archaeal proteins

Summary

Summary: Proteins found in any species of archaeon.

Top Publications

  1. pmc RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex
    Caryn R Hale
    Department of Biochemistry, University of Georgia, Athens, GA 30602, USA
    Cell 139:945-56. 2009
  2. pmc Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity
    Jing Zhang
    Biomedical Sciences Research Complex, University of St Andrews, Fife KY16 9ST, UK
    Mol Cell 45:303-13. 2012
  3. pmc A single-base resolution map of an archaeal transcriptome
    Omri Wurtzel
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Genome Res 20:133-41. 2010
  4. pmc Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis
    Hagen Richter
    Max Planck Institute for Terrestrial Microbiology, Karl von Frisch Strasse 10, D 35037 Marburg, Germany
    Nucleic Acids Res 40:9887-96. 2012
  5. pmc Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs
    Caryn R Hale
    Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
    Mol Cell 45:292-302. 2012
  6. ncbi Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota
    Anja Spang
    University of Vienna, Department of Genetics in Ecology, Althanstrasse 14, A 1090 Vienna, Austria
    Trends Microbiol 18:331-40. 2010
  7. ncbi Identification of genes that are associated with DNA repeats in prokaryotes
    Ruud Jansen
    Department of Infectious Diseases and Immunology, Bacteriology Division, Veterinary Faculty, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
    Mol Microbiol 43:1565-75. 2002
  8. pmc Characterization of the CRISPR/Cas subtype I-A system of the hyperthermophilic crenarchaeon Thermoproteus tenax
    André Plagens
    Institute of Biology, Microbiology I, University of Duisburg Essen, Essen, Germany
    J Bacteriol 194:2491-500. 2012
  9. ncbi Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling
    Alexander H Treusch
    University of Bergen, Department of Biology, Jahnebakken 5, N 5020 Bergen, Norway
    Environ Microbiol 7:1985-95. 2005
  10. pmc Phylogenomics of prokaryotic ribosomal proteins
    Natalya Yutin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 7:e36972. 2012

Research Grants

  1. FEN-1 and PCNA Complexes and Human Genome Stability
    John A Tainer; Fiscal Year: 2013
  2. Interrogation of systems level mechanisms controlling DNA repair processes
    Nitin S Baliga; Fiscal Year: 2010
  3. MOLECULAR SEQUENCE DATA
    Samuel Karlin; Fiscal Year: 2001
  4. Gene Expression Levels Across Diverse Genomes
    Samuel Karlin; Fiscal Year: 2006
  5. DNA RADICAL KINETICS
    Martin Newcomb; Fiscal Year: 2001
  6. MECHANISTIC PROBES FOR ENZYME-CATALYZED OXIDATIONS
    MARTIN E NEWCOMB; Fiscal Year: 2010
  7. INTERFACIAL ACTIVATION OF WATER SOLUBLE PHOSPHOLIPASES
    Mary Roberts; Fiscal Year: 2003
  8. ATP-DEPENDENT PROTEIN KINASES IN GRAM-POSITIVE BACTERIA
    Milton Saier; Fiscal Year: 2004
  9. MOLECULAR MECHANISM OF DYSKERATOSIS CONGENITA
    U Meier; Fiscal Year: 2008
  10. New Inhibitors of HIV Replication
    Gabriele Varani; Fiscal Year: 2005

Detail Information

Publications321 found, 100 shown here

  1. pmc RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex
    Caryn R Hale
    Department of Biochemistry, University of Georgia, Athens, GA 30602, USA
    Cell 139:945-56. 2009
    ..Our results indicate that prokaryotes possess a unique RNA silencing system that functions by homology-dependent cleavage of invader RNAs...
  2. pmc Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity
    Jing Zhang
    Biomedical Sciences Research Complex, University of St Andrews, Fife KY16 9ST, UK
    Mol Cell 45:303-13. 2012
    ..Both target and guide RNAs can be cleaved, although a single molecule of guide RNA can support the degradation of multiple targets...
  3. pmc A single-base resolution map of an archaeal transcriptome
    Omri Wurtzel
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Genome Res 20:133-41. 2010
    ..This study highlights transcriptome sequencing as a key tool for understanding the mechanisms and extent of RNA-based regulation in Bacteria and Archaea...
  4. pmc Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis
    Hagen Richter
    Max Planck Institute for Terrestrial Microbiology, Karl von Frisch Strasse 10, D 35037 Marburg, Germany
    Nucleic Acids Res 40:9887-96. 2012
    ..These effects will need to be considered for the application of CRISPR clusters that are designed to produce synthetic crRNAs...
  5. pmc Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs
    Caryn R Hale
    Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
    Mol Cell 45:292-302. 2012
    ..Our findings indicate that the CRISPR RNA-Cmr protein pathway may be exploited to cleave RNAs of interest...
  6. ncbi Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota
    Anja Spang
    University of Vienna, Department of Genetics in Ecology, Althanstrasse 14, A 1090 Vienna, Austria
    Trends Microbiol 18:331-40. 2010
    ....
  7. ncbi Identification of genes that are associated with DNA repeats in prokaryotes
    Ruud Jansen
    Department of Infectious Diseases and Immunology, Bacteriology Division, Veterinary Faculty, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
    Mol Microbiol 43:1565-75. 2002
    ..The spatial coherence of CRISPR and cas genes may stimulate new research on the genesis and biological role of these repeats and genes...
  8. pmc Characterization of the CRISPR/Cas subtype I-A system of the hyperthermophilic crenarchaeon Thermoproteus tenax
    André Plagens
    Institute of Biology, Microbiology I, University of Duisburg Essen, Essen, Germany
    J Bacteriol 194:2491-500. 2012
    ..These data provide insights into the specialized mechanisms of an archaeal CRISPR/Cas system and allow selective functional analyses of Cas protein complexes in the future...
  9. ncbi Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling
    Alexander H Treusch
    University of Bergen, Department of Biology, Jahnebakken 5, N 5020 Bergen, Norway
    Environ Microbiol 7:1985-95. 2005
    ..Taken together, our findings suggest that mesophilic terrestrial and marine crenarchaeota might be capable of ammonia oxidation under aerobic and potentially also under anaerobic conditions...
  10. pmc Phylogenomics of prokaryotic ribosomal proteins
    Natalya Yutin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 7:e36972. 2012
    ..These alignments, available for download, can be used as search profiles to improve genome annotation of r-proteins and for further comparative genomics studies...
  11. pmc Archaeal nitrification in the ocean
    Cornelia Wuchter
    Department of Marine Biogeochemistry and Toxicology, Royal Netherlands Institute for Sea Research NIOZ, P O Box 59, 1790 AB, Den Burg, The Netherlands
    Proc Natl Acad Sci U S A 103:12317-22. 2006
    ..Our data thus suggest a major role for Archaea in oceanic nitrification...
