Dr. Adrian R. Ferre-D'Amare

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Howard Hughes Medical Institute
Fred Hutchinson Cancer Research Center
InvestigatorAppointed: 2008
Fred Hutchinson Cancer Research Center
Division of Basic Sciences
MemberAppointed: 1999
University of Washington
School of Medicine
Department of Biochemistry
Affiliate Associate ProfessorAppointed: 1999
Professional Headshot of Adrian R. Ferre-D'Amare

Mailing Address

Howard Hughes Medical Insititue
Fred Hutchinson Cancer Research Center
1100 Fairview Avenue North
Seattle, Washington 98109-1024
United States

Contact Information

Phone: (206) 667-3622
Fax: (206) 667-3331
aferre@fhcrc.org

Qualifications

Ph.D., The Rockefeller University, Molecular Biophysics, 1995.
B.A., Instituto Tecnologico y de Estudios Superiores de Monterrey, Chemistry, 1990.

Expertise and Research Interests

Despite its chemical simplicity (compared to proteins) RNA can fold into intricate three-dimensional structures that can recognize other RNAs, proteins and small molecules with high affinity and specificity and carry out biological catalysis. We employ structural, biophysical, biochemical, and in vitro genetic techniques, as well as chemical synthesis, to study ribozymes, riboswitches, and ribonucleoprotein complexes.

We study ribozymes (catalytic RNAs), both cellular and in vitro selected, because they starkly demonstrate the chemical versatility of this nucleic acid. We study riboswitches. These are RNA elements of non-coding regions of messenger RNAs that can switch between two functional states, depending on whether they are bound to a metabolite. Riboswitches are used by bacteria and eukaryotes to regulate gene expression at the transcriptional, post-transcriptional, and translational levels. We study protein enzymes responsible for post-transcriptional modification of RNAs. These modifications expand the chemical repertoire of the nucleic acid; the enzymes responsible may also serve as chaperones, facilitating RNA folding in vivo. We study a family of protein enzymes called pseudouridine synthases. These are responsible for the most abundant and phylogenetically conserved modification of cellular RNAs.

Keywords

COS Keywords:

Biochemistry, Biochemistry, Proteins, Biophysics, Crystallography, Proteins and Macromolecules, RNA.

Additional Terms:

Catalytic RNA, Molecular Biophysics, X-ray Crystallography.

Memberships

American Alpine Club
RNA Society

Honors and Awards

2004, Eli Lilly & Co. Research Award, American Society for Microbiology, ASM
2003-2008, Distinguished Young Scholar in Medical Research, W.M. Keck Foundation
2001-2004, Rita Allen Foundation Scholar, Rita Allen Foundation
1995-1998, Jane Coffin Childs Postdoctoral Fellowship, J. Coffin Childs Memorial Fund, Yale University
1993-1995, David Rockefeller Predoctoral Fellowship, The Rockefeller University
1990, Summa cum Laude, Instituto Tecnologico y de Estudios Superiores de Monterrey

Previous Positions

1998-1999, Associate Research Scientist, Yale University, Molecular Biophysics and Biochemistry
1995-1998, Postdoctoral Fellow, Yale University, Molecular Biophysics and Biochemistry
1990-1995, Graduate Fellow, The Rockefeller University, Laboratory of Molecular Biophysics

