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  • Lunar and Planetary Science and Exploration  (18)
  • *Models, Molecular  (6)
  • 2010-2014  (24)
  • 1
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    Structural biology: The gatekeepers revealed (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-06-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Monya -- England -- Nature. 2010 Jun 10;465(7299):823-6. doi: 10.1038/465823a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20535212" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Computational Biology ; Computer Simulation ; Cryoelectron Microscopy ; Crystallization ; Crystallography, X-Ray ; Drug Design ; Humans ; Lipid Bilayers/chemistry/metabolism ; Magnetic Resonance Spectroscopy ; Mass Spectrometry ; Membrane Proteins/*chemistry/isolation & purification/*metabolism ; Membranes, Artificial ; *Models, Molecular ; Movement ; Protein Conformation ; Receptors, G-Protein-Coupled/chemistry/isolation & purification/metabolism ; Solubility ; Structure-Activity Relationship
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Computational design of proteins targeting the conserved stem region of influenza hemagglutinin (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-05-14
    Description: We describe a general computational method for designing proteins that bind a surface patch of interest on a target macromolecule. Favorable interactions between disembodied amino acid residues and the target surface are identified and used to anchor de novo designed interfaces. The method was used to design proteins that bind a conserved surface patch on the stem of the influenza hemagglutinin (HA) from the 1918 H1N1 pandemic virus. After affinity maturation, two of the designed proteins, HB36 and HB80, bind H1 and H5 HAs with low nanomolar affinity. Further, HB80 inhibits the HA fusogenic conformational changes induced at low pH. The crystal structure of HB36 in complex with 1918/H1 HA revealed that the actual binding interface is nearly identical to that in the computational design model. Such designed binding proteins may be useful for both diagnostics and therapeutics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3164876/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3164876/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fleishman, Sarel J -- Whitehead, Timothy A -- Ekiert, Damian C -- Dreyfus, Cyrille -- Corn, Jacob E -- Strauch, Eva-Maria -- Wilson, Ian A -- Baker, David -- AI057141/AI/NIAID NIH HHS/ -- AI058113/AI/NIAID NIH HHS/ -- GM080209/GM/NIGMS NIH HHS/ -- P01 AI058113/AI/NIAID NIH HHS/ -- P01 AI058113-07/AI/NIAID NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 May 13;332(6031):816-21. doi: 10.1126/science.1202617.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21566186" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Sequence ; Binding Sites ; Computational Biology ; *Computer Simulation ; Hemagglutinin Glycoproteins, Influenza Virus/chemistry/*metabolism ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; *Models, Molecular ; Molecular Sequence Data ; Mutation ; Peptide Library ; Protein Binding ; Protein Conformation ; *Protein Engineering ; Protein Interaction Domains and Motifs ; Protein Structure, Secondary ; Proteins/*chemistry/genetics/*metabolism ; Software
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    Solution structure of a minor and transiently formed state of a T4 lysozyme mutant (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-08-23
    Description: Proteins are inherently plastic molecules, whose function often critically depends on excursions between different molecular conformations (conformers). However, a rigorous understanding of the relation between a protein's structure, dynamics and function remains elusive. This is because many of the conformers on its energy landscape are only transiently formed and marginally populated (less than a few per cent of the total number of molecules), so that they cannot be individually characterized by most biophysical tools. Here we study a lysozyme mutant from phage T4 that binds hydrophobic molecules and populates an excited state transiently (about 1 ms) to about 3% at 25 degrees C (ref. 5). We show that such binding occurs only via the ground state, and present the atomic-level model of the 'invisible', excited state obtained using a combined strategy of relaxation-dispersion NMR (ref. 6) and CS-Rosetta model building that rationalizes this observation. The model was tested using structure-based design calculations identifying point mutants predicted to stabilize the excited state relative to the ground state. In this way a pair of mutations were introduced, inverting the relative populations of the ground and excited states and altering function. Our results suggest a mechanism for the evolution of a protein's function by changing the delicate balance between the states on its energy landscape. More generally, they show that our approach can generate and validate models of excited protein states.