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Anna Marie Pyle

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Spliceosomes

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TOP 3
Marco Marcia; Anna Marie Pyle
Visualizing group II intron catalysis through the stages of splicing.
Elisabeth Humphris-Narayanan; Anna Marie Pyle
Discrete RNA libraries from pseudo-torsional space.
Kevin S Keating; Anna Marie Pyle
RCrane: semi-automated RNA model building.

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All Publications

2012: Marco Marcia; Anna Marie Pyle
Visualizing group II intron catalysis through the stages of splicing.
Cell 2012;151(3):497-507.
2012: Elisabeth Humphris-Narayanan; Anna Marie Pyle
Discrete RNA libraries from pseudo-torsional space.
Journal of molecular biology 2012;421(1):6-26.
2012: Kevin S Keating; Anna Marie Pyle
RCrane: semi-automated RNA model building.
Acta crystallographica. Section D, Biological crystallography 2012;68(Pt 8):985-95.
2012: Russell T Chan; Anna Marie Pyle; Kanagalaghatta R Rajashankar; Aaron R Robart; Navtej Toor
Crystal structure of a group II intron in the pre-catalytic state.
Nature structural & molecular biology 2012;19(5):555-7.
2011: Kevin S Keating; Elisabeth L Humphris; Anna Marie Pyle
A new way to see RNA.
Quarterly reviews of biophysics 2011;44(4):433-66.
2011: Anna Marie Pyle
RNA helicases and remodeling proteins.
Current opinion in chemical biology 2011;15(5):636-42.
2011: Wenxiang Cao; Maria Magdalena Coman; Steve Ding; Arnon Henn; Elizabeth R Middleton; Michael J Bradley; Elizabeth Rhoades; David D Hackney; Anna Marie Pyle; Enrique M De La Cruz
Mechanism of Mss116 ATPase reveals functional diversity of DEAD-Box proteins.
Journal of molecular biology 2011;409(3):399-414.
2010: Nora Zingler; Amanda Solem; Anna Marie Pyle
Dual roles for the Mss116 cofactor during splicing of the ai5γ group II intron.
Nucleic acids research 2010;38(19):6602-9.
2010: Christian Matranga; Anna Marie Pyle
Double-stranded RNA-dependent ATPase DRH-3: insight into its role in RNAsilencing in Caenorhabditis elegans.
The Journal of biological chemistry 2010;285(33):25363-71.
2010: Anna Marie Pyle
The tertiary structure of group II introns: implications for biological function and evolution.
Critical reviews in biochemistry and molecular biology 2010;45(3):215-32.
2010: Kevin S Keating; Anna Marie Pyle
Semiautomated model building for RNA crystallography using a directed rotameric approach.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(18):8177-82.
2010: Olga Fedorova; Amanda Solem; Anna Marie Pyle
Protein-facilitated folding of group II intron ribozymes.
Journal of molecular biology 2010;397(3):799-813.
2010: Navtej Toor; Kevin S Keating; Olga Fedorova; Kanagalaghatta Rajashankar; Jimin Wang; Anna Marie Pyle
Tertiary architecture of the Oceanobacillus iheyensis group II intron.
RNA (New York, N.Y.) 2010;16(1):57-69.
2010: Kevin S Keating; Navtej Toor; Philip S Perlman; Anna Marie Pyle
A structural analysis of the group II intron active site and implications for the spliceosome.
RNA (New York, N.Y.) 2010;16(1):1-9.
2009: Anna Marie Pyle
How to drive your helicase in a straight line.
Cell 2009;139(3):458-9.
2009: Navtej Toor; Kevin S Keating; Anna Marie Pyle
Structural insights into RNA splicing.
Current opinion in structural biology 2009;19(3):260-6.
2009: Rudolf K F Beran; Brett D Lindenbach; Anna Marie Pyle
The NS4A protein of hepatitis C virus promotes RNA-coupled ATP hydrolysis by the NS3 helicase.
Journal of virology 2009;83(7):3268-75.
2009: Michael Roitzsch; Anna Marie Pyle
The linear form of a group II intron catalyzes efficient autocatalytic reverse splicing, establishing a potential for mobility.
RNA (New York, N.Y.) 2009;15(3):473-82.
