Laser ablation-miniature mass spectrometer for elemental and isotopic analysis of rocks.

A laser ablation-miniature mass spectrometer (LA-MMS) for the chemical and isotopic measurement of rocks and minerals is described. In the LA-MMS method, neutral atoms ablated by a pulsed laser are led into an electron impact ionization source, where they are ionized by a 70 eV electron beam. This results in a secondary ion pulse typically 10-100 µs wide, compared to the original 5-10 ns laser pulse duration. Ions of different masses are then spatially dispersed along the focal plane of the magnetic sector of the miniature mass spectrometer (MMS) and measured in parallel by a modified CCD array detector capable of detecting ions directly. Compared to conventional scanning techniques, simultaneous measurement of the ion pulse along the focal plane effectively offers a 100% duty cycle over a wide mass range. LA-MMS offers a more quantitative assessment of elemental composition than techniques that detect ions directly generated by the ablation process because the latter can be strongly influenced by matrix effects that vary with the structure and geometry of the surface, the wavelength of the laser beam, and the not well characterized ionization efficiencies of the elements in the process. The above problems attendant to the direct ion analysis has been minimized in the LA-MMS by analyzing the ablated neutral species after their post-ionization by electron impaction. These neutral species are much more abundant than the directly ablated ions in the ablated vapor plume and are, therefore, expected to be characteristic of the chemical composition of the solid. Also, the electron impact ionization of elements is well studied and their ionization cross sections are known and easy to find in databases. Currently, the LA-MMS limit of detection is 0.4 wt.%. Here we describe LA-MMS elemental composition measurements of various minerals including microcline, lepidolite, anorthoclase, and USGS BCR-2G samples. The measurements of high precision isotopic ratios including (41)K/(39)K (0.077 ± 0.004) and (29)Si/(28)Si (0.052 ± 0.006) in these minerals by LA-MMS are also described. The LA-MMS has been developed as a prototype instrument system for space applications for geochemical and geochronological measurements on the surface of extraterrestrial bodies.

H2O at the Phoenix landing site.

The Phoenix mission investigated patterned ground and weather in the northern arctic region of Mars for 5 months starting 25 May 2008 (solar longitude between 76.5 degrees and 148 degrees ). A shallow ice table was uncovered by the robotic arm in the center and edge of a nearby polygon at depths of 5 to 18 centimeters. In late summer, snowfall and frost blanketed the surface at night; H(2)O ice and vapor constantly interacted with the soil. The soil was alkaline (pH = 7.7) and contained CaCO(3), aqueous minerals, and salts up to several weight percent in the indurated surface soil. Their formation likely required the presence of water.

Detection of perchlorate and the soluble chemistry of martian soil at the Phoenix lander site.

The Wet Chemistry Laboratory on the Phoenix Mars Lander performed aqueous chemical analyses of martian soil from the polygon-patterned northern plains of the Vastitas Borealis. The solutions contained approximately 10 mM of dissolved salts with 0.4 to 0.6% perchlorate (ClO4) by mass leached from each sample. The remaining anions included small concentrations of chloride, bicarbonate, and possibly sulfate. Cations were dominated by Mg2+ and Na+, with small contributions from K+ and Ca2+. A moderately alkaline pH of 7.7 +/- 0.5 was measured, consistent with a carbonate-buffered solution. Samples analyzed from the surface and the excavated boundary of the approximately 5-centimeter-deep ice table showed no significant difference in soluble chemistry.

Evidence for calcium carbonate at the Mars Phoenix landing site.

Carbonates are generally products of aqueous processes and may hold important clues about the history of liquid water on the surface of Mars. Calcium carbonate (approximately 3 to 5 weight percent) has been identified in the soils around the Phoenix landing site by scanning calorimetry showing an endothermic transition beginning around 725 degrees C accompanied by evolution of carbon dioxide and by the ability of the soil to buffer pH against acid addition. Based on empirical kinetics, the amount of calcium carbonate is most consistent with formation in the past by the interaction of atmospheric carbon dioxide with liquid water films on particle surfaces.

Mars water-ice clouds and precipitation.

The light detection and ranging instrument on the Phoenix mission observed water-ice clouds in the atmosphere of Mars that were similar to cirrus clouds on Earth. Fall streaks in the cloud structure traced the precipitation of ice crystals toward the ground. Measurements of atmospheric dust indicated that the planetary boundary layer (PBL) on Mars was well mixed, up to heights of around 4 kilometers, by the summer daytime turbulence and convection. The water-ice clouds were detected at the top of the PBL and near the ground each night in late summer after the air temperature started decreasing. The interpretation is that water vapor mixed upward by daytime turbulence and convection forms ice crystal clouds at night that precipitate back toward the surface.

Carbon monoxide binding by de novo heme proteins derived from designed combinatorial libraries.

