reveals that water dynamics slows down in the hydration layer. Despite this general slowing down, water molecules in the vicinity of the second beta turn of this protein exhibit faster dynamics than those near other regions of the protein. Since this beta turn is believed to play a critical role in the receptor binding of this protein, the faster dynamics of water near the beta turn m ay have biological significance. The collective orientational dynamics of the water molecules in the protein solution exhibits a characteristic long time component of 27 ps, which agrees well with dielectric relaxation experiments.

Exploring use of climate information for optimal design of water resources infrastructure

We conducted surveys of fire and fuels managers at local, regional, and national levels to gain insights into decision processes and information flows in wildfire management. Survey results in the form of fire managers’ decision calendars show how climate information needs vary seasonally, over space, and through the organizational network, and help determine optimal points for introducing climate information and forecasts into decision processes. We identified opportunities to use climate information in fire management, including seasonal to interannual climate forecasts at all organizational levels, to improve the targeting of fuels treatments and prescribed burns, the positioning and movement of initial attack resources, and staffing and budgeting decisions. Longer-term (5–10 years) outlooks also could be useful at the national level in setting budget and research priorities. We discuss these opportunities and examine the kinds of organizational changes that could facilitate effective use of existing climate information and climate forecast capabilities.

Dynamic and thermodynamic anomalies of water at low temperatures: from bulk water to reverse micelles and DNA hydration layer

Liquid water is known to exhibit remarkable thermodynamic and dynamic anomalies, ranging from solvation properties in supercritical state to an apparent divergence of the linear response functions at a low temperature. Anomalies in various dynamic properties of water have also been observed in the hydration layer of proteins, DNA grooves and inside the nanocavity, such as reverse micelles and nanotubes. Here we report studies on the molecular origin of these anomalies in supercooled water, in the grooves of DNA double helix and reverse micelles. The anomalies have been discussed in terms of growing correlation length and intermittent population fluctuation of 4- and 5-coordinated species. We establish correlation between thermodynamic response functions and mean squared species number fluctuation. Lifetime analysis of 4- and 5-coordinated species reveals interesting differences between the role of the two species in supercooled and constrained water. The nature and manifestations of the apparent and much discussed liquid-liquid transition under confinement are found to be markedly different from that in the bulk. We find an interesting `faster than bulk' relaxation in reverse micelles which we attribute to frustration effects created by competition between the correlations imposed by surface interactions and that imposed by hydrogen bond network of water.