  12. ncbi Origin and evolution of DNA topoisomerases
    Patrick Forterre
    Institut de Genetique et Microbiologie, UMR8621, Universite Paris Sud 11, Bat 400 409, 91405 Orsay Cedex, France
    Biochimie 89:427-46. 2007
    ....
  13. ncbi Revealing the essentiality of multiple archaeal pcna genes using a mutant propagation assay based on an improved knockout method
    Changyi Zhang
    State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
    Microbiology 156:3386-97. 2010
    ..Because the only prerequisite for this assay is the generation of a MID transformant, this approach can be applied generally to any micro-organisms proficient in homologous recombination...
  14. ncbi The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
    N Ban
    Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, New Haven, CT 06520 8114, USA
    Science 289:905-20. 2000
    ..Most of the proteins stabilize the structure by interacting with several RNA domains, often using idiosyncratically folded extensions that reach into the subunit's interior...
  15. pmc A unique cell division machinery in the Archaea
    Ann Christin Lindås
    Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University, Norbyvagen 18C, SE 752 36, Uppsala, Sweden
    Proc Natl Acad Sci U S A 105:18942-6. 2008
    ....
  16. pmc A role for the ESCRT system in cell division in archaea
    Rachel Y Samson
    Medical Research Council MRC Cancer Cell Unit, Hills Road, Cambridge CB2 0XZ, UK
    Science 322:1710-3. 2008
    ..Overexpression of a catalytically inactive mutant Vps4 in Sulfolobus resulted in the accumulation of enlarged cells, indicative of failed cell division. Thus, the archaeal ESCRT system plays a key role in cell division...
  17. pmc Mechanism of gate opening in the 20S proteasome by the proteasomal ATPases
    Julius Rabl
    Fachbereich Biologie, Chemie, Pharmazie, Freie Universitat Berlin, Takustrasse 3, 14195 Berlin, Germany
    Mol Cell 30:360-8. 2008
    ..This mechanism differs from that of PA26/28, which lacks the HbYX motif and does not cause alpha subunit rotation. These findings demonstrated how the ATPases' C termini function to facilitate substrate entry...
  18. ncbi The HAMP domain structure implies helix rotation in transmembrane signaling
    Michael Hulko
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Cell 126:929-40. 2006
    ..coli chemotaxis receptor. Structural and functional studies show that the equilibrium between the two forms is dependent on the side-chain size of residue 291, which is alanine in the wild-type protein...
  19. pmc Development of additional selectable markers for the halophilic archaeon Haloferax volcanii based on the leuB and trpA genes
    Thorsten Allers
    Institute of Genetics, University of Nottingham, Queen s Medical Centre, Nottingham NG7 2UH, United Kingdom
    Appl Environ Microbiol 70:943-53. 2004
    ..We constructed both integrative and replicative plasmids carrying the leuB or trpA gene under control of a constitutive promoter. The use of these selectable markers in deletion of the lhr gene of H. volcanii is described...
  20. ncbi The mechanisms of HAMP-mediated signaling in transmembrane receptors
    Hedda U Ferris
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Structure 19:378-85. 2011
    ..These are correlated with activity and ligand response in vitro and in vivo by incorporating Af1503 HAMP into mycobacterial adenylyl cyclase assay systems...
  21. pmc Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes
    Iain Anderson
    Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
    PLoS ONE 6:e20237. 2011
    ..The extremely halophilic archaea are present worldwide in saline environments and have important biotechnological applications. Ten complete genomes of haloarchaea are now available, providing an opportunity for comparative analysis...
  22. ncbi Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary
    Annika C Mosier
    Department of Environmental Earth System Science, Stanford University, Stanford, CA 94305, USA
    Environ Microbiol 10:3002-16. 2008
    ..Overall, this study significantly enhances our understanding of estuarine ammonia-oxidizing microbial communities and highlights the environmental conditions and niches under which different AOA and beta-AOB phylotypes may thrive...
  23. ncbi Crystal structure of Argonaute and its implications for RISC slicer activity
    Ji Joon Song
    Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Science 305:1434-7. 2004
    ..The architecture of the molecule and the placement of the PAZ and PIWI domains define a groove for substrate binding and suggest a mechanism for siRNA-guided mRNA cleavage...
  24. ncbi The principle of gating charge movement in a voltage-dependent K+ channel
    Youxing Jiang
    Howard Hughes Medical Institute, Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Nature 423:42-8. 2003
    ..Our findings lead us to conclude that the voltage-sensor paddles operate somewhat like hydrophobic cations attached to levers, enabling the membrane electric field to open and close the pore...
  25. pmc Structure of Alba: an archaeal chromatin protein modulated by acetylation
    B N Wardleworth
    Centre for Biomolecular Science, St Andrews University, North Haugh, St Andrews, Fife KY16 9ST, UK
    EMBO J 21:4654-62. 2002
    ..We present a model for the Alba-DNA interaction consistent with the available structural, biophysical and electron microscopy data...
  26. ncbi A methylaspartate cycle in haloarchaea
    Maria Khomyakova
    Mikrobiologie, Fakultat Biologie, Universitat Freiburg, Schanzlestrasse 1, D 79104 Freiburg, Germany
    Science 331:334-7. 2011
    ..Moreover, it requires elevated intracellular glutamate concentrations, as well as coupling carbon assimilation with nitrogen metabolism...
  27. pmc The UCSC Archaeal Genome Browser
    Kevin L Schneider
    Biomolecular Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 34:D407-10. 2006
    ..We encourage submission of new experimental and bioinformatic analysis from contributors. The purpose of this tool is to aid biological discovery and facilitate greater collaboration within the archaeal research community...
  28. pmc Recognition and cleavage of a nonstructured CRISPR RNA by its processing endoribonuclease Cas6
    Yaming Shao
    Institute of Molecular Biophysics, Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
    Structure 21:385-93. 2013
    ..The distinct RNA binding and cleavage mechanisms underline the diversity in CRISPR RNA processing...
  29. pmc The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes
    Kira S Makarova
    National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, Maryland 20894, USA
    Biol Direct 7:7. 2012
    ..Here we present the results of in-depth phylogenomic analysis of RecJ homologs in archaea...
  30. ncbi Proteomic characterization of archaeal ribosomes reveals the presence of novel archaeal-specific ribosomal proteins
    Viter Marquez
    Gene Center and Department of Biochemistry, Ludwig Maximilians Universitat, Feodor Lynen Str 25, 81377 Munich, Germany
    J Mol Biol 405:1215-32. 2011
    ..The discovery of novel archaeal r-proteins and factors may be the first step to understanding how archaeal ribosomes cope with extreme environmental conditions...
