Search Results - "Ferre, R A"

Crystal structure of a hepatitis delta virus ribozyme by Doudna, Jennifer A, Ferré-D'Amaré, Adrian R, Zhou, Kaihong

“…The self-cleaving ribozyme of the hepatitis delta virus (HDV) is the only catalytic RNA known to be required for the viability of a human pathogen. We obtained…”
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Structure-Assisted Design of Mechanism-Based Irreversible Inhibitors of Human Rhinovirus 3C Protease with Potent Antiviral Activity against Multiple Rhinovirus Serotypes by Matthews, D A, Dragovich, P S, Webber, S E, Fuhrman, S A, Patick, A K, Zalman, L S, Hendrickson, T F, Love, R A, Prins, T J, Marakovits, J T, Zhou, R, Tikhe, J, Ford, C E, Meador, J W, Ferre, R A, Brown, E L, Binford, S L, Brothers, M A, DeLisle, D M, Worland, S T

“…Human rhinoviruses, the most important etiologic agents of the common cold, are messenger-active single-stranded monocistronic RNA viruses that have evolved a…”
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Use of Cis- and Trans-Ribozymes to Remove 5′ and 3′ Heterogeneities From Milligrams of In Vitro Transcribed RNA by Ferré-D'Amaré, Adrian R., Doudna, Jennifer A.

“…In vitro transcription with phage T7 RNA polymerase is the method of choice for obtaining multi-milligram quantities of RNA for structural studies. However,…”
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The hairpin ribozyme: from crystal structure to function by Ferré-D'amaré, A R, Rupert, P B

“…The hairpin ribozyme is one of four known natural catalytic RNAs that carry out sequence-specific cleavage of RNA. It is of particular biochemical interest…”
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structure and function of small nucleolar ribonucleoproteins by Reichow, Steve L, Hamma, Tomoko, Ferré-D'Amaré, Adrian R, Varani, Gabriele

“…Eukaryotes and archaea use two sets of specialized ribonucleoproteins (RNPs) to carry out sequence-specific methylation and pseudouridylation of RNA, the two…”
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Design, Synthesis, and Evaluation of Nonpeptidic Inhibitors of Human Rhinovirus 3C Protease by Webber, Stephen E., Tikhe, Jayashree, Worland, Stephen T., Fuhrman, Shella A., Hendrickson, Thomas F., Matthews, David A., Love, Robert A., Patick, Amy K., Meador, James W., Ferre, Rose Ann, Brown, Edward L., DeLisle, Dorothy M., Ford, Clifford E., Binford, Susan L.

“…The design, synthesis, and biological evaluation of reversible, nonpeptidic inhibitors of human rhinovirus (HRV) 3C protease (3CP) are reported. A novel series…”
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Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography by Stagno, J. R., Liu, Y., Bhandari, Y. R., Conrad, C. E., Panja, S., Swain, M., Fan, L., Nelson, G., Li, C., Wendel, D. R., White, T. A., Coe, J. D., Wiedorn, M. O., Knoska, J., Oberthuer, D., Tuckey, R. A., Yu, P., Dyba, M., Tarasov, S. G., Weierstall, U., Grant, T. D., Schwieters, C. D., Zhang, J., Ferré-D’Amaré, A. R., Fromme, P., Draper, D. E., Liang, M., Hunter, M. S., Boutet, S., Tan, K., Zuo, X., Ji, X., Barty, A., Zatsepin, N. A., Chapman, H. N., Spence, J. C. H., Woodson, S. A., Wang, Y.-X.

“…Femtosecond XFEL crystallography is used to identify dynamic changes in the adenine riboswitch aptamer domain, with at least four states identified in real…”
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Crystallization and structure determination of a hepatitis delta virus ribozyme: use of the RNA-binding protein U1A as a crystallization module by Ferré-D'Amaré, A R, Doudna, J A

“…Well-ordered crystals of a genomic hepatitis delta virus (HDV) ribozyme, a large, globular RNA, were obtained employing a new crystallization method. A…”
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Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis by Rupert, Peter B, Ferré-D'Amaré, Adrian R

“…The hairpin ribozyme catalyses sequence-specific cleavage of RNA. The active site of this natural RNA results from the docking of two irregular helices: stems…”
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Structure-Based Design, Synthesis, and Biological Evaluation of Irreversible Human Rhinovirus 3C Protease Inhibitors. 3. Structure−Activity Studies of Ketomethylene-Containing Peptidomimetics by Dragovich, Peter S, Prins, Thomas J, Zhou, Ru, Fuhrman, Shella A, Patick, Amy K, Matthews, David A, Ford, Clifford E, Meador, James W, Ferre, Rose Ann, Worland, Stephen T

“…The structure-based design, chemical synthesis, and biological evaluation of various ketomethylene-containing human rhinovirus (HRV) 3C protease (3CP)…”
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Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain by Ferré-D'Amaré, Adrian R, Prendergast, George C, Ziff, Edward B, Burley, Stephen K

