Search NASA⌕ Search

SEARCH · Search NASA

Results for “crystal structure refinement”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 records
All sourcesNASA NTRSDOE OSTI
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 NTRS1991

Center for Macromolecular Crystallography, University of Alabama in Birmingham

Porcine pancreatic elastase (PPE) crystals grown under microgravity conditions on mission STS-26 of the Space Shuttle Discovery were shown to diffract to considerably higher resolution than the best PPE crystals grown by us on the ground. We have now independently refined both the microgravity and ground-based data. Preliminary results of these refinements are summarized. These results show nearly a doubling of experimental diffraction data for this structure, exceeding 1.3 A resolution. Improved phase information derived from the refined structure of PPE based on this microgravity data has allowed us to interpret previously-uninterpretable electron density obtained from ground-based crystals of a complex of PPE with a chemically-reactive inhibitor. Intermediate stages in the enzyme-inhibitor reaction mechanism in the crystal can now be directly observed. Further refinement of PPE structures is in progress.

Navia, Manuel A.↗
NASA NTRS1996

Synthesis, Structure, and Characterization of Cu4S10(4-methylpyridine)4

The title compound, Cu4S10(4-methylpyridine)(sub 4) (dot) 4-methylpyridine was prepared by three different reactions: the oxidation of copper powder by sulfur and the reaction of copper (I) sulfide (or CuBr (dot) SMe2) with excess sulfur, both in the coordinating solvent, 4-methylpyridine. Red crystals of the compound obtained by layering with hexanes were subjected to single crystal X-ray diffraction. The structure was refined to R = 0.026 and R(sub w) = 0.036 in a space group P1bar (No. 2), with Z = 2, a = 13.983 (2) A, b = 15.384 (2) A, c = 9.660 (1) A, alpha = 93.87 (1)deg., beta = 93.38 (1)deg., gamma = 99.78 (1)deg., V = 2037.9 (9) A(exp 3). The compound has approximate S(sub 4) symmetry and consists of two pentasulfide chains linking four Cu(I) ions, each with a corrdinating 2-methylpyridine. The infrared spectrum was dominated by absorption due to coordinated 4-methylpyridine with several low-energy peaks attributable to S-S stretches, which were also observed by Raman spectroscopy. A featureless electronic absorption spectrum yielded a single peak in the near ultraviolet upon computer enhancement (lambda = 334 nm, epsilon = 10,000), most likely an intraligand transition. Cyclic voltammetry indicates that the polysulfide complex undergoes irrversible oxidation and reduction at +0.04 and -0.34 V vs. SCE, respectively, at 298 K in 4-methylpyridine when swept at 20 mV/sec. The electrochemical behavior was unvaried even at sweep rates as high as 100 V/sec.

Hepp, Aloysius F.↗
NASA NTRS2003

Crystal structures of pinoresinol-lariciresinol and phenylcoumaran benzylic ether reductases and their relationship to isoflavone reductases

Despite the importance of plant lignans and isoflavonoids in human health protection (e.g. for both treatment and prevention of onset of various cancers) as well as in plant biology (e.g. in defense functions and in heartwood development), systematic studies on the enzymes involved in their biosynthesis have only recently begun. In this investigation, three NADPH-dependent aromatic alcohol reductases were comprehensively studied, namely pinoresinol-lariciresinol reductase (PLR), phenylcoumaran benzylic ether reductase (PCBER), and isoflavone reductase (IFR), which are involved in central steps to the various important bioactive lignans and isoflavonoids. Of particular interest was in determining how differing regio- and enantiospecificities are achieved with the different enzymes, despite each apparently going through similar enone intermediates. Initially, the three-dimensional x-ray crystal structures of both PLR_Tp1 and PCBER_Pt1 were solved and refined to 2.5 and 2.2 A resolutions, respectively. Not only do they share high gene sequence similarity, but their structures are similar, having a continuous alpha/beta NADPH-binding domain and a smaller substrate-binding domain. IFR (whose crystal structure is not yet obtained) was also compared (modeled) with PLR and PCBER and was deduced to have the same overall basic structure. The basis for the distinct enantio-specific and regio-specific reactions of PCBER, PLR, and IFR, as well as the reaction mechanism and participating residues involved (as identified by site-directed mutagenesis), are discussed.

