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Adrian R. Ferré-D'Amaré, Ph.D.

Publications


Principal Investigator thumbnail image

Adrian R. Ferré-D'Amaré
Senior Investigator

P: +1 301 496 4096
adrian.ferre@nih.gov


Full Publications Listing

Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA.
Zhang J, Ferré-D'Amaré AR.
Nature. 2013 Aug 15;500(7462):363-6.
[Text Abstract on PubMed]

Glucosamine and glucosamine-6-phosphate derivatives: catalytic cofactor analogues for the glmS ribozyme.
Posakony JJ, Ferré-D'Amaré AR.
J Org Chem. 2013 May 17;78(10):4730-43.
[Text Abstract on PubMed]

Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches.
Baird NJ, Ferré-D'Amaré AR.
RNA. 2013 Feb ;19(2):167-76.
[Text Abstract on PubMed]

Allosteric tertiary interactions preorganize the c-di-GMP riboswitch and accelerate ligand binding.
Wood S, Ferré-D'Amaré AR, Rueda D.
ACS Chem. Biol. 2012 May 18;7(5):920-7.
[Text Abstract on PubMed]

YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops.
Baird NJ, Zhang J, Hamma T, Ferré-D'Amaré AR.
RNA. 2012 Apr;18(4):759-70.
[Text Abstract on PubMed]

Riboswitches: discovery of drugs that target bacterial gene-regulatory RNAs.
Deigan KE, Ferré-D'Amaré AR.
Acc. Chem. Res. 2011 Dec 20;44(12):1329-38.
[Text Abstract on PubMed]

Use of a coenzyme by the glmS ribozyme-riboswitch suggests primordial expansion of RNA chemistry by small molecules.
Ferré-D'Amaré AR.
Philos. Trans. R. Soc. Lond., B, Biol. Sci. 2011 Oct 27;366(1580):2942-8.
[Text Abstract on PubMed]

The glmS ribozyme tunes the catalytically critical pK(a) of its coenzyme glucosamine-6-phosphate.
Gong B, Klein DJ, Ferré-D'Amaré AR, Carey PR.
J. Am. Chem. Soc. 2011 Sep 14;133(36):14188-91.
[Text Abstract on PubMed]

Protein synthesis: Stop the nonsense.
Ferré-D'Amaré AR.
Nature. 2011 Jun 16;474(7351):289-90.
[Text Abstract on PubMed]

Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe C.
Edwards TE, Cekan P, Reginsson GW, Shelke SA, Ferré-D'Amaré AR, Schiemann O, Sigurdsson ST.
Nucleic Acids Res. 2011 May;39(10):4419-26.
[Text Abstract on PubMed]

The roles of metal ions in regulation by riboswitches.
Ferré-D'Amaré AR, Winkler WC.
Met Ions Life Sci. 2011;9:141-73.
[Text Abstract on PubMed]

SEWAL: an open-source platform for next-generation sequence analysis and visualization.
Pitt JN, Rajapakse I, Ferré-D'Amaré AR.
Nucleic Acids Res. 2010 Dec;38(22):7908-15.
[Text Abstract on PubMed]

Ribozymes and riboswitches: modulation of RNA function by small molecules.
Zhang J, Lau MW, Ferré-D'Amaré AR.
Biochemistry. 2010 Nov 2;49(43):9123-31.
[Text Abstract on PubMed]

The glmS ribozyme: use of a small molecule coenzyme by a gene-regulatory RNA.
Ferré-D'Amaré AR.
Q. Rev. Biophys. 2010 Nov;43(4):423-47.
[Text Abstract on PubMed]

Rapid construction of empirical RNA fitness landscapes.
Pitt JN, Ferré-D'Amaré AR.
Science. 2010 Oct 15;330(6002):376-9.
[Text Abstract on PubMed]

Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAs.
Ferré-D'Amaré AR.
Methods. 2010 Oct;52(2):159-67.
[Text Abstract on PubMed]

RNA methods: from sequence to structure and dynamics.
Ferré-D'Amaré AR.
Methods. 2010 Oct;52(2):123-4.
[Text Abstract on PubMed]

Riboswitch function: flipping the switch or tuning the dimmer?
Baird NJ, Kulshina N, Ferré-D'Amaré AR.
RNA Biol. 2010 May-Jun;7(3):328-32.
[Text Abstract on PubMed]

Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis.
Baird NJ, Ferré-D'Amaré AR.
RNA. 2010 Mar;16(3):598-609.
[Text Abstract on PubMed]

The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modification.
Hamma T, Ferré-D'Amaré AR.
J. Biol. Chem. 2010 Jan 8;285(2):805-9.
[Text Abstract on PubMed]

Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch.
Kulshina N, Edwards TE, Ferré-D'Amaré AR.
RNA. 2010 Jan;16(1):186-96.
[Text Abstract on PubMed]

Synthetic biology: an RNP switch raises a roadblock.
Ferré-D'Amaré AR.
Nat. Chem. Biol. 2010 Jan;6(1):5-6.
[Text Abstract on PubMed]

Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch.
Kulshina N, Baird NJ, Ferré-D'Amaré AR.
Nat. Struct. Mol. Biol. 2009 Dec;16(12):1212-7.
[Text Abstract on PubMed]

Structure-guided engineering of the regioselectivity of RNA ligase ribozymes.
Pitt JN, Ferré-D'Amaré AR.
J. Am. Chem. Soc. 2009 Mar 18;131(10):3532-40.
[Text Abstract on PubMed]

Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase.
Klein DJ, Edwards TE, Ferré-D'Amaré AR.
Nat. Struct. Mol. Biol. 2009 Mar;16(3):343-4.
[Text Abstract on PubMed]

Crystallization of the glmS ribozyme-riboswitch.
Klein DJ, Ferré-D'Amaré AR.
Methods Mol. Biol. 2009;540:129-39.
[Text Abstract on PubMed]

Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch.
Xiao H, Edwards TE, Ferré-D'Amaré AR.
Chem. Biol. 2008 Oct 20;15(10):1125-37.
[Text Abstract on PubMed]

Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme.
Xiao H, Murakami H, Suga H, Ferré-D'Amaré AR.
Nature. 2008 Jul 17;454(7202):358-61.
[Text Abstract on PubMed]

Essential role of an active-site guanine in glmS ribozyme catalysis.
Klein DJ, Been MD, Ferré-D'Amaré AR.
J. Am. Chem. Soc. 2007 Dec 5;129(48):14858-9.
[Text Abstract on PubMed]

Requirement of helix P2.2 and nucleotide G1 for positioning the cleavage site and cofactor of the glmS ribozyme.
Klein DJ, Wilkinson SR, Been MD, Ferré-D'Amaré AR.
J. Mol. Biol. 2007 Oct 12;373(1):178-89.
[Text Abstract on PubMed]

Riboswitches: small-molecule recognition by gene regulatory RNAs.
Edwards TE, Klein DJ, Ferré-D'Amaré AR.
Curr. Opin. Struct. Biol. 2007 Jun;17(3):273-9.
[Text Abstract on PubMed]

The structure and function of small nucleolar ribonucleoproteins.
Reichow SL, Hamma T, Ferré-D'Amaré AR, Varani G.
Nucleic Acids Res. 2007;35(5):1452-64.
[Text Abstract on PubMed]

Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure.
Hoang C, Chen J, Vizthum CA, Kandel JM, Hamilton CS, Mueller EG, Ferré-D'Amaré AR.
Mol. Cell. 2006 Nov 17;24(4):535-45.
[Text Abstract on PubMed]

Pseudouridine synthases.
Hamma T, Ferré-D'Amaré AR.
Chem. Biol. 2006 Nov;13(11):1125-35.
[Text Abstract on PubMed]

Structural basis of glmS ribozyme activation by glucosamine-6-phosphate.
Klein DJ, Ferré-D'Amaré AR.
Science. 2006 Sep 22;313(5794):1752-6.
[Text Abstract on PubMed]

Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition.
Edwards TE, Ferré-D'Amaré AR.
Structure. 2006 Sep;14(9):1459-68.
[Text Abstract on PubMed]

The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPs.
Hamma T, Reichow SL, Varani G, Ferré-D'Amaré AR.
Nat. Struct. Mol. Biol. 2005 Dec;12(12):1101-7.
[Text Abstract on PubMed]

Precursor complex structure of pseudouridine synthase TruB suggests coupling of active site perturbations to an RNA-sequestering peripheral protein domain.
Hoang C, Hamilton CS, Mueller EG, Ferré-D'Amaré AR.
Protein Sci. 2005 Aug;14(8):2201-6.
[Text Abstract on PubMed]