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3706084/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3706084/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bouvignies, Guillaume -- Vallurupalli, Pramodh -- Hansen, D Flemming -- Correia, Bruno E -- Lange, Oliver -- Bah, Alaji -- Vernon, Robert M -- Dahlquist, Frederick W -- Baker, David -- Kay, Lewis E -- R01 GM092802/GM/NIGMS NIH HHS/ -- Canadian Institutes of Health Research/Canada -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 Aug 21;477(7362):111-4. doi: 10.1038/nature10349.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Genetics, The University of Toronto, Toronto, Ontario M5S 1A8, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21857680" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage T4/*enzymology/*genetics ; Evolution, Molecular ; Hydrophobic and Hydrophilic Interactions ; Ligands ; *Models, Molecular ; Muramidase/*chemistry/*genetics ; *Mutation ; Protein Binding ; Temperature
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Improved molecular replacement by density- and energy-guided protein structure optimization (2011)
    Nature Publishing Group (NPG)
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    Publication Date: 2011-05-03
    Description: Molecular replacement procedures, which search for placements of a starting model within the crystallographic unit cell that best account for the measured diffraction amplitudes, followed by automatic chain tracing methods, have allowed the rapid solution of large numbers of protein crystal structures. Despite extensive work, molecular replacement or the subsequent rebuilding usually fail with more divergent starting models based on remote homologues with less than 30% sequence identity. Here we show that this limitation can be substantially reduced by combining algorithms for protein structure modelling with those developed for crystallographic structure determination. An approach integrating Rosetta structure modelling with Autobuild chain tracing yielded high-resolution structures for 8 of 13 X-ray diffraction data sets that could not be solved in the laboratories of expert crystallographers and that remained unsolved after application of an extensive array of alternative approaches. We estimate that the new method should allow rapid structure determination without experimental phase information for over half the cases where current methods fail, given diffraction data sets of better than 3.2 A resolution, four or fewer copies in the asymmetric unit, and the availability of structures of homologous proteins with 〉20% sequence identity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365536/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365536/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DiMaio, Frank -- Terwilliger, Thomas C -- Read, Randy J -- Wlodawer, Alexander -- Oberdorfer, Gustav -- Wagner, Ulrike -- Valkov, Eugene -- Alon, Assaf -- Fass, Deborah -- Axelrod, Herbert L -- Das, Debanu -- Vorobiev, Sergey M -- Iwai, Hideo -- Pokkuluri, P Raj -- Baker, David -- 082961/Wellcome Trust/United Kingdom -- 5R01GM092802/GM/NIGMS NIH HHS/ -- GM074898/GM/NIGMS NIH HHS/ -- P01 GM063210/GM/NIGMS NIH HHS/ -- P41RR002250/RR/NCRR NIH HHS/ -- R01 GM092802/GM/NIGMS NIH HHS/ -- U54 GM074898/GM/NIGMS NIH HHS/ -- U54 GM074958/GM/NIGMS NIH HHS/ -- U54 GM094586/GM/NIGMS NIH HHS/ -- U54GM074958/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- Wellcome Trust/United Kingdom -- England -- Nature. 2011 May 26;473(7348):540-3. doi: 10.1038/nature09964. Epub 2011 May 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Washington, Department of Biochemistry and HHMI, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21532589" target="_blank"〉PubMed〈/a〉
    Keywords: Computational Biology/*methods ; Crystallography, X-Ray ; Databases, Protein ; Electrons ; *Models, Molecular ; Proteins/*chemistry ; Sequence Alignment ; Sequence Homology, Amino Acid ; *Structural Homology, Protein
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
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    Principles for designing ideal protein structures (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-11-09
    Description: Unlike random heteropolymers, natural proteins fold into unique ordered structures. Understanding how these are encoded in amino-acid sequences is complicated by energetically unfavourable non-ideal features--for example kinked alpha-helices, bulged beta-strands, strained loops and buried polar groups--that arise in proteins from evolutionary selection for biological function or from neutral drift. Here we describe an approach to designing ideal protein structures stabilized by completely consistent local and non-local interactions. The approach is based on a set of rules relating secondary structure patterns to protein tertiary motifs, which make possible the design of funnel-shaped protein folding energy landscapes leading into the target folded state. Guided by these rules, we designed sequences predicted to fold into ideal protein structures consisting of alpha-helices, beta-strands and minimal loops. Designs for five different topologies were found to be monomeric and very stable and to adopt structures in solution nearly identical to the computational models. These results illuminate how the folding funnels of natural proteins arise and provide the foundation for engineering a new generation of functional proteins free from natural evolution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3705962/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3705962/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koga, Nobuyasu -- Tatsumi-Koga, Rie -- Liu, Gaohua -- Xiao, Rong -- Acton, Thomas B -- Montelione, Gaetano T -- Baker, David -- U54 GM094597/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Nov 8;491(7423):222-7. doi: 10.1038/nature11600.