2009: Victor Serebrov; Rudolf K F Beran; Anna Marie Pyle
Establishing a mechanistic basis for the large kinetic steps of the NS3 helicase.
The Journal of biological chemistry 2009;284(4):2512-21.
2008: Kevin S Keating; Navtej Toor; Anna Marie Pyle
The GANC tetraloop: a novel motif in the group IIC intron structure.
Journal of molecular biology 2008;383(3):475-81.
2008: Navtej Toor; Kanagalaghatta Rajashankar; Kevin S Keating; Anna Marie Pyle
Structural basis for exon recognition by a group II intron.
Nature structural & molecular biology 2008;15(11):1221-2.
2008: Rudolf K F Beran; Anna Marie Pyle
Hepatitis C viral NS3-4A protease activity is enhanced by the NS3 helicase.
The Journal of biological chemistry 2008;283(44):29929-37.
2008: Olga Fedorova; Anna Marie Pyle
A conserved element that stabilizes the group II intron active site.
RNA (New York, N.Y.) 2008;14(6):1048-56.
2008: Navtej Toor; Kevin S Keating; Sean D Taylor; Anna Marie Pyle
Crystal structure of a self-spliced group II intron.
Science (New York, N.Y.) 2008;320(5872):77-82.
2008: Christina Waldsich; Anna Marie Pyle
A kinetic intermediate that regulates proper folding of a group II intron RNA.
Journal of molecular biology 2008;375(2):572-80.
2008: Nora Zingler; Amanda Solem; Anna Marie Pyle
Protein-facilitated ribozyme folding and catalysis.
Nucleic acids symposium series (2004) 2008;(52):67-8.
2008: Anna Marie Pyle
Translocation and unwinding mechanisms of RNA and DNA helicases.
Annual review of biophysics 2008;37():317-36.
2008: Alexandre de Lencastre; Anna Marie Pyle
Three essential and conserved regions of the group II intron are proximal to the 5'-splice site.
RNA (New York, N.Y.) 2008;14(1):11-24.
2007: Rudolf K F Beran; Victor Serebrov; Anna Marie Pyle
The serine protease domain of hepatitis C viral NS3 activates RNA helicase activity by promoting the binding of RNA substrate.
The Journal of biological chemistry 2007;282(48):34913-20.
2007: Leven M Wadley; Kevin S Keating; Carlos M Duarte; Anna Marie Pyle
Evaluating and learning from RNA pseudotorsional space: quantitative validation of a reduced representation for RNA structure.
Journal of molecular biology 2007;372(4):942-57.
2007: Brett D Lindenbach; Béla M Prágai; Roland Montserret; Rudolf K F Beran; Anna Marie Pyle; François Penin; Charles M Rice
The C terminus of hepatitis C virus NS4A encodes an electrostatic switch that regulates NS5A hyperphosphorylation and viral replication.
Journal of virology 2007;81(17):8905-18.
2007: Christopher L Tang; Emil Alexov; Anna Marie Pyle; Barry Honig
Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides.
Journal of molecular biology 2007;366(5):1475-96.
2007: Olga Fedorova; Christina Waldsich; Anna Marie Pyle
Group II intron folding under near-physiological conditions: collapsing to the near-native state.
Journal of molecular biology 2007;366(4):1099-114.
2007: Anna Marie Pyle; Olga Fedorova; Christina Waldsich
Folding of group II introns: a model system for large, multidomain RNAs?
Trends in biochemical sciences 2007;32(3):138-45.
2007: Gunter Wagner; Anna Marie Pyle
Tinkering with transcription factor proteins: the role of transcription factor adaptation in developmental evolution.
Novartis Foundation symposium 2007;284():116-25; discussion 125-9, 158-63.
2007: Roland K O Sigel; Anna Marie Pyle
Alternative roles for metal ions in enzyme catalysis and the implications for ribozyme chemistry.
Chemical reviews 2007;107(1):97-113.
2007: Christina Waldsich; Anna Marie Pyle
A folding control element for tertiary collapse of a group II intron ribozyme.
Nature structural & molecular biology 2007;14(1):37-44.
2006: Amanda Solem; Nora Zingler; Anna Marie Pyle
A DEAD protein that activates intron self-splicing without unwinding RNA.
Molecular cell 2006;24(4):611-7.
2006: Stephanie Hamill; Anna Marie Pyle
The receptor for branch-site docking within a group II intron active site.
