NILS WALTER

Summary

Affiliation: University of Michigan
Country: USA

Publications

  1. ncbi request reprint Probing non-selective cation binding in the hairpin ribozyme with Tb(III)
    N G Walter
    Markey Center for Molecular Genetics, Department of Microbiology and Molecular Genetics, The University of Vermont, 306 Stafford Hall, Burlington, VT, 05405, USA
    J Mol Biol 298:539-55. 2000
  2. pmc Do-it-yourself guide: how to use the modern single-molecule toolkit
    Nils G Walter
    Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, USA
    Nat Methods 5:475-89. 2008
  3. ncbi request reprint Under the microscope: single molecule symposium at the University of Michigan, 2006
    Nils G Walter
    Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, MI 48109 1055, USA
    Biopolymers 85:106-14. 2007
  4. ncbi request reprint Future of biomedical sciences: single molecule microscopy
    Nils G Walter
    Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 N University Avenue, Ann Arbor, MI 48109 1055, USA
    Biopolymers 85:103-5. 2007
  5. pmc Ribozyme catalysis revisited: is water involved?
    Nils G Walter
    Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48019 1055, USA
    Mol Cell 28:923-9. 2007
  6. pmc Ribozymes: catalytic RNAs that cut things, make things, and do odd and useful jobs
    Nils G Walter
    The University of Michigan, Ann Arbor 48109, USA
    Biologist (London) 49:199-203. 2002
  7. ncbi request reprint In the fluorescent spotlight: global and local conformational changes of small catalytic RNAs
    N G Walter
    Department of Chemistry, The University of Michigan, 930 N University, Ann Arbor 48109 1055, USA
    Biopolymers 61:224-42. 2001
  8. ncbi request reprint A base change in the catalytic core of the hairpin ribozyme perturbs function but not domain docking
    N G Walter
    Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109 1055, USA
    Biochemistry 40:2580-7. 2001
  9. ncbi request reprint Structural dynamics of catalytic RNA highlighted by fluorescence resonance energy transfer
    N G Walter
    Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109 1055, USA
    Methods 25:19-30. 2001
  10. pmc Trapped water molecules are essential to structural dynamics and function of a ribozyme
    Maria M Rhodes
    Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109 1055, USA
    Proc Natl Acad Sci U S A 103:13380-5. 2006

Collaborators

  • Jiri Sponer
  • D P Millar
  • Joel Swanson
  • Markos Koutmos
  • Sohee Jeong
  • Ari Gafni
  • GARY GLICK
  • Mark A Burns
  • Hashim M Al-Hashimi
  • XIAOWEI contact ZHUANG
  • Stefanie Redemann
  • Vinod K Misra
  • Bohdan Schneider
  • Daniel Svozil
  • David Rueda
  • Rebecca A Tinsley
  • Mark A Ditzler
  • Dinari A Harris
  • Jana Sefcikova
  • Maryna V Krasovska
  • Miguel J B Pereira
  • S Elizabeth McDowell
  • Meredith Newby Lambert
  • Maria M Rhodes
  • Chamaree de Silva
  • Gregory Bokinsky
  • John Hsieh
  • John A H Hoerter
  • Sean M Langelier
  • Matthew S Marek
  • Anthony J Manzo
  • Nicole Michelotti
  • Mario Blanco
  • Michal Otyepka
  • Pavel Banas
  • Carol A Fierke
  • Melissa J Bobeck
  • Shixin Liu
  • Kamila Réblová
  • Melissa E Gondert
  • Sarah A Uhler
  • Phillip T Sekella
  • Alexander Johnson-Buck
  • Eric Livak-Dahl
  • Brian N Johnson
  • Kristin S Koutmou
  • Jesse M Jun
  • Alexander E Johnson-Buck
  • Richard A Collins
  • Kristina Hakansson
  • Veronika Hánosová
  • Evgenia N Nikolova
  • Lubomír Rulísek
  • Jingjie Mo
  • Shawna L Hiley
  • Dominic Jaikaran
  • Jennifer R W Furchak
  • Elvin A Alemán
  • Arivalagan Gajraj
  • Eva Vöcker
  • Jens Christian Meiners
  • Seth Blumberg
  • Nad a Spacková
  • Jeremy J Day-Storms
  • Michael J Rust
  • Katrin Wick
  • Carina Figge
  • Dawen Cai
  • Hazen P Babcock
  • Andrew Gordus
  • Yunfang Man