NASA Discipline Plant Biology↗
NASA NTRS1993

Zaoyang chondrite cooling history from pyroxene Fe(2+)-Mg intracrystalline ordering and exolutions

The Zaoyang ordinary chondrite fell as a single 14.15-kg mass in Hubey province (China) in October 1984 and was classified as a non-brecciated H5 chondrite, shock facies b. Cooling rate in pyroxenes can be calculated down to about 1000 C by using fine textures and at still lower temperatures (700 to 200 C) by intracrystalline ordering processes. The crystal chemistry of clinopyroxene and orthopyroxene from the matrix of the H5 Zaoyang chondrite has been investigated by X-ray structure refinement and detailed microprobe analysis. By comparison with terrestrial pyroxenes cell and polyhedral volumes in clino- and orthopyroxenes show a low crystallization pressure. Fe(2+) and Mg are rather disordered in M1 and M2 sites of clino- and orthopyroxenes; the closure temperatures of the exchange reaction are 600 and 512 C respectively, which is consistent with a quite fast cooling rate, estimated of the order of one degree per day. The closure temperature for the intercrystalline Ca-Mg exchange reaction for clino- and orthopyroxene showing clinopyroxene lamellae about 10 microns thick. Kinetic evaluations based on the thickness of exolved lamellae give a cooling rate of not more than a few degrees per 10(exp 4) years. The different cooling rates obtained from Fe(2+)-Mg intracrystalline partitioning and exolution lamellae suggest an initial episode of slow cooling at 900 C, followed by faster cooling at temperatures of 600-500 C at low pressure conditions. The most probable scenario of the meteorite history seems that the exolved orthopyroxene entered the parental chondrite body after exolution had taken place at high temperature. Subsequent fast cooling occurred at low temperature after the formation of the body.

Molin, G. M.↗
NASA NTRS1985

Structural basis for stabilization of Z-DNA by cobalt hexaammine and magnesium cations

In the equilibrium between B-DNA and Z-DNA in poly(dC-dG), the [Co(NH3)6]3+ ion stabilizes the Z form 4 orders of magnitude more effectively than the Mg2+ ion. The structural basis of this difference is revealed in Z-DNA crystal structures of d(CpGpCpGpCpG) stabilized by either Na+/Mg2+ or Na+/Mg2+ plus [Co(NH3)6]3+. The crystals diffract X-rays to high resolution, and the structures were refined at 1.25 A. The [Co(NH3)6]3+ ion forms five hydrogen bonds onto the surface of Z-DNA, bonding to a guanine O6 and N7 as well as to a phosphate group in the ZII conformation. The Mg2+ ion binds through its hydration shell with up to three hydrogen bonds to guanine N7 and O6. Higher charge, specific fitting of more hydrogen bonds, and a more stable complex all contribute to the great effectiveness of [Co(NH3)6]3+ in stabilizing Z-DNA.

NASA Discipline Exobiology↗
NASA NTRS2001

First Protein Crystallization Experiments on The International Space Station: Sweet Success in Space With Thaumatin

We determined the room temperature 1.2 A structure of thaumatin using a crystal grown in the first protein crystallization experiment conducted aboard the International Space Station (ISS). The crystals were grown in the Enhanced Gaseous Nitrogen Dewar (EGN) developed by Alexander McPherson and co-workers. EGN transports frozen solutions contained in tygon tubing in a liquid nitrogen Dewar to ISS where the tubes then thaw. Batch, free interface diffusion (FID), or vapor diffusion crystallization occurs after thawing. EGN was flown to the ISS on STS-106 on September 8, 2000. This was a "risk mitigation" flight that tested EGN performance and the process of conducting experiments on ISS. We focused on how to map a hanging drop crystallization recipe to the EGN FID method. Thaumatin was chosen as the test system. Three series of crystallization recipes were set-up. Each series tested different volume ratios of protein-rich solution to precipitant-rich solution. The series differed from each other by fixing either the protein concentration or the amount of protein in the solutions. Upon return of the samples to Earth on October 24 by STS-92, bubbles that spanned the diameter of the tubing were observed in all tubes. Such bubbles interrupt liquid-liquid diffusion and force vapor diffusion equilibration to occur instead. Nonetheless, crystals grew in 9 of 30 tubes. Many large crystals were grown, the largest being 2.0 x 1.1 x 1.0 cubic mm. The largest crystal was used to collect data at room temperature on beamline 7-1 of the Stanford Synchrotron Radiation Source to a maximum resolution of 1.2 A. The structure was refined anisotropically using SHELX with a data to parameter ratio of 4.5 to give an R(sub factor) of 15.8% (R(sub free) = 18.2%) for ail reflections without generated hydrogens. This refinement is proceeding. Comparisons of this 1.2 A microgravity structure to previous reports of the thaumatin structure at 1.75 A and to ground control crystals will be presented.

