N B Leontis

Summary

Affiliation: Bowling Green State University
Country: USA

Publications

  1. pmc Geometric nomenclature and classification of RNA base pairs
    N B Leontis
    Chemistry Department and Center for Biomolecular Sciences, Bowling Green State University, Ohio 43403, USA
    RNA 7:499-512. 2001
  2. pmc Computational simulation of the docking of Prochlorothrix hollandica plastocyanin to potosystem I: modeling the electron transfer complex
    Eugene Myshkin
    Department of Biological Sciences, Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
    Biophys J 82:3305-13. 2002
  3. pmc The RNA Ontology Consortium: an open invitation to the RNA community
    Neocles B Leontis
    RNA 12:533-41. 2006
  4. ncbi request reprint Specific RNA self-assembly with minimal paranemic motifs
    Kirill A Afonin
    Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
    J Am Chem Soc 130:93-102. 2008
  5. ncbi request reprint Analysis of RNA motifs
    Neocles B Leontis
    Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
    Curr Opin Struct Biol 13:300-8. 2003
  6. pmc The non-Watson-Crick base pairs and their associated isostericity matrices
    Neocles B Leontis
    Chemistry Department and Center for Biomolecular Sciences, Overman Hall, Bowling Green State University, Bowling Green, OH 43403, USA
    Nucleic Acids Res 30:3497-531. 2002
  7. ncbi request reprint Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules
    N B Leontis
    Chemistry Department and Center for Biomolecular Sciences, Overman Hall, Bowling Green State University, Bowling Green, OH 43403, USA
    Biochimie 84:961-73. 2002
  8. pmc Classification and energetics of the base-phosphate interactions in RNA
    Craig L Zirbel
    Department of Mathematics and Statistics, Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
    Nucleic Acids Res 37:4898-918. 2009
  9. ncbi request reprint A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs
    N B Leontis
    Chemistry Department, Bowling Green State University, Bowling Green, OH, 43403, USA
    J Mol Biol 283:571-83. 1998
  10. pmc Frequency and isostericity of RNA base pairs
    Jesse Stombaugh
    Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
    Nucleic Acids Res 37:2294-312. 2009