  31. ncbi How do thermophilic proteins deal with heat?
    S Kumar
    Laboratory of Experimental and Computational Biology, NCI Frederick, Maryland 21702, USA
    Cell Mol Life Sci 58:1216-33. 2001
    ..At the same time, surface loop deletion contributes to decreased conformational entropy and decreased heat capacity change between the folded and unfolded states of the protein...
  32. pmc DNA bending, compaction and negative supercoiling by the architectural protein Sso7d of Sulfolobus solfataricus
    Alessandra Napoli
    Institute of Protein Biochemistry and Enzymology, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Naples, Italy
    Nucleic Acids Res 30:2656-62. 2002
    ..The proposed biological relevance of these observations is that these proteins might model the behaviour of DNA in constrained chromatin environments...
  33. pmc E1- and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in archaea
    Hugo V Miranda
    Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611 0700, USA
    Proc Natl Acad Sci U S A 108:4417-22. 2011
    ..In sulfur transfer, SAMP1 and SAMP2 appear specific for MoCo biosynthesis and the thiolation of tRNA, respectively. Overall, this study provides a fundamental insight into the diverse cellular functions of the Ubl system...
  34. ncbi Molecular mechanisms of proteasome assembly
    Shigeo Murata
    Laboratory of Protein Metabolism, Department of Integrated Biology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Nat Rev Mol Cell Biol 10:104-15. 2009
    ..By contrast, little is known about the assembly of the 19S regulatory particles, but several hints have emerged...
  35. ncbi Diversity and spatio-temporal distribution of ammonia-oxidizing Archaea and Bacteria in sediments of the Westerschelde estuary
    Emel Sahan
    Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
    FEMS Microbiol Ecol 64:175-86. 2008
    ..Variability in net primary production rates was also correlated with species composition of both groups, but changes in the nitrite concentration only to the distribution of the AOA...
  36. pmc Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group
    Takuro Nunoura
    Subsurface Geobiology and Advanced Research Project, Institute of Biogeosciences, Japan Agency for Marine Earth Science and Technology, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Nucleic Acids Res 39:3204-23. 2011
    ..The presence of such a eukaryote-type system is unprecedented in prokaryotes, and indicates that a prototype of the eukaryotic protein modifier system is present in the Archaea...
  37. ncbi X-ray structure of a voltage-dependent K+ channel
    Youxing Jiang
    Howard Hughes Medical Institute, Laboratory of Molecular Neurobiology and Biophysics, Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Nature 423:33-41. 2003
    ..Flexible hinges suggest that the voltage-sensor paddles move in response to membrane voltage changes, carrying their positive charge across the membrane...
  38. pmc Enigmatic, ultrasmall, uncultivated Archaea
    Brett J Baker
    Department of Earth and Planetary Science and Environmental Science, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 107:8806-11. 2010
    ..2009) ISME J 3:159-167], and many genes previously only affiliated with Crenarchaea or Bacteria indicate extensive unique physiology in organisms that branched close to the time that Cren- and Euryarchaeotal lineages diverged...
  39. ncbi Structural basis for 5'-end-specific recognition of guide RNA by the A. fulgidus Piwi protein
    Jin Biao Ma
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Nature 434:666-70. 2005
    ....
  40. pmc Improved and versatile transformation system allowing multiple genetic manipulations of the hyperthermophilic archaeon Thermococcus kodakaraensis
    Takaaki Sato
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    Appl Environ Microbiol 71:3889-99. 2005
    ..Likewise, a triple deletion mutant, KUWH1 (DeltapyrF DeltatrpE DeltahisD), could also be constructed. The transformation systems developed here now provide the means for extensive genetic studies in this hyperthermophilic archaeon...
  41. pmc Extrachromosomal element capture and the evolution of multiple replication origins in archaeal chromosomes
    Nicholas P Robinson
    Medical Research Council Cancer Cell Unit, Hutchison Medical Research Council Research Center, Hills Road, Cambridge CB2 0XZ, United Kingdom
    Proc Natl Acad Sci U S A 104:5806-11. 2007
    ....
  42. pmc Diversity in chemotaxis mechanisms among the bacteria and archaea
    Hendrik Szurmant
    Department of Biochemistry, College of Medicine, University of Illinois, Urbana, IL 61801, USA
    Microbiol Mol Biol Rev 68:301-19. 2004
    ..coli and B. subtilis have been discovered in other organisms. This review emphasizes those used by B. subtilis and these other organisms but also gives an account of the mechanism in E. coli...
  43. pmc A novel strategy to engineer DNA polymerases for enhanced processivity and improved performance in vitro
    Yan Wang
    Department of Research and Development, MJ Bioworks Inc, 7000 Shoreline Court, South San Francisco, CA 94080, USA
    Nucleic Acids Res 32:1197-207. 2004
    ..This technology has the potential to broadly improve the performance of nucleic acid modifying enzymes...
  44. pmc The relationship of protein conservation and sequence length
    David J Lipman
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 2:20. 2002
    ..However, additional evolutionary forces that affect the length of a protein may be revealed by studying the length distributions of proteins evolving under weaker functional constraints...
  45. pmc Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes
    R S Gupta
    Department of Biochemistry, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
    Microbiol Mol Biol Rev 62:1435-91. 1998
    ..In this model, the ancestral eukaryotic cell is a chimera that resulted from a unique fusion event between the two separate groups of prokaryotes followed by integration of their genomes...
  46. pmc Crystal structure of the crenarchaeal conserved chromatin protein Cren7 and double-stranded DNA complex
    Yingang Feng
    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People s Republic of China
    Protein Sci 19:1253-7. 2010
    ....
  47. ncbi Structural insights into the interaction of the crenarchaeal chromatin protein Cren7 with DNA
    Zhenfeng Zhang
    State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No 1 West Beichen Road, Chaoyang District, Beijing 100101, China
    Mol Microbiol 76:749-59. 2010
    ..Structural comparison of Cren7-DNA complexes with Sac7d-DNA complexes reveals significant differences between the two proteins in DNA binding surface, suggesting that Cren7 and Sul7d serve distinct functions in chromosomal organization...
  48. ncbi The structure and function of MCM from archaeal M. Thermoautotrophicum
    Ryan J Fletcher
    Department of Biochemistry and Molecular Genetics, University of Colorado Health Science Center, School of Medicine, Denver, Colorado 80262, USA
    Nat Struct Biol 10:160-7. 2003
    ..Yeast bypass experiments using MCM5 mutant proteins support the hypothesis for the bypass mechanism...
  49. pmc Evolution of diverse cell division and vesicle formation systems in Archaea
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Nat Rev Microbiol 8:731-41. 2010
    ..By contrast, eukaryotes seem to have inherited all three ancestral systems...