Kundrot, Craig E.↗
NASA NTRS2000

R6 Hexameric Insulin Complexed with m-Cresol or Rescorcinol

The structures of three R6 human insulin hexamers have been determined. Crystals of monoclinic m-cresol/insulin, monoclinic resorcinol/insulin, and rhombohedral m-cresol/insulin crystals diffracted to 1.9, 1.9 and 1,78 Angstroms, respectively, and have been refined to residuals of 0.195, 0.179, and 0.200, respectively. In all three structures, a phenolic derivative is found to occupy the phenolic binding site where it forms hydrogen bonds to the carbonyl oxygen of A6 Cys and the nitrogen of A11 Cys. Two additional phenolic derivative binding sites were identified within or between hexamers. The structures of all three hexamers are nearly identical although a large displacement of the N-terminus of one B-chain in both monoclinic structures results from coordination to a sodium ion which is located between symmetry related hexamers. Other minor differences in structure are a consequence of differences in packing in the monoclinic cell as compared to the rhombohedral cell. Based upon the differences in conformation of the B13 Glu side chains in T6, T3R3, and R6 hexamers, the deprotonation of these side chains appears to be associated with the T (right arrow) R conformational transition.

Smith, G. David↗
NASA NTRS2005

Neutron Diffraction Study Oxygen Dissolution Alpha(sub 2)-Ti3Al

Rietveld refinements of neutron powder diffraction data on alpha(sub 2)-Ti3Al have been performed to determine the crystal structure as a function of interstitial oxygen (O) concentration for three alloys with a Ti/Al ratio of approximately equal to 2.34 and O concentrations of 0.25%, 3.99% and 7.71%. The structures of the allows are hexagonal in space group P6(sub 3)/mmc where Ti and Al atoms populate unique sites with excess Al at the Ti site and O atoms occupy octahedral interstitial sites surrounded by six Ti sites. The length of the c-axis was found to increase linearly as the O occupancy of the interstitial sites increased; this lattice lengthening effect was much less pronounced along the alpha axis. Correspondingly, the increases in the lengths of Ti-Al and Ti-Ti bonds with a major component of their direction parallel to the c-axis were roughly an order of magnitude greater than the increases in the lengths of Ti-al and Ti-Ti bonds more closely aligned with the alpha-axis. Densities calculated form the lattice parameters and occupancy factors fall in the range (4.118 plus or minus 0.004) grams per cubic centimeter to (4.194 plus or minus 0.004) grams per cubic centimeter, and exhibit a nearly linear increase with oxygen concentration. Measured densities of (4.113 plus or minus 0.001) grams per cubic centimeter, (4.146 plus or minus 0.009) grams per cubic centimeter, and (4.191 plus or minus 0.002) grams per cubic centimeter for these alloys agree with the results of the refinements.

Jones, Camille Y.↗
NASA NTRS2007

Investigation of Synthetic Mg(1.3)V(1.7)O4 Spinel with MgO Inclusions: Case Study of a Spinel with an Apparently occupied Interstitial Site

A magnesium vanadate spinel crystal, ideally MgV2O4, synthesized at 1 bar, 1200 C and equilibrated under FMQ + 1.3 log f(sub o2) condition, was investigated using single-crystal X-ray diffraction, electron microprobe, and electron backscatter (EBSD). The initial X-ray structure refinements gave tetrahedral and octahedral site occupancies, along with the presence of 0.053 apfu Mg at an interstitial octahedral site . Back-scattered electron (BSE) images and electron microprobe analyses revealed the existence of an Mg-rich phase in the spinel matrix, which was too small (less than or equal to 3microns) for an accurate chemical determination. The EBSD analysis combined with X-ray energy dispersive spectroscop[y (XEDS) suggested that the Mg-rich inclusions are periclase oriented coherently with the spinel matrix. The final structure refinements were optimized by subtracting the X-ray intensity contributions (approx. 9%) of periclase reflections, which eliminated the interstitial Mg. This study provides insight into possible origins of refined interstitial cations reported in the the literature for spinel, and points to the difficulty of using only X-ray diffraction data to distinguish a spinel with interstitial cations from one with coherently oriented MgO inclusions.