Detail Information

Publications57

  1. ncbi request reprint Probing non-selective cation binding in the hairpin ribozyme with Tb(III)
    N G Walter
    Markey Center for Molecular Genetics, Department of Microbiology and Molecular Genetics, The University of Vermont, 306 Stafford Hall, Burlington, VT, 05405, USA
    J Mol Biol 298:539-55. 2000
    ..Our findings, therefore, illuminate general principles of non-selective outer-sphere cation binding in RNA structure and function that may have prevailed in primitive ribozymes of an early "RNA world"...
  2. pmc Do-it-yourself guide: how to use the modern single-molecule toolkit
    Nils G Walter
    Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, USA
    Nat Methods 5:475-89. 2008
    ..We also provide guidelines for choosing the right approach from the available single-molecule toolkit for applications as diverse as structural biology, enzymology, nanotechnology and systems biology...
  3. ncbi request reprint Under the microscope: single molecule symposium at the University of Michigan, 2006
    Nils G Walter
    Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, MI 48109 1055, USA
    Biopolymers 85:106-14. 2007
    ....
  4. ncbi request reprint Future of biomedical sciences: single molecule microscopy
    Nils G Walter
    Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 N University Avenue, Ann Arbor, MI 48109 1055, USA
    Biopolymers 85:103-5. 2007
    ..This issue of Biopolymers presents a first set of reviews that aim to highlight the accomplishments and future prospects of single molecule microscopies...
  5. pmc Ribozyme catalysis revisited: is water involved?
    Nils G Walter
    Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48019 1055, USA
    Mol Cell 28:923-9. 2007
    ..Recent evidence suggests that some may also judiciously place structural water molecules to shuttle protons in acid-base catalyzed reactions...
  6. pmc Ribozymes: catalytic RNAs that cut things, make things, and do odd and useful jobs
    Nils G Walter
    The University of Michigan, Ann Arbor 48109, USA
    Biologist (London) 49:199-203. 2002
    ..Are they also an avenue to the development of new catalysts to recreate evolution, or to use as therapeutics and molecule sensors...
  7. ncbi request reprint In the fluorescent spotlight: global and local conformational changes of small catalytic RNAs
    N G Walter
    Department of Chemistry, The University of Michigan, 930 N University, Ann Arbor 48109 1055, USA
    Biopolymers 61:224-42. 2001
    ..The structural transitions observed in these two small catalytic RNAs are likely to be found in many other biological RNAs, and the described fluorescence techniques promise to be broadly applicable...
  8. ncbi request reprint A base change in the catalytic core of the hairpin ribozyme perturbs function but not domain docking
    N G Walter
    Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109 1055, USA
    Biochemistry 40:2580-7. 2001
    ..These data appear to invoke a mechanism of functional interference by a single base mutation, in which the ribozyme-substrate complex becomes trapped in a nativelike fold preceding the chemical transition state...
  9. ncbi request reprint Structural dynamics of catalytic RNA highlighted by fluorescence resonance energy transfer
    N G Walter
    Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109 1055, USA
    Methods 25:19-30. 2001
    ..Similar domain docking events are expected to be at the heart of many biological functions of RNA, and the described FRET techniques promise to be adaptable to most of the involved RNA systems...
  10. pmc Trapped water molecules are essential to structural dynamics and function of a ribozyme
    Maria M Rhodes
    Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109 1055, USA
    Proc Natl Acad Sci U S A 103:13380-5. 2006
    ..Our observations suggest important, still underappreciated roles for specifically bound water molecules in the structural dynamics and function of noncoding RNAs...
  11. pmc RNA dynamics: it is about time
    Hashim M Al-Hashimi
    Department of Chemistry and Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109 1055, United States
    Curr Opin Struct Biol 18:321-9. 2008
    ..Here, we review recent advances in our understanding of RNA dynamics as highlighted by biophysical tools...
  12. doi request reprint Program review. The Interdisciplinary Biophysics Graduate Program at the University of Michigan
    Ari Gafni
    Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA
    Biopolymers 89:256-61. 2008
    ..in the academic and the industrial settings...
  13. doi request reprint Flexible casting of modular self-aligning microfluidic assembly blocks
    Sean M Langelier
    Department of Chemical Engineering, University of Michigan, 2300 Hayward St 3074 H H Dow Building, Ann Arbor, MI 48109 2136, USA
    Lab Chip 11:1679-87. 2011
    ..Finally, several exemplary applications of these MABs are demonstrated in chemical gradient synthesis, droplet generation, and total internal reflection fluorescence microscopy...
  14. ncbi request reprint Diffusely bound Mg2+ ions slightly reorient stems I and II of the hammerhead ribozyme to increase the probability of formation of the catalytic core
    David Rueda
    Department of Chemistry and Biophysics Research Division, The University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109 1055, USA
    Biochemistry 42:9924-36. 2003
