Research TopicsSpecies | Structural bases of the functions of RNA-protein machinesSummaryPrincipal Investigator: THOMAS ARTHUR STEITZ Abstract: DESCRIPTION (provided by applicant): The objective of this Program is to develop a fundamental physical and chemical understanding of the mechanisms by which RNA molecules and their complexes with proteins carry out their biological functions. During the next five years, several different systems that are involved in the processes of protein synthesis by ribosomes, catalysis by RNA enzymes, RNA helicases and ribo-switches will be studied. While the primary technique used will be single crystal X-ray diffraction, these structural studies will be integrated with genetic, biochemical, chemical and computational approaches. A major goal will be to capture these macromolecular machines at each step of the various processes they carry out, enabling the production of movies showing the molecular motions involved in these mechanisms. Of special interest are the motions that occur in the course of protein synthesis as the ribosome proceeds through its elongation cycle, the co-translational passage of secreted proteins through membranes, the remodeling of RNA by a DEAD box helicase, the mechanisms of riboswitches and other RNAs using allosteric mechanisms, the allosteric consequence of aminoacyl-tRNA synthetase recognition of the tRNA anticodon, and the mechanism of catalysis by a group I intron RNA. Also of interest will be the ways in which the structures and properties of RNA molecules can be utilized to carry out various biological functions often analogous to those performed by proteins. Funding Period: 1997-04-01 - 2015-03-31 more information: NIH RePORT Top Publications
Research Grants
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Publications
Diamonds in the rough: a strong case for the inclusion of weak-intensity X-ray diffraction dataJimin Wang
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
Acta Crystallogr D Biol Crystallogr 70:1491-7. 2014..Averaging starts with uniform density inside double-shelled spherical masks and NCS matrices that are derived from bound heavy-atom clusters at the vertices of cuboctahedrally symmetric protein particles...- The bacterial second messenger c-di-GMP: probing interactions with protein and RNA binding partners using cyclic dinucleotide analogsCarly A Shanahan
Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
Org Biomol Chem 10:9113-29. 2012..Efforts towards the synthesis of c-di-GMP and its analogs are discussed as well as studies aimed at targeting these macromolecular effectors with chemically synthesized cyclic dinucleotide analogs... - Crystal structure of the dimeric coiled-coil domain of the cytosolic nucleic acid sensor LRRFIP1Jennifer B Nguyen
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
J Struct Biol 181:82-8. 2013..The structure of LRRFIP1-CC constitutes a valuable tool for probing the mechanism of LRRFIP1 signaling and for structural studies of larger LRRFIP1 constructs... - MDA5 assembles into a polar helical filament on dsRNAIan C Berke
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
Proc Natl Acad Sci U S A 109:18437-41. 2012..We conclude that MDA5 is a polymerization-dependent signaling platform that uses the amyloid-like self-propagating properties of MAVS to amplify signaling... - The hexameric helicase DnaB adopts a nonplanar conformation during translocationOrnchuma Itsathitphaisarn
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
Cell 151:267-77. 2012..We propose a hand-over-hand mechanism in which sequential hydrolysis of NTP causes a sequential 5' to 3' movement of the subunits along the helical axis of the staircase, resulting in the unwinding of two nucleotides per subunit... - Expression, purification, crystallization and preliminary crystallographic studies of Rhagium inquisitor antifreeze proteinAaron Hakim
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
Acta Crystallogr Sect F Struct Biol Cryst Commun 68:547-50. 2012..X-ray diffraction data were collected to 1.3 Å resolution using a synchrotron-radiation source. The crystals belonged to the trigonal space group P3(1)21 (or P3(2)21), with unit-cell parameters a = b = 46.46, c = 193.21 Å... - Identification of ligand analogues that control c-di-GMP riboswitchesKazuhiro Furukawa
Department of Molecular, Cellular and Developmental Biology, Yale University, P O Box 208103, New Haven, CT 06520 8103, USA
ACS Chem Biol 7:1436-43. 2012..Moreover, we demonstrate the potential of an engineered allosteric ribozyme for the rapid screening of chemical libraries for compounds that bind c-di-GMP riboswitches... - Quantification of the affinities and kinetics of protein interactions using silicon nanowire biosensorsXuexin Duan
Department of Electrical Engineering, Yale University, New Haven, Connecticut 06520, USA
Nat Nanotechnol 7:401-7. 2012.... - How hibernation factors RMF, HPF, and YfiA turn off protein synthesisYury S Polikanov
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
Science 336:915-8. 2012..The binding of RMF and HPF, but not YfiA, to the ribosome induces a conformational change of the 30S head domain that promotes 100S dimer formation... - Engineered allosteric ribozymes that sense the bacterial second messenger cyclic diguanosyl 5'-monophosphateHongzhou Gu
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States
Anal Chem 84:4935-41. 2012..Moreover, these ribozymes could be employed in high-throughput screens to identify compounds that trigger c-di-GMP riboswitch function... - Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosomeMatthieu G Gagnon
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
Science 335:1370-2. 2012..This structure gives insights into the mechanism of YaeJ function and provides a basis for understanding how it rescues stalled ribosomes... 