  50. pmc Structure of the archaeal Cascade subunit Csa5: relating the small subunits of CRISPR effector complexes
    Judith Reeks
    Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, UK
    RNA Biol 10:762-9. 2013
    ..A definitive answer awaits structural studies of further small subunits from other CRISPR effector complexes. ..
  51. pmc Structure of a dimeric crenarchaeal Cas6 enzyme with an atypical active site for CRISPR RNA processing
    Judith Reeks
    Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
    Biochem J 452:223-30. 2013
    ....
  52. pmc Crenarchaeal chromatin proteins Cren7 and Sul7 compact DNA by inducing rigid bends
    Rosalie P C Driessen
    Molecular Genetics, Leiden Institute of Chemistry and Cell Observatory, Physics of Life Processes, Leiden Institute of Physics and Cell Observatory, Leiden University, 2333 CC Leiden, The Netherlands
    Nucleic Acids Res 41:196-205. 2013
    ..Moreover, we investigate the flexibility of the bending angle induced by Cren7 and Sul7 and show that the protein-DNA complexes differ in flexibility from analogous bacterial and eukaryotic DNA-bending proteins...
  53. pmc A genetic investigation of the KEOPS complex in halophilic Archaea
    Adit Naor
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
    PLoS ONE 7:e43013. 2012
    ..volcanii. Deletion of pcc1 led to pleiotropic phenotypes, including decreased growth rate, reduced levels of t(6)A modification, and elevated levels of intra-cellular glycation products...
  54. ncbi Change of carbon source causes dramatic effects in the phospho-proteome of the archaeon Sulfolobus solfataricus
    D Esser
    Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Faculty of Chemistry, University of Duisburg Essen, Universitätsstraße 5, 45141 Essen, Germany
    J Proteome Res 11:4823-33. 2012
    ....
  55. pmc Characterization of DNA primase complex isolated from the archaeon, Thermococcus kodakaraensis
    Wiebke Chemnitz Galal
    Program of Molecular Biology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    J Biol Chem 287:16209-19. 2012
    ..Supplementation of such reactions with the DNA primase complex supported lagging strand formation as well...
  56. pmc Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin
    J Salgado-Garrido
    EMBL, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    EMBO J 18:3451-62. 1999
    ..We also identified archaeal proteins related to Sm and Sm-like proteins...
  57. pmc Atomic structure of the KEOPS complex: an ancient protein kinase-containing molecular machine
    Daniel Y L Mao
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
    Mol Cell 32:259-75. 2008
    ..Lastly, as Bud32 lacks the conventional substrate-recognition infrastructure of eukaryotic protein kinases including an activation segment, Bud32 may provide a glimpse of the evolutionary history of the protein kinase family...
  58. pmc Crystal structure of the Mre11-Rad50-ATPγS complex: understanding the interplay between Mre11 and Rad50
    Hye Seong Lim
    Department of Life Science, Pohang University of Science and Technology, Pohang, South Korea
    Genes Dev 25:1091-104. 2011
    ..Our structural and biochemical data provide insights into understanding the interplay between Mre11 and Rad50 to facilitate efficient DNA damage repair...
  59. ncbi The role of the DNA sliding clamp in Okazaki fragment maturation in archaea and eukaryotes
    Thomas R Beattie
    Sir William Dunn School of Pathology, Oxford University, South Parks Road, Oxford OX1 3RE, UK
    Biochem Soc Trans 39:70-6. 2011
    ..This conformational malleability may be key to the co-ordination of these enzymes' activities...
  60. ncbi The archaeal DNA primase: biochemical characterization of the p41-p46 complex from Pyrococcus furiosus
    L Liu
    Department of Molecular Biology, Binomolecular Engineering Research Institute, Suita, Osaka 565 0874, Japan
    J Biol Chem 276:45484-90. 2001
    ..furiosus, in a similar fashion to the eukaryotic polymerase alpha-primase complex...
  61. pmc The archaeal eIF2 homologue: functional properties of an ancient translation initiation factor
    Nadia Pedullà
    Department of Cellular Biotechnology and Hematology, University of Rome La Sapienza Viale Regina Elena 324, 00161 Rome, Italy
    Nucleic Acids Res 33:1804-12. 2005
    ..The detailed analysis of the complete trimer and of its isolated subunits is discussed in light of the evolutionary history of the eIF2-like proteins...
  62. pmc The impact of CRISPR repeat sequence on structures of a Cas6 protein-RNA complex
    Ruiying Wang
    Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
    Protein Sci 21:405-17. 2012
    ..Substitutions of these bases result in structural changes in the protein-RNA complex including its oligomerization state...
  63. ncbi Distinct regulators control the expression of methanol methyltransferase isozymes in Methanosarcina acetivorans C2A
    Arpita Bose
    Department of Microbiology, University of Illinois at Urbana Champaign, B103 CLSL, 601 S Goodwin, Urbana, IL 61801, USA
    Mol Microbiol 67:649-61. 2008
    ..We refer to these genes as methanol-specific regulators and designate MA0459, MA0460, MA4383, MA4397 and MA4398 as msrA, msrB, msrC, msrD and msrE respectively...
  64. pmc Archaeal intrinsic transcription termination in vivo
    Thomas J Santangelo
    Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
    J Bacteriol 191:7102-8. 2009
    ....
  65. pmc The P. furiosus mre11/rad50 complex promotes 5' strand resection at a DNA double-strand break
    Ben B Hopkins
    The Howard Hughes Medical Institute, Department of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, TX 78712, USA
    Cell 135:250-60. 2008
    ..This work elucidates how the conserved Mre11/Rad50 complex promotes DNA end resection in archaea and may serve as a model for DSB processing in eukaryotes...
  66. ncbi Diversity and spatial distribution of amoA-encoding archaea in the deep-sea sediments of the tropical West Pacific Continental Margin
    H Dang
    Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
    J Appl Microbiol 106:1482-93. 2009
    ..Our aim was to study the diversity, structure and distribution of the AEA community in the sediments of the tropical West Pacific Continental Margin, to develop a general view of the AEA biogeography in the deep-sea extreme environment...
  67. ncbi The evolutionary history of archaeal MCM helicases: a case study of vertical evolution combined with hitchhiking of mobile genetic elements
    Mart Krupovic
    Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    Mol Biol Evol 27:2716-32. 2010
    ....
  68. pmc Crystal structure of the archaeal ammonium transporter Amt-1 from Archaeoglobus fulgidus
    Susana L A Andrade
    Institut fur Mikrobiologie und Genetik, Abteilung Molekulare Strukturbiologie, Georg August Universitat, Justus von Liebig Weg 11, 37077 Gottingen, Germany
    Proc Natl Acad Sci U S A 102:14994-9. 2005
    ..In this model, GlnB-1 binds tightly to the cytoplasmic face of the transporter, effectively blocking conduction through the three individual substrate channels...