    ..We propose that the role of diffusely bound Mg(2+) is to increase the probability of formation of a properly aligned catalytic core, thus compensating for the absence of naturally occurring kissing-loop interactions...
  15. pmc Molecular dynamics simulations of RNA: an in silico single molecule approach
    S Elizabeth McDowell
    Biophysics Research Division, Single Molecule Analysis Group, University of Michigan, 930 N University Avenue, Ann Arbor, MI 48109 1055, USA
    Biopolymers 85:169-84. 2007
    ..Such cooperation will open the door to a fundamental understanding of the structure-function relationships in diverse and complex RNA molecules. ...
  16. ncbi request reprint Catalytic core structure of the trans-acting HDV ribozyme is subtly influenced by sequence variation outside the core
    Melissa E Gondert
    Department of Chemistry, The University of Michigan, 930 North University, Ann Arbor, Michigan 48109 1055, USA
    Biochemistry 45:7563-73. 2006
    ..Our results demonstrate that the trefoil turn of the HDV ribozyme catalytic core is in a state of dynamic equilibrium not captured by static crystal structures and is highly sensitive to the identity of the 5' sequence and Mg2+ ions...
  17. pmc Mg2+-induced compaction of single RNA molecules monitored by tethered particle microscopy
    Meredith Newby Lambert
    Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, Michigan 48109 1055, USA
    Biophys J 90:3672-85. 2006
    ..Both effects are nonspecific, however, as they are dampened in the presence of higher concentrations of monovalent cations...
  18. pmc Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation
    Rebecca A Tinsley
    Department of Chemistry, University of Michigan, Ann Arbor, MI 48109 1055, USA
    RNA 12:522-9. 2006
    ..Taken together, our data showcase the potential of pyrrolo-C as an effective fluorescent probe to study RNA structure, dynamics, and function, complementary to the popular 2-aminopurine ribonucleoside...
  19. pmc The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis
    Jana Sefcikova
    Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109 1055, USA
    Nucleic Acids Res 35:1933-46. 2007
    ..Strikingly, we find that the common structural U-turn motif serves distinct functions in the HDV and hammerhead ribozymes...
  20. ncbi request reprint Focus on function: single molecule RNA enzymology
    Mark A Ditzler
    Biophysics Research Division, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA
    Biopolymers 87:302-16. 2007
    ..This review surveys the current status of our understanding of RNA catalysis at the single molecule level and discusses the existing challenges and opportunities in developing suitable assays...
  21. pmc Single VS ribozyme molecules reveal dynamic and hierarchical folding toward catalysis
    Miguel J B Pereira
    Department of Chemistry, Single Molecule Analysis Group, 930 N University Ave, University of Michigan, Ann Arbor, MI 48109 1055, USA
    J Mol Biol 382:496-509. 2008
    ..This preference is expected to facilitate processing of the multimeric RNA replication intermediate into circular VS RNA, which is the predominant form observed in vivo...
  22. pmc Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations
    S Elizabeth McDowell
    Biophysics, University of Michigan, Ann Arbor, Michigan 48109 1055, USA
    RNA 16:2414-26. 2010
    ....
  23. ncbi request reprint Local conformational changes in the catalytic core of the trans-acting hepatitis delta virus ribozyme accompany catalysis
    Dinari A Harris
    Department of Chemistry, The University of Michigan, 930 North University, Ann Arbor, MI 48109 1055, USA
    Biochemistry 41:12051-61. 2002
    ..Our data show that, at least in the trans-acting HDV ribozyme, C(75) becomes positioned for reaction chemistry only along the trajectory from precursor to product...
  24. pmc A biosensor for theophylline based on fluorescence detection of ligand-induced hammerhead ribozyme cleavage
    Phillip T Sekella
    Department of Chemistry, University of Michigan, Ann Arbor 48109 1055, USA
    RNA 8:1242-52. 2002
    ..Additionally, time-resolved FRET measurements on the biosensor ribozyme in complex with a noncleavable substrate analog reveal no significant changes in fluorophore distance distribution upon binding of effector...
  25. pmc A bird's eye view tracking slow nanometer-scale movements of single molecular nano-assemblies
    Nicole Michelotti
    Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
    Methods Enzymol 475:121-48. 2010
    ..These experiments demonstrate the promise of fluorescent particle tracking as a tool for the detailed characterization of synthetic molecular nanosystems at the single-molecule level...
  26. pmc Analysis of complex single-molecule FRET time trajectories
    Mario Blanco
    Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
    Methods Enzymol 472:153-78. 2010
    ..Finally, the application of these techniques to studies of pre-mRNA conformational changes during eukaryotic splicing is discussed...
  27. pmc A divalent cation stabilizes the active conformation of the B. subtilis RNase P x pre-tRNA complex: a role for an inner-sphere metal ion in RNase P
    John Hsieh
    Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
    J Mol Biol 400:38-51. 2010
    ....
  28. ncbi request reprint RNA degradation in cell extracts: real-time monitoring by fluorescence resonance energy transfer
    Sarah A Uhler
    Department of Chemistry, University of Michigan, Ann Arbor, MI 48109 1055, USA
