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NASA NTRS1989

Molecular modeling of calmodulin: a comparison with crystallographic data

Two methods of side-chain placement on a modeled protein have been examined. Two molecular models of calmodulin were constructed that differ in the treatment of side chains prior to optimization of the molecule. A virtual bond analysis program developed by Purisima and Scheraga was used to determine the backbone conformation based on 2.2 angstroms resolution C alpha coordinates for the molecules. In the first model, side chains were initially constructed in an extended conformation. In the second model, a conformational grid search technique was employed. Calcium ions were treated explicitly during energy optimization using CHARMM. The models are compared to a recently published refined crystal structure of calmodulin. The results indicate that the initial choices for side-chains, but also significant effects on the main-chain conformation and supersecondary structure. The conformational differences are discussed. Analysis of these and other methods makes possible the formulation of a methodology for more appropriate side-chain placement in modeled proteins.

NASA Discipline Exobiology↗

NASA NTRS1993

Evolution in vitro: analysis of a lineage of ribozymes

Background: Catalytic RNAs, or ribozymes, possessing both a genotype and a phenotype, are ideal molecules for evolution experiments in vitro. A large, heterogeneous pool of RNAs can be subjected to multiple rounds of selection, amplification and mutation, leading to the development of variants that have some desired phenotype. Such experiments allow the investigator to correlate specific genetic changes with quantifiable alterations of the catalytic properties of the RNA. In addition, patterns of evolutionary change can be discerned through a detailed examination of the genotypic composition of the evolving RNA population. Results: Beginning with a pool of 10(13) variants of the Tetrahymena ribozyme, we carried out in vitro evolution experiments that led to the generation of ribozymes with the ability to cleave an RNA substrate in the presence of Ca2+ ions, an activity that does not exist for the wild-type molecule. Over the course of 12 generations, a seven-error variant emerged that has substantial Ca(2+)-dependent RNA-cleavage activity. Advantageous mutations increased in frequency in the population according to three distinct dynamics--logarithmic, linear and transient. Through a comparative analysis of 31 individual variants, we infer how certain mutations influence the catalytic properties of the ribozyme. Conclusions: In vitro evolution experiments make it possible to elucidate important aspects of both evolutionary biology and structural biochemistry on a reasonable short time scale.

Non-NASA Center↗

NASA NTRS1995

Modeling transport kinetics in clinoptilolite-phosphate rock systems

Nutrient release in clinoptilolite-phosphate rock (Cp-PR) systems occurs through dissolution and cation-exchange reactions. Investigating the kinetics of these reactions expands our understanding of nutrient release processes. Research was conducted to model transport kinetics of nutrient release in Cp-PR systems. The objectives were to identify empirical models that best describe NH4, K, and P release and define diffusion-controlling processes. Materials included a Texas clinoptilolite (Cp) and North Carolina phosphate rock (PR). A continuous-flow thin-disk technique was used. Models evaluated included zero order, first order, second order, parabolic diffusion, simplified Elovich, Elovich, and power function. The power-function, Elovich, and parabolic-diffusion models adequately described NH4, K, and P release. The power-function model was preferred because of its simplicity. Models indicated nutrient release was diffusion controlled. Primary transport processes controlling nutrient release for the time span observed were probably the result of a combination of several interacting transport mechanisms.

NASA Center JSC↗

NASA NTRS1993

Solubility and cation exchange in phosphate rock and saturated clinoptilolite mixtures

Mixtures of zeolite and phosphate rock (PR) have the potential to provide slow-release fertilization of plants in synthetic soils by dissolution and ion-exchange reactions. This study was conducted to examine solubility and cation-exchange relationships in mixtures of PR and NH4- and K-saturated clinoptilolite (Cp). Batch-equilibration experiments were designed to investigate the effect of PR source, the proportion of exchangeable K and NH4, and the Cp to PR ratio on solution N, P, K, and Ca concentrations. The dissolution and cation-exchange reactions that occurred after mixing NH4- and K-saturated Cp with PR increased the solubility of the PR and simultaneously released NH4 and K into solution. The more reactive North Carolina (NC) PR rendered higher solution concentrations of NH4 and K when mixed with Cp than did Tennessee (TN) PR. Solution P concentrations for the Cp-NC PR mixture and the Cp-TN PR mixture were similar. Solution concentrations of N, P, K, and Ca and the ratios of these nutrients in solution varied predictably with the type of PR, the Cp/PR ratio, and the proportions of exchangeable K and NH4 on the Cp. Our research indicated that slow-release fertilization using Cp/PR media may provide adequate levels of N, P, and K to support plant growth. Solution Ca concentrations were lower than optimum for plant growth.