  69. pmc The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
    Richard Bonneau
    New York University, Biology Department, Center for Comparative Functional Genomics, New York, NY 10003, USA
    Genome Biol 7:R36. 2006
    ..Several specific regulatory predictions were experimentally tested and verified...
  70. pmc ABC ATPase signature helices in Rad50 link nucleotide state to Mre11 interface for DNA repair
    Gareth J Williams
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    Nat Struct Mol Biol 18:423-31. 2011
    ....
  71. ncbi Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study
    Suvobrata Chakravarty
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    Biochemistry 41:8152-61. 2002
    ..At buried sites, statistically significant hydrophobic amino acid substitutions are typically consistent with decreased side chain conformational entropy...
  72. ncbi Reconstitution, activities, and structure of the eukaryotic RNA exosome
    Quansheng Liu
    Structural Biology Program, Sloan Kettering Institute, New York, NY 10021, USA
    Cell 127:1223-37. 2006
    ..To elucidate the architecture of a eukaryotic exosome, its conserved surfaces, and the structural basis for RNA decay, we report the X-ray structure determination for the 286 kDa nine-subunit human exosome at 3.35 A...
  73. pmc Archaeal ribosomal protein L7 is a functional homolog of the eukaryotic 15.5kD/Snu13p snoRNP core protein
    Jeffrey F Kuhn
    Department of Molecular and Structural Biochemistry, North Carolina State University, Box 7622, Raleigh, NC 27695 7622, USA
    Nucleic Acids Res 30:931-41. 2002
    ..L7 functioning as both an sRNP core protein and a ribosomal protein could potentially regulate and coordinate sRNP assembly with ribosome biogenesis...
  74. pmc Global occurrence of archaeal amoA genes in terrestrial hot springs
    Chuanlun L Zhang
    Department of Marine Sciences, University of Georgia, Athens, Georgia 30602, USA
    Appl Environ Microbiol 74:6417-26. 2008
    ..Our study demonstrates the global occurrence of putative archaeal amoA genes in a wide variety of terrestrial hot springs and suggests that geography may play an important role in selecting different assemblages of AOA...
  75. ncbi The interaction of Alba, a conserved archaeal chromatin protein, with Sir2 and its regulation by acetylation
    Stephen D Bell
    Medical Research Council MRC Cancer Cell Unit, The Hutchison MRC Research Centre, Hills Road, Cambridge, CB2 2QH, UK
    Science 296:148-51. 2002
    ..These data provide a paradigm for how Sir2 family proteins influence transcription and suggest that modulation of chromatin structure by acetylation arose before the divergence of the archaeal and eukaryotic lineages...
  76. pmc Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes
    Toshiaki Fukui
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    Genome Res 15:352-63. 2005
    ....
  77. pmc Biogeography of the Sulfolobus islandicus pan-genome
    Michael L Reno
    Department of Microbiology and Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Proc Natl Acad Sci U S A 106:8605-10. 2009
    ..islandicus exposes the process of allopatric speciation in thermophilic Archaea and brings us closer to a generalized framework for understanding microbial genome evolution in a spatial context...
  78. ncbi The many faces of the helix-turn-helix domain: transcription regulation and beyond
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Room 5N50, Bethesda, MD 20894, USA
    FEMS Microbiol Rev 29:231-62. 2005
    ..This differential relationship of their basal and specific transcriptional machinery poses an apparent conundrum regarding the origins of their transcription apparatus...
  79. ncbi Archaeal DNA replication and repair
    Zvi Kelman
    University of Maryland Biotechnology Institute, Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
    Curr Opin Microbiol 8:669-76. 2005
    ..Recent biochemical and structural studies of the proteins that participate in archaeal DNA replication and repair have increased our understanding of these processes...
  80. ncbi Structure and function in the uracil-DNA glycosylase superfamily
    L H Pearl
    Section of Structural Biology and CRC DNA Repair Enzyme Group, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, SW3 6JB, London, UK
    Mutat Res 460:165-81. 2000
    ....
  81. pmc A novel DNA nuclease is stimulated by association with the GINS complex
    Zhuo Li
    Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 39:6114-23. 2011
    ..This novel archaeal nuclease, designated GINS-associated nuclease (GAN), also forms a complex in vivo with the euryarchaeal-specific DNA polymerase D. Roles for GAN in replisome assembly and DNA replication are discussed...
  82. pmc The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
    Brigitte Boeckmann
    Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
    Nucleic Acids Res 31:365-70. 2003
    ..Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to SWISS-PROT at swiss-prot@expasy.org...
  83. ncbi Diversity and spatial distribution of sediment ammonia-oxidizing crenarchaeota in response to estuarine and environmental gradients in the Changjiang Estuary and East China Sea
    Hongyue Dang
    Centre for Bioengineering and Biotechnology, China University of Petroleum East China, Qingdao 266555, China
    Microbiology 154:2084-95. 2008
    ..Besides freshwater, nutrients, organic matter and suspended particles, the Changjiang Diluted Water might also contribute to the transport of terrestrial archaea into the seawater and sediments along its flow path...
  84. ncbi Methanococcus aeolicus sp. nov., a mesophilic, methanogenic archaeon from shallow and deep marine sediments
    Melissa M Kendall
    Biology Department, Portland State University, PO Box 751, Portland, OR 97207 0751, USA
    Int J Syst Evol Microbiol 56:1525-9. 2006
    ..The name Methanococcus aeolicus sp. nov. is proposed, with strain Nankai-3(T) (=OCM 812(T)=DSM 17508(T)) as the type strain...
  85. pmc Spatial variability in nitrification rates and ammonia-oxidizing microbial communities in the agriculturally impacted Elkhorn Slough estuary, California
    Scott D Wankel
    Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138, USA
    Appl Environ Microbiol 77:269-80. 2011
    ..This is the first report measuring AOA and β-AOB amoA abundance in conjunction with (15)N-based nitrification rates in estuary sediments...
  86. ncbi Genetic technologies for Archaea
    Michael Rother
    Institut fur Mikrobiologie, Johann Wolfgang Goethe Universitat, Marie Curie Strasse 9, D 60439 Frankfurt Main, Germany
    Curr Opin Microbiol 8:745-51. 2005
    ....
  87. pmc Crystal structure of a near-full-length archaeal MCM: functional insights for an AAA+ hexameric helicase
    Aaron S Brewster
    Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
    Proc Natl Acad Sci U S A 105:20191-6. 2008
    ..These structural and biochemical results provide a basis for future study of the helicase mechanisms of the archaeal and eukaryotic MCM complexes in DNA replication...