How RNA closes a Diel.
Pitt JN, Ferré-D'Amaré AR.
Nat. Struct. Mol. Biol. 2005 Mar;12(3):206-8.
[Text Abstract on PubMed]

A novel ARH splice site mutation in a Mexican kindred with autosomal recessive hypercholesterolemia.
Canizales-Quinteros S, Aguilar-Salinas CA, Huertas-Vázquez A, Ordóñez-Sánchez ML, Rodríguez-Torres M, Venturas-Gallegos JL, Riba L, Ramírez-Jimenez S, Salas-Montiel R, Medina-Palacios G, Robles-Osorio L, Miliar-García A, Rosales-León L, Ruiz-Ordaz BH, Zentella-Dehesa A, Ferré-D'Amare A, Gómez-Pérez FJ, Tusié-Luna MT.
Hum. Genet. 2005 Jan;116(1-2):114-20.
[Text Abstract on PubMed]

Crystal structure of the highly divergent pseudouridine synthase TruD reveals a circular permutation of a conserved fold.
Hoang C, Ferre-D'Amare AR.
RNA. 2004 Jul;10(7):1026-33.
[Text Abstract on PubMed]

Structure of protein L7Ae bound to a K-turn derived from an archaeal box H/ACA sRNA at 1.8 A resolution.
Hamma T, Ferré-D'Amaré AR.
Structure. 2004 May;12(5):893-903.
[Text Abstract on PubMed]

The hairpin ribozyme.
Ferré-D'Amaré AR.
Biopolymers. 2004 Jan;73(1):71-8.
[Text Abstract on PubMed]

Crystallization of the hairpin ribozyme: illustrative protocols.
Rupert PB, Ferré-D'Amaré AR.
Methods Mol. Biol. 2004;252:303-11.
[Text Abstract on PubMed]

U1A RNA-binding domain at 1.8 A resolution.
Rupert PB, Xiao H, Ferré-D'Amaré AR.
Acta Crystallogr. D Biol. Crystallogr. 2003 Aug;59(Pt 8):1521-4.
[Text Abstract on PubMed]

RNA-modifying enzymes.
Ferré-D'Amaré AR.
Curr. Opin. Struct. Biol. 2003 Feb;13(1):49-55.
[Text Abstract on PubMed]

Transition state stabilization by a catalytic RNA.
Rupert PB, Massey AP, Sigurdsson ST, Ferré-D'Amaré AR.
Science. 2002 Nov 15;298(5597):1421-4.
[Text Abstract on PubMed]

The hairpin ribozyme: from crystal structure to function.
Ferré-D'amaré AR, Rupert PB.
Biochem. Soc. Trans. 2002 Nov;30(Pt 6):1105-9.
[Text Abstract on PubMed]

Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme.
Hoang C, Ferré-D'Amaré AR.
Cell. 2001 Dec 28;107(7):929-39.
[Text Abstract on PubMed]

Direct pK(a) measurement of the active-site cytosine in a genomic hepatitis delta virus ribozyme.
Lupták A, Ferré-D'Amaré AR, Zhou K, Zilm KW, Doudna JA.
J. Am. Chem. Soc. 2001 Sep 5;123(35):8447-52.
[Text Abstract on PubMed]

Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis.
Rupert PB, Ferré-D'Amaré AR.
Nature. 2001 Apr 12;410(6830):780-6.
[Text Abstract on PubMed]

SRPrises in RNA-protein recognition.
Rupert PB, Ferré-D'amaré AR.
Structure. 2000 May 15;8(5):R99-104.
[Text Abstract on PubMed]

Crystallization and structure determination of a hepatitis delta virus ribozyme: use of the RNA-binding protein U1A as a crystallization module.
Ferré-D'Amaré AR, Doudna JA.
J. Mol. Biol. 2000 Jan 21;295(3):541-56.
[Text Abstract on PubMed]

A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes.
Wadkins TS, Perrotta AT, Ferré-D'Amaré AR, Doudna JA, Been MD.
RNA. 1999 Jun;5(6):720-7.
[Text Abstract on PubMed]

RNA folds: insights from recent crystal structures.
Ferré-D'Amaré AR, Doudna JA.
Annu Rev Biophys Biomol Struct. 1999;28:57-73.
[Text Abstract on PubMed]