    J Am Chem Soc 125:14230-1. 2003
    ..Finally, gel electrophoretic FRET analysis confirms that HeLa cell extract is dominated by 5' to 3' exonucleolytic activity...
  29. pmc Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance
    David Rueda
    Department of Chemistry, University of Michigan, Ann Arbor, 48109, USA
    Proc Natl Acad Sci U S A 101:10066-71. 2004
    ..Our findings also have broad implications for applications such as the action of drugs and ligands distal to the active site or the engineering of allostery into RNA...
  30. ncbi request reprint Magnesium dependence of the amplified conformational switch in the trans-acting hepatitis delta virus ribozyme
    Rebecca A Tinsley
    Department of Chemistry, The University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, USA
    Biochemistry 43:8935-45. 2004
    ..Thus, a consistent picture emerges in which divalent metal ions and RNA functional groups are intimately intertwined in affecting structural dynamics and catalysis in the HDV ribozyme...
  31. pmc Leakage and slow allostery limit performance of single drug-sensing aptazyme molecules based on the hammerhead ribozyme
    Chamaree de Silva
    Biophysics, University of Michigan, Ann Arbor, Michigan 48109 1055, USA
    RNA 15:76-84. 2009
    ..Our single molecule FRET approach also monitors in real time the previously elusive equilibrium docking dynamics of the hammerhead ribozyme between several inactive conformations and the active, long-lived, Y-shaped conformer...
  32. ncbi request reprint Long-range impact of peripheral joining elements on structure and function of the hepatitis delta virus ribozyme
    Rebecca A Tinsley
    Department of Chemistry, University of Michigan, Ann Arbor, MI 48109 1055, USA
    Biol Chem 388:705-15. 2007
    ....
  33. doi request reprint Probing RNA structural dynamics and function by fluorescence resonance energy transfer (FRET)
    Nils G Walter
    University of Michigan, Ann Arbor, Michigan, USA
    Curr Protoc Nucleic Acid Chem . 2003
    ..Considerations for selecting appropriate RNA, fluorophores, and labeling strategies are discussed in detail in the commentary...
  34. doi request reprint Probing RNA structure and metal-binding sites using terbium(III) footprinting
    Dinari A Harris
    University of Michigan, Ann Arbor, Michigan, USA
    Curr Protoc Nucleic Acid Chem . 2003
    ....
  35. pmc Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in
    Mark A Ditzler
    Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109 1055, USA
    Acc Chem Res 43:40-7. 2010
    ..The examples given in this Account showcase how the judicious use of basic MD simulations has already served as a powerful tool to help evaluate the role of structural dynamics in biological function of RNA...
  36. pmc A rugged free energy landscape separates multiple functional RNA folds throughout denaturation
    Mark A Ditzler
    Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
    Nucleic Acids Res 36:7088-99. 2008
    ..Our results demonstrate a surprising longevity of molecular heterogeneity and advance our current understanding beyond that of non-functional misfolds of RNA kinetically trapped on a rugged folding-free energy landscape...
  37. ncbi request reprint Structural modeling of sequence specificity by an autoantibody against single-stranded DNA
    Melissa J Bobeck
    Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109 1055, USA
    Biochemistry 46:6753-65. 2007
    ..These data-driven 11F8.ssDNA models provide testable hypotheses concerning interactions that mediate sequence specificity in 11F8 and the effects of somatic mutation on ssDNA recognition...
  38. ncbi request reprint Significant kinetic solvent isotope effects in folding of the catalytic RNA from the hepatitis delta virus
    Rebecca A Tinsley
    Department of Chemistry, University of Michigan, Ann Arbor, MI 48109 1055, USA
    J Am Chem Soc 125:13972-3. 2003
    ..They also suggest that an unusual proton inventory may provide a signature for a conformational change contributing to the rate-limiting step...
  39. ncbi request reprint Terbium-mediated footprinting probes a catalytic conformational switch in the antigenomic hepatitis delta virus ribozyme
    Dinari A Harris
    Department of Chemistry, The University of Michigan, 930 N University, Ann Arbor, MI 48109 1055, USA
    J Mol Biol 341:389-403. 2004
    ....
  40. ncbi request reprint Dynamics inherent in helix 27 from Escherichia coli 16S ribosomal RNA
    John A H Hoerter
    Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109 1055, USA
    Biochemistry 43:14624-36. 2004
    ..This begs the question of how these inherent structural dynamics are suppressed within the context of the ribosome...
  41. pmc Solution probing of metal ion binding by helix 27 from Escherichia coli 16S rRNA
    Meredith Newby Lambert
    Department of Chemistry, University of Michigan, Ann Arbor, 48109 1055, USA
    RNA 11:1688-700. 2005
    ..Our studies thus highlight an example for differences between RNA-metal ion interactions observed in solution and in crystals...
  42. ncbi request reprint The 5' leader of precursor tRNAAsp bound to the Bacillus subtilis RNase P holoenzyme has an extended conformation
    David Rueda
    Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
    Biochemistry 44:16130-9. 2005
    ..These results reveal a structural basis for the P protein dependent discrimination between precursor and mature tRNAs...