Collaborators

Detail Information

Publications25

  1. pmc Geometric nomenclature and classification of RNA base pairs
    N B Leontis
    Chemistry Department and Center for Biomolecular Sciences, Bowling Green State University, Ohio 43403, USA
    RNA 7:499-512. 2001
    ..Graphical conventions are proposed for displaying non-Watson-Crick interactions on a secondary structure diagram. The utility of the classification in homology modeling of RNA tertiary motifs is illustrated...
  2. pmc Computational simulation of the docking of Prochlorothrix hollandica plastocyanin to potosystem I: modeling the electron transfer complex
    Eugene Myshkin
    Department of Biological Sciences, Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
    Biophys J 82:3305-13. 2002
    ..hollandica Pc-PSI complex that can be extended for the study of other cyanobacterial Pc/PSI reaction pairs...
  3. pmc The RNA Ontology Consortium: an open invitation to the RNA community
    Neocles B Leontis
    RNA 12:533-41. 2006
    ....
  4. ncbi request reprint Specific RNA self-assembly with minimal paranemic motifs
    Kirill A Afonin
    Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
    J Am Chem Soc 130:93-102. 2008
    ..The 3HT motif appears suitable for specific, programmable, and reversible tecto-RNA self-assembly for constructing artificial RNA molecular machines...
  5. ncbi request reprint Analysis of RNA motifs
    Neocles B Leontis
    Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
    Curr Opin Struct Biol 13:300-8. 2003
    ..It is therefore crucial, when analyzing a three-dimensional RNA structure in order to identify and compare motifs, to first classify its non-Watson-Crick base pairs geometrically...
  6. pmc The non-Watson-Crick base pairs and their associated isostericity matrices
    Neocles B Leontis
    Chemistry Department and Center for Biomolecular Sciences, Overman Hall, Bowling Green State University, Bowling Green, OH 43403, USA
    Nucleic Acids Res 30:3497-531. 2002
    ..This format makes apparent the recurrent geometric patterns that are observed and helps identify isosteric pairs that co-vary or interchange in sequences of homologous molecules while maintaining conserved three-dimensional motifs...
  7. ncbi request reprint Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules
    N B Leontis
    Chemistry Department and Center for Biomolecular Sciences, Overman Hall, Bowling Green State University, Bowling Green, OH 43403, USA
    Biochimie 84:961-73. 2002
    ....
  8. pmc Classification and energetics of the base-phosphate interactions in RNA
    Craig L Zirbel
    Department of Mathematics and Statistics, Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
    Nucleic Acids Res 37:4898-918. 2009
    ..Bases that form BPh interactions, which are conserved in the rRNA 3D structures are also conserved in homologous rRNA sequence alignments...
  9. ncbi request reprint A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs
    N B Leontis
    Chemistry Department, Bowling Green State University, Bowling Green, OH, 43403, USA
    J Mol Biol 283:571-83. 1998
    ..Besides its presence in the hairpin ribozyme, the loop E motif is also apparent in helix P10 of bacterial RNase P, in domain P7 of one sub-group of group I introns, and in domain 3 of one subgroup of group II introns...
  10. pmc Frequency and isostericity of RNA base pairs
    Jesse Stombaugh
    Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
    Nucleic Acids Res 37:2294-312. 2009
    ..In order to improve the statistics from the 3D structures, we also derive base pair occurrence frequencies from rRNA sequence alignments...
  11. ncbi request reprint Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding
    K Csaszar
    Chemistry Department and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
    J Mol Biol 313:1073-91. 2001
    ..Sodium cation coordination sites with occupancies above 50 % were also observed...
  12. pmc Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericities
    Ali Mokdad
    Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, OH 43403, USA
    Bioinformatics 22:2168-70. 2006
    ..1 (SP3) or higher installed version. A stand-alone version is also available for the PC platform. AVAILABILITY: http://rna.bgsu.edu/ribostral...
  13. pmc Structural and evolutionary classification of G/U wobble basepairs in the ribosome
    Ali Mokdad
    Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, OH 43403, USA
    Nucleic Acids Res 34:1326-41. 2006
    ..MD simulations were carried out on eight P-interactions. The specific GU/CG signature of this interaction observed in structure and sequence analysis was rationalized, and can now be used for improving sequence alignments...
  14. pmc FR3D: finding local and composite recurrent structural motifs in RNA 3D structures
    Michael Sarver
    Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA
    J Math Biol 56:215-52. 2008
    ..The search algorithms have been optimized for speed to allow users to search the non-redundant RNA 3D structure database on a personal computer in a matter of minutes...
  15. ncbi request reprint The building blocks and motifs of RNA architecture
    Neocles B Leontis
    Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, OH 43402, USA
    Curr Opin Struct Biol 16:279-87. 2006
    ..This follows the biologically relevant motivation, which is to identify RNA structural characteristics that are subject to sequence constraints and that thus relate RNA architectures to sequences...
  16. pmc Controlling RNA self-assembly to form filaments
    Lorena Nasalean
    Department of Chemistry, Bowling Green State University, OH 43402, USA
    Nucleic Acids Res 34:1381-92. 2006
    ..This work emphasizes the potential of RNA as a scaffold for designing and engineering new controllable biomaterials mimicking modern cytoskeletal proteins...
  17. pmc The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure
    N B Leontis
    Chemistry Department, Bowling Green State University, Ohio 43403, USA
    RNA 4:1134-53. 1998
    ..The latter covariations may indicate transitions between related but distinctive motifs within the loop E of 5S ribosomal RNA...
  18. pmc TokenRNA: a new type of sequence-specific, label-free fluorescent biosensor for folded RNA molecules
    Kirill A Afonin
    Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
    Chembiochem 9:1902-5. 2008
  19. pmc Generating new specific RNA interaction interfaces using C-loops
    Kirill A Afonin
    Department of Chemistry and Center for Bimolecular Sciences, Bowling Green State University, Bowling Green, Ohio 43402, USA
    J Am Chem Soc 128:16131-7. 2006
    ..Binding affinities for most C-loop-containing molecules were generally equal or higher than those for the parent molecules lacking C-loops...
  20. pmc Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E
    Kamila Réblová
    National Center for Biomolecular Research, Brno, Czech Republic
    Biophys J 84:3564-82. 2003
    ..The ordered hydration is intimately connected with RNA local conformational variations...
  21. ncbi request reprint Unique tertiary and neighbor interactions determine conservation patterns of Cis Watson-Crick A/G base-pairs
    Jiri Sponer
    Institute of Biophysics, Academy of Sciences of the Czech Republic and National Center for Biomolecular Research, Kralovopolska 135, 612 65 Brno, Czech Republic
    J Mol Biol 330:967-78. 2003
    ..C. A/G base-pairs requires a detailed analysis of the relation between the molecular structures and the energetics of interactions at a level of single H-bonds and contacts...
  22. ncbi request reprint Ribosomal RNA kink-turn motif--a flexible molecular hinge
    Filip Razga
    National Centre for Biomolecular Research, Kotlarska 2, 61137 Brno, Czech Republic
    J Biomol Struct Dyn 22:183-94. 2004
    ..They can for example be involved in mediation of large-scale motions or they can allow a smooth assembling of the other parts of the ribosome...
  23. pmc Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex
    Kamila Réblová
    National Centre for Biomolecular Research, Faculty of Sciences, Masaryk University, Kotlarska 2, 61137 Brno, Czech Republic
    Biophys J 87:3397-412. 2004
    ..Long-residency hydration sites thus represent important elements of the three-dimensional structure of rRNA...
  24. pmc Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments
    Aurelie Lescoute
    Institut de Biologie Moleculaire et Cellulaire du CNRS, UPR 9002, Université Louis Pasteur 15 rue René Descartes, F 67084 Strasbourg CEDEX, France
    Nucleic Acids Res 33:2395-409. 2005
    ..The conservations observed in Isostericity Matrices form a predictive basis for identifying motifs in sequences...
  25. pmc Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases
    Filip Razga
    National Centre for Biomolecular Research, Brno, Czech Republic
    Biophys J 88:3466-85. 2005
    ..We suggest that some K-turns are flexible elements mediating large-scale ribosomal motions during the protein synthesis cycle...