Research Topics
Genomes and Genes | ADRIAN R FERRE-D'AMARESummaryAffiliation: Fred Hutchinson Cancer Research Center Country: USA Publications
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Publications
The hairpin ribozyme: from crystal structure to functionA 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...
Small self-cleaving ribozymesADRIAN 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...- The glmS ribozyme: use of a small molecule coenzyme by a gene-regulatory RNAADRIAN 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.... - Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAsADRIAN 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.... - The roles of metal ions in regulation by riboswitchesADRIAN 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... - RNA-modifying enzymesADRIAN 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... - The hairpin ribozymeADRIAN 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.... - Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structureCharmaine 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... - Pseudouridine synthasesTomoko Hamma
Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
Chem Biol 13:1125-35. 2006.... - Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitchNadia Kulshina
Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195, USA
RNA 16:186-96. 2010.... 
Crystallization of the glmS ribozyme-riboswitchDaniel 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...- Structural basis of glmS ribozyme activation by glucosamine-6-phosphateDaniel 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... - Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozymeHong 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... - Precursor complex structure of pseudouridine synthase TruB suggests coupling of active site perturbations to an RNA-sequestering peripheral protein domainCharmaine 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... - The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modificationTomoko 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... - Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitchNadia Kulshina
Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, USA
Nat Struct Mol Biol 16:1212-7. 2009.... - Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitchHong 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... - Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobaseDaniel 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.... - The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPsTomoko 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... - Structure-guided engineering of the regioselectivity of RNA ligase ribozymesJason 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... - Rapid construction of empirical RNA fitness landscapesJason 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... - Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognitionThomas 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... - Ribozymes and riboswitches: modulation of RNA function by small moleculesJinwei Zhang
Howard Hughes Medical Institute, Seattle, Washington 98109 1024, USA
Biochemistry 49:9123-31. 2010.... - Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysisNathan 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... - Structure of protein L7Ae bound to a K-turn derived from an archaeal box H/ACA sRNA at 1.8 A resolutionTomoko 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... - SEWAL: an open-source platform for next-generation sequence analysis and visualizationJason 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... - 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... - Crystal structure of the highly divergent pseudouridine synthase TruD reveals a circular permutation of a conserved foldCharmaine 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 Grants
- MSC BLUE-3 AND MSC PURPLE-3 CONFOCAL X-RAY OPTICSADRIAN 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. ..
- Structural Biology of RNAADRIAN 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. ..
- Structural Biology of RNAADRIAN 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. ..
- Structural Biology of RNAADRIAN 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. ..