Molecular cell 2006;23(6):831-40.
2006: Rudolf K F Beran; Michael M Bruno; Heath A Bowers; Eckhard Jankowsky; Anna Marie Pyle
Robust translocation along a molecular monorail: the NS3 helicase from hepatitis C virus traverses unusually large disruptions in its track.
Journal of molecular biology 2006;358(4):974-82.
2006: Sophie Dumont; Wei Cheng; Victor Serebrov; Rudolf K F Beran; Ignacio Tinoco; Anna Marie Pyle; Carlos Bustamante
RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP.
Nature 2006;439(7072):105-8.
2005: Olga Fedorova; Anna Marie Pyle
Linking the group II intron catalytic domains: tertiary contacts and structural features of domain 3.
The EMBO journal 2005;24(22):3906-16.
2005: Anna Marie Pyle
Capping by branching: a new ribozyme makes tiny lariats.
Science (New York, N.Y.) 2005;309(5740):1530-1.
2005: Alexandre de Lencastre; Stephanie Hamill; Anna Marie Pyle
A single active-site region for a group II intron.
Nature structural & molecular biology 2005;12(7):626-7.
2005: Phillip S Pang; Eckhard Jankowsky; Leven M Wadley; Anna Marie Pyle
Prediction of functional tertiary interactions and intermolecular interfaces from primary sequence data.
Journal of experimental zoology. Part B, Molecular and developmental evolution 2005;304(1):50-63.
2005: Linhui J. Su; Christina Waldsich; Anna Marie Pyle
An obligate intermediate along the slow folding pathway of a group II intron ribozyme.
Nucleic acids research 2005;33(21):6674-87.
2005: Jane Kawaoka; Anna Marie Pyle
Choosing between DNA and RNA: the polymer specificity of RNA helicase NPH-II.
Nucleic acids research 2005;33(2):644-9.
2004: Victor Serebrov; Anna Marie Pyle
Periodic cycles of RNA unwinding and pausing by hepatitis C virus NS3 helicase.
Nature 2004;430(6998):476-80.
2004: Jane Kawaoka; Eckhard Jankowsky; Anna Marie Pyle
Backbone tracking by the SF2 helicase NPH-II.
Nature structural & molecular biology 2004;11(6):526-30.
2004: Roland K O Sigel; Dipali G Sashital; Dana L. Abramovitz; Arthur G Palmer; Samuel E Butcher; Anna Marie Pyle
Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif.
Nature structural & molecular biology 2004;11(2):187-92.
2004: Leven M Wadley; Anna Marie Pyle
The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery.
Nucleic acids research 2004;32(22):6650-9.
2003: Linhui J. Su; Michael Brenowitz; Anna Marie Pyle
An alternative route for the folding of large RNAs: apparent two-state folding by a group II intron ribozyme.
Journal of molecular biology 2003;334(4):639-52.
2003: Carlos M Duarte; Leven M Wadley; Anna Marie Pyle
RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space.
Nucleic acids research 2003;31(16):4755-61.
2003: Olga Fedorova; Therese Mitros; Anna Marie Pyle
Domains 2 and 3 interact to form critical elements of the group II intron active site.
Journal of molecular biology 2003;330(2):197-209.
2003: Catherine Adamidi; Olga Fedorova; Anna Marie Pyle
A group II intron inserted into a bacterial heat-shock operon shows autocatalytic activity and unusual thermostability.
Biochemistry 2003;42(12):3409-18.
2003: Yasunori Aizawa; Qing Xiang; Alan M Lambowitz; Anna Marie Pyle
The pathway for DNA recognition and RNA integration by a group II intron retrotransposon.
Molecular cell 2003;11(3):795-805.
2003: Roland K O Sigel; Anna Marie Pyle
Lanthanide ions as probes for metal ions in the structure and catalytic mechanism of ribozymes.
Metal ions in biological systems 2003;40():477-512.
2002: Olga Fedorova; Linhui J. Su; Anna Marie Pyle
Group II introns: highly specific endonucleases with modular structures and diverse catalytic functions.
Methods (San Diego, Calif.) 2002;28(3):323-35.
2002: Anna Marie Pyle
Metal ions in the structure and function of RNA.
Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry 2002;7(7-8):679-90.