Carbon monoxide binding was studied in a collection of de novo heme proteins derived from combinatorial libraries of sequences designed to fold into 4-helix bundles. The design of the de novo sequences was based on the previously reported "binary code" strategy, in which the patterning of polar and nonpolar amino acids is specified explicitly, but the exact identities of the side chains are varied extensively.(1) The combinatorial mixture of amino acids included histidine and methionine, which ligate heme iron in natural proteins. However, no attempt was made to explicitly design a heme binding site. Nonetheless, as reported previously, approximately half of the binary code proteins bind heme.(2) This collection of novel heme proteins provides a unique opportunity for an unbiased assessment of the functional potentialities of heme proteins that have not been prejudiced either by explicit design or by evolutionary selection. To assess the capabilities of the de novo heme proteins to bind diatomic ligands, we measured the affinity for CO, the kinetics of CO binding and release, and the resonance Raman spectra of the CO complexes for eight de novo heme proteins from two combinatorial libraries. The CO binding affinities for all eight proteins were similar to that of myoglobin, with dissociation constants (K(d)) in the low nanomolar range. The CO association kinetics (k(on)) revealed that the heme environment in all eight of the de novo proteins is partially buried, and the resonance Raman studies indicated that the local environment around the bound CO is devoid of hydrogen-bonding groups. Overall, the CO binding properties of the de novo heme proteins span a narrow range of values near the center of the range observed for diverse families of natural heme proteins. The measured properties of the de novo heme proteins can be considered as a "default" range for CO binding in alpha-helical proteins that have neither been designed to bind heme or CO, nor subjected to genetic selections for heme or CO binding.

Self-assembled monolayers from a designed combinatorial library of de novo beta-sheet proteins.

A variety of naturally occurring biomaterials owe their unusual structural and mechanical properties to layers of beta-sheet proteins laminated between layers of inorganic mineral. To explore the possibility of fabricating novel two-dimensional protein layers, we studied the self-assembly properties of de novo proteins from a designed combinatorial library. Each protein in the library has a distinct 63 amino acid sequence, yet they all share an identical binary pattern of polar and nonpolar residues, which was designed to favor the formation of six-stranded amphiphilic beta-sheets. Characterization of proteins isolated from the library demonstrates that (i) they self assemble into monolayers at an air/water interface; (ii) the monolayers are dominated by beta-sheet secondary structure, as shown by both circular dichroism and infrared spectroscopies; and (iii) the measured areas (500- 600 A(2)) of individual protein molecules in the monolayers match those expected for proteins folded into amphiphilic beta-sheets. The finding that similar structures are formed by distinctly different protein sequences suggests that assembly into beta-sheet monolayers can be encoded by binary patterning of polar and nonpolar amino acids. Moreover, because the designed binary pattern is compatible with a wide variety of different sequences, it may be possible to fabricate beta-sheet monolayers by using combinations of side chains that are explicitly designed to favor particular applications of novel biomaterials.

Evidence that the reactivity of the martian soil is due to superoxide ions.

The Viking Landers were unable to detect evidence of life on Mars but, instead, found a chemically reactive soil capable of decomposing organic molecules. This reactivity was attributed to the presence of one or more as-yet-unidentified inorganic superoxides or peroxides in the martian soil. Using electron paramagnetic resonance spectroscopy, we show that superoxide radical ions (O2-) form directly on Mars-analog mineral surfaces exposed to ultraviolet radiation under a simulated martian atmosphere. These oxygen radicals can explain the reactive nature of the soil and the apparent absence of organic material at the martian surface.

Cooperative thermal denaturation of proteins designed by binary patterning of polar and nonpolar amino acids.

We previously reported a combinatorial strategy for designing alpha-helical proteins by assigning only the binary patterning of polar or nonpolar residues [Kamtekar, S., Schiffer, J. M., Xiong, H. Y., Babik, J. M., and Hecht, M. H. (1993) Science 262, 1680-1685]. Here we describe the finding that approximately half of the proteins in the original collection display some level of cooperativity in their thermal denaturation profiles. Many are monomeric in solution, demonstrating that the observed cooperativity is not merely a consequence of oligomerization. These findings demonstrate that although the combinatorial nature of the design strategy precludes explicit design of side-chain packing, binary patterning incorporates sufficient sequence information to generate de novo proteins with cooperatively folded structures. As binary partitioning of polar and nonpolar amino acids is an intrinsic part of the genetic code, these findings may bear on the early evolution of native proteins.

Nature disfavors sequences of alternating polar and non-polar amino acids: implications for amyloidogenesis.