  88. ncbi Nitrogen fixation at 92 degrees C by a hydrothermal vent archaeon
    Mausmi P Mehta
    School of Oceanography, University of Washington, Seattle, WA 98195, USA
    Science 314:1783-6. 2006
    ..This increase in the temperature limit of nitrogen fixation could reveal a broader range of conditions for life in the subseafloor biosphere and other nitrogen-limited ecosystems than previously estimated...
  89. pmc The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation
    Jan P Erzberger
    Biochemistry and Molecular Biology Division, Department of Molecular and Cell Biology, 229 Stanley Hall, University of California, Berkeley, CA 94720, USA
    EMBO J 21:4763-73. 2002
    ....
  90. ncbi Characterization of Sac10a, a hyperthermophile DNA-binding protein from Sulfolobus acidocaldarius
    Stephen P Edmondson
    Laboratory for Structural Biology, Department of Chemistry, Graduate Program in Biotechnology and Bioengineering, University of Alabama in Huntsville, Huntsville, Alabama 35899, USA
    Biochemistry 43:13026-36. 2004
    ..Sac10a shows no sequence similarity to the other Sulfolobus chromatin proteins Sac7d, Sac8, Sso10b2, and Alba...
  91. pmc A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability
    Amy K Schmid
    Institute for Systems Biology, Seattle, WA 98103 8904, USA
    Mol Syst Biol 5:282. 2009
    ..Simultaneous analysis of metabolic and gene regulatory network architectures suggests an ongoing process of co-evolution in which TrmB integrates the expression of metabolic enzyme-coding genes of diverse origins...
  92. pmc A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq
    Elizabeth G Wilbanks
    University of California Davis, Department of Biomedical Engineering and Genome Center, One Shields Avenue, Davis, CA 95616, USA
    Nucleic Acids Res 40:e74. 2012
    ..While this study focuses on the application of ChIP-seq in H. salinarum sp. NRC-1, our workflow can also be adapted for use in other archaea and bacteria with basic genetic tools...
  93. pmc The Mre11 protein interacts with both Rad50 and the HerA bipolar helicase and is recruited to DNA following gamma irradiation in the archaeon Sulfolobus acidocaldarius
    Achim Quaiser
    Univ Paris Sud, Institut de Genetique et Microbiologie, CNRS UMR 8621, Batiment 409, F 91405 Orsay cedex, France
    BMC Mol Biol 9:25. 2008
    ..Since genetic tools for hyperthermophilic archaea are just emerging, we utilized immuno-detection approaches to get the first in vivo data on the role(s) of these proteins in the hyperthermophilic crenarchaeon Sulfolobus acidocaldarius...
  94. pmc The core and unique proteins of haloarchaea
    Melinda D Capes
    Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland, 701 East Pratt Street, Baltimore, MD 21202 USA
    BMC Genomics 13:39. 2012
    ..However, few previous attempts have been made to identify novel genes that would permit survival in such extreme conditions...
  95. pmc DNA replication: archaeal oriGINS
    Stephen D Bell
    Sir William Dunn School of Pathology, Oxford OX1 3RE, UK
    BMC Biol 9:36. 2011
    ..The structure reveals the anticipated similarity to the previously determined eukaryotic complex but also has some intriguing differences in the relative disposition of subunit domains...
  96. ncbi Tantalizing evidence for caspase-like protein expression and activity in the cellular stress response of Archaea
    Kelly A Bidle
    Department of Biology, Rider University, Lawrenceville, NJ, USA
    Environ Microbiol 12:1161-72. 2010
    ..By playing a role in normal cell function, caspase-like proteases in Archaea appear to have co-evolved with other metabolic pathways, broadening their biological roles beyond apoptosis and cell death...
  97. pmc Genetic and biochemical analysis of the twin-arginine translocation pathway in halophilic archaea
    Kieran Dilks
    Department of Biology, University of Pennsylvania, Philadelphia, 19104, USA
    J Bacteriol 187:8104-13. 2005
    ..Using size exclusion chromatography to further characterize cytoplasmic and membrane TatA proteins, we find these proteins present in high-molecular-weight complexes in both cellular fractions...
  98. pmc Identification and characterization of an archaeon-specific riboflavin kinase
    Zahra Mashhadi
    Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
    J Bacteriol 190:2615-8. 2008
    ..Some divalent metals were found to be potent inhibitors of the reaction. The enzyme represents a unique CTP-dependent family of kinases...
  99. ncbi Archaeal RNA polymerase is sensitive to intrinsic termination directed by transcribed and remote sequences
    Thomas J Santangelo
    Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
    J Mol Biol 355:196-210. 2006
    ....
  100. ncbi Nucleoid-associated proteins in Crenarchaea
    Rosalie P C Driessen
    Leiden Institute of Chemistry, Gorlaeus Laboratories, Laboratory of Molecular Genetics and Cell Observatory, Leiden University, P O Box 9502, 2300 RA Leiden, The Netherlands
    Biochem Soc Trans 39:116-21. 2011
    ..It relies on the action of a large set of small, abundant and generally basic proteins to compact and organize their genome and to modulate its activity...
  101. pmc Structure and catalysis of acylaminoacyl peptidase: closed and open subunits of a dimer oligopeptidase
    Veronika Harmat
    Laboratory of Structural Chemistry and Biology and HAS ELTE Protein Modeling Group, Institute of Chemistry, Eotvos Lorand University, Pázmány P sétány 1 A, H 1117 Budapest, Hungary
    J Biol Chem 286:1987-98. 2011
    ..The mutations affected the closed, active form of the enzyme, disrupting its catalytic triad. We concluded that the two forms are at equilibrium and the substrates bind by the conformational selection mechanism...

Research Grants62

  1. FEN-1 and PCNA Complexes and Human Genome Stability
    John A Tainer; Fiscal Year: 2013
    ..Targeted experiments on human and archaeal proteins will allow efficient and systematic analyses fundamental to understanding FEN, XPG, and ligase activities ..
  2. Interrogation of systems level mechanisms controlling DNA repair processes
    Nitin S Baliga; Fiscal Year: 2010
    ..e. a predictive model for regulatory mechanisms for repair. This basic model will serve as a template for designing systems approaches to model higher complexities of eukaryotic repair processes. ..
  3. MOLECULAR SEQUENCE DATA
    Samuel Karlin; Fiscal Year: 2001
    ..by spacings between repeats, and by properties of repeat families (intergenic, coding, direct, inverted, mixed). ..
  4. Gene Expression Levels Across Diverse Genomes
    Samuel Karlin; Fiscal Year: 2006
    ..A third major objective of our research will be to extend our codon usage methods for predicting gene expression levels to eukaryotic genomes, including yeast, D. melanogaster, C. elegans, and human. [unreadable] [unreadable]..