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Washington, Department of Biochemistry and Howard Hughes Medical Institute, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23135467" target="_blank"〉PubMed〈/a〉
    Keywords: *Computer Simulation ; *Models, Molecular ; *Protein Folding ; *Protein Stability ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/*chemistry ; Thermodynamics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
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    Atomic model of the type III secretion system needle (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-06-16
    Description: Pathogenic bacteria using a type III secretion system (T3SS) to manipulate host cells cause many different infections including Shigella dysentery, typhoid fever, enterohaemorrhagic colitis and bubonic plague. An essential part of the T3SS is a hollow needle-like protein filament through which effector proteins are injected into eukaryotic host cells. Currently, the three-dimensional structure of the needle is unknown because it is not amenable to X-ray crystallography and solution NMR, as a result of its inherent non-crystallinity and insolubility. Cryo-electron microscopy combined with crystal or solution NMR subunit structures has recently provided a powerful hybrid approach for studying supramolecular assemblies, resulting in low-resolution and medium-resolution models. However, such approaches cannot deliver atomic details, especially of the crucial subunit-subunit interfaces, because of the limited cryo-electron microscopic resolution obtained in these studies. Here we report an alternative approach combining recombinant wild-type needle production, solid-state NMR, electron microscopy and Rosetta modelling to reveal the supramolecular interfaces and ultimately the complete atomic structure of the Salmonella typhimurium T3SS needle. We show that the 80-residue subunits form a right-handed helical assembly with roughly 11 subunits per two turns, similar to that of the flagellar filament of S. typhimurium. In contrast to established models of the needle in which the amino terminus of the protein subunit was assumed to be alpha-helical and positioned inside the needle, our model reveals an extended amino-terminal domain that is positioned on the surface of the needle, while the highly conserved carboxy terminus points towards the lumen.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3598588/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3598588/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Loquet, Antoine -- Sgourakis, Nikolaos G -- Gupta, Rashmi -- Giller, Karin -- Riedel, Dietmar -- Goosmann, Christian -- Griesinger, Christian -- Kolbe, Michael -- Baker, David -- Becker, Stefan -- Lange, Adam -- 1R01GM092802-01/GM/NIGMS NIH HHS/ -- R01 GM092802/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 May 20;486(7402):276-9. doi: 10.1038/nature11079.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22699623" target="_blank"〉PubMed〈/a〉
    Keywords: *Bacterial Secretion Systems ; HeLa Cells ; Humans ; Microscopy, Electron ; *Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Protein Structure, Secondary ; Salmonella typhimurium/*chemistry
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
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    MESSENGER Observations of Extreme Loading and Unloading of Mercury's Magnetic Tail (2010)
    In:  CASI
    Details
    Publication Date: 2018-06-06
    Description: During MESSENGER's third flyby of Mercury, a series of 2-3 minute long enhancements of the magnetic field in the planet's magnetotail were observed. Magnetospheric substorms at Earth are powered by similar tail loading, but the amplitude is approximately 10 times less and the durations are 1 hr. These observations of extreme loading imply that the relative intensity of substorms at Mercury must be much larger than at Earth. The correspondence between the duration of tail enhancements and the calculated approximately 2 min Dungey cycle, which describes plasma circulation through Mercury's magnetosphere, suggests that such circulation determines substorm timescale. A key aspect of tail unloading during terrestrial substorms is the acceleration of energetic charged particles. Such signatures are puzzlingly absent from the MESSENGER flyby measurements.