Structural basis of innate immune recognition of viral RNAIan C Berke
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
Cell Microbiol 15:386-94. 2013..Many open questions remain including the role of proteolytic activation in RNA recognition by TLR3 and how unanchored ubiquitin chains contribute to RNA recognition by RIG-I and MDA5...- Selective pressure causes an RNA virus to trade reproductive fitness for increased structural and thermal stability of a viral enzymeMoshe Dessau
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
PLoS Genet 8:e1003102. 2012.... - Structural models of the membrane anchors of envelope glycoproteins E1 and E2 from pestivirusesJimin Wang
Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA Electronic address
Virology 454:93-101. 2014..The membrane anchor models provide structural constraints for the disulfide bonding pattern and overall backbone conformation of the E1 ectodomain. .. - A widespread self-cleaving ribozyme class is revealed by bioinformaticsAdam Roth
1 Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA 2 Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA 3
Nat Chem Biol 10:56-60. 2014..The twister ribozyme motif provides another example of a natural RNA catalyst and calls attention to the potentially varied biological roles of this and other classes of widely distributed self-cleaving RNAs. .. - Riboswitches in eubacteria sense the second messenger c-di-AMPJames W Nelson
Department of Chemistry, Yale University, New Haven, Connecticut, USA
Nat Chem Biol 9:834-9. 2013..Our findings resolve the mystery regarding the primary ligand for this extremely common riboswitch class and expose a major portion of the super-regulon of genes that are controlled by the widespread bacterial second messenger c-di-AMP. .. - Viral membrane fusion and nucleocapsid delivery into the cytoplasm are distinct events in some flavivirusesAdel M Nour
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
PLoS Pathog 9:e1003585. 2013..Virus entry modulates intracellular calcium release and phosphatidylinositol-3-phosphate kinase signaling. Moreover, the broadly cross-reactive therapeutic antibody scFv11 binds to virus-like particles and inhibits fusion. .. - Peroxiredoxin-1 from the human hookworm Ancylostoma ceylanicum forms a stable oxidized decamer and is covalently inhibited by conoidin AJennifer B Nguyen
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
Chem Biol 20:991-1001. 2013..This work demonstrates the promise of conoidin compounds as probes to evaluate peroxiredoxins as drug targets in human parasites. .. - The initiation of mammalian protein synthesis and mRNA scanning mechanismIvan B Lomakin
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 8114, USA
Nature 500:307-11. 2013..Conformational changes associated with the captured functional states reveal the dynamics of the interactions in the P site of the ribosome. These results have functional implications for the mechanism of mRNA scanning. .. - Crystal structure of glycoprotein E2 from bovine viral diarrhea virusYue Li
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
Proc Natl Acad Sci U S A 110:6805-10. 2013..From the structure of E2, we propose alternative possible membrane fusion mechanisms. We expect the pestivirus fusion apparatus to be conserved in hepatitis C virus... - Crystal structure of an insect antifreeze protein and its implications for ice bindingAaron Hakim
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
J Biol Chem 288:12295-304. 2013..By matching several planes of hexagonal ice, these waters may help freeze the AFP to the ice surface, thus providing the molecular basis of ice binding... - Crystal structure of glycoprotein C from Rift Valley fever virusMoshe Dessau
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
Proc Natl Acad Sci U S A 110:1696-701. 2013..Unanticipated similarities between G(C) and flavivirus envelope proteins reveal an evolutionary link between the two virus families and provide insights into the organization of G(C) in the outer shell of RVFV... - Identification of c-di-GMP derivatives resistant to an EAL domain phosphodiesteraseCarly A Shanahan
Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
Biochemistry 52:365-77. 2013..This suggests a general strategy for designing c-di-GMP derivatives with increased enzymatic stability that also possess desirable properties for development as chemical probes of c-di-GMP signaling... - Mechanism and distribution of glmS ribozymesPhillip J McCown
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