2002: Phillip S Pang; Eckhard Jankowsky; Paul J Planet; Anna Marie Pyle
The hepatitis C viral NS3 protein is a processive DNA helicase with cofactor enhanced RNA unwinding.
The EMBO journal 2002;21(5):1168-76.
2002: Dong-Chul Kang; Rahul V Gopalkrishnan; Qingping Wu; Eckhard Jankowsky; Anna Marie Pyle; Paul B Fisher
mda-5: An interferon-inducible putative RNA helicase with double-stranded RNA-dependent ATPase activity and melanoma growth-suppressive properties.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(2):637-42.
2002: Jennifer F Swisher; Linhui J. Su; Michael Brenowitz; Vernon E Anderson; Anna Marie Pyle
Productive folding to the native state by a group II intron ribozyme.
Journal of molecular biology 2002;315(3):297-310.
2001: V T Chu; Catherine Adamidi; Q Liu; Philip S Perlman; Anna Marie Pyle
Control of branch-site choice by a group II intron.
The EMBO journal 2001;20(23):6866-76.
2001: Jennifer F Swisher; Carlos M Duarte; Linhui J. Su; Anna Marie Pyle
Visualizing the solvent-inaccessible core of a group II intron ribozyme.
The EMBO journal 2001;20(8):2051-61.
2001: Linhui J. Su; PZ Qin; W J Michels; Anna Marie Pyle
Guiding ribozyme cleavage through motif recognition: the mechanism of cleavage site selection by a group ii intron ribozyme.
Journal of molecular biology 2001;306(4):655-68.
2001: Eckhard Jankowsky; C H Gross; Stewart Shuman; Anna Marie Pyle
Active disruption of an RNA-protein interaction by a DExH/D RNA helicase.
Science (New York, N.Y.) 2001;291(5501):121-5.
2000: Roland K O Sigel; A Vaidya; Anna Marie Pyle
Metal ion binding sites in a group II intron core.
Nature structural biology 2000;7(12):1111-6.
2000: marc boudvillain; Alexandre de Lencastre; Anna Marie Pyle
A tertiary interaction that links active-site domains to the 5' splice site of a group II intron.
Nature 2000;406(6793):315-8.
2000: Eckhard Jankowsky; C H Gross; Stewart Shuman; Anna Marie Pyle
The DExH protein NPH-II is a processive and directional motor for unwinding RNA.
Nature 2000;403(6768):447-51.
2000: Anna Marie Pyle; V T Chu; Eckhard Jankowsky; marc boudvillain
Using DNAzymes to cut, process, and map RNA molecules for structural studies or modification.
Methods in enzymology 2000;317():140-6.
1999: K Chin; K A Sharp; Barry Honig; Anna Marie Pyle
Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function.
Nature structural biology 1999;6(11):1055-61.
1999: PZ Qin; Anna Marie Pyle
Antagonistic substrate binding by a group II intron ribozyme.
Journal of molecular biology 1999;291(1):15-27.
1999: P Z Qin; Anna Marie Pyle
Site-specific labeling of RNA with fluorophores and other structural probes.
Methods (San Diego, Calif.) 1999;18(1):60-70.
1998: Carlos M Duarte; Anna Marie Pyle
Stepping through an RNA structure: A novel approach to conformational analysis.
Journal of molecular biology 1998;284(5):1465-78.
1998: B B Konforti; Q Liu; Anna Marie Pyle
A map of the binding site for catalytic domain 5 in the core of a group II intron ribozyme.
The EMBO journal 1998;17(23):7105-17.
1998: marc boudvillain; Anna Marie Pyle
Defining functional groups, core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: a NAIM analysis.
The EMBO journal 1998;17(23):7091-104.
1998: V T Chu; Q Liu; Mircea Podar; Philip S Perlman; Anna Marie Pyle
More than one way to splice an RNA: branching without a bulge and splicing without branching in group II introns.
RNA (New York, N.Y.) 1998;4(10):1186-202.
1998: PZ Qin; Anna Marie Pyle
The architectural organization and mechanistic function of group II intron structural elements.
Current opinion in structural biology 1998;8(3):301-8.
1998: John D Wagner; Eckhard Jankowsky; M Company; Anna Marie Pyle; John Abelson
The DEAH-box protein PRP22 is an ATPase that mediates ATP-dependent mRNA release from the spliceosome and unwinds RNA duplexes.