  5. DNA RADICAL KINETICS
    Martin Newcomb; Fiscal Year: 2001
    ....
  6. MECHANISTIC PROBES FOR ENZYME-CATALYZED OXIDATIONS
    MARTIN E NEWCOMB; Fiscal Year: 2010
    ..A better understanding of the fundamental nature of the reactive species formed in the enzymes and the mechanisms of their reactions is expected to lead to lead ultimately to health-related advances in disease treatment and drug design. ..
  7. INTERFACIAL ACTIVATION OF WATER SOLUBLE PHOSPHOLIPASES
    Mary Roberts; Fiscal Year: 2003
    ..abstract_text> ..
  8. ATP-DEPENDENT PROTEIN KINASES IN GRAM-POSITIVE BACTERIA
    Milton Saier; Fiscal Year: 2004
    ..abstract_text> ..
  9. MOLECULAR MECHANISM OF DYSKERATOSIS CONGENITA
    U Meier; Fiscal Year: 2008
    ..The results of this application will allow pinpointing the molecular consequences of DC mutations on several basic cellular functions and thereby provide the basis for small molecule/drug development. ..
  10. New Inhibitors of HIV Replication
    Gabriele Varani; Fiscal Year: 2005
    ..While the project is challenging and partly untested, the introduction of new structures leading to therapeutic options for treating drug-resistant viruses would have substantial impact. ..
  11. Energy metabolism and virulence of Bordetella species
    Imke Schroeder; Fiscal Year: 2008
    ..The relative contributions of cytochrome oxidase to the infectious cycle will be analyzed in Aim 3 using high-resolution animal models of respiratory tract infection. ..
  12. Development of a HTS system:topoisomerase targets (RMI)
    Yuk Ching Tse Dinh; Fiscal Year: 2004
    ..The screening system should also be applicable for targeting topoisomerases in pathogenic bacteria relevant for biodefense. ..
  13. Structure-Function Studies of Annexin I and II
    Hartmut Luecke; Fiscal Year: 2006
    ..5) Co-crystallize annexin with t-PA and solve the structure of this complex after characterizing complex formation in solution. ..
  14. Redox Regulation of Auxillary B subunits of BK Channels
    Christopher Lingle; Fiscal Year: 2006
    ..Furthermore, BK channels may play a key role as neuroprotectants during ischemic conditions. This work will provide important insight into the mechanisms by which this role of BK channels may occur. ..
  15. Propeptide-Mediated Protein Folding
    Masayori Inouye; Fiscal Year: 2006
    ..Another emphasis is to investigate how the nascent folding intermediate can be activated with small peptide substrates. ..
  16. AUTOMATED PROTEIN FOLD MODEL GENERATION
    Temple Smith; Fiscal Year: 2003
    ..In addition, these libraries and their associated analysis tools will provide valuable data to aid in the experimental design to test predictions about the cellular roles of such proteins. ..
  17. Atomic structures of chemotaxis receptors and complexes
    Sung Hou Kim; Fiscal Year: 2010
    ....
  18. FUNCTION AND MECHANISM OF DNA TOPOISOMERASE
    Tao Shih Hsieh; Fiscal Year: 2010
    ..This will also allow us to examine the mechanistic basis of a number of anti-cancer drugs that affect the equilibrium of DNA cleavage and religation. ..
  19. Refinement of Macromolecular Assembly Structure using Electron Microscopy
    Michael S Chapman; Fiscal Year: 2010
    ..A second goal is a more detailed mechanistic understanding of biomolecular complexes, going beyond domain movements to the internal conformational changes that drive them. ..
  20. PROTEIN NMR STRUCTURE AND DYNAMICS VIA ISOTOPIC LABELING
    DAVID LEMASTER; Fiscal Year: 2002
    ..This labeling pattern is likewise well suited for more conventional NOE-based solution structure determinations and its range of utility will be demonstrated ..
  21. STRUCTURAL STUDIES OF THE BACTERIORHODOPSIN PHOTOCYCLE
    Hartmut Luecke; Fiscal Year: 2002
    ....
  22. Structural Basis for Sporulation in Bacillus
    Seth A Darst; Fiscal Year: 2010
    ..4. Structurally characterize the ?F regulatory system (?F/SpollAA/SpollAB/SpollE) controlling the initiation of Bacillus sporulation. ..
  23. Recombinant archaeal organelles of SIV and HIV antigens
    Elizabeth Stuart; Fiscal Year: 2002
    ....
  24. X-RAY CRYSTALLOGRAPHIC STUDIES OF TAQ RNA POLYMERASE
    Seth Darst; Fiscal Year: 2008
    ..Determine the crystal structure of RNAP with the transcription elongation factor GreA/B; 5. Determine the crystal structure of T. thermophilus sigma (E) holoenzyme. ..
  25. Engineering new RNA-binding proteins by selection and design
    Gabriele Varani; Fiscal Year: 2010
    ..abstract_text> ..
  26. Structure of ribonucleoprotein: telomerase
    Gabriele Varani; Fiscal Year: 2007
    ..The design and execution of new biochemical and functional experiments, grounded onto the structural results, that will address the biological function of these protein-RNA complexes. ..
  27. Role of cytochrome oxidases in Bordetella pathogenesis
    Imke Schroeder; Fiscal Year: 2007
    ..Jeffrey F. Miller as co-investigator. Although this study is exploratory in nature Dr. Miller brings extensive expertise on Bordetella genetics and pathogen-animal host interaction to the project. [unreadable] [unreadable]..
  28. Histones and Nucleosomes in Archaea
    JOHN REEVE; Fiscal Year: 2007
    ..abstract_text> ..
  29. Signal Transduction by Histidine Kinases and their Response Regulators
    Masayori Inouye; Fiscal Year: 2009
    ..abstract_text> ..
  30. Improvement of RNAi efficacy by blocking RNAi inhibitors
    ERIK SONTHEIMER; Fiscal Year: 2007
    ..Development of compounds that boost RNAi performance in general will have significant impact on public health. [unreadable] [unreadable] [unreadable] [unreadable]..
  31. MICROBIAL METABOLISM OF REDUCED PHOSPHORUS COMPOUNDS
    WILLIAM METCALF; Fiscal Year: 2008
    ..unreadable] [unreadable]..
  32. RNA Silencing Complex Assembly and Function
    ERIK SONTHEIMER; Fiscal Year: 2008
    ..Accordingly, a deeper understanding of RNA silencing pathways will accelerate many aspects of biomedical research and disease treatment. ..
