ADRIAN R FERRE-D'AMARE

Summary

Affiliation: Fred Hutchinson Cancer Research Center
Country: USA

Publications

  1. ncbi The hairpin ribozyme: from crystal structure to function
    A R Ferré-D'amaré
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109 1024, USA
    Biochem Soc Trans 30:1105-9. 2002
  2. pmc Small self-cleaving ribozymes
    ADRIAN R FERRE-D'AMARE
    Howard Hughes Medical Institute and Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 8109 1024, USA
    Cold Spring Harb Perspect Biol 2:a003574. 2010
  3. pmc The glmS ribozyme: use of a small molecule coenzyme by a gene-regulatory RNA
    ADRIAN R FERRE-D'AMARE
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 1024, USA
    Q Rev Biophys 43:423-47. 2010
  4. pmc Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAs
    ADRIAN R FERRE-D'AMARE
    Howard Hughes Medical Institute and Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 1024, USA
    Methods 52:159-67. 2010
  5. pmc The roles of metal ions in regulation by riboswitches
    ADRIAN R FERRE-D'AMARE
    Howard Hughes Medical Institute and Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 1024, USA
    Met Ions Life Sci 9:141-73. 2011
  6. ncbi RNA-modifying enzymes
    ADRIAN R FERRE-D'AMARE
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 1024, USA
    Curr Opin Struct Biol 13:49-55. 2003
  7. ncbi The hairpin ribozyme
    ADRIAN R FERRE-D'AMARE
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 1024, USA
    Biopolymers 73:71-8. 2004
  8. ncbi Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure
    Charmaine Hoang
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Mol Cell 24:535-45. 2006
  9. ncbi Pseudouridine synthases
    Tomoko Hamma
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
    Chem Biol 13:1125-35. 2006
  10. pmc Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch
    Nadia Kulshina
    Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195, USA
    RNA 16:186-96. 2010

Research Grants

  1. MSC BLUE-3 AND MSC PURPLE-3 CONFOCAL X-RAY OPTICS
    ADRIAN FERRE D AMARE; Fiscal Year: 2001
  2. Structural Biology of RNA
    ADRIAN FERRE D AMARE; Fiscal Year: 2007
  3. Structural Biology of RNA
    ADRIAN FERRE D AMARE; Fiscal Year: 2005
  4. Structural Biology of RNA
    ADRIAN FERRE D AMARE; Fiscal Year: 2009