The EMBO journal 1998;17(10):2926-37.
1998: Q Xiang; PZ Qin; W J Michels; K Freeland; Anna Marie Pyle
Sequence specificity of a group II intron ribozyme: multiple mechanisms for promoting unusually high discrimination against mismatched targets.
Biochemistry 1998;37(11):3839-49.
1998: Mircea Podar; V T Chu; Anna Marie Pyle; Philip S Perlman
Group II intron splicing in vivo by first-step hydrolysis.
Nature 1998;391(6670):915-8.
1998: B B Konforti; Dana L. Abramovitz; Carlos M Duarte; Alexander Karpeisky; Leonid Beigelman; Anna Marie Pyle
Ribozyme catalysis from the major groove of group II intron domain 5.
Molecular cell 1998;1(3):433-41.
1997: PZ Qin; Anna Marie Pyle
Stopped-flow fluorescence spectroscopy of a group II intron ribozyme reveals that domain 1 is an independent folding unit with a requirement for specific Mg2+ ions in the tertiary structure.
Biochemistry 1997;36(16):4718-30.
1997: Q Liu; J B Green; A Khodadadi; Peter Haeberli; Leonid Beigelman; Anna Marie Pyle
Branch-site selection in a group II intron mediated by active recognition of the adenine amino group and steric exclusion of non-adenine functionalities.
Journal of molecular biology 1997;267(1):163-71.
1997: Dana L. Abramovitz; Anna Marie Pyle
Remarkable morphological variability of a common RNA folding motif: the GNRA tetraloop-receptor interaction.
Journal of molecular biology 1997;266(3):493-506.
1996: Dana L. Abramovitz; R A Friedman; Anna Marie Pyle
Catalytic role of 2'-hydroxyl groups within a group II intron active site.
Science (New York, N.Y.) 1996;271(5254):1410-3.
1996: D L Daniels; W J Michels; Anna Marie Pyle
Two competing pathways for self-splicing by group II introns: a quantitative analysis of in vitro reaction rates and products.
Journal of molecular biology 1996;256(1):31-49.
1996: Anna Marie Pyle
Role of metal ions in ribozymes.
Metal ions in biological systems 1996;32():479-520.
1995: E A Griffin; Z Qin; W J Michels; Anna Marie Pyle
Group II intron ribozymes that cleave DNA and RNA linkages with similar efficiency, and lack contacts with substrate 2'-hydroxyl groups.
Chemistry & biology 1995;2(11):761-70.
1995: Anna Marie Pyle; J B Green
RNA folding.
Current opinion in structural biology 1995;5(3):303-10.
1995: K Chin; Anna Marie Pyle
Branch-point attack in group II introns is a highly reversible transesterification, providing a potential proofreading mechanism for 5'-splice site selection.
RNA (New York, N.Y.) 1995;1(4):391-406.
1995: W J Michels; Anna Marie Pyle
Conversion of a group II intron into a new multiple-turnover ribozyme that selectively cleaves oligonucleotides: elucidation of reaction mechanism and structure/function relationships.
Biochemistry 1995;34(9):2965-77.
1994: Anna Marie Pyle; J B Green
Building a kinetic framework for group II intron ribozyme activity: quantitation of interdomain binding and reaction rate.
Biochemistry 1994;33(9):2716-25.
1993: Anna Marie Pyle
Ribozymes: a distinct class of metalloenzymes.
Science (New York, N.Y.) 1993;261(5122):709-14.
1992: Thomas R Cech; Daniel Herschlag; Joseph A Piccirilli; Anna Marie Pyle
RNA catalysis by a group I ribozyme. Developing a model for transition state stabilization.
The Journal of biological chemistry 1992;267(25):17479-82.
1990: Anna Marie Pyle; James McSwiggen; Thomas R Cech
Direct measurement of oligonucleotide substrate binding to wild-type and mutant ribozymes from Tetrahymena.
Proceedings of the National Academy of Sciences of the United States of America 1990;87(21):8187-91.
1989: K Uchida; Anna Marie Pyle; T Morii; Jacqueline K Barton
High resolution footprinting of EcoRI and distamycin with Rh(phi)2(bpy)3+, a new photofootprinting reagent.
Nucleic acids research 1989;17(24):10259-79.