  33. Pyrrolysine, a novel genetically encoded amino acid
    Joseph Krzycki; Fiscal Year: 2008
    ..Finally, transposon mutagenesis will be used to identify unknown genes with anticipated or unanticipated functions during UAG translation as pyrrolysine. [unreadable] [unreadable]..
  34. Structure/Function of the Bacterial TRCF
    Seth Darst; Fiscal Year: 2008
    ..3. Determine the structural basis for the specific transcription termination activity of TRCF through structural studies of an RNAP ternary elongation complex (RNAP/DNA/RNA) with TRCF. ..
  35. PHOSPAGEN KINASE STRUCTURE, MECHANISM AND SPECIFICITY
    Michael Chapman; Fiscal Year: 2002
    ....
  36. Mechanism of Ligand Gating in Potassium Channels
    Youxing Jiang; Fiscal Year: 2008
    ..We will use structure-based mutagenesis combined with single channel electrophysiological recordings to analyze the energetic process of ligand gating. ..
  37. Transcriptional Nitrogen Regulation in Methanococcus
    JOHN LEIGH; Fiscal Year: 2007
    ..These studies in Archaea have wide importance, as regulatory mechanisms are central to human development and disease. ..
  38. Eukaryotic Membrane Protein Folding in E. coli
    John Spudich; Fiscal Year: 2006
    ..Submitted in response to PA-03-100 High Impact/High Risk Research and PA-02-060 Structural Biology of Membrane Proteins. ..
  39. Intelligent Information Systems for Systems Biology
    Leroy Hood; Fiscal Year: 2003
    ..Finally, we propose some novel educational programs designed to put graduate students together into interdisciplinary teams for problem solving. ..
  40. REGULATORY DOMAINS OF PROTEIN PHOSPHATASE-1
    PETER KENNELLY; Fiscal Year: 2004
    ..The realization of these aims will contribute to our long-term goal of mapping and modeling the molecular interplay of a complete signal transduction/regulatory network on a cellular scale. ..
  41. STRESS RESPONSE AND ADAPTATION IN ESCHERICHIA COLI
    Masayori Inouye; Fiscal Year: 2003
    ..The proposed research will provide important insight into the fundamental principles of stress response and adaptation in prokaryotes. ..
  42. PERMEATION MECHANISMS IN POTASSIUM CHANNELS
    Roderick MacKinnon; Fiscal Year: 2003
    ..The third specific aim focuses on a structural component of the HERG K+ channel that controls its gating. The HERG K+ channel governs electrical activity of the heart; its malfunction is a cause of sudden death by cardiac arrhythmia. ..
  43. GENOME SEQUENCE AND REGULATION IN M MARIPALUDIS
    JOHN LEIGH; Fiscal Year: 2002
    ..Genes will be identified that either vary in expression with changing conditions, or change in expression after mutagenesis of regulatory genes. ..
  44. STRUCTURE/FUNCTION IN MOLECULAR COMMUNICATION
    Sung Hou Kim; Fiscal Year: 2002
    ..The objective of these studies is to resolve the conflicting evidence about the mechanism of transmembrane signaling in dimeric receptors. ..
  45. Conference: Diffraction Methods in Structural Biology
    Michael Chapman; Fiscal Year: 2002
    ..Junior participation will be encouraged with a new policy of 3 mini-talks each day invited from the poster-presentations by the day's session chairs. ..
  46. ION CHANNELS, ACTION POTENTIALS, AND QUANTAL SECRETION
    Christopher Lingle; Fiscal Year: 2001
    ....
  47. STRUCTURAL PARAMETERS OF E COLI RNA POLYMERASE
    Seth Darst; Fiscal Year: 2001
    ....
  48. Cold Shock Vectors for Single Protein Production
    Masayori Inouye; Fiscal Year: 2004
    ..The proposed vector-host system will be highly useful not only for structural biology but also for medicinal research involving human proteins, which can not be obtained by conventional expression systems. ..
  49. REVERSE TRANSCRIPTASES IN THE PROKARYOTES
    Masayori Inouye; Fiscal Year: 2004
    ....
  50. The mechanism of signal transduction in photoreceptors
    Hartmut Luecke; Fiscal Year: 2006
    ..5. Determine the crystal structure of the primary Anabaena photoreceptor in the ground and signaling state. 6. Determine the structure of the complex of the Anabaena photoreceptor with its putative transducer. [unreadable] [unreadable]..
  51. Upgrade of in-house X-ray diffraction equipment
    Seth Darst; Fiscal Year: 2006
    ..unreadable] [unreadable]..
  52. CALCIUM-ACTIVATED POTASSIUM CHANNELS
    Christopher Lingle; Fiscal Year: 2006
    ....
  53. Crystallographic Analysis of GHMP kinases
    Hong Zhang; Fiscal Year: 2005
    ....
  54. Crystallographic Analysis of NMN Adenylytransferases
    Hong Zhang; Fiscal Year: 2005
    ..influenzae, and the crystallization trials are in progress. Elucidating the structures of NadR in its various ligand-bound forms and its complex with DNA will reveal how its conformation and function are modulated by both NAD and ATP. ..
  55. 750 Mhz NMR Console
    Gabriele Varani; Fiscal Year: 2005
    ..Furthermore, the new console will reduce the inevitable downtime associated with console failure, which are becoming increasingly common as the spectrometer ages. ..
  56. KINETIC CONTROL IN THIOREDOXINS AND DISULFIDE ISOMERASES
    DAVID LEMASTER; Fiscal Year: 2001
    ..abstract_text> ..
  57. Support for 2002 GRC on Photosensory Receptors & Signal
    John Spudich; Fiscal Year: 2002
    ..We expect the conference will stimulate exciting discussion of emerging insights, general principles, and the most engaging mysteries on the cutting edge of photosensory signal transduction. ..
  58. Archaeal gene recruitment by the Chlamydiales
    David Graham; Fiscal Year: 2008
    ..Results from these experiments will support future microbiological studies of the role of this system in chlamydial infection and survival in the host cell. [unreadable] [unreadable] [unreadable]..
  59. SIGNAL TRANSDUCTION MECHANISMS IN BACTERIAL CHEMOTAXIS
    Richard Stewart; Fiscal Year: 2009
    ..Our results will help to define general concepts about regulation and clustering of receptor-kinase complexes. ..
  60. Structure and function of SRP RNA
    Christian Zwieb; Fiscal Year: 2006
    ..These studies will focus on the specific features of two critical interactions and define their dynamic relationship to SRP function. [unreadable] [unreadable]..
  61. ENZYMOLOGY OF ACETOTROPHIC METHANOGENESIS
    JAMES FERRY; Fiscal Year: 2003
    ..The results are expected to contribute not only to a deeper understanding of the acetate fermentation pathway, but more importantly to the broader field of anaerobic microbiology and beyond. ..