NASA Discipline Number 61-10↗

NASA NTRS1992

Modelling the Phanerozoic carbon cycle and climate: constraints from the 87Sr/86Sr isotopic ratio of seawater

A numerical model describing the coupled evolution of the biogeochemical cycles of carbon, sulfur, calcium, magnesium, phosphorus, and strontium has been developed to describe the long-term changes of atmospheric carbon dioxide and climate during the Phanerozoic. The emphasis is on the effects of coupling the cycles of carbon and strontium. Various interpretations of the observed Phanerozoic history of the seawater 87Sr/86Sr ratio are investigated with the model. More specifically, the abilities of continental weathering, volcanism, and surface lithology in generating that signal are tested and compared. It is suggested that the observed fluctuations are mostly due to a changing weatherability over time. It is shown that such a conclusion is very important for the modelling of the carbon cycle. Indeed, it implies that the conventional belief that the evolution of atmospheric carbon dioxide and climate on a long time scale is governed by the balance between the volcanic input of CO2 and the rate of silicate weathering is not true. Rather carbon exchanges between the mantle and the exogenic system are likely to have played a key role too. Further, the increase of the global weathering rates with increasing surface temperature and/or atmospheric CO2 pressure usually postulated in long-term carbon cycle and climate modelling is also inconsistent with the new model. Other factors appear to have modulated the weatherability of the continents through time, such as mountain building and the existence of glaciers and ice sheets. Based on these observations, a history of atmospheric carbon dioxide and climate during Phanerozoic time, consistent with the strontium isotopic data, is reconstructed with the model and is shown to be compatible with paleoclimatic indicators, such as the timing of glaciation and the estimates of Cretaceous paleotemperatures.

NASA Discipline Number 52-30↗

NASA NTRS2002

Formation of ferrihydrite and associated iron corrosion products in permeable reactive barriers of zero-valent iron

Ferrihydrite, which is known to form in the presence of oxygen and to be stabilized by the adsorption of Si, PO4 and SO4, is ubiquitous in the fine-grained fractions of permeable reactive barrier (PRB) samples from the U.S. Coast Guard Support Center (Elizabeth City, NC) and the Denver Federal Center (Lakewood, CO) studied by high-resolution transmission electron microscopy and selected area electron diffraction. The concurrent energy-dispersive X-ray data indicate a strong association between ferrihydrite and metals such as Si, Ca, and Cr. Magnetite, green rust 1, aragonite, calcite, mackinawite, greigite and lepidocrocite were also present, indicative of a geochemical environment that is temporally and spatially heterogeneous. Whereas magnetite, which is known to form due to anaerobic Fe0 corrosion, passivates the Fe0 surface, ferrihydrite precipitation occurs away from the immediate Fe0 surface, forming small (<0.1 microm) discrete clusters. Consequently, Fe0-PRBs may remain effective for a longer period of time in slightly oxidized groundwater systems where ferrihydrite formation occurs compared to oxygen-depleted systems where magnetite passivation occurs. The ubiquitous presence of ferrihydrite suggests that the use of Fe0-PRBs may be extended to applications that require contaminant adsorption rather than, or in addition to, redox-promoted contaminant degradation.

Metals/chemistry↗

NASA NTRS1990

Partial purification and characterization of a Ca(2+)-dependent protein kinase from the green alga, Dunaliella salina

A calcium-dependent protein kinase was partially purified and characterized from the green alga Dunaliella salina. The enzyme was activated at free Ca2+ concentrations above 10(-7) molar. and half-maximal activation was at about 3 x 10(-7) molar. The optimum pH for its Ca(2+)-dependent activity was 7.5. The addition of various phospholipids and diolein had no effects on enzyme activity and did not alter the sensitivity of the enzyme toward Ca2+. The enzyme was inhibited by calmodulin antagonists, N-(6-aminohexyl)-1-naphthalene sulfonamide and N-(6-aminohexyl)-5-chloro-1-naphthalene sulfonamide in a dose-dependent manner while the protein kinase C inhibitor, sphingosine, had little effect on enzyme activity up to 800 micromolar. Immunoassay showed some calmodulin was present in the kinase preparations. However, it is unlikely the kinase was calmodulin regulated, since it still showed stimulation by Ca2+ in gel assays after being electrophoretically separated from calmodulin by two different methods. This gel method of detection of the enzyme indicated that a protein band with an apparent molecular weight of 40,000 showed protein kinase activity at each one of the several steps in the purification procedure. Gel assay analysis also showed that after native gel isoelectric focusing the partially purified kinase preparations had two bands with calcium-dependent activity, at isoelectric points 6.7 and 7.1. By molecular weight, by isoelectric point, and by a comparative immunoassay, the Dunaliella kinase appears to differ from at least some of the calcium-dependent, but calmodulin and phospholipid independent kinases described from higher plants.

Non-NASA Center↗