Collaborators

Detail Information

Publications28

  1. ncbi The hairpin ribozyme: from crystal structure to function
    A R Ferré-D'amaré
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109 1024, USA
    Biochem Soc Trans 30:1105-9. 2002
    ..It remains to be established whether this RNA enzyme relies exclusively on binding energy to carry out catalysis, or whether some other mechanism, such as general acid-base catalysis, is being employed...
  2. pmc Small self-cleaving ribozymes
    ADRIAN R FERRE-D'AMARE
    Howard Hughes Medical Institute and Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 8109 1024, USA
    Cold Spring Harb Perspect Biol 2:a003574. 2010
    ..This versatility explains the abundance of ribozymes in contemporary organisms and also supports a role for catalytic RNAs early in evolution...
  3. pmc The glmS ribozyme: use of a small molecule coenzyme by a gene-regulatory RNA
    ADRIAN R FERRE-D'AMARE
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 1024, USA
    Q Rev Biophys 43:423-47. 2010
    ....
  4. pmc Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAs
    ADRIAN R FERRE-D'AMARE
    Howard Hughes Medical Institute and Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 1024, USA
    Methods 52:159-67. 2010
    ....
  5. pmc The roles of metal ions in regulation by riboswitches
    ADRIAN R FERRE-D'AMARE
    Howard Hughes Medical Institute and Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 1024, USA
    Met Ions Life Sci 9:141-73. 2011
    ..In this chapter, we discuss how the intimate physicochemical relationship between metal ions and nucleic acids is important for the structure and function of metal ion- and metabolite-sensing regulatory RNAs...
  6. ncbi RNA-modifying enzymes
    ADRIAN R FERRE-D'AMARE
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 1024, USA
    Curr Opin Struct Biol 13:49-55. 2003
    ..Recent structure determinations have included two types of RNA nucleobase modifying enzyme: pseudouridine synthases and tRNA guanine transglycosylases...
  7. ncbi The hairpin ribozyme
    ADRIAN R FERRE-D'AMARE
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 1024, USA
    Biopolymers 73:71-8. 2004
    ....
  8. ncbi Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure
    Charmaine Hoang
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Mol Cell 24:535-45. 2006
    ..Sequence and structural comparisons suggest that pseudouridine synthases of the RluA, RsuA, and TruA families employ an equivalent arginine for base flipping...
  9. ncbi Pseudouridine synthases
    Tomoko Hamma
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
    Chem Biol 13:1125-35. 2006
    ....
  10. pmc Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch
    Nadia Kulshina
    Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195, USA
    RNA 16:186-96. 2010
    ....
  11. doi Crystallization of the glmS ribozyme-riboswitch
    Daniel J Klein
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109 1024, USA
    Methods Mol Biol 540:129-39. 2009
    ..Although their details are specific to the glmS ribozyme, these general strategies may be useful for analyzing and improving crystals of other RNAs...
  12. ncbi Structural basis of glmS ribozyme activation by glucosamine-6-phosphate
    Daniel J Klein
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 1024, USA
    Science 313:1752-6. 2006
    ..Our structures suggest that the amine group of the glmS ribozyme-bound coenzyme performs general acid-base and electrostatic catalysis...
  13. doi Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme
    Hong Xiao
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109 1024, USA
    Nature 454:358-61. 2008
    ..Such a mechanism would be reminiscent of the mutually induced fit of tRNA and protein employed by some aminoacyl-tRNA synthetases to increase specificity...
  14. pmc Precursor complex structure of pseudouridine synthase TruB suggests coupling of active site perturbations to an RNA-sequestering peripheral protein domain
    Charmaine Hoang
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 1024, USA
    Protein Sci 14:2201-6. 2005
    ..This may allow the peripheral RNA-binding domain to monitor progress of the pseudouridylation reaction...
  15. pmc The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modification
    Tomoko Hamma
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    J Biol Chem 285:805-9. 2010
    ..This analysis reveals how the protein components distort the RNA component of the RNP, enabling productive docking of the substrate RNA into the enzymatic active site...
  16. pmc Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch
    Nadia Kulshina
    Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, USA
    Nat Struct Mol Biol 16:1212-7. 2009
    ....
  17. pmc Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch
    Hong Xiao
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 1024, USA
    Chem Biol 15:1125-37. 2008
    ..The three-helix junction, h-shaped architecture of this artificial RNA is more complex than those of most aptamers and is reminiscent of the structures of some natural riboswitches...
  18. pmc Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase
    Daniel J Klein
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109 1024, USA
    Nat Struct Mol Biol 16:343-4. 2009
    ....
  19. ncbi The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPs
    Tomoko Hamma
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109 1024, USA
    Nat Struct Mol Biol 12:1101-7. 2005
    ..Mutagenesis results implicate an adjacent basic patch in RNA binding. This tripartite RNA-binding surface may function as a molecular bracket that organizes the multihelical H/ACA and telomerase RNAs...
  20. pmc Structure-guided engineering of the regioselectivity of RNA ligase ribozymes
    Jason N Pitt
    Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195, USA
    J Am Chem Soc 131:3532-40. 2009
    ..These results demonstrate how local geometry inherent to the substrate-template duplexes controls the regioselectivity of ribozyme-catalyzed RNA ligation reactions...
  21. pmc Rapid construction of empirical RNA fitness landscapes
    Jason N Pitt
    Howard Hughes Medical Institute and Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 1024, USA
    Science 330:376-9. 2010
    ..High-throughput mapping between genotype and phenotype may apply to artificial selections, host-pathogen interactions, and other biomedically relevant evolutionary phenomena...
  22. ncbi Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition
    Thomas E Edwards
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Structure 14:1459-68. 2006
    ..In the pyrithiamine complex, the pyrophosphate binding site is largely unstructured. These results show how the riboswitch can bind to various metabolites, and why the thi-box preferentially binds thiamine pyrophosphate...
  23. pmc Ribozymes and riboswitches: modulation of RNA function by small molecules
    Jinwei Zhang
    Howard Hughes Medical Institute, Seattle, Washington 98109 1024, USA
    Biochemistry 49:9123-31. 2010
    ....
  24. pmc Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis
    Nathan J Baird
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109 1024, USA
    RNA 16:598-609. 2010
    ..It is possible that the range of behaviors observed by SAXS, rather than being a biophysical idiosyncrasy, reflects adaptation of riboswitches to the regulatory requirements of their individual genomic context...
  25. ncbi Structure of protein L7Ae bound to a K-turn derived from an archaeal box H/ACA sRNA at 1.8 A resolution
    Tomoko Hamma
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 USA
    Structure 12:893-903. 2004
    ..Comparison with the 15.5 kDa/Snu13-RNA complex structure suggests why the eukaryotic homolog does not recognize terminal stem loop L7Ae binding sites...
  26. pmc SEWAL: an open-source platform for next-generation sequence analysis and visualization
    Jason N Pitt
    Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 1024, USA
    Nucleic Acids Res 38:7908-15. 2010
    ..Source code, executable files and links to sample data sets are available at http://www.sourceforge.net/projects/sewal...
  27. pmc Riboswitch function: flipping the switch or tuning the dimmer?
    Nathan J Baird
    Howard Hughes Medical Institute, USA
    RNA Biol 7:328-32. 2010
    ..The range of observed behaviors suggests that in response to the evolutionary need for precise genetic regulation, riboswitches may be tuned to function more as dimmers or rheostats than binary on/off switches...
  28. pmc Crystal structure of the highly divergent pseudouridine synthase TruD reveals a circular permutation of a conserved fold
    Charmaine Hoang
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 1024, USA
    RNA 10:1026-33. 2004
    ..Because the sequence of the permuted segment, a beta-strand that bisects the catalytic domain, is conserved among orthologs from bacteria, archaea and eukarya, the permutation likely happened early in evolution...

Research Grants10

  1. MSC BLUE-3 AND MSC PURPLE-3 CONFOCAL X-RAY OPTICS
    ADRIAN FERRE D AMARE; Fiscal Year: 2001
    ..We are requesting funds to purchase MSC/Max-Flux confocal optics that will result in up to 27-fold increase in useable X-ray flux, relative to the current configuration. ..
  2. Structural Biology of RNA
    ADRIAN FERRE D AMARE; Fiscal Year: 2007
    ..These 'molecular movies' will provide the basic understanding that will help manipulate the functions of RNAs in human health and disease, and in the life cycle of pathogenic organisms. ..
  3. Structural Biology of RNA
    ADRIAN FERRE D AMARE; Fiscal Year: 2005
    ..Finally, we will employ biochemistry and crystallography to analyze how, in eukaryotes, certain nucleolar RNAs scaffold the assembly of psi synthases and accessory proteins into versatile catalytic machines. ..
  4. Structural Biology of RNA
    ADRIAN FERRE D AMARE; Fiscal Year: 2009
    ..These 'molecular movies' will provide the basic understanding that will help manipulate the functions of RNAs in human health and disease, and in the life cycle of pathogenic organisms. ..