A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor.
Basu S, Rambo RP, Strauss-Soukup J, Cate JH, Ferré-D'Amaré AR, Strobel SA, Doudna JA.
Nat. Struct. Biol. 1998 Nov;5(11):986-92.
[Text Abstract on PubMed]

Crystal structure of a hepatitis delta virus ribozyme.
Ferré-D'Amaré AR, Zhou K, Doudna JA.
Nature. 1998 Oct 8;395(6702):567-74.
[Text Abstract on PubMed]

A general module for RNA crystallization.
Ferré-D'Amaré AR, Zhou K, Doudna JA.
J. Mol. Biol. 1998 Jun 12;279(3):621-31.
[Text Abstract on PubMed]

Co-crystal structure of sterol regulatory element binding protein 1a at 2.3 A resolution.
Párraga A, Bellsolell L, Ferré-D'Amaré AR, Burley SK.
Structure. 1998 May 15;6(5):661-72.
[Text Abstract on PubMed]

Mitfmi-enu122 is a missense mutation in the HLH dimerization domain.
Steingrímsson E, Favor J, Ferré-D'Amaré AF, Copeland NG, Jenkins NA.
Mamm. Genome. 1998 Mar;9(3):250-2.
[Text Abstract on PubMed]

Establishing suitability of RNA preparations for crystallization. Determination of polydispersity.
Ferré-d'Amaré AR, Doudna JA.
Methods Mol. Biol. 1997;74:371-7.
[Text Abstract on PubMed]

The semidominant Mi(b) mutation identifies a role for the HLH domain in DNA binding in addition to its role in protein dimerization.
Steingrímsson E, Nii A, Fisher DE, Ferré-D'Amaré AR, McCormick RJ, Russell LB, Burley SK, Ward JM, Jenkins NA, Copeland NG.
EMBO J. 1996 Nov 15;15(22):6280-9.
[Text Abstract on PubMed]

Use of cis- and trans-ribozymes to remove 5' and 3' heterogeneities from milligrams of in vitro transcribed RNA.
Ferré-D'Amaré AR, Doudna JA.
Nucleic Acids Res. 1996 Mar 1;24(5):977-8.
[Text Abstract on PubMed]

Ferré-D'Amaré, A.R. 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 (1995).

Canne, L.E., Ferré-D'Amaré, A.R., Burley, S.K. & Kent, S.B.H. Total chemical synthesis of a unique transcription factor protein: cMyc-Max. J. Am. Chem. Soc. 117, 2998-3007 (1995).

Anti-cooperative biphasic equilibrium binding of transcription factor upstream stimulatory factor to its cognate DNA monitored by protein fluorescence changes.
Sha M, Ferré-D'Amaré AR, Burley SK, Goss DJ.
J. Biol. Chem. 1995 Aug 18;270(33):19325-9.
[Text Abstract on PubMed]

Probing the solution structure of the DNA-binding protein Max by a combination of proteolysis and mass spectrometry.
Cohen SL, Ferré-D'Amaré AR, Burley SK, Chait BT.
Protein Sci. 1995 Jun;4(6):1088-99.
[Text Abstract on PubMed]

Molecular basis of mouse microphthalmia (mi) mutations helps explain their developmental and phenotypic consequences.
Steingrímsson E, Moore KJ, Lamoreux ML, Ferré-D'Amaré AR, Burley SK, Zimring DC, Skow LC, Hodgkinson CA, Arnheiter H, Copeland NG.
Nat. Genet. 1994 Nov;8(3):256-63.
[Text Abstract on PubMed]

Use of dynamic light scattering to assess crystallizability of macromolecules and macromolecular assemblies.
Ferré-D'Amaré AR, Burley SK.
Structure. 1994 May 15;2(5):357-9.
[Text Abstract on PubMed]

Structure and function of the b/HLH/Z domain of USF.
Ferré-D'Amaré AR, Pognonec P, Roeder RG, Burley SK.
EMBO J. 1994 Jan 1;13(1):180-9.
[Text Abstract on PubMed]

Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain.
Ferré-D'Amaré AR, Prendergast GC, Ziff EB, Burley SK.
Nature. 1993 May 6;363(6424):38-45.
[Text Abstract on PubMed]

X-ray crystallographic studies of eukaryotic transcription factors.
Burley SK, Clark KL, Ferré-D'Amaré A, Kim JL, Nikolov DB.
Cold Spring Harb. Symp. Quant. Biol. 1993;58:123-32.
[Text Abstract on PubMed]