Recent experiments with combinatorial libraries of de novo proteins have demonstrated that sequences designed to contain polar and non-polar amino acid residues arranged in an alternating pattern form fibrillar structures resembling beta-amyloid. This finding prompted us to probe the distribution of alternating patterns in the sequences of natural proteins. Analysis of a database of 250,514 protein sequences (79,708,024 residues) for all possible binary patterns of polar and non-polar amino acid residues revealed that alternating patterns occur significantly less often than other patterns with similar compositions. The under-representation of alternating binary patterns in natural protein sequences, coupled with the observation that such patterns promote amyloid-like structures in de novo proteins, suggests that sequences of alternating polar and non-polar amino acids are inherently amyloidogenic and consequently have been disfavored by evolutionary selection.

De novo amyloid proteins from designed combinatorial libraries.

Amyloid deposits are associated with several neurodegenerative diseases, including Alzheimer's disease and the prion diseases. The amyloid fibrils isolated from these different diseases share similar structural features. However, the protein sequences that assemble into these fibrils differ substantially from one disease to another. To probe the relationship between amino acid sequence and the propensity to form amyloid, we studied a combinatorial library of sequences designed de novo. All sequences in the library were designed to share an identical pattern of alternating polar and nonpolar residues, but the precise identities of these side chains were not constrained and were varied combinatorially. The resulting proteins self-assemble into large oligomers visible by electron microscopy as amyloid-like fibrils. Like natural amyloid, the de novo fibrils are composed of beta-sheet secondary structure and bind the diagnostic dye, Congo red. Thus, binary patterning of polar and nonpolar residues arranged in alternating periodicity can direct protein sequences to form fibrils resembling amyloid. The model amyloid fibrils assemble and disassemble reversibly, providing a tractable system for both basic studies into the mechanisms of fibril assembly and the development of molecular therapies that interfere with this assembly.

H-bonding maintains the active site of type 1 copper proteins: site-directed mutagenesis of Asn38 in poplar plastocyanin.

Type I Cu proteins maintain a trigonal N2S coordination group (with weak axial ligation) in both oxidation states of the Cu2+/+ ion, thereby reducing the reorganization energy for electron transfer. Requirements for maintaining this coordination group were investigated in poplar plastocyanin (Pcy) by mutation of a conserved element of the type 1 architecture, an asparagine residue (Asn38) adjacent to one of the ligating histidines. The side chain of this asparagine forms an active site clasp via two H-bonds with the residue (Ser85) adjacent to the ligating cysteine (Cys84). In addition, the main chain NH of Asn38 donates an H-bond to the thiolate ligand. We have investigated the importance of these interactions by mutating Asn38 to Gln, Thr, and Leu. The mutant proteins are capable of folding and binding Cu2+, but the blue color fades; the rate of fading increases in the order Gln < Thr < Leu. The color is not restored by ferricyanide, showing that the protein is modified irreversibly, probably by oxidation of Cys84. The more stable mutants N38Q and N38T were characterized spectroscopically. The wild-type properties are slightly perturbed for N38Q, but N38T shows remarkable similarity to another type 1 Cu protein, azurin (Azu) from Pseudomonas aeruginosa. The Cu-S(Cys) bond is longer in Azu than in Pcy, and the NH H-bond to the ligating S atom is shorter. Molecular modeling suggests a similar effect for N38T because the threonine residue shifts toward Ser85 in order to avoid a steric clash and to optimize H-bonding. These results demonstrate that H-bonding adjacent to the type 1 site stabilizes an architecture which both modulates the electronic properties of the Cu, and suppresses side reactions of the cysteine ligand.

Electrochemistry on Mars.

NASA: Researchers describe research design and equipment for electrochemical analysis of Martian soil. The Wet Chemistry Laboratory (WCL) was designed for the Mars Surveyor 2001 Lander by the Mars Environmental Compatibility Assessment (MECA) team. The WCL consists of four beakers, each containing an integral array of electrochemical sensors. In addition to describing WCL design, the article discusses WCL sensor selection and design, analytical goals of the MECA experiments, expected composition of the Martian regolith, survival and performance testing, and reference electrode selection. The description of the research design describes experiment initiation, warm-up, leaching solution, calibration, sampling, analysis, reagent addition, and data analysis.^ieng

Detecting native-like properties in combinatorial libraries of de novo proteins.