“…The three-dimensional structure of the basic/helix-loop-helix/leucine zipper domain of the transcription factor Max complexed with DNA has been determined by…”
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Molecular basis of mouse microphthalmia ( mi ) mutations helps explain their developmental and phenotypic consequences by Burley, Stephen K, Sanders Zimring, Debra C, Arnheiter, Heinz, Lamoreux, M. Lynn, Moore, Karen J, Copeland, Neal G, Steingrímsson, Eiríkur, Hodgkinson, Colin A, Ferré-D'Amaré, Adrian R, Skow, Loren C, Jenkins, Nancy A

“…Mutations in the mouse microphthalmia (mi) gene affect the development of a number of cell types including melanocytes, osteoclasts and mast cells. Recently,…”
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Structure and function of the b/HLH/Z domain of USF by Ferré‐D'Amaré, A.R., Pognonec, P., Roeder, R.G., Burley, S.K.

“…The basic/helix‐loop‐helix/leucine zipper (b/HLH/Z) transcription factor upstream stimulatory factor (USF) and its isolated DNA binding domain undergo a random…”
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Structure-Based Design, Synthesis, and Biological Evaluation of Irreversible Human Rhinovirus 3C Protease Inhibitors. 4. Incorporation of P1 Lactam Moieties as l-Glutamine Replacements by Dragovich, Peter S, Prins, Thomas J, Zhou, Ru, Webber, Stephen E, Marakovits, Joseph T, Fuhrman, Shella A, Patick, Amy K, Matthews, David A, Lee, Caroline A, Ford, Clifford E, Burke, Benjamin J, Rejto, Paul A, Hendrickson, Thomas F, Tuntland, Tove, Brown, Edward L, Meador, James W, Ferre, Rose Ann, Harr, James E. V, Kosa, Maha B, Worland, Stephen T

“…The structure-based design, chemical synthesis, and biological evaluation of various human rhinovirus (HRV) 3C protease (3CP) inhibitors which incorporate P1…”
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A general module for RNA crystallization by Ferré-D’Amaré, Adrian R, Zhou, Kaihong, Doudna, Jennifer A

“…Crystallization of RNA molecules other than simple oligonucleotide duplexes remains a challenging step in structure determination by X-ray crystallography…”
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Cocrystal Structure of a tRNA psi 55 Pseudouridine Synthase: Nucleotide Flipping by an RNA-Modifying Enzyme by Hoang, C, Ferre-D'Amare, A R

“…Pseudouridine ( psi ) synthases catalyze the isomerization of specific uridines in cellular RNAs to pseudouridines and may function as RNA chaperones. TruB is…”
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The Crystal Structure of the RNA-Dependent RNA Polymerase from Human Rhinovirus: A Dual Function Target for Common Cold Antiviral Therapy by Love, Robert A, Maegley, Karen A, Yu, Xiu, Ferre, Rose Ann, Lingardo, Laura K, Diehl, Wade, Parge, Hans E, Dragovich, Peter S, Fuhrman, Shella A

“…Human rhinoviruses (HRV), the predominant members of the Picornaviridae family of positive-strand RNA viruses, are the major causative agents of the common…”
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Structure-based design of irreversible, tripeptidyl human rhinovirus 3C protease inhibitors containing N-methyl amino acids by Dragovich, Peter S, Webber, Stephen E, Prins, Thomas J, Zhou, Ru, Marakovits, Joseph T, Tikhe, Jayashree G, Fuhrman, Shella A, Patick, Amy K, Matthews, David A, Ford, Clifford E, Brown, Edward L, Binford, Susan L, Meador, James W, Ferre, Rose Ann, Worland, Stephen T

“…Tripeptide-derived molecules incorporating N-methyl amino acid residues and C-terminal Michael acceptor moieties were evaluated as irreversible inhibitors of…”
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Structure-Based Design, Synthesis, and Biological Evaluation of Irreversible Human Rhinovirus 3C Protease Inhibitors. 1. Michael Acceptor Structure−Activity Studies by Dragovich, Peter S, Webber, Stephen E, Babine, Robert E, Fuhrman, Shella A, Patick, Amy K, Matthews, David A, Lee, Caroline A, Reich, Siegfried H, Prins, Thomas J, Marakovits, Joseph T, Littlefield, Ethel S, Zhou, Ru, Tikhe, Jayashree, Ford, Clifford E, Wallace, Michael B, Meador, James W, Ferre, Rose Ann, Brown, Edward L, Binford, Susan L, Harr, James E. V, DeLisle, Dorothy M, Worland, Stephen T

“…The structure-based design, chemical synthesis, and biological evaluation of peptide-derived human rhinovirus (HRV) 3C protease (3CP) inhibitors are described…”
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Transition State Stabilization by a Catalytic RNA by Rupert, Peter B., Massey, Archna P., Snorri Th. Sigurdsson, Ferré-D'Amaré, Adrian R.

“…The hairpin ribozyme catalyzes sequence-specific cleavage of RNA through transesterification of the scissile phosphate. Vanadate has previously been used as a…”
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