Uchida, Hinako↗
NASA NTRS1999

Fabrication of Pop-up Detector Arrays on Si Wafers

High sensitivity is a basic requirement for a new generation of thermal detectors. To meet the requirement, close-packed, two-dimensional silicon detector arrays have been developed in NASA Goddard Space Flight Center. The goal of the task is to fabricate detector arrays configured with thermal detectors such as infrared bolometers and x-ray calorimeters to use in space fliGht missions. This paper focuses on the fabrication and the mechanical testing of detector arrays in a 0.2 mm pixel size, the smallest pop-up detectors being developed so far. These array structures, nicknamed "PUDS" for "Pop-Up Detectors", are fabricated on I pm thick, single-crystal, silicon membranes. Their designs have been refined so we can utilize the flexibility of thin silicon films by actually folding the silicon membranes to 90 degrees in order to obtain close-packed two-dimensional arrays. The PUD elements consist of a detector platform and two legs for mechanical support while also serving as electrical and thermal paths. Torsion bars and cantilevers connecting the detector platform to the legs provide additional flexures for strain relief. Using micro-electromechanical structure (MEMS) fabrication techniques, including photolithography, anisotropic chemical etching, reactive-ion etching, and laser dicing, we have fabricated PLTD detector arrays of fourteen designs with a variation of four parameters including cantilever length, torsion bar length and width, and leg length. Folding tests were conducted to test mechanical stress distribution for the array structures. We obtained folding yields and selected optimum design parameters to reach minimal stress levels. Computer simulation was also employed to verify mechanical behaviors of PUDs in the folding process. In addition, scanning electron microscopy was utilized to examine the flatness of detectors and the alignment of detector pixels in arrays. The fabrication of thermistors and heaters on the pop-up detectors is under way, preparing us for the next step of the experiment, the thermal test.

Li, Mary J.↗
NASA NTRS1993

The Crystal and Molecular Structure of an Asymmetric Diacetylene Monomer, 6-(2-methyl-4-nitroanilino)-2,4-hexadiyne-1-ol

The crystal and molecular structure of an asymmetric diacetylene monomer has been determined from x-ray diffraction data. The crystals, obtained from an acetone/pentane solution, are orthorhombic, Fdd2 with Z = 16 in a unit cell having dimensions of a = 42.815(6) A, b = 22.224(5) A, c = 4.996(l) A. The structure was solved by direct methods and refined by least- squares techniques to an R(sub F) of 6.4% for 988 reflections and 171 variables. The diacetylene chains are disposed in the unit cell in a complex manner in order to satisfy the hydrogen- bonding, crystal packing, and symmetry requirements of the system. The solid state polymerization mechanism is discussed with respect to the geometric disposition of the diacetylene chains. These chains are far apart and incorrectly oriented with respect to each other to permit polymerization in the crystal by means of 1,4-addition, consistent with the Baughman mechanistic model.

Vlasse, Marcus↗
NASA NTRS2003

Crystal Structure of the Catalytic Domain of a Serine Threonine Protein Phosphatase

Reversible phosphorylation of serine and threonine residues is a well-recognized mechanism in eukaryotic cells for the regulation of cell-cycle progression, cell growth and metabolism. Human serine/threonine phosphatases can be placed into two major families, PPP and PPM. To date the structure on one PPP family member (PPl) has been determined. Here we present the structure of a 323-residue catalytic domain of a second phosphatase belonging to the PPP family of enzyme. catalytic domain of the enzyme has been determined to 1.60Angstrom resolution and refined to R=17.5 and Rfree = 20.8%. The catalytic domain possesses a unique fold consisting of a largely monolithic structure, divisible into closely-associated helical and sheet regions. The catalytic site contains two manganese ions that are involved in substrate binding and catalysis. The enzyme crystallizes as a dimer that completely buries catalytic surfaces of both monomers, Also, the structure shows evidence of some flexibility around the active site cleft that may be related to substrate specificity of this enzyme.