Publications

  • Klein, D.J., Ferre-D'Amare A.R. (2009) Crystallization of the glms ribozyme-riboswitch, Methods in Molecular Biology, 540, 129-139
  • Klein, D.J., Edwards, T.E., Ferré-D'Amaré, A.R. (2009) Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase, Nature Structural and Molecular Biology, 16, 343-344
  • Pitt, J.N., Ferré-D'Amaré, A.R. (2009) Structure-guided engineering of the regioselectivity of RNA ligase ribozymes, Journal of the American Chemical Society, 131, 3532-3540
  • E.G. Mueller, A.R. Ferré-D'Amaré (2009) Pseudouridine formation, the most common transglycosylation in RNA, DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution, Austin, Landes Bioscience, 363-376 pages, ISBN=978-1-58706-3 (bookchapter)
  • Xiao, H., Edwards, T.E., Ferré-D'Amaré, A.R. (2008) Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch, Chemistry & Biology, 15, 1125-1137
  • Xiao, H, Murakami, H., Suga, H., Ferré-D'Amaré, A.R. (2008) Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme, Nature, 454, 358-361
  • Ferré-D'Amaré, A.R. (2008) RNA-modifying enzymes, Protein-Nucleic Acid Interactions, First Edition, Cambridge, Royal Society of Chemistry, 367-381 pages, ISBN=978-0-85404-2 (bookchapter)
  • Klein, D.J., Been, M.D., Ferré-D'Amaré, A.R. (2007) Essential role of an active-site guanine in glmS ribozyme catalysis, Journal of the American Chemical Society, 129, 14858-14859
  • Klein, D.J., Wilkinson, S.R., Been, M.D., Ferré-D'Amaré, A.R. (2007) Requirement of helix P2.2 and nucleotide G1 for positioning the cleavage site and cofactor of the glmS ribozyme, Journal of Molecular Biology, 373, 178-189
  • Reichow, S.L., Hamma, T., Ferré-D'Amaré, A.R., Varani, G. (2007) The structure and function of small nucleolar ribonucleoproteins, Nucleic Acids Research, 35, 1125-1135
  • Edwards, T.E., Klein, D.J., Ferré-D'Amaré, A.R (2007) Riboswitches: small molecule recognition by gene-regulatory RNAs, Current Opinion in Structural Biology, 15, 273-279
  • Hamma, T., Ferré-D'Amaré, A.R. (2006) Pseudouridine synthases, Chemistry and Biology, 13, 1125-1135
  • Hoang, C., Chen, J., Vizthum, C.A., Kandel, J.M., Hamilton, C.S., Mueller, E.G., Ferré-D'Amaré, A.R. (2006) Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure, Molecular Cell, 24, 535-545
  • Klein, D.J., Ferré-D'Amaré, A.R. (2006) Structural basis of glmS ribozyme activation by glucosamine-6-phosphate, Science, 313, 1752-1756
  • Edwards, T.E., Ferré-D'Amaré, A.R. (2006) Crystal structure of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition, Structure, 14, 1459-1468
  • Pitt, J.N., Ferré-D'Amaré, A.R. (2005) How RNA closes a Diel, Nature Structural and Molecular Biology, 12, 206-208
  • Hoang, C., Hamilton, C.S., Mueller, E.G., Ferré-D'Amaré, A.R. (2005) Precursor complex structure of pseudouridine synthase TruB suggests coupling of active site perturbations to an RNA-sequestering peripheral domain, Protein Science, 14, 2201-2206
  • Hamma, T, Reichow, S.L., Varani, G., Ferré-D'Amaré, A.R. (2005) The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPs, Nature Structural and Molecular Biology, 12, 1101-1107
  • Hoang, C., Ferré-D'Amaré, A.R (2004) Crystal structure of the highly divergent pseudouridine synthase TruD reveals a circular permutation of a conserved fold, RNA, 10, 1026-1033
  • Hamma, T., Ferré-D'Amaré, A.R. (2004) Structure of protein L7Ae bound to a K-turn derived from an archaeal box H/ACA sRNA at 1.8 Ĺ resolution, Structure, 12, 893-903
  • Ferré-D'Amaré, A.R (2004) The hairpin ribozyme, Biopolymers, 73, 71-78
  • Rupert, P.B., Ferré-D'Amaré, A.R. (2004) Crystallization of the hairpin ribozyme: illustrative protocols, Methods in Molecular Biology, 252, 303-311
  • Rupert, P.B., Xiao, H., Ferré-D'Amaré, A.R (2003) U1A RNA-binding domain at 1.8 Ĺ resolution, Acta Crystallographica, D59, 1521-1524
  • Ferré-D'Amaré, A.R (2003) RNA-modifying enzymes, Current Opinion in Structural Biology, 13, 49-55
  • Rupert, P.B., Ferré-D'Amaré, A.R (2002) The hairpin ribozyme: From crystal structure to function, Biochemical Society Transactions, 30, 1105-1109
  • Rupert, P.B., Massey, A.P., Sigurdsson, S.Th., Ferré-D'Amaré, A.R (2002) Transition state stabilization by a catalytic RNA, Science, 298, 1421-1424
  • Rupert, P.B., Ferré-D'Amaré, A.R (2001) Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis, Nature, 410, 780-786
  • Hoang, C., Ferré-D'Amaré, A.R. (2001) Cocrystal structure of a tRNA psi55 pseudouridine synthase: Nucleotide flipping by an RNA-modifying enzyme, Cell, 107, 929-939
  • Luptak, A., Ferré-D'Amaré, A.R., Zhou, K., Doudna, J.A. (2001) Direct pKa measurement of the active-site cytosine ina a genomic hepatitis delta virus ribozyme, Journal of the American Chemical Society, 123, 8447-8452