  43. ncbi request reprint Single molecule fluorescence control for nanotechnology
    David Rueda
    Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109 1055, USA
    J Nanosci Nanotechnol 5:1990-2000. 2005
    ..The future will see a merger of these two separate research thrusts, as single molecule detection will afford optimal control over the assembly and performance of individual nanoscale devices...
  44. ncbi request reprint Reaction pathway of the trans-acting hepatitis delta virus ribozyme: a conformational change accompanies catalysis
    Miguel J B Pereira
    Department of Chemistry, The University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109 1055, USA
    Biochemistry 41:730-40. 2002
    ..Our observations may present the structural basis of the recently described utilization of intrinsic substrate binding energy to the overall catalytic rate enhancement by the trans-acting HDV ribozyme...
  45. pmc Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme
    Mark A Ditzler
    University of Michigan, Ann Arbor, 48109 1055, USA
    RNA 15:560-75. 2009
    ....
  46. ncbi request reprint Impact of an extruded nucleotide on cleavage activity and dynamic catalytic core conformation of the hepatitis delta virus ribozyme
    Jana Sefcikova
    Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 N University Avenue, Ann Arbor, MI 48109 1055, USA
    Biopolymers 85:392-406. 2007
    ..Terbium(III) footprinting and additional MD show that the activity differences between N76 mutants of this ribozyme are related instead to changes in average conformation and modified cross-correlations in the trefoil turn...
  47. pmc Trans-acting glmS catalytic riboswitch: locked and loaded
    Rebecca A Tinsley
    Department of Chemistry, University of Michigan, Ann Arbor, MI 48109 1055, USA
    RNA 13:468-77. 2007
    ..These findings suggest that the glmS ribozyme is fully folded in solution prior to binding its activating ligand, supporting recent observations in the crystalline state...
  48. pmc The shape-shifting quasispecies of RNA: one sequence, many functional folds
    Matthew S Marek
    Department of Chemistry, 930 N University Ave, University of Michigan, Ann Arbor, MI 48109 1055, USA
    Phys Chem Chem Phys 13:11524-37. 2011
    ..Embracing that one sequence can give rise to multiple native folds, we hypothesize that this phenomenon imparts adaptive advantages on any functionally evolving RNA quasispecies...
  49. ncbi request reprint Fluorescent energy transfer readout of an aptazyme-based biosensor
    David Rueda
    Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
    Methods Mol Biol 335:289-310. 2006
    ..The chapter should therefore facilitate the implementation of RNA-based biosensor components for other analytes of interest...
  50. ncbi request reprint Trans-acting hepatitis delta virus ribozyme: catalytic core and global structure are dependent on the 5' substrate sequence
    Sohee Jeong
    Department of Chemistry, The University of Michigan, 930 North University, Ann Arbor, Michigan 48109 1055, USA
    Biochemistry 42:7727-40. 2003
    ..Our results suggest a structural basis for the previously observed impact of the 5' substrate sequence on catalytic activity...
  51. ncbi request reprint Correlating structural dynamics and function in single ribozyme molecules
    Xiaowei Zhuang
    Department of Physics, Stanford University, Stanford, CA 94305, USA
    Science 296:1473-6. 2002
    ..The complex structural dynamics quantitatively explain the heterogeneous cleavage kinetics common to many catalytic RNAs. The intimate coupling of structural dynamics and function is likely a general phenomenon for RNA...
  52. pmc Single-molecule transition-state analysis of RNA folding
    Gregory Bokinsky
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 100:9302-7. 2003
    ..Such a compact transition state without well formed tertiary contacts may be a general property of elementary RNA folding reactions...
  53. pmc Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic "fingerprinting"
    Shixin Liu
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 104:12634-9. 2007
    ..These results underscore the kinetic interdependence of reversible steps on an enzymatic reaction pathway and demonstrate a potentially general route to dissect them...
  54. ncbi request reprint Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations
    Maryna V Krasovska
    National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
    J Mol Biol 351:731-48. 2005
    ....
  55. pmc Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme
    Maryna V Krasovska
    Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic
    Biophys J 91:626-38. 2006
    ..Monovalent cations bind to the active site and elsewhere assisted by structurally bridging long-residency water molecules, but are generally delocalized...
  56. pmc General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility
    Pavel Banas
    Department of Physical Chemistry and Center for Biomolecules and Complex Molecular Systems, Palacky University, tr Svobody 26, 771 46, Olomouc, Czech Republic
    J Phys Chem B 112:11177-87. 2008
    ..The calculated energy barrier of the proposed mechanism, approximately 20 kcal/mol, would lower the reaction barrier by approximately 15 kcal/mol compared with the uncatalyzed reaction and is in good agreement with experimental data...
  57. ncbi request reprint Michaelis-Menten is dead, long live Michaelis-Menten!
    Nils G Walter
    Nat Chem Biol 2:66-7. 2006