Swinglel, Mark↗
NASA NTRS1997

The Structure and Function of Non-Collagenous Bone Proteins

The research done under the cooperative research agreement for the project titled 'The structure and function of non-collagenous bone proteins' represented the first phase of an ongoing program to define the structural and functional relationships of the principal noncollagenous proteins in bone. An ultimate goal of this research is to enable design and execution of useful pharmacological compounds that will have a beneficial effect in treatment of osteoporosis, both land-based and induced by long-duration space travel. The goals of the now complete first phase were as follows: 1. Establish and/or develop powerful recombinant protein expression systems; 2. Develop and refine isolation and purification of recombinant proteins; 3. Express wild-type non-collagenous bone proteins; 4. Express site-specific mutant proteins and domains of wild-type proteins to enhance likelihood of crystal formation for subsequent solution of structure.

Hook, Magnus↗
NASA NTRS1987

Multistep modeling of protein structure: application towards refinement of tyr-tRNA synthetase

The scope of multistep modeling (MSM) is expanding by adding a least-squares minimization step in the procedure to fit backbone reconstruction consistent with a set of C-alpha coordinates. The analytical solution of Phi and Psi angles, that fits a C-alpha x-ray coordinate is used for tyr-tRNA synthetase. Phi and Psi angles for the region where the above mentioned method fails, are obtained by minimizing the difference in C-alpha distances between the computed model and the crystal structure in a least-squares sense. We present a stepwise application of this part of MSM to the determination of the complete backbone geometry of the 321 N terminal residues of tyrosine tRNA synthetase to a root mean square deviation of 0.47 angstroms from the crystallographic C-alpha coordinates.

NASA Discipline Exobiology↗
NASA NTRS2004

Intricate Crystal Structure of Dihydrolipoamide Dehydrogenase (E3) with its Binding Protein: Multiple Copies, Dynamic and Static Disorders

Human E3 and binding protein E3BP are two components of the pyruvate dehydrogenase complex. Crystallization of E3 with 221-amino acid fragment of E3BP (E3BPdd) led to crystals that diffracted to a resolution of 2.6 Angstroms. Structure determination involved molecular replacement using a dimer of E3 homolog as a search model and de novo building of the E3BPdd peptide. Solution was achieved by inclusion of one E3 dimer at a time, followed by refinement until five E3 dimers were located. This complete content of E3 provided electron density maps suitable for tracing nine peptide chains of E3BPdd, eight of them being identified with partial occupancies. Final content of the asymmetric unit consists of five E3 dimers, each binding one E3BPdd molecule. In four of these molecular complexes, E3BPdd is in static disorder resulting in E3BPdd binding to either one or the other monomer of the E3 dimer. However, E3BPdd of the fifth E3 dimer forms specific contacts that lock it at one monomer. In addition to this static disorder, E3BPdd reveals high mobility in the limited space of the crystal lattice. Support from NIH and NASA.

Makal, A.↗
NASA NTRS1994

A full-coordinate model of the polymerase domain of HIV-1 reverse transcriptase and its interaction with a nucleic acid substrate

We present a full-coordinate model of residues 1-319 of the polymerase domain of HIV-I reverse transcriptase. This model was constructed from the x-ray crystallographic structure of Jacobo-Molina et al. (Jacobo-Molina et al., P.N.A.S. USA 90, 6320-6324 (1993)) which is currently available to the degree of C-coordinates. The backbone and side-chain atoms were constructed using the MAXSPROUT suite of programs (L. Holm and C. Sander, J. Mol. Biol. 218, 183-194 (1991)) and refined through molecular modeling. A seven base pair A-form dsDNA was positioned in the nucleic acid binding cleft to represent the template-primer complex. The orientation of the template-primer complex in the nucleic acid binding cleft was guided by the positions of phosphorus atoms in the crystal structure.

Non-NASA Center↗
NASA NTRS1979

Layered synthetic microstructures - Properties and applications in X-ray astronomy

Refinements in vacuum deposition technology have made it possible to produce structures in which two materials are arranged in alternating layers of uniform thickness and as thin as 5 A. Such structures act as Bragg diffractors or 'artificial crystals' for X-rays, as well as they may be regarded as multilayer interference coatings. A dynamical theory is used to show how the properties of layered synthetic microstructures are dependent on the layer materials and thicknesses and how these properties can be tailored to specific applications. Laboratory results at various X-ray wavelengths are presented. In particular, specific X-ray astronomy applications in spectroscopy, imaging, polarimetry and laboratory calibration are discussed.

Underwood, J. H.↗