    Keywords: Lunar and Planetary Science and Exploration
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  • 8
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    Lunar Flashlight: Mapping Lunar Surface Volatiles Using a Cubesat (2014)
    In:  CASI
    Details
    Publication Date: 2019-07-19
    Description: Water ice and other volatiles may be located in the Moon's polar regions, with sufficient quantities for in situ extraction and utilization by future human and robotic missions. Evidence from orbiting spacecraft and the LCROSS impactor suggests the presence of surface and/or nearsurface volatiles, including water ice. These deposits are of interest to human exploration to understand their potential for use by astronauts. Understanding the composition, quantity, distribution, and form of water/H species and other volatiles associated with lunar cold traps is identified as a NASA Strategic Knowledge Gap (SKG) for Human Exploration. These polar volatile deposits could also reveal important information about the delivery of water to the Earth- Moon system, so are of scientific interest. The scientific exploration of the lunar polar regions was one of the key recommendations of the Planetary Science Decadal Survey. In order to address NASA's SKGs, the Advanced Exploration Systems (AES) program selected three lowcost 6-U CubeSat missions for launch as secondary payloads on the first test flight (EM1) of the Space Launch System (SLS) scheduled for 2017. The Lunar Flashlight mission was selected as one of these missions, specifically to address the SKG associated with lunar volatiles. Development of the Lunar Flashlight CubeSat concept leverages JPL's Interplanetary Nano- Spacecraft Pathfinder In Relevant Environment (INSPIRE) mission, MSFC's intimate knowledge of the Space Launch System and EM-1 mission, small business development of solar sail and electric propulsion hardware, and JPL experience with specialized miniature sensors. The goal of Lunar Flashlight is to determine the presence or absence of exposed water ice and its physical state, and map its concentration at the kilometer scale within the permanently shadowed regions of the lunar south pole. After being ejected in cislunar space by SLS, Lunar Flashlight deploys its solar panels and solar sail and maneuvers into a low-energy transfer to lunar orbit. The solar sail and attitude control system work to bring the satellite into an elliptical polar orbit spiraling down to a perilune of 30-10 km above the south pole for data collection. Lunar Flashlight uses its solar sail to shine reflected sunlight into permanently shadowed regions, measuring surface albedo with a four-filter point spectrometer at 1.1, 1.5 1.9, and 2.0 microns. Water ice will be distinguished from dry regolith from these measurements in two ways: 1) spatial variations in absolute reflectance (water ice is much brighter in the continuum channels), and 2) reflectance ratios between absorption and continuum channels. Derived reflectance and reflectance ratios will be mapped onto the lunar surface in order to distinguish the composition of the PSRs from that of the sunlit terrain. Lunar Flashlight enables a low-cost path to in-situ resource utilization (ISRU) by identifying operationally useful deposits (if there are any), which is a game-changing capability for expanded human exploration.
    Keywords: Lunar and Planetary Science and Exploration
    Type: M14-3629 , NASA''s Solar System Exploration Research Virtual Institute Exploration Science Forum; Jul 21, 2014 - Jul 23, 2014; Moffett Field, CA; United States
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  • 9
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    A Search for Amino Acids and Nucleobases in the Martian Meteorite Roberts Massif 04262 Using Liquid Chromatography-Mass Spectrometry (2013)
    In:  CASI
    Details
    Publication Date: 2019-07-13
    Description: The investigation into whether Mars contains signatures of past or present life is of great interest to science and society. Amino acids and nucleobases are compounds that are essential for all known life on Earth and are excellent target molecules in the search for potential Martian biomarkers or prebiotic chemistry. Martian meteorites represent the only samples from Mars that can be studied directly in the laboratory on Earth. Here, we analyzed the amino acid and nucleobase content of the shergottite Roberts Massif (RBT) 04262 using liquid chromatography-mass spectrometry. We did not detect any nucleobases above our detection limit in formic acid extracts; however, we did measure a suite of protein and nonprotein amino acids in hot-water extracts with high relative abundances of beta-alanine and gamma-amino-eta-butyric acid. The presence of only low (to absent) levels of several proteinogenic amino acids and a lack of nucleobases suggest that this meteorite fragment is fairly uncontaminated with respect to these common biological compounds. The distribution of straight-chained amine-terminal eta-omega-amino acids in RBT 04262 resembled those previously measured in thermally altered carbonaceous meteorites. A carbon isotope ratio of -24(0/00) +/- 6(0/00) for beta-alanine in RBT 04262 is in the range of reduced organic carbon previously measured in Martian meteorites (Steele et al. 2012). The presence of eta-omega-amino acids may be due to a high temperature Fischer-Tropschtype synthesis during igneous processing on Mars or impact ejection of the meteorites from Mars, but more experimental data are needed to support these hypotheses.
    Keywords: Lunar and Planetary Science and Exploration
    Type: GSFC-E-DAA-TN8169 , Meteoritics & Planetary Science; 48; 5; 786-795
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  • 10
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    Lunar Flashlight: Mapping Lunar Surface Volatiles Using a Cubesat (2014)
    In:  CASI
    Details
    Publication Date: 2019-07-13
    Description: No abstract available
    Keywords: Lunar and Planetary Science and Exploration
    Type: M14-3827 , NASA''s Solar System Exploration Research Virtual Institute (NASA SSERVI) Exploration Science Forum; Jul 21, 2014 - Jul 23, 2014; Moffett Field, CA; United States
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