Methods Mol Biol 848:113-29. 2012..Representatives of glmS ribozymes also serve as excellent experimental models to elucidate how RNAs fold to recognize small molecule ligands and promote chemical transformations... - MDA5 cooperatively forms dimers and ATP-sensitive filaments upon binding double-stranded RNAIan C Berke
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
EMBO J 31:1714-26. 2012..We propose a signalling model in which the CARDs on MDA5-RNA filaments nucleate the assembly of MAVS filaments with the same polymeric geometry... - Structural and biochemical characterization of linear dinucleotide analogues bound to the c-di-GMP-I aptamerKathryn D Smith
Department of Chemistry, Yale University, New Haven, Connecticut 06520 8321, United States
Biochemistry 51:425-32. 2012..These data reveal principles that, along with published work, will contribute to the design of c-di-GMP analogues with properties desirable for use as chemical tools and potential therapeutics... - Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosomeGregor Blaha
Department of Molecular Biophysics, Yale University, New Haven, CT 06520, USA
Science 325:966-70. 2009..EF-P facilitates the proper positioning of the fMet-tRNA(i)(fMet) for the formation of the first peptide bond during translation initiation... - A structural view on the mechanism of the ribosome-catalyzed peptide bond formationMiljan Simonovic
Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, MBRB 1170, 900 S Ashland Ave, Chicago, IL 60607, USA
Biochim Biophys Acta 1789:612-23. 2009..A current understanding of the mechanism of the ribosome-catalyzed peptide bond formation is the focus of this review. Implications on the mechanism of peptide release are discussed as well... - U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosomeGüliz Gürel
Department of Chemistry, Yale University, New Haven, CT 06520, USA
J Mol Biol 389:146-56. 2009..In the ribosome, the position of U2504 is controlled by its interactions with neighboring nucleotides, whose identities vary among kingdoms... - Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozymeJesse C Cochrane
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
Biochemistry 48:3239-46. 2009.... - Mutations outside the anisomycin-binding site can make ribosomes drug-resistantGregor Blaha
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
J Mol Biol 379:505-19. 2008..The conformational effects of some mutations of the second kind propagate through the ribosome for considerable distances and are reversed when A-site substrates bind to the ribosome... - RNA catalysis: ribozymes, ribosomes, and riboswitchesScott A Strobel
Yale University, Department of Molecular Biophysics and Biochemistry, New Haven, CT 06520 8114, USA
Curr Opin Chem Biol 11:636-43. 2007..This catalytic breadth raises intriguing evolutionary questions about how RNA lost its biological role in some cases, but not in others, and what catalytic roles RNA might still be playing in biology... - Negamycin binds to the wall of the nascent chain exit tunnel of the 50S ribosomal subunitSusan J Schroeder
Department of Chemistry, Yale University, New Haven, Connecticut 06520 8107, USA
Antimicrob Agents Chemother 51:4462-5. 2007..The mechanism of antibiotic action and the function of this unexplored tunnel region remain intriguingly elusive... - Structural metals in the group I intron: a ribozyme with a multiple metal ion coreMary R Stahley
Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Ave, New Haven, CT 06520 8114, USA
J Mol Biol 372:89-102. 2007..The structural data are correlated to the biochemical results to further understand the role of metal ions in group I intron structure and function... - The structures of antibiotics bound to the E site region of the 50 S ribosomal subunit of Haloarcula marismortui: 13-deoxytedanolide and girodazoleSusan J Schroeder
Department of Chemistry, Yale University, New Haven, CT 06520 8107, USA
J Mol Biol 367:1471-9. 2007..Girodazole is specific for eukarytes and archaea because it makes interactions with L15 that are not possible in eubacteria... - Structural investigation of the GlmS ribozyme bound to Its catalytic cofactorJesse C Cochrane
Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520, USA
Chem Biol 14:97-105. 2007..This demonstrates that RNA, like protein enzymes, can employ the chemical diversity of small molecules to promote catalytic activity... - Structural basis of ligand binding by a c-di-GMP riboswitchKathryn D Smith
Department of Chemistry, Yale University, New Haven, Connecticut, USA