  • Rupert, P.B.,, Ferré-D'Amaré, A.R. (2000) SRPrises in RNA-protein recognition, Structure, 8, R99-R104
  • Ferré-D'Amaré, A.R., Doudna, J.A. (2000) Crystallization and structure determination of a hepatitis delta virus ribozyme: Use of the RNA-binding protein U1A as a crystallization module, Journal of Molecular Biology, 295, 541-556
  • Ferré-D'Amaré, A.R., Doudna, J.A. (1999) RNA folds: Insights from recent crystal structures, Annual Review of Biophysics and Biomolecular Structure, 28, 57-73
  • Ferré-D'Amaré, A.R (1999) Book Review: Crystallization of Biological Macromolecules, RNA, 5, 847-848
  • Basu, S., Rambo, R.P., Strauss-Soukup, J., Cate, J.H., Ferré-D'Amaré, A.R., Strobel, S.A., Doudna, J.A (1998) A specific monovalent metal ion integral to the A-A platform of the RNA tetraloop receptor, Nature Structural Biology, 5, 986-992
  • Ferré-D'Amaré A.R., Zhou K., Doudna, J.A. (1998) A general module for RNA crystallization, Journal of Molecular Biology, 279, 621-631
  • Ferré-D'Amaré A.R., Zhou K., Doudna, J.A. (1998) Crystal structure of a hepatitis delta viurs ribozyme, Nature, 395, 567-574
  • Steingrímsson, E., Favor, J., Ferré-D'Amaré, A.R., Copeland, N.G., Jenkins, N.A (1998) Mitfmi-enu122 is a missense mutation in the HLH dimerization domain, Mammalian Genome, 9, 250-252
  • Párraga, A., Bellsolell, L., Ferré-D'Amaré, A.R. (1998) Co-crystal structure of sterol regulatory element binding protein 1a at 2.3 Ĺ resolution, Structure, 6, 661-672
  • Ferré-D'Amaré, A.R., Burley, S.K. (1997) Dynamic light scattering in evaluating crystallizability of macromolecules, Methods in enzymology, 276, 157-166
  • Ferré-D'Amaré, A.R., Doudna, J.A. (1997) Establishing suitability of RNA preparations for crystallization, Methods in Molecular Biology, 74, 371-377
  • Steingímsson, E., Nii, A., Fisher, D.F., Ferré-D'Amaré, A.R., McCormick, R.J., Russell, L.B., Burley, S.K., Ward, J.M., Jenkins, N.A. (1996) The semidominant Mib mutation identifies a role for the HLH domain in DNA binding in addition to its role in protein dimerization, EMBO Journal, 15, 6280-6289
  • Ferré-D'Amaré, A.R., Doudna, J.A. (1996) Use of cis- and trans-ribozymes to remove 5' and 3' heterogeneities from milligrams of in vitro transcribed RNA, Nucleic Acids Research, 24, 977-978
  • Ferré-D'Amaré, A.R., Burley, S.K. (1995) DNA recognition by helix-loop-helix proteins, Nucleic Acids and Molecular Biology, 9, 285-298
  • Canne, L.E., Ferré-D'Amaré, A.R., Burley, S.K., Kent, S.B.H. (1995) Total chemical synthesis of a unique transcription factor protein: cMyc-Max, Journal of the American Chemical Society, 117, 2998-3007
  • Sha, M., Ferré-D'Amaré, A.R., Burley, S.K., Goss, D.J. (1995) Anti-cooperative biphasic equilibrium binding of transcription factor upstream stimulatory factor to its cognate DNA monitored by protein fluorescence changes, Journal of Biological Chemistry, 270, 19325-19329
  • Cohen, S.L., Ferré-D'Amaré, A.R., Burley, S.K., Chait, B. (1995) Probing the solution structure of the DNA-binding protein Max by a combination of proteolysis and mass spectrometry, Protein Science, 4, 1088-1099
  • Ferré-D'Amaré, A.R. (1995) Prospección ecológica de los arrecifes coralinos de Cayos Arcas y Triángulos, Campeche, México. Impacto ambiental de una década de actividades de la industria petrolera, Sian Ka'an Serie Documentos, 4, 40-48
  • Steingrímsson, E., Moore, K.J., Lamoreux, M.L., Ferré-D'Amaré, A.R., Burley, S.K., Sanders Zimring, D.C., Skow, L.C., Hodgkinson, C.A., Arnheiter, H., Copeland, N.G. (1994) Molecular basis of mouse microphthalmia (mi) mutations helps explain their developmental and phenotypic consequences, Nature Genetics, 8, 256-268
  • Ferré-D'Amaré, A.R., Burley, S.K. (1994) Use of dynamic light scattering to assess crystallizability of macromolecules and macromolecular assemblies, Structure, 2, 357-359
  • Ferré-D'Amaré, A.R., Pognonec, P., Roeder, R.G., Burley, S.K. (1994) Structure and function of the b/HLH/Z domain of USF, EMBO Journal, 13, 180-189
  • Burley, S.K., Clark, K.L., Ferré-D'Amaré, A., Kim, J.L. (1993) X-ray crystallographic studies of eukaryotic transcription factors, Cold Spring Harbor Symposia on Quantitative Biology, 58, 123-132
  • Ferré-D'Amaré, A.R., Prendergast, G.C., Ziff, E.B., Burley, S.K. (1993) Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain, Nature, 363, 38-45
  • Ferré-D'Amaré, A.R (1985) Coral reefs of the Mexican Atlantic: a review, Proceedings of the Fifth International Coral Reef Symposium, 6, 349-354

Profile Details

Last Updated: 7/26/2009

COS Expertise ID #675640
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