BACKGROUND: Combinatorial methods based on binary patterning of polar and nonpolar residues have been used to generate large libraries of de novo alpha-helical proteins. Within such libraries, the ability to find structures that resemble natural proteins requires a rapid method to sort through large collections of proteins and detect those possessing 'native-like' features. The current paper presents such a method and applies it to an initial collection of de novo proteins. RESULTS: We present a method to identify proteins with native-like properties from libraries of de novo sequences expressed in vivo. A novel 'rapid prep' freeze/thaw procedure was used to prepare samples; chromatographic purification was not required. The semi-crude samples were analyzed for native-like features by one-dimensional 1H NMR spectroscopy. Using this method, we demonstrate that native-like features can readily be observed for several proteins among a collection of sequences designed by binary patterning of polar and nonpolar amino acids. CONCLUSIONS: Native-like properties can be detected using a method that requires neither isotopic enrichment nor chromatographic purification. The method is inexpensive, rapid, and suitable for parallel processing. It can therefore be employed to screen for native-like properties among large collections of de novo sequences. Using this method, we demonstrate that although the binary code strategy does not explicitly design tertiary packing, it can nonetheless generate proteins that possess native-like properties. The use of combinatorial methods to produce large collections of proteins coupled with the availability of a rapid assay for detecting native-like properties will facilitate the design and isolation of novel proteins with desirable properties.

De novo heme proteins from designed combinatorial libraries.

We previously reported the design of a library of de novo amino acid sequences targeted to fold into four-helix bundles. The design of these sequences was based on a "binary code" strategy, in which the patterning of polar and nonpolar amino acids is specified explicitly, but the exact identities of the side chains is varied extensively (Kamtekar S, Schiffer JM, Xiong H, Babik JM, Hecht MH, 1993, Science 262:1680-1685). Because of this variability, the resulting collection of amino acid sequences may include de novo proteins capable of binding biologically important cofactors. To probe for such binding, the de novo sequences were screened for their ability to bind the heme cofactor. Among an initial collection of 30 binary code sequences, 15 are shown to bind heme and form bright red complexes. Characterization of several of these de novo heme proteins demonstrated that their absorption spectra and resonance Raman spectra resemble those of natural cytochromes. Because the design of these sequences is based on global features of polar/ nonpolar patterning, the finding that half of them bind heme highlights the power of the binary code strategy, and demonstrates that isolating de novo heme proteins does not require explicit design of the cofactor binding site. Because bound heme plays a key role in the functions of many natural proteins, these results suggest that binary code sequences may serve as initial prototypes for the development of large collections of functionally active de novo proteins.

Sequence replacements in the central beta-turn of plastocyanin.

The role of beta-turns in dictating the structure of a beta-barrel protein is assessed by probing the tolerance of the central beta-turn of poplar plastocyanin to substitution by arbitrary sequences. Native plastocyanin binds copper and is colored bright blue. However, when the wild-type Pro47-Ser48-Gly49-Val50 turn sequence is replaced by arbitrary tetrapeptides, the vast majority (92/98 = 94%) of mutant proteins cannot fold into the native blue structure. Characterization of the colorless mutant proteins demonstrates that the majority of substitutions in this type II beta-turn disrupt the native structure severely. Gross structural changes are indicated by major differences in the CD spectra of the mutants relative to the wild-type protein, and by the much larger apparent size of mutant proteins in gel filtration experiments. These mutant proteins do not bind copper. Furthermore, Cys84 forms a disulfide bond readily in the colorless mutant proteins, indicating that it has moved away from the buried position it occupies in the native copper binding site and has become exposed. These results indicate that the central beta-turn in plastocyanin is not merely a default structure arising in response to the surrounding context; rather, sequence information in this turn plays an active role in dictating the location of a chain reversal in the beta-barrel structure. These findings are discussed in terms of their implications for the folding of natural proteins, as well as the design of de novo proteins.

Binary patterning of polar and nonpolar amino acids in the sequences and structures of native proteins.

Protein sequences can be represented as binary patterns of polar ([symbol: see text]) and nonpolar ([symbol: see text]) amino acids. These binary sequence patterns are categorized into two classes: Class A patterns match the structural repeat of an idealized amphiphilic alpha-helix (3.6 residues per turn), and class B patterns match the structural repeat of an idealized amphiphilic beta-strand (2 residues per turn). The difference between these two classes of sequence patterns has led to a strategy for de novo protein design based on binary patterning of polar and nonpolar amino acids. Here we ask whether similar binary patterning is incorporated in the sequences and structures of natural proteins. Analysis of the Protein Data Bank demonstrates the following. (1) Class A sequence patterns occur considerably more frequently in the sequences of natural proteins that would be expected at random, but class B patterns occur less often than expected. (2) Each pattern is found predominantly in the secondary structure expected from the binary strategy for protein design. Thus, class A patterns are found more frequently in alpha-helices than in beta-strands, and class B patterns are found more frequently in beta-strands than in alpha-helices. (3) Among the alpha-helices of natural proteins, the most commonly used binary patterns are indeed the class A patterns. (4) Among all beta-strands in the database, the most commonly used binary patterns are not the expected class B patterns. (5) However, for solvent-exposed beta-strands, the correlation is striking: All beta-strands in the database that contain the class B patterns are exposed to solvent.(ABSTRACT TRUNCATED AT 250 WORDS)