Research Grants16

  1. Trekking with the Ribognome: Single Molecule Microscopy of Intracellular miRNPs
    Nils G Walter; Fiscal Year: 2010
    ..What are the lower limits for DNA repeat sequence and protein polymerization detection and can these limits be further pushed? Can multiple different biopolymers be detected in parallel and how does this affect detection limits? ..
  2. U-turn of the Hepatitis Delta Virus Ribozyme
    Nils G Walter; Fiscal Year: 2010
    ....
  3. U-turn of the Hepatitis Delta Virus Ribozyme
    NILS WALTER; Fiscal Year: 2009
    ....
  4. U-turn of the Hepatitis Delta Virus Ribozyme
    NILS WALTER; Fiscal Year: 2007
    ....
  5. Trekking with the Ribognome: Single Molecule Microscopy of Intracellular miRNPs
    NILS WALTER; Fiscal Year: 2007
    ..concept? What are the lower limits for DNA repeat sequence and protein polymerization detection and can these limits be further pushed? Can multiple different biopolymers be detected in parallel and how does this affect detection limits? ..
  6. FOLDING AND FUNCTION OF HAMMERHEAD AND DELTA RIBOZYMES
    NILS WALTER; Fiscal Year: 2005
    ....
  7. U-turn of the Hepatitis Delta Virus Ribozyme
    Nils G Walter; Fiscal Year: 2010
    ....