Nat Struct Mol Biol 16:1218-23. 2009.... - Plasticity of the RNA kink turn structural motifAlexandra H Antonioli
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 8114, USA
RNA 16:762-8. 2010..Such plasticity suggests that the K-turn is not a primary element in RNA folding, but instead is shaped by other structural elements within the RNA or ribonucleoprotein assembly... - Prospects for riboswitch discovery and analysisRonald R Breaker
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520 8103, USA
Mol Cell 43:867-79. 2011..Some of the greatest prospects for riboswitch research and some of the more interesting mysteries are discussed in this review... - Differential analogue binding by two classes of c-di-GMP riboswitchesCarly A Shanahan
Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
J Am Chem Soc 133:15578-92. 2011..These data suggest an explanation for the predicted preferential use of the class I motif over the class II motif in the c-di-GMP signaling pathway... - Structural basis of cooperative ligand binding by the glycine riboswitchEthan B Butler
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
Chem Biol 18:293-8. 2011..These interactions provide a structural basis for how the glycine riboswitch cooperatively regulates gene expression... - Interactions of the c-di-GMP riboswitch with its second messenger ligandKathryn D Smith
Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520, USA
Biochem Soc Trans 39:647-51. 2011..The binding kinetics reveal that this is a kinetically controlled riboswitch and mutations to the riboswitch lead to increases in the off-rate. This riboswitch is therefore flexible in sequence as well as kinetic properties... - An expanded collection and refined consensus model of glmS ribozymesPhillip J McCown
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520 8103, USA
RNA 17:728-36. 2011..These findings reveal that glmS ribozymes have a broader phylogenetic distribution than previously known and suggest that additional rare structural variants may remain to be discovered... - Association of OLE RNA with bacterial membranes via an RNA-protein interactionKirsten F Block
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
Mol Microbiol 79:21-34. 2011..Therefore, the majority of the complex structure formed by OLE RNA may perform a biochemical function that requires membrane localization... - An allosteric self-splicing ribozyme triggered by a bacterial second messengerElaine R Lee
Department of Molecular, Cellular, and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520 8103, USA
Science 329:845-8. 2010..Our findings indicate that some self-splicing ribozymes are not selfish elements but are harnessed by cells as metabolite sensors and genetic regulators... - Structural and biochemical determinants of ligand binding by the c-di-GMP riboswitch Kathryn D Smith
Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
Biochemistry 49:7351-9. 2010..Many mutants retain sufficient c-di-GMP affinity for the RNA to remain biologically relevant, which suggests that this motif is quite resilient to mutation... - A eubacterial riboswitch class that senses the coenzyme tetrahydrofolateTyler D Ames
Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520 8103, USA
Chem Biol 17:681-5. 2010..These findings expand the number of coenzymes that are directly sensed by RNA and reveal possible riboswitch-controlled regulons that respond to changes in single-carbon metabolism... - The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosomeRobin E Stanley
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
Nat Struct Mol Biol 17:289-93. 2010.... - A fast and efficient procedure to produce scFvs specific for large macromolecular complexesSi Wu
Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
J Immunol Methods 318:95-101. 2007..We also describe a fast and easy method to overcome the abundance of amber stop codons in the positive phage clones. The resulting antibodies have been used in ELISA and Western blot analysis...
Research Grants
- DEGENERATIVE AND DEMENTING DISEASES OF AGINGStanley B Prusiner; Fiscal Year: 2013..The ultimate goal of all the proposed studies is to define the molecular events that feature in the formation of human prions in order to develop therapeutics that cure the human prion diseases. ..
- HORMONAL REGULATION OF BLOOD PRESSUREMichal Laniado Schwartzman; Fiscal Year: 2013..ular tone, in the pathophysiology of hypertension and cardiovascular disease. ..
- Inflammatory responses of vascular cellsPaul L Fox; Fiscal Year: 2013..abstract_text> ..